Complete Release Notes

Version 1.51 23 April 2018 (download)

• 1.51w 13 March 2018
  • Thanks to Stein Rorvik, added the setOption("InvertY",boolean) and is("InvertY”) macro functions.
  • Thanks to Pradeep Rajasekhar and Jan Eglinger, fixed a 1.51v regression that caused the ‘OK’ and ‘Cancel’ buttons in the Bioformats importer dialog box to be missing.
• 1.51v 9 March 2018
  • Thanks to Norbert Vischer, extended the Plot class to make it relatively simple to draw the x and y values on plots. For examples, refer to Custom Plot Symbols and Bar Charts in the Help>Examples>Plots menu.
  • Thanks to Michael Schmid, added the Dialog.addToSameRow() macro function, which makes the next item added to a GenericDialog appear on the same row as the previous item (example).
  • Thanks to Salim Kanoun, added the Overlay.selectable(boolean) method which can be used to make an overlay non-selectable (example).
  • Thanks to Salim Kanoun, added the Overlay.setLabelFont(font,true) method, which causes labels in overlays to scale as the image is zoomed.
  • Thanks to Michael Schmid, the GenericDialog class automatically generates unique labels for macro recording.
  • Thanks to Michael Schmid, on Linux, the "OK" button in GenericDialogs is now on the right, as it is on Macs.
  • Added a setFontSize() method to the MontageMaker class.
  • Thanks to Michael Schmid, fixed a bug that caused symbols in plots to be drawn at the left or bottom border if there was a NaN value.
  • Thanks to Wilhelm Burger, fixed a bug on Java 9 that caused Plugins>Compile and Run to not work with .class files not in the default package.
  • Thanks to Jerome Mutterer, fixed a 1.51u regression that caused macro calls similar to newArray(a.length) to always return 1.
  • Thanks to Rob Lees, fixed a 1.51u regression that caused the close(pattern) macro function to close the ROI Manager if 'pattern' did not have a wildcard.
  • Thanks to Norbert Vischer, fixed a 1.51u regression that caused the close("\\Others") to not work.
  • Thanks to Rob Lees, fixed a 1.51s regression that caused multi-point deletion with “Show all” enabled to not function correctly.
• 1.51u 13 February 2018
  • Thanks to Norbert Vischer, added support for plotting rectangles, vertical and horizontal bar charts, and vertical and horizontal boxes and whiskers. Use the Bar Charts and Shapes commands in the Help>Examples>Plots menu to see examples.
  • Thanks to Norbert Vischer, zooming in and out of plot windows using the "+" and "-" keys works better.
  • Thanks to Norbert Vischer, added the Help>Examples>Open as Panel command.
  • Thanks to Norbert Vischer, added the Plot.appendToStack() function. The Dynamic Plot and Dynamic Plot 2D macros in the Help>Examples>Plots menu and the Dynamic Plot script in the Help>Examples>JavaScript menu demonstrate how to use it.
  • Thanks to Norbert Vischer, added support for multi-line labels in plots. For an example, see Help>Examples>Plots>BarCharts.
  • Added the Help>Examples>Plots>Histograms example macro, which demonstrates how to use the new Plot.add("bars",x,y) macro function to draw histograms.
  • The File>Save As>Gif command now works with RGB images and stacks, saving stacks as animated GIFs (example1, example2).
  • The Plugins>Utilities>Control Panel now requires a double click to run a command.
  • Thanks to Stein Rorvik, when moving the mouse pointer, or creating a selection, on spatially calibrated images, the uncalibrated x and y pixel coordinates are shown in parenthesis in the status bar.
  • Thanks to Jerome Mutterer, the focus is reset to the prompt when either the backspace or delete key is pressed in the macro functions finder.
  • Thanks to Norbert Vischer, the close(pattern) macro function closes windows whose title matches 'pattern'. Non-image windows, like "Roi Manager" have to be specified without wildcards. For text windows, wildcards are allowed if 'pattern' ends with ".txt", ".ijm" etc. Use close(pattern, "keep") to close only unchanged windows.
  • Thanks to Michael Schmid, added the Recorder.fixString() method, which is used to escape strings passed to the recorder.
  • Thanks to Michael Schmid, the delete key on Windows keyboards can be used as a substitute for backspace as a shortcut for the Image>Clear command, for deleting ROIs from overlays and for deleting lines in Results Tables and in the Log window. In addition, the ',' key on european numeric keypads is mapped to the '.' key.
  • Thanks to Norbert Vischer, added the Plot.drawShapes() and Plot.drawGrid macro functions.
  • Thanks to Gregory Jefferis, fixed a bug that caused the run("Scale...", "...") macro function to fail in Fiji headless mode.
  • Thanks to Stein Rorvik, fixed a bug that caused the min/max constrast values to be lost when duplicating virtual stacks.
  • Thanks to Michael Schmid, fixed a bug that caused incorrect log x axis coordinates to be displayed at the bottom of plot windows.
  • Thanks to Andrew Shum, fixed a bug that caused the File>Batch>Macro and File>Batch>Virtual Stack commands to not be correctly recorded.
  • Thanks to Philippe Carl and Jan Eglinger, fixed a bug that caused the newArray() macro function to fail if there were multiple arguments and the first argument was not a number.
  • Thanks to Stein Rorvik, fixed a bug on Windows that sometimes caused strings to be pasted in the wrong position in text windows.
  • Thanks to Michael Schmid, fixed a bug that caused the Process>Filters>Variance command to sometimes generate negative values with 32-bit images.
  • Thanks to Tobias Starborg, fixed a bug that caused the Image>Stacks>Animation>Animation Options command to not work in batch mode macros.
• 1.51t 31 December 2017
  • Thanks to Norbert Vischer, the Plot class now supports filled plots. Run Help>Examples>Macro>Damped Wave Plot to see an example.
  • Thanks to Norbert Vischer, when a macro error occurs, the line number is copied to the clipboard and the error message is displayed in the "Debug" window.
  • Added "Synthetic Images" and "Spiral Rotation" examples, in Macro and JavaScript versions, to the Help>Examples menu.
  • Added a "hidden" checkbox to the plot window More>>Contents Style dialog.
  • The Process>Math>Macro command and the ImageProcessor.applyMacro() method automatically add "v=" if it is missing.
  • Thanks to Norbert Vischer, the seed set by the random("seed",n) macro function is now used when creating images with random content and by Process>Noise commands, allowing reproducible test situations to be created (examples).
  • Thanks to Francois Gannier, the x and y-axis labels are used as the first two column headings in the table created by the plot window "List" command when these labels start and end with a space character.
  • Thanks to Jan Brocher, fixed a bug that caused the ColorThresholder.RGBtoYUV() method to not work as expected.
  • Thanks to Stein Rorvik, fixed a bug that caused function key and numeric kaypad macro shortcuts to not work as expected when "Require control key for shortcuts" was enabled in the Edit>Options>Misc dialog.
  • Thanks to Christophe Leterrier, worked around a macOS High Sierra/APFS bug that caused LUTs listed in the Image>Lookup Tables menu and file names returned by the getFileList() macro function to not be sorted.
  • Thanks to Michael Kaul, fixed a v1.51s regression that could cause ImageJ to fail to quit properly if there was an Action Bar launched at startup.
  • Thanks to Norbert Vischer, fixed a v1.51r26 regression that caused the setBatchMode("show") macro function to not work as expected.
• 1.51s 5 December 2017
  • Thanks to Philippe Carl, added support for diamond symbols to the Plot class.
  • Added the Help>Examples>JavaScript>Event Listener example.
  • Incresed the default plot size from 450x200 to 530x300.
  • Thanks to 'graukatze', line length measurements are now much faster when all measurements are disabled in the Set Measurents dialog.
  • Thanks to Jean Christophe Taveau, ECMAScript 6 is used when running JavaScript code on Java 9 (more info).
  • Thanks to Ron DeSpain, the File.directory() macro function (OpenDialog.getLastDirectory() method) now returns the path to the directory that a macro was loaded from.
  • Thanks to Lorenzo Cangiano, fixed a bug that could cause the "Apply" button in the Image>Adjust>Brightness/Contrast dialog to throw an exception with 16-bit images.
  • Thanks to Rob Lees and Jan Eglinger, fixed a bug that, when deleting a point from a point selection on a stack, could cause an overlaping invisible point in another slice to be deleted.
  • Thanks to 'WaDoMa', fixed a bug that caused ImagePlus.setAntialiasRendering() calls to be ignored when rendering arrows in flattened images.
  • Thanks to Jean Christophe Taveau, fixed a bug that caused scripts installed in the plugins menu to be aborted if the user clicked "Cancel" in a GenericDialog.
  • Thanks to Klaus Michel, fixed a bug that caused the ROI Manager's More>Translate command to not work correctly if one of the ROIs being translated was active.
  • Thanks to Stein Rorvik, fixed bugs that caused the RunAtStartup, AutoRun and command line macros to interfere with each other, causing &variable expansion in run() calls to not work. To avoid this interference, the RunAtStartup macro (created by Edit>Options>Startup), the AutoRun macro (in StartupMacros) and command line macros now all run on the same thread.
  • Thanks to Stein Rorvik, fixed a bug that caused the Startup Macros command in the >> toolbar menu to not work as expected if the StartupMacros file had an ".ijm" extension.
  • Thanks to Alban Favre and Jan Eglinger, fixed a bug that caused the getResult() macro function to not work with tables created by plugins using the ResultsTable.setValue(column,row,value) method.
  • Thanks to Stein Rorvik, fixed a bug that caused forward slash separators to not work with default directories on Windows.
  • Thanks to Adrian Daerr, fixed a bug that caused raw virtual stacks to be opened incorrectly if the number of images specified in the dialog was greater than the actual number of images.
  • Thanks to 'tigers1964', fixed bugs that sometimes caused File>Import>Raw to not correctly zero fill when the specified image size was greater than the file size.
  • Thanks to Michael Kaul, fixed a bug that caused the ImagePlus.setProcessor() method to sometimes not work as expected with stacks.
  • Thanks to 'graukatze', fixed a bug that caused Plot Z-axis Profile, in "Live" mode, to interfere with the Measure command.
  • Thanks to Bjorn Marsen, fixed a v1.51 regression that caused run("Set Measurements...","...") to reset the measurement counter when used in a macro run from the command line using the -batch option.
• 1.51r 15 October 2017
  • Thanks to Norbert Vischer, custom symbols in plots are now supported. Refer to the Help>Examples>Macro>Custom Plot Symbols command for an example.
  • Thanks to Philippe Carl, replaced the min/max threshold value labels in the "Threshold" dialog by editable text fields and removed the "Set" button. New values are validated once the user hits the enter key. Also added mouse wheel and arrow key support to the min and max sliders. The up/down keys increase/decrease the threshold values when the cursor is within one of the text fields.
  • The "Save column headers" and "Save row numbers" options in the Edit>Options>Input/Output dialog are always enabled on startup.
  • Thanks to Mathieu Prouveur, ImageJ displays an error message when a macro function attempts to return a string enclosed in parenthesis.
  • Thanks to Roger Leigh, fixed bugs that prevented ImageJ from running on Java 9.
  • Thanks to Derek Xu and Michael Schmid, fixed a bug that could cause the Orthogonal Views command to throw an exception.
  • Thanks to Jerome Parent, fixed a bug that caused the median filter to not work correctly with 32-bit images containing NaN values.
  • Thanks to Ron DeSpain, fixed a bug that could cause startup macro shortcuts to be disabled when opening a macro in the macro editor.
  • Thanks to Kees Straatman, fixed a bug that caused the run("Set Measurements...", options) macro function to not work as expected if used after a run("Analyze Particles...", options) call that was missing 'display ' in the options string.
  • Thanks to Jeremy Adler, fixed a bug that caused the run("Stack to Images") macro function to not make the last opened image active.
  • Thanks to Michael Schmid, fixed bugs that sometimes caused the the wrong image to be activated after an image is deleted in a macro.
  • Thanks to Michael Schmid, fixed a 1.51q regression that could cause an exception when creating a plot.
• 1.51q 18 September 2017
  • Plot enhancements, thanks to Michael Schmid:
    • Plots saved as tiff or zip include the data, so the plot range can be modified (zooming, etc.) and the data can be listed after loading the plot from a file.
    • Changing the axis or label font size of a plot keeps the image size constant and modifies the plot frame size (previously, the plot frame size was constant).
    • Slightly more space for numbers at the left, enough for scientific notation. ImageJ switches to a smaller font if more significant digits are required.
    • Added Plot.getFrameBounds(x, y, width, height) macro function.
    • The default font for plots is now Arial, not Helvetica (Arial is available on more platforms).
    • When opening a plot on a computer where a given font is not available, try to replace fonts by similar ones. This should make the appearance on different platforms more similar.
    • The ImageProcessor getStringWidth() and getStringBounds() methods use the more accurate GlyphVector class.
  • Thanks to Norbert Vischer, the Edit>Selection>Straighten and Image>Duplicate commands work with rotated rectangle selections.
  • Thanks to Jerome Parent, added the Image>Stacks>Plot XY Profile command.
  • Thanks to Jerome Parent, added a "Show unit" checkbox to the Analyze>Tools>Calibration Bar dialog box.
  • Thanks to Stein Rorvik, newly opened editor windows are larger and, on Linux and Windows, are less likely to cover the main ImageJ window.
  • Thanks to Norbert Vischer, added a "Smooth if thresholded" option to the Wand tool dialog (example).
  • Thanks to Kenneth Sloan, added a recordable ZProjector.run() method (examples).
  • Thanks to Norbert Vischer, added the makeRotatedRectangle(x1,y1,x2,y2,width) macro function.
  • Thanks to Norbert Vischer, added the List.toArrays(keys,values), List.fromArrays(keys,values) and List.indexOf(key) macro functions.
  • Thanks to Max Leiter, fixed a bug that caused RoiListeners to not be notified when an ROI was created.
  • Thanks to Alvaro Folgado, fixed an OS X command injection vulnerability in the BrowserLauncher.
  • Thanks to Alison Walter, fixed a bug that caused the "Spline fit" checkbox in the "Line Width" dialog to convert angle selections to polygons.
  • Thanks to Chris Lamb, fixed a typo in MemoryMonitor.java where a constant that should have been 1024 was 1204.
  • Thanks to Norbert Vischer, fixed a bug in the Array.resample() macro function that caused it to throw an exception if the langth of the input was 0 or 1.
  • Thanks to John Loveland and Lukas Kvasnica, fixed a v1.51o regression that caused plugins that create virtual stacks without implementing the VirtualStack class to throw an exception.
  • Thanks to Tim Huang, fixed a bug that caused the Image>Overlay>Flatten command to not work correctly with high-resolution images.
  • Thanks to Norbert Vischer, fixed a bug with the Debug>Abort command in the macro editor that caused it to display a bogus error message.
  • Thanks to Stefan Helfrich and Azman Rashid, fixed a bug that caused ImageJ to not correctly read TIFF files created by the Bfconvert command line tool.
  • Thanks to Jan Eglinger, fixed a bug that caused the popup menu (e.g. right-click > Rename...) and the "Dev" menu tool to not get recorded.
  • Thanks to Sethur, fixed a bug that caused scroll wheel zooming in image stacks (enabled using control or shift key) to not work correctly.
  • Thanks to Steffen Schmidt, fixed a bug that caused scale bars to not be correctly positioned with large font sizes.
  • Thanks to Vanessa King and Jan Eglinger, fixed a bug that caused the "List" option in plot windows to sometimes not list all X columns when the columns differed in length.
  • Thanks to Carne Draug, fixed several problems related to building the ImageJ Debian package.
  • Thanks to Salim Kanoun, fixed a bug that caused overlay titles to be selectable when a new ROI was being constructed.
  • Thanks to Norbert Vischer, fixed a bug than caused the Analyze>Gels>Select Next Lane command to sometimes create duplicate plots.
  • Thanks to Michael Kaul, fixed a v1.51o regression that caused the ImagePlus.flatten() method to be much slower.
  • Fixed a 1.51e regression that caused the "Auto" buttion in the Brightness/Contrast dialog to not increase contrast with repeated clicks.
• 1.51p 22 June 2017
  • When adding a hyperstack ROI to the ROI Manager, the channel position is set to 0 (display in all channels) if the display mode is "Composite".
  • Added the setOption("ConvertToMicrons",boolean) macro function. When this option is set, units in TIFF images are converted to microns if the pixel width is less than 0.0001 cm.
  • Thanks to Norbert vischer, worked around a bug in Java 8 on OS X that sometimes caused painting of GenericDialogs to be incomplete.
  • Thanks to Rainer Engel, fixed a bug that caused macros that passed variables using "&" notation to fail if they used the Process>Math>Macro command to process a stack.
  • Thanks to Philippe Carl, fixed a 1.51o regression that sometimes caused ImageJ to freeze on Windows when opening or processing images.
• 1.51o 7 June 2017
  • Added a Command Finder tool to the >> toolbar menu.
  • Thanks to Hermann-Josef Roeser, histograms of RGB images are now labeled with the histogram type ("Intensity (weighted)", "Intensity (unweighted)" or "R+G+B") and the "RGB" button cycle includes these three histogram types.
  • Updated the VirtualStack class to support frequency domain FFT images (example macros).
  • Worked around bugs with Windows 10 Creators Update that caused the file open dialog to freeze and the "ImageJ" window to be taller than normal.
  • Thanks to Michael Kaul, added the Roi.setPosition(ImagePlus) method.
  • Worked around a bug with Java 8 on Mac OS X that caused the buttons in histogram windows to be partially hidden.
  • Thanks to Wilhelm Burger and Tiago Ferreira, fixed a bug that caused coordinates used by the ImageProcessor.getLine() method to retrieve pixel values to be offset by 0.5 pixel when interpolation was not enabled.
  • Thanks to Wilhelm Burger, fixed a bug that caused the ImageProcessor.setColor() method to ignore RGB component weights when setting the associated drawing (i.e., gray) value of non-RGB grayscale images.
  • Thanks to Robert Atwood, fixed a bug that caused the "Auto" option in the Image>Adjust>Threshold tool to sometimes not work as expected with 16-bit stacks.
  • Thanks to Christian Tischer, fixed a bug that caused the Image>Transform>Bin command to change the calibation of the source image.
  • Thanks to Theresa Swayne, fixed a bug that caused the ROI Manager's Multi-Measure command (in "append" mode) to not reset its saved results when the Results Table was cleared.
  • Thanks to Norbert Vischer, fixed a bug that caused screen updates of images with complex overlays to be very slow with Java 8 on Mac OS X.
  • Thanks to Don Levin, fixed a bug that caused the File>Save As>PGM to not correctly save 16-bit images.
  • Thanks to Rob Beetel, fixed a regression that caused the ROI to be deleted after using "Apply" on RGB images in the Brightness/Contrast, Window/Level and Color Balance dialogs.
• 1.51n 1 May 2017
  • Fixed a 1.51m regression that caused the "+" command (Image>Zoom>In) to sometimes not work as expected.
• 1.51m 30 April 2017
  • Images are scaled to fit when windows are resized.
  • Added the Image>Zoom>Maximize command.
  • Thanks to Agathe Robisson, added a "Center grid on image" checkbox to the Analyze>Tools>Grid dialog.
  • A Plugins>Why are Plugins Missing? command is added to the Plugins menu if plugins were not loaded due to macOS Path Randomization.
  • Added the Help>Examples>JavaScript>TeraByte VirtualStack example script.
  • Changed the default extension when saving tables from ".xls" to ".csv" (coma-separated values) and added support for opening and saving tables in ".tsv" (tab-delimited values) format.
  • The Macros>Evaluate JavaScript command in the text editor now respects the "use strict" directive (Java 8 only) to indicate that the code should be executed in "strict mode". In strict mode, you can not, for example, use undeclared variables.
  • Thanks to Michael Schmid, the Analyze>Plot Profile command remembers whether the alt key was down (used for verticall plotting) when initialized so "Live" plots continue to be vertical.
  • Thanks to Michael Schmid, the AVI Reader tries to recover data from truncated files.
  • Thanks to Jerome Mutterer, added the setOption("SaveBatchOutput",false) macro function, which can be used in Process>Batch>Virtual Stack macros to prevent slices from being written to the output virtual stack.
  • Thanks to Stephan Preibisch, removed the limit of 25 sliders in GenericDialogs.
  • Thanks to Norbert Vischer, added the Array.rotate() and Array.getVertexAngles() macro functions and added an optional edgeMode argument to the Array.findMaxima() function (example1, example2, example1).
  • Added the Roi.hasHyperStackPosition() method.
  • Thanks to Stefan Helfrich and Mojo Dodo, fixed a bug that caused the Image>Color>Arrange Channels command to not close the source image in batch mode macros.
  • Thanks to Robert Dougherty, fixed a bug that caused the "Overlay" checkbox in the Analyze>Tools>Calibration Bar dialog box to not be remenbered.
  • Thanks to Robert Dougherty, fixed a bug that caused the backgrounds of scrollbars to be white when running on Windows 10 and Java 6.
  • Thanks to Martin Hohne, fixed a bug that caused the run("Point Tool...", "...") macro function to not work as expected.
  • Thanks to Stefan Helfrich, fixed a bug that caused the GroupedZProjector to always generate a time series regardless of the input stack format.
  • Thanks to lcsglvr, fixed a bug that caused slow drawing of 16-bit and 32-bit multi-channel composite color images in "Color" mode.
  • Thanks to Michael Schmid, fixed a bug in the AVI Reader that caused the file to not be closed in case of a cancelled dialog or some IO errors.
  • Thanks to Wilhelm Burger, fixed bugs with the PointIterator on line and point selections that caused incorrect point coordinates to be returned.
  • Fixed a bug on Mac OS X that caused the position of the "ImageJ" window to not be remembered if it was located partially offscreen to the right.
• 1.51k 1 March 2017
  • Added the Plugins>Utilities>Capture Delayed command.
  • Thanks to Yaman al-Yousof, added Macro and JavaScript "Custom Measurement" examples to the Help>Examples menu.
  • Added this note to the Help>Examples>Macro>Sphere example:
    "JavaScript on Java 8 runs this code 30 times faster than the macro language when 'size' is set to 4096."
  • Thanks to Norbert Vischer, worked around OSX/Java 8 bugs that caused the toolbar to not be updated after clicking on a new tool with the recorder running, caused newly opened image windows to obscure the ImageJ status and progress bars and caused the selectImage() macro function to sometimes be very slow.
  • Thanks to Florian Jug and Curtis Rueden, fixed a bug that caused ImageJ to incorrectly open TIFF stacks created by Bio-Formats.
  • Thanks to Stein Rorvik, fixed bugs that caused Windows file paths starting with "C:/� to not work in the open() and runMacro() macro functions.
  • Thanks to Stein Rorvik, fixed bugs that caused min/max values to be lost when resampling virtual stacks.
  • Thanks to Stein Rorvik, fixed a bug that caused z-scaling of 8-bit stacks to not retain the min,max contrast setting.
  • Thanks to Stein Rorvik, fixed a bug that caused Edit>Selection>Rotate to not work for straight line selections if "Rotate around image center" was enabled.
  • Thanks to Stefan Woerz, fixed a bug that caused profile plots to not be displayed if the min and max pixels values were non-zero and equal.
  • Thanks to Volker Baecker, fixed a bug that caused the print("[text-window]", "...") macro function to not work as expected if "text-window" had been saved and re-opened.
  • Thanks to Puifai Santisakultarm, fixed a bug that caused the IJ.run(imp,"RGB Color","") method to not work as expected with non-displayed images.
  • Thanks to Michael Cammer, fixed a bug that caused the run("3D Project...",options) macro function to not work reliably with hyperstacks.
  • Thanks to Edward Muir and and Curtis Rueden, fixed a bug that caused the "Out of memory" error message to incorrectrly report the amount of available memory.
• 1.51j 4 February 2017
  • Added the Rotated Rectangle selection tool.
  • Added the Edit>Detab command and the Edit>Tab Key Inserts Spaces Checkbox menu item to the text editor;
  • Thanks to Stein Rorvik, added the Macros>Evaluate Macro command to the text editor.
  • Thanks to Jerome Mutterer, added the Help>Examples>Macro>Star Tool example macro tool, just in time for this holiday season.
  • Thanks to Michael Schmid, the File>New>Image command displays a progress bar when creating single RGB images filled with noise.
  • Added JavaScript and Java "plasma cloud" recursion examples to the Help>Examples menu, based on PlasmaCloud.java, from the book Introduction to Programming in Java by Robert Sedgewick and Kevin Wayne.
  • Thanks to Michael Schmid, added the "Save window locations" option to theEdit>Options>Misc dialog (only on Linux). Enable this option to workaround a bug with some Linux window managers that causes windows to wander down the screen when they are repeatedly opened and closed.
  • Added the random("gaussian") and Overlay.measure macro functions.
  • Added the Roi.setStrokeColor(r,g,b), Roi.setStrokeColor(rgb), Roi.setFillColor(r,g,b) and Roi.setFillColor(rgb) macro functions.
  • Thanks to Norbert Vischer, add the getBoolean(message, yesLabel, noLabel) macro function.
  • Added the ImageProcessor.fillRect() method.
  • Added the Overlay.measure(ImagePlus) method.
  • Thanks to Michael Schmid, the ColorProcessor.filter(type) method supports the additional types FIND_EDGES, MEDIAN_FILTER, MIN and MAX.
  • Thanks to Norbert Vischer, fixed a bug that caused the particle analyzer to be very slow in batch mode macros if the "Add to manager" option was enabled.
  • Thanks to Michael Schmid, fixed a bug that caused Process>Smooth to not process the edges.
  • Thanks to Salim Kanoun, fixed a bug that caused the getMetadata("info") macro function to sometimes not work as expected with stacks.
• 1.51h 9 November 2016
  • Thanks to Stein Rorvik, the Image>Stacks>Z-axis Profile and Image>Stacks>Tools>Make Substack commands display a progress bar if the stack has more than 400 slices or is a virtual stack.
  • Thanks to Christiane, the Results table, for each point in a multi-point selection, displays the counter associated with the point and the count for that counter.
  • A selection in an overlay can be activated by double clicking the corresponding row in the Image>Overlay>List Elements list.
  • Thanks to Michael Schmid, added the Prefs.splineFitLines flag, set by the "Spline fit" checkbox in the "Line Width" dialog, opened by double clicking on the line tool icon.
  • Thanks to Thorsten Wagner, TIFF files with cm units are now converted to µm units if the pixel width is less than 0.0001 cm. In earlier versions of ImageJ they were only converted when importing an image sequence as a virtual stack.
  • Thanks to Gilles Carpentier, error messages displayed by the Plugins>Compile and Run command now include ImageJ, Java and OS version information.
  • Thanks to Stein Rorvik, added the setOption("AntialiasedText",boolean) macro function and the TextRoi.setAntialiasedText(boolean) method, which control the "Antialiased text" option in the Edit>Options>Fonts dialog.
  • Thanks to Avital Steinberg, fixed a bug that caused the ImageProcessor.getStatistics() method to sometimes not work as expected with ShapeRois.
  • Thanks to krami79, fixed a bug that could cause an exception when closing a live plot window.
  • Thanks to Jan Eglinger, fixed a bug that could cause plugins and scripts using the GenericDialog.getMessage() method to throw an exception.
  • Thanks to Norbert Vischer, fixed a bug that caused dots in plots to be drawn outside the frame.
  • Thanks to Ron Paletzki, fixed a bug that caused Image>Scale and Image>Adjust>Size to not work as expected with z scale factors less than 0.5 when Interpolation was set to None.
  • Thanks to Gilles Carpentier, fixed a 1.50i regression that caused the Edit>Selection>Enlarge command to sometimes not work as expected when shrinking very small selections.
• 1.51g 22 September 2016
  • Thanks to Michael Schmid, added the Image>Adjust>Coordinates command, which allows the user to set the corner coordinates of the selection bounds or the full image. This modifies the image scale (pixelWidth, pixelHeight) and the xOrigin, yOrigin. If a single point is selected, the coordinates of the point can be specified, which only sets xOrigin and yOrigin. The units for x and y can be also selected.
  • Thanks Marcel Krzan, increased the font size in GenericDialog text areas (Options>Startup, Analyze>Calibrate, Filters>Convolve and Batch>Macros) to 14 points.
  • Thanks to Thomas Boudier, when creating a new stack, a status message and progress bar are only displayed when the stack is 250 MB or larger.
  • Thanks to Norbert Vischer, added the List.setMeasurements("limit") macro function.
  • Thanks to Curtis Rueden, fixed a bug that caused the run("From ROI Manager") macro function to not transfer the selection positions to the overlay.
  • Thanks to Jinghan Chen, fixed a bug that caused the multi-point tool to sometimes fail when using multiple counters.
  • Thanks to Curtis Rueden, fixed bugs that caused the "Run single instance listener" option in Edit>Options>Misc to not work as expected.
• 1.51f 17 August 2016
  • Thanks to 'mls' and Jan Eglinger, the Image>Stacks>Tools>Combine command now works with hyperstacks.
  • Thanks to Eduardo Kropnick, fixed a 1.51e regression that caused the List.setMeasurements macro function to not work as expected.
• 1.51e 5 August 2016
  • Added a "Don't set Mac menu bar" option to the Edit>Option>Misc dialog. When this option is set, ImageJ does not set the ImageJ menu bar when image windows are activated. This may prevent ImageJ from becoming unresponsive due to setMenuBar() becoming slower and slower over time. To recover the menu bar, click on the "ImageJ" window or press return, the shortcut for the Window>Main Window command.
  • When running Java 8 on OS X, the "Don't set Mac menu bar" option in Edit>Option>Misc is automatically set when it the setMenuBar() method takes more than two seconds.
  • Thanks to Gabriel Landini, when selecting rectangular ROI handles, the buffer zone is larger on screens wider than 1280 pixels.
  • Thanks to Patrick Darby Parker, plot windows created by macros calling run("Plot Z-axis Profile") now include a "Live" button.
  • Thanks to Philippe Carl, the Plugins>Compile and Run command adds jar files in the plugins/jars folder with "_" in their names to the javac classpath.
  • Added the ImagePlus.crop() method (example).
  • Thanks to Jean-Yves Tineves, added the VirtualStack(width,height,slices) constructor that creates a virtual stack with no backing store (example).
  • Thanks to Ignacio Garcia Gonzalez, fixed a bug that caused ROIs with coordinates greater 65535 to be corrupted when saved and reopened.
  • Thanks to Jens Kriese, fixed a bug that caused the slices of new "Random" stacks to be copies of the first slice.
  • Thanks to Ondrej Sebesta, fixed a bug that caused the roiManager("Select",index) macro function to fail if setKeyDown("Shift") was previously called.
  • Thanks to Marcel, fixed a bug that caused the "Propagate to all open images" option in the "Set" dialog of the Image>Adjust>Window/Level widget to fail.
  • Thanks to Philippe Carl, fixed a bug that caused the Image>Stacks>Tools>Concatenate command to not be correctly recorded when the Recorder was not in "Macro" mode.
  • Thanks to Jan Eglinger, fixed a bug that caused the Image>Color>Channels Tool widget to not work as expected in "Color" mode when using Java 8 on Mac OS X.
  • Thanks to Steve, fixed a bug in the Image>Stacks>Make Montage command that caused it to not work as expected if "Border width" was greater than 0.
  • Thanks to Michael Schmid, fixed a bug that caused the ImageCanvas.setSourceRect() method to sometimes modify the Rectangle passed to it.
  • Thanks to Michael Schmid, fixed a bug that caused the ImageJ menu bar on Mac OS X to disappear when cliking on the "B&C" window to activate it.
  • Thanks to Stefan Helfrich, fixed a bug that caused inconsistent handling of the animation rate if it was set to less than 0.1 fps.
  • Thanks to Stefan Helfrich, fixed a bug that caused the Image>Stacks>Label command to not work as expected with hyperstacks if the "Use overlay" option was enabled.
  • Thanks to Gabriel Landini, fixed a v1.51d regression that caused the ImagePlus.getStatistics() method to be much slower.
  • Thanks to Jean-Yves Tineves, fixed a v1.47 regression that caused overlays to not work with custom virtual stacks.
  • Thanks to jbrazill and Jan Eglinger, fixed a regression that caused the Image>Overlay>Flatten command to not work with non-RGB images without a selection or overlay.
• 1.51d 16 June 2016
  • Fixed a bug that caused the Measure command to ignore the "Invert Y coordinates" setting in Analyze>Set Measurements when measuring the centroid of stright line selections.
  • Thanks to Aleksandr Mironov, fixed a bug that caused the multi-point tool to fail when creating a second multi-point selection.
  • Thanks to Nuno Martins, fixed a 1.51b regression that caused the run("Duplicate","duplicate") macro function to not work as expected when operating on stacks.
• 1.51c 7 June 2016
  • Thanks to A Schain, the Plugins>Macros>Startup Macros command opens StartupMacros.fiji.ijm if StartupMacros.txt or StartupMacros.ijm are not found.
  • Thanks to Eduardo Kropnick, fixed a 1.51b regression that caused the List.setMeasurements macro function to fail.
• 1.51b 5 June 2016
  • Thanks to Gabriel Landini, when using Image>Duplicate to duplicate a single slice of a stack, the title of the resulting image is derived from the slice label.
  • Added the Help>Examples>JavaScript>Gamma Adjuster example script, which demonstrates how to interactively update an image that has been added to a GenericDialog.
  • Thanks to Ralph Albuquerque, the "Add to overlay" option in Analyze>Set Measurements now causes the overlay elements to be labeled by default.
  • Thanks to Curtis Rueden, replaced the Command Finder tooltips, which could cause an exception, with a "Help" button.
  • Thanks to Alex Doe, the GenericDialog.repaint() method now repaints images that have been added to the dialog (example).
  • Thanks to Joe Pickard, the backspace (delete) key is ignored in the Gel Analyzer to prevent inadvertent erasure of the contents of the selection rectangle.
  • Added the ImagePlus.getRawStatistics(), ImageStatistics.getStatistics(ip) and ImageProcessor.getHistogram(nbins) methods.
  • Thanks to Jerome Mutterer, fixed a bug that caused Roi change listeners to not be notified when a line's width was adjusted and a bug that caused Analyze>Measure to report incorrect values for 'min' and 'max' when "Limit to threshold" was enabled and 'area' was zero.
  • Fixed a bug that made it impossible to unset "Show labels" in the Image>Overlay>Labels dialog box if "Use names as labels" was enabled.
  • Thanks to Jerome Mutterer, fixed a bug that caused the Roi.getContainedPoints() macro function and Roi.getContainedFloatPoints() method to throw exceptions with rectangular selections.
  • Thanks to Ezemiron, fixed a bug that caused the Image>Scale command to throw an exception when processing a stack with an overlay.
  • Thanks to Curtis Rueden, fixed bugs that caused Image>Overlay>Add Image to not set the stack position and Image>Scale to not correctly scale ImageRois in overlays.
  • Thanks to Robert Haase, fixed a bug that caused the Edit>Selection>Create Selection command to throw an exception on Java 8 if there were no thresholded pixels.
  • Thanks to Ondrej Sebesta, fixed a bug that caused the File>Open Next command to sometimes incorrectly preserve the isHyperstack flag.
  • Thanks to Ondrej Sebesta, fixed a bug that caused macro code recorded by the Plugins>Shortcuts>Add Shortcut command to not work as expected if the command name contained brackets (e.g., "In [+]").
  • Thanks to Arttu Miettinen, fixed a bug that caused garbage results when perfprming multiple simultaneous reslice operations.
  • Thanks to Elton Rexhepaj, fixed a bug that caused the ChannelSplitter to create ImageStacks with non-working getVoxel() methods.
  • Thanks to Arttu Miettinen, fixed a bug that could cause the IJ.d2s() method to throw an exception.
  • Thanks to Wilhelm Burger, fixed a bug that caused the ImageProcessor.drawDot() method to not remove the ROI that it sets.
  • Thanks to Matthias Kirsch and Curtis Rueden, fixed 1.50d regressions that caused the Edit>Selection>Create Selection and Edit>Selection>Enlarge commands to not work correctly with multi-point selections.
• 1.51a 3 May 2016
  • Thanks to Michael Schmid, added a plot window dialog called by More>>Contents Style that allows users to modify the color, line thickness and symbol (line/dots/crosses/circles, etc.) of plot curves.
  • Thanks to Wilhelm Burger and Dimitri Vanhecke, added the Roi.getContainedPoints() macro function, Roi.getContainedPoints() method and Roi.getContainedFloatPoints() method (macro example, JavaScript example).
  • Thanks to Wilhelm Burger, Java plugins can now iterate over the points contained in a selection using "for (Point p : roi) {//process}" (example).
  • Thanks to Avital Steinberg and Jan Eglinger, the ImageProcessor.getStatistics() method now calculates all statistics.
  • Thanks to Elton Rexhepaj, the ImageStack.getVoxel(x,y,z) method now throws an IndexOutOfBoundsException if x, y or z are beyong the stack limits.
  • Thanks to Michael Schmid, added the ImageProcessor.isSigned16Bit() method.
  • Thanks to Ved Sharma, fixed a bug that caused the Image>Stacks>Combine command to not maintain the calibration of the source images.
  • Thanks to Elton Rexhepaj, fixed a bug that caused the ImageProcessor.getRoi() method to return an empty rectangle with FloatProcessors created using the FloatProcessor(int[][]) constructor.
  • Thanks to moreglia, fixed a bug that caused an exception when saving FFTs of RGB images in TIFF format.
  • Thanks to Marton Gulyas, fixed a bug that caused overlays to not work as expected on AVI virtual stacks.
  • Thanks to Curtis Rueden, fixed a bug that sometimes caused macros to not be correctly terminated when an error occurred.
  • Thanks to Greg Reneff, fixed a v1.50d regression that caused Process>Math>Macro to not work as expected with signed 16-bit images.

Version 1.50 26 March 2016 (download)

• 1.50i 26 March 2016
  • The ImageJ website (imagej.net/ij) will soon start using encryption incompatible with Java so sample images and updates are now downloaded from wsr.imagej.net and URLs used to open images and text files are redirected to mirror.imagej.net.
  • Thanks to Thorsten Wagner, added the is("global calibration") macro function.
  • Thanks to Philippe Carl, added the RoiManager.rename(index,name) method.
  • Thanks to Nicolas Cedilnik and Mark Hiner, fixed a bug that could cause an exception when saving a virtual stack.
  • Thanks to Kees Straatman, fixed a bug that caused the ROI Manager's "Multi Measure" command to sometimes not work as expected when the "append" option was used.
  • Fixed a bug that caused the "Decimal Places" field in the Analyze>Set Measurements dialog to be ignored after the value was set to zero.
  • Thanks to Stein Rorvik, fixed a 1.50d regression that caused duplicated images to lose their density calibration.
• 1.50h 14 March 2016
  • Thanks to Tiago Ferreira, improved the Command Finder (Plugins>Utilities>Find Commands).
    • Resizable and reduced screen "footprint"
    • Auto-scrolling using keystrokes
    • Tooltip that hints at navigation shortcuts
    • Scriptable
  • Thanks to Ajay Sood, the ROI Manager's OR (Combine) command now uses a progress bar and runs on a separate thread.
  • Thanks to Philippe Carl, the Converter class, which mplements the commands in the Image>Type submenu, now displays a messaged in the "Log" window if the image is locked. This error is typically caused by plugins that mistakenly implement the PlugInFilter interface and call IJ.run() methods.
  • Thanks to Norbert Vischer, the Window>Tile command displays an errow message if there is an unfrozen plot window open. To freeze a plot wondow, use the More>>Freeze Plot command.
  • Thanks to Gabriel Landini, the image size shown in the Window menu is updated when the image is converted to a different type.
  • Thanks to Norbert Vischer, the Dialog.addNumber("Prompt:",NaN) function now creates a blank field instead of showing "NaN".
  • Thanks to Norbert Vischer, added the Plot.setBackgroundColor() macro function (example).
  • Added the ij.plugin.ImageInfo class as a replacement for ij.plugin.filter.info.
  • Thanks to Jeff Hanson, fixed a bug that caused the showMessage() macro function to work with the <html> tag but not with <HTML>.
  • Thanks to Arttu Miettinen, fixed a bug that could cause image corruption if the slice selector scrollbar was used while a stack operation was being performed.
  • Thanks to Ryota Homma, fixed a bug that caused the ROI Manager's More>Remove Positions command to fail.
  • Thanks to Gabriel Landini, fixed a bug that caused the Image>Rename command to sometimes not correctly update the Window menu.
  • Thanks to Herbie Gluender, fixed a v1.50f regression that caused the Process>FFT>Swap Quadrants command to disappear.
  • Thanks to S. Rothery, fixed a 1.50f regression that caused the Multi Measure command in the ROI Manager to not work correctly with hyperstacks.
  • Thanks to Mark Hiner, fixed a 1.50d regression that caused the multi-point tool to not correctly place points on zoomed images.
  • Thanks to Gilles Carpentier, fixed a 1.50g regression that caused macros that used the run("Copy") function on images with overlays to not work as expected.
  • Thanks to Ryota Homma, fixed a 1.49i regression that caused selection subtraction by drawing with the alt key down to not work reliably.
• 1.50g 13 February 2016
  • Thanks to Norbert Vischer, added an "R" (Reset Range) button to the lower left corner of plot windows, and, in the More>>Set Limits dialog, numeric fields can be left empty for automatic range calculation.
  • Thanks to Michael Schmid, changed the name of the Profile Plot Options command to Plots and created a "Profile Plot Options" section at the bottom of the dialog.
  • Thanks to Dorai Iyer, multi-point selections are constrained to a horizontal or vertical line when the shift key is down.
  • Thanks to Michael Schmid, the ROI Manager's "Multi Measure" command displays a progress bar when "One row per slice" is checked.
  • Thanks to Stefan Worz, the Image>Duplicate, Image>Scale, Image>Adjust>Size, Image>Stacks>Stack to Images and Image>Stacks>Images to Stack commands no longer ignore image overlays.
  • Thanks to Christian Irgens, points selections selected in the ROI Manager are no longer moved when they are outside the image boundary.
  • Thanks to Christophe Leterrier, ImageJ now uses the Nashorn JavaScript engine when running on Java 8.
  • Thanks to Mike Davidson, added the call("ij.plugin.frame.ThresholdAdjuster.setMode",mode) macro function and the ThresholdAdjuster.setMode(mode) method, where 'mode' is "Red", "B&W" or "Over/Under".
  • Fixed a bug that caused the Compile and Run command to fail on Java 8 when compiling plugins with errors.
  • Thanks to Jan Eglinger, fixed a bug that caused an exception when saving multi-point selections.
  • Thanks to Rajeev Chaudhary, fixed a bug that caused the Edit>Copy and Edit>Copy to System commands to not correctly handle images with overlays.
  • Thanks to Dan White, fixed a bug that caused the Brightness/Contrast tool to not correctly display min and max values greater than 99999.
  • Thanks to Marc Lartaud, fixed a v1.50c regression that caused the More>>Save command in the ROI Manager to fail if there were duplicate ROI names.
  • Thanks to Michael Schmid and Dan White, fixed a 1.50d regression that caused the File>Save As>AVI command to create files that could not by opened by the Windows Media Player.
• Ved Sharma has released HyperStackReg, a plugin for the alignment (registration) of images in a multichannel hyperstack (C>1, Z>=1, T>1).
• 1.50f 3 January 2016
  • Added the Analyze>Tools>Grid command, which creates a non-destructive grid of lines, crosses, circles or points on the current image.
  • Thanks to Michael Elbaum, added the Process>FFT>Make Circular Selection command.
  • Thanks to Daniel Chung, text images can now be opened by dragging and dropping them on the ">>" icon in the toolbar.
  • Thanks to Stein Rorvik, with spatially calibrated images, the raw width and height are shown in parenthesis as a selection is being created.
  • Thanks to Sho Fujisawa, the ROI Manager uses 5 digits for y-coordinates in ROI names if the image height is greater than 9999 pixels.
  • With RGB images, the Image>Adjust>Threshold command (and shift-t shortcut) no longer runs the ColorThresholder plugin. Instead, it displays a dialog that suggest splitting the image into three grayscale images.
  • Thanks to Norbert Vischer, added the Stack.setOrthoViews(x,y,z), Stack.getOrthoViewsID() and Stack.stopOrthoViews() macro functions (example).
  • Thanks to Stein Rorvik, added the getInfo("macro.filepath") macro function.
  • Thanks to Norbert Vischer, Image>Stacks>Orthoganal Views is faster and more reliable when working with hyperstacks.
  • The getInfo(key) macro function returns "Invalid key" if a value associated with the key is not found.
  • Thanks to Gabriel Landini, added the ImageProcessor.drawLine4(x1,y1,x2,y2) method, which draws 4-connected lines.
  • Added the static RoiManager.getRoiManager() method, which returns a reference to the ROI Manager and opens the "ROI Manager" window if it is not already open.
  • Thanks to Nicolas Stifani, fixed bugs that could cause the getResultLabel(row) and getResultString("Label",row) macro functions to fail.
  • Thanks to MartinH, fixed a bug that caused montages created using Image>Stacks>Make Montage to lose their pixel dimensions.
  • Thanks to Norbert Vischer, fixed a bug that caused the Pixel Inspector tool to not work correctly with blank 32-bit images.
  • Thanks Kees Straatman, fixed a bug that caused Process>Find Maxima, with "Count" output, to sometimes display unwanted results.
  • Thanks to Romain Guiet, fixed a bug in the ROI Manager that caused it to ignore an ROI name if the name was 9 character in length and it had a "-" in the middle.
  • Thanks to Stein Rorvik, fixed a bug that caused macros run from the command line to fail if the argument contained parenthesis.
  • Fixed a 1.50c regression that caused the deprecated RoiManager.getROIs() method to return null.
• 1.50e 19 November 2015
  • Thanks to Curtis Rueden and Brandon Hurr, the Stack to Images, Window>Tile and Window>Cascade commands, and non-batch mode macros that process multiple images, run faster on Macs (test macro).
  • Pressing "i" (Image>Show Info) when no images are open now displays useful information instead of a "No images are open" error.
  • Added a "Show all" checkbox and a "Help" button to the multi-point tool's options dialog box.
  • Thanks to Peter Haub, the Selection Rotator tool, available in the toolbar's ">>" menu, now rotates about the selection centroid and is recordable.
  • Thanks to Radoslaw Ejsmont, ImageJ's directory chooser, on Mac OS X, now uses the JFileChooser when the "Use JFileChoose to open/save" option is enabled in Edit>Options>Input/Output. Unlike the native directory chooser, JFileChooser still has a title bar on OS X 10.11 (El Capitan).
  • Thanks to Anton Jormescu and John Wolodzko, you can again change the views in Image>Stacks>Orthoganal Views by clicking, but not dragging, in the YZ and XZ planes.
  • Thanks to John Wolodzko, added the Plot.showValues macro function, which displays plot window values in the Results table.
  • Thanks to Peter Haub, added the Roi.getContourCentroid() method.
  • Thanks to Jan Eglinger, fixed a bug that caused Image>Adjust>Size, when using bilinear or bicubic interpolation, to shift positions of pixels by 1.0 in X, 0.5 in Y and 0.5 in Z.
  • Thanks to Michael Schmid, fixed a bug that caused the Brightness/Contrast adjuster's "Apply" function to not be undoable for full images or rectangular selections with 8-bit and 16-bit images.
  • Thanks to Michael Schmid, fixed a bug that caused the Brightness/Contrast adjuster to hang with RGB images when there was a non-rectangular selection extending beyond image boundary.
  • Thanks to Bob Hamilton, fixed bugs that caused the Run to Insertion Point macro debugger command to fail and the debugger to sometimes behave erratically.
  • Thanks to David Gault, fixed a memory leak when closing composite color images.
  • Thanks to Jan Eglinger, fixed a bug with the "d" (Draw) keyboard shortcut that caused it to not be correctly recorded.
  • Thanks to Anton Jormescu, fixed a bug in the Image>Stack>Tools>Grouped Z Project command that changed the Z and T dimensions of the original stack, which caused the Duplicate and Synchronize Windows commands to not work as expected.
  • Thanks to Carl Vandewater, fixed a bug that could cause Image>Color>Merge Channels to throw an exception when an input file name was shorter than three characters.
  • Thanks to Till Bretschneider, fixed a bug on OS X and Java 8 that caused copying of text from the macro recorder to fail.
  • Thanks to Saibal Mitra, fixed a v1.50d regression that caused the Process>Math>Macro command to not work correctly with 32-bit images.
  • Thanks to Michael Schmid, fixed a v1.49 regression that caused NaN values to not be correctly handled in plots.
• 1.50d 25 October 2015
  • Thanks to Peter Haub, added the Selection Rotator tool to the Toolbar's ">>" menu. To move the selection with this tool, hold down the alt or shift key.
  • The Edit>Options>Point Tool dialog, in multi-point mode, is now non-modal and has a "Counter" drop down menu. As a shortcut for opening this dialog, double click on the multi-point tool icon.
  • A point in a polygon, polyline or point selection can now be deleted by either alt-clicking or control-clicking.
  • The File>Import>Raw command now uses "smart recording" (default options are not recorded).
  • Added the Help>Examples>Autorun checkbox menu item.
  • Thanks to Michael Schmid, the AVI Reader now opens most oversized (>4GB) ImageJ AVI 1 files and the AVI Writer uses the AVI 2 format, which is AVI 1 compatible for files up to approx 0.9 GB. Use the Virtual Test Stack plugin to create multi-gigabyte test stacks.
  • Thanks to Bill Christens-Barry, added the WaitForUserDialog.setNextLocation(x,y) method (macro example).
  • Added the add(Roi,name) and remove(name) methods to the Overlay class.
  • Added the ThresholdAdjuster.setMethod() method.
  • Thanks to Kota Miura, worked around Java 8 bugs that caused cut, copy and paste to not work in the curve fitter (Analyze>Tools>Curve Fitting).
  • Thanks to Jan Eglinger, fixed a bug that caused the Image>Scale command to ignore the "z=" option when run from a macro.
  • Thanks to Stein Rorvik, fixed a bug that caused calibration bars (Analyze>Tools>Calibration Bar) to remove existing overlays.
  • Fixed a bug that caused the Process>Math>Macro command to not work correctly with 16-bit and 32-bit images if the macro code called the getPixel() function.
  • Fixed a bug that caused the Rotate 90 Degrees Right and Rotate 90 Degrees Left commands to not correctly handle non-zero origins.
  • Fixed a bug that caused polygon and polyline selections to lose properties like stroke color and stroke width after one of the selection's points had been deleted.
  • Thanks to Vytas Bindokas, fixed a bug that caused the waitForUser() macro function to fail on Windows.
• 1.50c 27 September 2015
  • The Image>Stacks>Make Montage command now uses "smart recording" (default options are not recorded).
  • Worked around Java 8 bugs that caused the 't' shortcut (Edit>Selection>Add to Manager) and ROI Manager arrow key and mouse wheel scrolling to not work as expected on OS X.
  • Fixed a bug that caused the "ImageJ" window to expand to full screen on Windows and Linux when you double clicked on the title bar.
  • Thanks to Jens Kriese, fixed a bug that caused no more that 99 menu entries in a plungins.config file to be loaded.
  • Thanks to Jochen Reichel, fixed several RGB-related bugs in the Brightness/Contrast dialog.
  • Thanks to Jan Eglinger, fixed a bug that caused the getResultString() macro function to return "null" on re-opened Results tables if the first column was non-numeric and all other columns were numeric.
  • Thanks to Avital Steinberg, fixed a bug that caused the particle analyzer to alter the Results table counter if the "Display results" option was not enabled.
  • Thanks to John Wolodzko, fixed bugs that prevented ImageJ from correctly opening .csv and .xls tables with cells containing commas.
  • Thanks to Linda Fothergill, fixed a bug that caused selections to change when rotated and then rotated back by the same angle.
  • Fixed a bug that caused the Image>Lookup Tables>Apply LUT command to not work with 16-bit images.
  • Thanks to Martin Hoehne, fixed a bug that caused the run("ROI Manager...") macro function to not work as expected in batch mode macros with hidden ROI Managers.
  • Fixed a 1.50b7 regression that caused the ROI Manager's "Sort" command to not work correctly.
• 1.50b 26 August 2015
  • Folders and AVI files dropped on the toolbar's ">>" icon open as virtual stacks.
  • Thanks to Jerome Mutterer, added the Help>Examples>Macro>Grab Viridis Colormap example macro.
  • Thanks to Norbert Vischer, added the "Dual Progress Demo" example macro and JavaScript to the Help>Examples> menu.
  • Added the "Non-numeric Table" example macro and JavaScript to the Help>Examples> menu.
  • Added the "Image with Overlay" example image to the File>Open Samples> menu.
  • Thanks to Xiuxia Zhang, the Process>Batch>Convert command and IJ.openImage(path) method work with text images.
  • The Image>Overlay>Overlay Options command uses the 'Y' keyboard shortcut and it adds "Show labels" and "Hide" checkboxes to its dialog box if the current image has an ovelay.
  • Assigned the 'W'' shortcut to the File>Close All command.
  • The "Use virtual stack" option in the AVI Reader is set by default.
  • Thanks to Jochen Reichel, fixed a bug that caused the makeSelection("line", xpoints, ypoints) macro function to throw an exception if either array contained a non-integer value.
  • Thanks to Aryeh Weiss, worked around a Java 8 bug that caused the Memory Monitor to fail.
  • Thanks to Hermann-Josef Roser, fixed a bug that caused some imported RGB TIFFs to be read incorrectly.
  • Thanks to Michael Cammer, fixed a v1.44 regression that caused the setLineWidth() macro function to sometimes not work as expected if the global line width set in the Edit>Options>Line Width dialog was not 1.
  • Thanks to Aryeh Weiss, worked around a Java 8 bug on Macs that sometimes caused ImageJ to freeze when clicking on "Show All" in the "ROI Manager" dialog.
  • Thanks to Michael Entrup, fixed a bug that caused the x-axis label of plots to be cut off on Windows.
  • Thanks to Ved Sharma, fixed a bug that caused the macro code "if (false) Array.invert(a);" to generate an error.
  • Thanks to John Wolodzko, fixed a bug that caused the Plot.setLimitsToFit() macro function to sometimes not work as expected.
• 1.50a 21 July 2015
  • Thanks to Gerald Torgersen, added the Plugins>Shortcuts>Add Shortcut by Name command and removed the obsolete Plugins>Shortcuts>Install Plugin command.
  • Thanks to SyntonicC, add a "Rotate around image center" option to the Edit>Selection>Rotate command.
  • Thanks to Thomas Julou, cursor coordinates are displayed in pixels in the status bar if either the alt or shift keys are down.
  • Thanks to Radoslaw Ejsmont, the ChannelSplitter.getChannel() method works with RGB images and stacks and it throws an illegal argument exception if the channel argument is out of range.
  • Added the setThreshold(lower,upper,"raw") macro function and the IJ.setRawThreshold(imp,lower,upper,mode) method.
  • Fixed a bug that caused JavaScripts to sometimes unexpectadly display values in the Log window on Java 8.
  • Fixed a bug that caused the eval("js",code) macro function to fail on Java 8.
  • Fixed a bug that sometimes caused the setThreshold() macro function to throw an exception with 16-bit images.
  • Thanks to Megan Hagenauer, fixed a bug that caused incorrect line selection measurements on density calibrated (global) images.
  • Thanks to Jerome Mutterer, fixed bugs that caused a new dialog to be opened each time you pressed shift-ctrl-f in an editor window to open the macro function finder and caused focus to be lost when you closed the dialog.
  • Thanks to Michael Schmid, fixed a bug that caused the particle analyzer to ignore selections on RGB images.
  • Worked around a Java 8 bug on Macs that caused ImageJ to freeze when changing the display mode in the "Channels" dialog.
  • Thanks to Takashi Abe, worked around a Java 8 bug that caused mirrored cursors in synched windows to not be visible.
  • Thanks to Thorsten Wagner, fixed a bug that caused the "Use names as labels" setting in the ROI Manager's More>>Labels dialog to not be persistent.
  • Thanks to Jerome Mutterer, fixed a 1.49o regression that caused live profile plots of wide lines to flicker.

Version 1.49 23 June 2015

• 1.49v 23 June 2015
  • Thanks to Jan Eglinger, the open(path) macro function opens a folder of images as a stack. Use open(path,"virtual") to open a folder as a virtual stack.
  • Thanks to Ilan Tal, added the WindowManager.getAllNonImageWindows() method.
  • Thanks to Jan Eglinger, fixed a bug that caused the recorder to display a warning message when recording Image>Properties or Analyze>Set Scale and the unit was "µm".
  • Thanks to Christophe Leterrier, fixed a bug that caused the DirectoryChooser, when using Java 7 or later, to not use the native Mac OS X file chooser.
  • Thanks Thorsten Wagner, fixed a bug in the RoiManager that caused the "Labels" checkbox to be ignored when the "Use ROI names as labels" option was enabled.
  • Thanks to Olivier Burri, fixed a bug that caused the run("Merge Channels...","...") macro function to not correctly handle missing arguments.
  • Thanks to Megan Hagenauer, fixed a 1.49t regression that caused plot windows to disable global calibration.
  • Thanks to Jan Eglinger, fixed a 1.49t regression that caused Image>Properties to change Y and Z units to "pixel".
• 1.49u 13 June 2015
  • Added the Help>Examples sub-menu and an Examples menu to the text editor. When opening an example macro or script, hold the shift, control or alt key down to also run it. The examples are also available at wsr.imagej.net/download/Examples/.
  • The Wand Tool Options dialog (opened by double clicking on the Wand tool) now has a "Tolerance" slider that dynamically updates the selection.
  • Added the "NaN empty cells" option to the Analyze>Measurements Options dialog.
  • Thanks to Michael Schmid, the Curve Fitter (Analyze>Tools>Curve Fitting), to avoid aliasing, will use more than 100 points to draw the fitted curve.
  • Thanks to Michael Cammer, the Image>Hyperstacks>Hyperstack to Stack command now works with composite color images.
  • Thanks to Aaron Schain, the Image>Stacks>Tools>Concatenate command maintains hyperstack calibration.
  • Added the Array.getSequence() macro function (example).
  • Added the add(shape,xpoints,ypoints), addLegend(labels), addLegend(labels,options), setColor(String) and getPlot() methods to the Plot class.
  • Added the ImagePlus.isThreshold() and ResultsTable.setNaNEmptyCells() methods.
  • Thanks to Kerry Krugh, Image>Show Info now displays the first 60 characters of UN (Unknown) Value Representation DICOM tags.
  • Thanks to Megan Hagenauer, fixed bugs that caused the Analyze>Measure command to not work as expected with line selections when "Limit to threshold" was enabled in Analyze>SetMeasurements.
  • Thanks to Michael Schmid and Timothy Feinstein, fixed a bug that caused the setSelectionLocation() and Roi.move() macro functions to sometimes not work with straight line selections.
  • Thanks to Gabriel Landini and Michael Schmid, fixed a bug that caused the brush tool to sometimes not work as expected on Linux.
  • Thanks to Jan Eglinger, fixed a bug that caused Process>Batch>Convert to throw an exception when converting stacks to TIFF format.
  • Thanks to Laurent Gelman, fixed a 1.49t regression that caused the Image>Adjust>Canvas Size command to not work as expected with plot windows.
• 1.49t 12 May 2015
  • Michael Schmid contributed a greatly improved Plot class with many new features (demo macro):
    • Plot windows can be resized.
    • Use Image>Zoom>View 100% or More>>Reset Format to revert to the size defined in Edit>Options>Profile Plot Options.
    • Image>Zoom>In, or the '+' key, zooms in (both x&y) and Image>Zoom>Out, or the '-' key, zooms out.
    • Put the cursor below the x axis to zoom in/out horizontally and put it left of the y axis to zoom in/out vertically.
    • With the cursor below or left of the plot, arrows appear, which can be clicked on to to shift the limit.
    • With a selection, the '+' key, Image>Zoom>In and Image>Zoom>To Selection set the data range to the selection.
    • Image>Zoom>Original Scale reverts to the original data range.
    • Image>Zoom>Scale to Fit sets the scale to fit all data.
    • Use the hand tool (or drag with the space bar down) to shift the display range.
    • Select whether axes should have ticks, grids etc. in More>>Axis Options.
    • Adjust the font size in More>>Axis Options or in Profile Plot Options (for future plots).
    • Plots can now have a legend, and with "Legend Position" set to "Auto", the legend tries to not cover any data.
    • You can create a high-resolution (publication-quality) version of a plot by using the More>>High-Resolution Plot command.
  • Thanks to Malgosia Pakulska, the "Apply" button in the Image>Adjust>Brightness/Contrast dialog works with 16-bit images.
  • Thanks to Nicolas Brouilly, the getResult() macro function works with tables that are not named "Results".
  • The "Save..." button in plot windows uses the "File extension for tables" from Edit>Options>Input/Output as the default extension.
  • Image>Adjust>Color Threshold uses the ColorSpaceConverter class (Image>Type>Lab Stack) to do RGB to Lab conversions.
  • Thanks to Vytas Bindokas, fixed a bug that sometimes caused 16-bit to 8-bit conversion of composte color images to fail.
  • Added the getValue("results.count") macro function.
  • Added the TextPanel.getOrCreateResultsTable() method.
  • Fixed a bug that caused the default "File extension for tables" in the Edit>Options>Input/Output dialog to be set to ".csv" when it was actually ".xls".
  • Thanks to Avital Steinberg, fixed a bug that caused an exception when saving composite selections with properties.
  • Thanks to Gabriel Landini, fixed a bug that caused the Make Binary and Convert to Mask commands to not work correctly with thresholded RGB images.
  • Christoph Derigo fixed bugs that caused the Calibrate.setYUnit() and Calibrate.setZUnit() methods to not convert "um" to "µm".
• 1.49r 21 April 2015
  • Thanks to Jerome Mutterer, measurements done using the Set Measurements "Limit to threshold" option add two columns ("MinThr" and "MaxThr") to the Results table.
  • Thanks to Nicolas Brouilly, a progress bar is displayed when large images are resized.
  • The Image>Show Info command (press "i" as a shortcut) displays additional information, including the ImageJ version, java version, OS version, memory in use and the image size.
  • The ROI Manager's "Save..." command is faster and displays a progress bar.
  • The quality of montages created by Image>Stacks>Make Montage is better due to use of bilinear interpolation and averaging when reducing.
  • Added an "Average when reducing" option to the Process>Batch>Convert dialog box.
  • Thanks to Norbert Vischer, the macro editor aborts any existing macro before running or debugging another one.
  • The Image>Stacks>Plot Z-axis Profile command now works with line selections.
  • The macro editor replaces right curly quotes with standard double quotes.
  • Thanks to Jan Eglinger, fixed a bug that caused an exception to be thrown when selecting an image from the Window menu.
  • Thanks to Daisuke Kinose, fixed a bug that caused GenericDialogs without "OK" buttons to throw exceptions.
  • Thanks to Norbert Vischer, fixed a bug that caused pasted image selections to sometimes become permanent before they could be moved.
  • Thanks to Michael Schmid, fixed a bug that caused the OpenDialog.setDefaultDirectory() method to not work as expected on Windows with file paths that ended in slashes instead of backslashes.
  • Thanks to Jurriaan Holzenspies, fixed a bug that caused an exception to be thrown when measuring the perimeter of selections created by the Edit>Selection>Make Rectangular Selection Rounded command in Fiji.
  • Fixed a bug that caused the Process>Batch>Convert progress bar to not work.
  • Thanks to Tomm, fixed a bug the caused the saveAs("Text",filepath) macro function to not work as expected if 'filepath' ended in ".csv".
  • Thanks to Bill Heeschen, fixed a bug that caused macro 'break' and 'continue' statements to not work as expected in 'for' and 'while' loops with inner loops.
  • Thanks to Gilles Carpentier, fixed a 1.49q regression that caused the File>Import>Image Sequence command to ignore overlays.
  • Thanks to Vassilis Kehayas, fixed a 1.45 regression that caused the Histogram command to loss the ability to generate stack histograms of composite color stacks.
• 1.49q 27 March 2015
  • The File>New>Hyperstack command embeds the channel, slice, frame and stack index into the pixel data.
  • Thanks to Michael Schmid and Michael Doube, the 'invertY' calibration flag is now saved in TIFF headers.
  • The options of the ROI Manager's "Multi Measure" command are recorded if the Recorder is in "Macro" mode.
  • The Image>Color>Merge Channels command now deletes the source images after displaying the merged composite image.
  • The run("Subtract Background...","...") macro function no longer changes the default settings in the Process>Subtract Background dialog.
  • Added the Roi.copy() and Roi.paste() macro functions.
  • The Opener.openLut() method now works with URLs (JavaScript example).
  • Thanks to Francis OBrien, added the ChannelArranger.run() method (JavaScript example).
  • Added the IJ.getDir() method, as an alias for IJ.getDirectory().
  • Thanks to Chris Pudney and Michael Schmid, fixed a bug that caused the PARALLELIZE_IMAGES flag of the PlugInFilter interface to return incorrect ROIs when using non-rectangular masks.
  • Thanks to Kurt Bockhorst, fixed a bug that caused Image>Stacks>Images to Stack to sometimes not work correctly with inverted LUT images.
  • Fixed a bug that caused the Image>Color>Arrange Channels command to not work with overlays.
  • Thanks to Jan Eglinger, fixed a bug that caused the run("Quit") macro function to sometimes not work as expected.
  • Fixed a bug that caused extremely large images (e.g. 25000x25000 pixels) to not be displayed correctly because the minimum zoom of 3.1% was not low enough.
  • Thanks to Kees Straatman, fixed a bug that sometimes caused 8-bit images to be incorrectly converted to 16-bits.
  • Thanks to Christophe Deroulers, fixed a bug that sometimes caused the ROI Manager's "Translate" command to not work as expected.
  • Fixed a bug that caused the IJ.openVirtual() method to throw an exception if the file was not found.
  • Thanks to Curtis Rueden, fixed a bug that could cause a StackOverflowError exception on ImageJ startup on systems with three monitors.
  • Thanks to Michael Schmid, fixed a bug in the curve fitter that caused the RODBARD fit to not fit some data.
  • Thanks to Michael Schmid, fixed a bug that caused the Analyze>Tools>Curve Fitting command to sometimes not correctly scale plots.
  • Thanks to Jorge Valero, fixed a 1.49n regression that caused an exception when measuring an area out of the threshold limits in a 16 bit image and "Limit to threshold" was enabled in "Set Measurements".
• 1.49p 28 February 2015
  • Stacks open and save in less time due to faster IJ.showStatus() method.
  • Added the Image>Type>Lab Stack command, which converts an RGB image into a L*a*b* stack using code from Duane Schwartzwald's Color Space Converter plugin.
  • Thanks to Ferdinando Pucci, the Image>Stacks>Tools>Concatenate command works with images that differ in width or height.
  • The Image>Overlay>To ROI Manager command starts numbering at 1 instead of 0.
  • Thanks to Curtis Rueden, Image>Stacks>Images to Stack suggest using Image>Stacks>Tools>Concatenate if the user attempts to combine two or more stacks.
  • The IJ.showStatus() method is up to a 1000 times faster (example).
  • ImageJ displays a better error message when attempting to run a plugin with a missing library.
  • Added the getList("image.titles") macro function.
  • Thanks to Norbert Vischer, added the Roi.setPolygonSplineAnchors(), Roi.setPolylineSplineAnchors() and Roi.getSplineAnchors() macro functions (example).
  • Thanks to Philippe Carl, added the RoiManager.isSelected() method (JavaScript example).
  • Thanks to Philippe Carl, fixed a bug that caused plugins using the NonBlockingGenericDialog to hang when they were called using the run() macro function.
  • Thanks to Matt Jackson, fixed a bug that caused the Image>Zoom>To Selection command to sometimes not work as expected (window does not expand) when the alt key is down.
  • Thanks to Analia Lourenco, fixed a bug that caused ROI Manager outlines created by the particle analyzer to not be displayed in batch mode macros.
  • Thanks to Neil Fazel, fixed a bug that caused File>Import>Text Image to not correctly open files containing "nan" (lower case "NaN") values.
  • Thanks to Philippe Carl, fixed a bug that caused the Edit>Selection>Restore Selection command to not work as expected after making a selection in the ROI Manager.
  • Thanks to Ilan Tal, fixed a bug that could cause the "Close All" command to throw an exception and cause ImageJ to hang.
  • Thanks to Leon Espinosa, fixed a 1.49k regression in the behavior, when processing stacks, of the Process>Binary>Convert to Mask command and "Threshold" widget's "Apply" option.
  • Thanks to Philippe Carl, fixed a regression that caused the ROI Manager's "Show All" and "Labels" buttons to not be recorded.
• 1.49o 21 January 2015
  • Michael Schmid extended the HTMLDialog class to support more text (wrapping lines, scrollbar) and hypertext links. This allows for longer GenericDialog help messages and "About this Plugin" dialogs (Java example).
  • Thanks to Michael Schmid, "Live" mode z-axis profile plots and histograms are updated when you use a command in the Edit>Selection menu, such as shift-a (Select None).
  • Thanks to Michael Schmid, y-units and z-units are saved with and read from tiff/zip files and special characters are preserved in units and description strings.
  • When opening AVI files, the open() macro function no longer displays a dialog box. To open an AVI as a virtual stack, use run("AVI...", "open=file_path use").
  • The measured values (left column) in the Analyze>Calibrate dialog are now validated. With 8-bit images, the values must be in the 0-255 range. With 16-bit images, they must be in the 0-65535 range.
  • Thanks to Cyril Turies, added a Dialog.setLocation(x,y) macro function.
  • Added the IJ.openVirtual(path) method, which opens a TIFF file as a virtual stack.
  • Thanks to Xavier Colome, added the GenericDialog.addImage(ImagePlus) method.
  • Added the setDisplayMode(), getDisplayMode() and setActiveChannels() methods to the ImagePlus class.
  • Added the ij.gui.RoiListener interface.
  • Thanks to Neil Fazel, fixed a bug the caused the ROI Manager's More>>Remove Positions command to sometimes not work as expected.
  • Thanks to Norbert Vischer, fixed a bug that caused the open() macro function to fail when downloading .jar files from https servers.
  • Thanks to Roland Nussbaumer, fixed a bug that caused the "Channels" tool to not be correctly recorded except in "Macro" mode.
  • Thanks to Cong-Xin Qiu, fixed bugs in the FileSaver and RoiManager classes that caused files to not be properly closed when errors occured.
  • Thanks to William Nicolas, fixed a bug that caused the waitForUser() dialog to be closed when the active image was closed.
  • Thanks to Marius Krause, fixed a bug that caused the File>Save As>Image Sequence command to not save overlays when saving in TIFF format.
  • Thanks to Philip Ershler, fixed a bug that caused the Image>Stacks>Plot X-axis Profile command, when plotting a time series stack, to not work if the interframe interval was 0.
  • Thanks to Michael Schmid, fixed a bug that could result in a confusing error message when running a plugin and a class is not found.
  • Thanks to Michael Schmid, fixed a bug that caused updated "Width" and "Height" fields of the Image>Adjust>Size dialog to not be rounded.
  • Thanks to Tokamoto, fixed a 1.49n regression that caused the saveAs("Results",path) macro function to sometimes not work as expected.
  • Thanks to Gilles Carpentier, fixed a 1.49k regression that caused the setupUndo() macro function to not work as expected.
• 1.49n 17 December 2014
  • 16-bit image statistics are calculated faster, using less memory.
  • Thanks to Michael Schmid, overlays modified by PluginFilters are now restored if the dialog is canceled or preview is disabled.
  • Added the Opener.openLut() method (JavaScript example).
  • Thanks to Avital Steinberg, added a runCommand(ImagePlus,String) method to the ROI Manager (JavaScript example).
  • Thanks to Michael Schmid, fixed a bug with frequency domain FFT images that caused a slight (1-pixel) shift between the position indicated in the status bar and the cursor.
  • Thanks to Felix Keber, fixed a bug that sometimes caused the "Threshold" widget to not work correctly with 16-bit stacks.
  • Thanks to Norbert Vischer, fixed a bug that caused the shift-a shortcut for Edit>Selection>Select None to not work as expected after using Analyze>Plot Profile and clicking "Live" in the plot window.
  • Thanks to Olivier Burri and Peter Bankhead, fixed a bug that caused the Image>Type>32-bit command to sometimes incorrectly convert 8-bit images to 32-bit.
  • Thanks to Kay Schink, fixed bugs that caused the particle analyzer to not work correctly with hyperstacks.
  • Thanks to Jared Windover, fixed a bug that sometimes caused the saveAs("Results",path) macro function to not work as expected.
  • Thanks to Gabriel Landini, fixed a 1.49k regression that could cause a plugin using the ImageCalculator class to fail when the plugin was called from a batch mode macro.
  • Thanks to Marc Lartaud, fixed a 1.49k regression that made it difficult to modify and update an ROI selected in the ROI Manager.
• 1.49m 24 November 2014
  • Fixed a bug that caused ImageJ to incorrectly read 3 and 4 channel 16-bit planar TIFFs.
  • Thanks to Dawid Krzempek and Michael Schmid, fixed bugs that caused the setFunction() and setCTable() methods of the Calibration class to sometimes not work as expected.
  • Thanks to Rodrigo Goncalves, fixed a bug that caused the size of maximized windows to be reset when they were moved on Windows 7 and Windows 8.
  • Fixed a 1.49k regression that could cause the imageCalculator() macro function to fail when processing stacks in batch mode macros.
  • Thanks to Frank Ogletree, fixed a 1.48 regression that caused 16-bit Zeiss SEM images to not open correctly.
  • Thanks to Graeme Awcock, fixed a 1.49c regression that caused GIFs with color LUTs to open as RGB images.
• 1.49k 9 November 2014
  • Thanks to Hermann-Josef Roeser, the Histogram command does a better job of plotting histograms with more than 256 bins. To get a dialog that allows you to specify the number of bins, run the Histogram command by pressing alt-h.
  • Thanks to Michael Schmid, the Process>FFT>FD Math command limits the image choices to power of 2 sizes and spatially calibrates the output image.
  • The table created by clicking on "List" in histogram windows is now a results table.
  • Thanks to Michael Schmid, the "B&C" tool no longer disables undo.
  • When running on Java 8, ImageJ uses the Rhino JavaScript engine instead of the built in, but incompatible, Nashorn engine.
  • Thanks to Christophe Leterrier and Johannes Schindelin, the JavaScript interpreter now supports the load() function.
  • Thanks to Philippe Carl, an ROI selected in the ROI Manager is deselected when it is removed from the image as long as the alt or shift keys are not held down.
  • Thanks to Thomas Templier, the ImageCanvas.setSourceRect() method now sets the magnification and is more robust (JavaScript example).
  • Thanks to Johannes Schindelin, added the ij.macro.Debugger interface.
  • Thanks to Glen MacDonald, the run("Make Binary") macro function now supports a 'slice' option that allows stacks to be converted to binary using custom thresholding methods (example).
  • Thanks to Glen MacDonald, fixed several bugs in the Make Binary and Convert to Mask commands.
  • Thanks to Gerhard Hahm, fixed a bug that caused the imageCalculator() macro function to not select the first (output) image in batch mode macros.
  • Thanks to Johan, fixed a bug that caused the calibration to not be updated after updating an existing plot window using the Plot.update() macro function.
  • Thanks to Michael Schmid, fixed a bug that caused Edit>Selection>Create Mask to not maintain the spatial calibration when converting selections into masks.
  • Thanks to Hermann-Josef Roeser, fixed a bug that caused ImageJ to not correctly open 16-bit, 4 samples per pixel TIFFs, such as those created by VueScan.
• 1.49j 25 October 2014
  • Thanks to Ulf Dittmer, pixel hex values are displayed in the status bar when the cursor is moved over RGB images and over the color picker.
  • Thanks to Ved Sharma, added a "File name contains" option to the Process>Batch>Macro dialog box. As with File>Import>Image Sequence, regular expressions must be enclosed in parenthesis.
  • Thanks to Stamatis Pagakis, the "Do not save X values" option in the Edit>Options>Profile Plot Options dialog now works with multiple plots.
  • Thanks to Michael Schmid, fixed a bug that caused the setThreshold(t1,t2) macro function, when t1 and t2 were equal, to not work as expected when used with the Create Mask command.
  • Thanks to Matthew Taylor, fixed a bug that caused Process>Math>Log and the log() macro function to not correctly process values less than or equal to zero in 32 bit images.
  • Thanks to Robert Atwood, fixed a v1.49i regression that could cause the Measure command to throw an exception.
• 1.49i 13 October 2014
  • Impoved Results table auto-formatting.
  • Thanks to Norbert Vischer, the mouse behaves like an eraser if the alt key is held down while creating a polygon, freehand, polyline, freeline or angle selection.
  • Thanks to Stamatis Pagakis, duplicate x columns in profile plot results tables are no longer repeated (example).
  • "Live" and "RGB" buttons are no longer added to stack histogram windows.
  • Thanks to Norbert Vischer, when the color picker background panel is in front, it is labeled "B" and the foreground panel is labeled "F".
  • Thanks to Michael Schmid, added the Array.fourier() macro function and FHT.fourier1D() method (example).
  • Added the ResultsTable.setDecimalPlaces(column,digits) method.
  • Thanks to Matt Pearson, fixed a bug that caused the particle analyzer to not work as expected when processing stacks using the "Overlay Outlines" or "Overlay Masks" options.
  • Thanks to Matt Pearson, fixed a bug that sometimes caused the wrong image to be activated after using the Split Channels command in macros not running in batch mode.
  • Thanks to Christian Tischer and Kota Miura, fixed a bug that caused the BatchProcessor to not ignore hidden Thumbs.db files.
  • Thanks to Christian Tischer, fixed a bug that caused calibration bars to not be displayed correctly on contrast enhanced 8-bit images.
  • Thanks to Bill Christens-Barry, fixed a bug that caused rounded rectangle selections to not be drawn correctly.
  • Thanks to Gadea Mata, fixed a bug that caused the "Intermodes" thresholding method to sometimes not work as expected.
  • Thanks to Konrad Rokicki, fixed bugs that could cause Fiji headless mode exceptions.
  • Thanks to Philippe Gendre and Michael Schmid, fixed a bug that caused the RankFilters.rank(ip,radius,filterType,whichOutliers,threshold) method to ignore the 'threshold' argument.
  • Thanks to Neil Fazel, fixed a v1.49h regression that caused selections moved using the arrow keys to not be drawn correctly.
• 1.49h 19 September 2014
  • Selections in the ROI Manager and in overlays can be dragged by their labels. To show labels in the ROI Manager, click on the "Labels" checkbox. To show labels in an overlay, enable "Show labels" in the Image>Overlay>Labels dialog.
  • Thanks to Jeremy Adler, added "Type" and "Add to overlay" options to Edit>Options>Point Tool dialog. Note that the "Add to overlay" option is not available if the multi-point tool is active.
  • Thanks to Ilan Tal, single macro tools in the macros/toolsets folder added to the toolbar using the toolbar's ">>" menu are restored to the toolbar when ImageJ restarts, as long as the file name matches the tool name and there is a free toolbar slot.
  • Thanks to Philippe Carl and Jerome Mutterer, added the Roi.contains(x,y) macro function.
  • Thanks to Thomas Siegmund, the RoiManager's getRoisAsArray() method is now synchronized.
  • Thanks to Pedro Pepe, fixed a bug that caused the "Sum Method" of Image>Stacks>Z Project to not work correctly with signed 16-bit stacks.
  • Fixed a bug that caused the makePoint(x,y) macro function to not work correctly with non-integer coordinates.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused setThreshold() to fail in batch mode macros.
  • Thanks to Pedro Ramos Cabrer and Michael Schmid, fixed a 1.46 regression that caused 4 or 5 parameter custom curve fits to be much slower.
  • Fixed a regression than sometimes caused the Image>Duplicate command to not be correctly recorded.
• 1.49g 25 August 2014
  • Thanks to Jon Harman, pinch to zoom works on Windows 8 tablets and touch screen laptops.
  • Thanks to Sean Smith, mouse wheel scrolling is faster on Windows.
  • Improved script-mode recording of commands in the Edit>Selection submenu.
  • Thanks to Neil Fazel, fixed a bug that caused the Analyze>Tools>Save XY Coordinates command to not work with NaN backgrounds.
  • Thanks to Richard Pastrick, fixed a bug in the TiffDecoder that caused it to sometimes incorrectly read the XResolution and YResolution tags.
  • Thanks to Jan Eglinger, fixed a 1.49f regression that caused Image>Overlay>Flatten to fail with composite images.
• 1.49f 18 August 2014
  • Thanks to George H, the particle analyzer's "Summary" window has an associated ResultsTable and has "Rename" and "Duplicate" commands in its File and contextual (right-click) menus (macro example, JavaScript example).
  • Thanks to Gabriel Schweighause and Michael Schmid, the second argument (delimiters) of the split() macro function can be a regular expression enclosed in parentheses.
  • Thanks to Aaron Schain, fixed bugs that caused layout problems when resizing hyperstacks, especially when "Scale to Fit" resizing by holding down the alt key.
  • Thanks to Gilles Carpentier, fixed a 1.49e regression that caused the split() macro function to sometimes not behave as expected.
  • Thanks to Biafra Ahanonu, fixed a 1.47 regression in the Image>Scale command that caused unwanted cross-talk in the x,y plane when downsampling in z.
  • Thanks to Olivier Burri, fixed a regression that sometimes caused Image>Stacks>Add Slice to throw an exception when adding a channel to a hyperstack.
• 1.49e 2 August 2014
  • Added the Edit>Options>Startup command.
  • Thanks to Norbert Vischer, added an "Adjust interval to match" option to the Edit>Selection>Interpolate dialog. This option adjusts the interval so that the steps between the first and last point are equidistant.
  • Thanks to Philippe Carl, the ROI Manager now insures that a selection activated by clicking on its label in the image is made visible in the list.
  • Thanks to Ilan Tal, plugin tools can now have right-click popup menus (example).
  • Thanks to Norbert Vischer, you can select a function name in the macro editor and use Macros>Macro Functions to get a description of that function.
  • Thanks to Christophe Deroulers, added a deselect() method to the RoiManager class.
  • Thanks to Neil Fazel, fixed a bug that caused error bars added using the Plot.add() macro function to not appear if the data points were added using Plot.add() (example).
  • Thanks to Marc Lartaud and Michael Schmid, fixed a bug that caused Feret's diameter of selections created with the selection brush tool on spatially calibrated images to be reported in pixels.
  • Thanks to Vytas Bindokas, fixed a bug that caused Edit>Selection>Create Mask to create a blank mask when it was used with a thresholded image in "select all" mode.
  • Thanks to Nikolaus Szeverenyi, fixed a bug that caused upper threshold values entered into the Image>Adjust>Threshold "Set" dialog to be reset to the highest pixel value in the image.
  • Thanks to Gabriel Schweighause and Michael Schmid, fixed a bug that caused the split() macro function to not correctly parse lines with empty cells in comma-delimited CSV files.
  • Thanks to Ilan Tal, fixed a bug that caused plugin tools with hints in parenthesis to not be installed when ImageJ restarted.
  • Thanks to Gilles Carpentier, fixed a v1.48 regression that caused IJ.log("\n") to not add a blank line to the Log window.
  • Thanks to Christophe Deroulers, fixed a v1.49c regression that caused ROI Manager list selections to not be recorded.
• 1.49d 9 July 2014
  • Thanks to Philippe Carl and Neil Fazel, horizontal error bars can now be added to plots (example).
  • Thanks to Alan Brooks, non-uniform x and y units are now used in image subtitles (example) and by the Show Info, Specify, Rotate Right, Rotate Left and Surface Plot commands.
  • Added a "Translate" command to the ROI Manager.
  • Plugins>Install now installs tools with names ending in "Tool.txt", "Tool.ijm" and Tool.class" in the toolbar and saves a copy of the tool in the plugins/Tools folder.
  • Thanks to Neil Fazel, the Overlay.drawString() macro function supports multiline strings.
  • Thanks to Michael Schmid, added the getInfo("window.title") macro function.
  • Thanks to Michael Schmid, added the FHT.transform1D() and FHT.inverseTransform1D()methods (example).
  • Thanks to David Gauntt, fixed bugs that could cause the DicomDecoder#getFileInfo() method to hang when attempting to open non-DICOM files.
  • Fixed a bug that caused Help>Refresh Menus and Plugins>Install to delete macros installed in the Plugins>Macros menu.
  • Thanks to Jan Brocher, fixed a bug that caused RoiManager methods called from plugins to be recorded.
  • Thanks to Andrew Porter, fixed a v1.49 regression that caused some imported TIFF stacks to open incorrectly.
• Thanks to Mark Tsuchida, OS X 10.7 and later no longer displays an "ImageJ is damaged and can't be opened" error message. Instead, it displays an "ImageJ can't be opened because it is from an unidentified developer" message, which can be bypassed by right clicking and selecting "Open" from the drop down menu.
• 1.49c 27 June 2014
  • Selections added to an overlay by the Measure command are removed when the corresponding rows in the Results table are cleared.
  • Animated GIFs can now be opened using File>Open and drag and drop.
  • Overlays are rendered when saving images as GIFs or stacks as animated GIFs.
  • The Analyze>Label command now displays a dialog box that suggests using the "Add to manager" option in Analyze>Set Measurements.
  • Thanks to Lars Damgaard, the run("Image Sequence... ", "...") macro function (File>Save As>Image Sequence) works with single images.
  • When duplicating virtual stacks, progress information is displayed in the status bar.
  • Added the setOption("ShowAngle",boolean) macro function, which determines whether or not "Angle" is reported when measuring straight line lengths.
  • Added the IJ.getFullVersion() macro function.
  • Thanks to Philippe Mailly, added a public multiMeasure() method to the ROI Manager and upgraded the recorder to support this method (example).
  • Thanks to Nicolas Casadei, fixed a bug that caused macros to not reset the "escapePressed" flag, which sometimes caused "INTERRUPTED" to be displayed in the status bar and the macro to not work as expected.
  • Thanks to Christian Renicke, fixed a bug that caused the Brightness/Contrast and Color Balance tools to not work as expected on RGB stacks after an "Apply" operation.
  • Thanks to Matthew Pearson, fixed a bug in the IJ.renameResults() macro function that caused it to sometimes not work as expected if a column had been added using setResult() calls.
  • Thanks to Bryan Callahan and Curtis Rueden, fixed a bug that caused the run("Profile Plot Options...","...") macro function to throw an exception in Fiji headless mode.
  • Thanks to Neil Fazel, fixed a bug that caused Analyze>Plot Profile to not correctly display plot x and y coordinates at the bottom of the plot window when a fixed y-axis scale was used.
  • Thanks to Antoine Vandecreme, fixed a bug that caused ImageJ to incorrectly open non-8bit TIFFs that were missing the BitsPerSample tag.
  • Thanks to Norbert Vischer, fixed a bug in Image>Show Info that caused it to display the pixel size using inadequate precision.
  • Thanks to Philippe Carl, fixed a bug in the setThreshold() macro function that caused it to not update the "Threshold" window.
  • Thanks to Philippe Carl, fixed a bug in the "Threshold" window's "Set" option that caused the plot and scrollbars to not be updated.
  • Thanks to Grimper, fixed a bug that caused the setForegroundColor() macro function to not work in headless mode.
  • Thanks to Tara Ficken and Simon Runde, fixed bugs that sometimes caused ImageJ to incorrectly import TIFF stacks.
  • Thanks to Philippe Carl, fixed ROI Manager bugs that caused it to unexpectedly move selections when using the arrow keys, and to not deselect when switching between images.
  • Thanks to Tiago Ferreira, fixed a v1.48m regression that sometimes caused the "List..." button in plot windows to display an empty table.
  • Thanks to Gabriel Landini, fixed a v1.49 regression that caused cached versions of the blobs.gif sample image to open without an inverting LUT.
  • Thanks to Kees Straatman, fixed a regression that caused the straight line tool to not be recorded.
• 1.49b 30 May 2014
  • Thanks to Jeff Spector, Image>Stacks>Reslice can now create multichannel kymographs from time-lapse 4D hyperstacks (c>1,z=1,t>1) .
  • Thanks to Kenneth Sloan, the width and color of the paintbrush tool can be set using macros (example).
  • The Gel Analyzer now labels lanes with a white number on a black background.
  • The "Fixed y-axis scale" option in the Edit>Options>Profile Plot Options dialog is no longer saved in the preferences file.
  • Thanks to Gabriel Landini, the Plugins>Compile and Run command compiles plugins that us the 3D Viewer. (example).
  • Thanks to Christopher Coulon, fixed a bug that caused Image>Overlay>Flatten to not transfer metadata to the output image.
  • Thanks to Christophe Leterrier, fixed a bug that caused Process>Enhance Contrast to sometimes not correctly set the display range of stacks when "Normalize" was enabled.
  • Thanks to Sidnei Paciornik, fixed a bug that caused the "n_situ" particle analyzer option to not work as expected when analyzing a single stack image (example).
  • Thanks to Sidnei Paciornik, fixed a bug that caused the particle analyzer to hang when processing an 8-bit image and the threshold was set to 0-255.
  • Thanks to Marcel Austenfeld, fixed a bug that caused Image>Stacks>Orthogonal Views to sometimes freeze and/or throw a StackOverflow exception when the user dragged in the "XZ" or "YZ" windows.
  • Fixed bugs related to cropping and projecting stacks with labeled overlays.
  • Thanks to Tara Ficken, fixed bugs that caused some float and int32 TIFFs to be read incorrectly.
  • Thanks to Jeremy Walker, fixed a v1.47o regression that caused the getResult() macro function to not be able retrieve numbers added as strings to the results table.
  • Thanks to Christophe Deroulers, fixed a v1.49a regression that sometimes caused progress bars to not work as expected.
• 1.49a 15 May 2014
  • Thanks to Kenneth Sloan, added a "Paint on overlay" option to the built in brush tool's options dialog. Add the built in brush tool to the toolbar by selecting "Brush" from the toolbar's ">>" menu.
  • Thanks to Daniel Pensold, Analyze>Tools>Save XY Coordinates saves the coordinates and values of pixels inside selections to a .csv file.
  • Thanks to Volker Wirth, added a "Title:" field to the dialog displayed by Edit>Selection>Straighten when the line width is one or when processing a stack.
  • Selections created by the selection brush tool are deleted after they are added to an overlay.
  • Thanks to Jon Harman, Plugins>Install recognizes .zip files.
  • Thanks to Jerome Mutterer, added the makeArrow() macro function (example).
  • Thanks to Federico Luzzati, added the Stack.toggleChannel() macro function (example).
  • Thanks to Norbert Vischer, the showProgress(progress) macro function displays subordinate progress bars as moving dots when 'progress' is negative (macro example, script example).
  • Thanks to Messaoudi Cedric, Edit>Options>Memory & Threads no longer limits the number of threads to 32.
  • Thanks to Wilhelm Burger, added the IJ.setProperty(String,Object) and IJ.getProperty(String) methods, which are useful for passing data between plugins.
  • Thanks to Stephan Preibisch, added the MultiLineLabel#setText() method (example).
  • Fixed a bug that caused the recording mode to not be saved when quitting ImageJ with the Recorder open.
  • Thanks to Mats Nilsson, fixed a bug that caused the getInfo() macro function and ImagePlus#getStringProperty() method to not work with DICOM tags containing letters.
  • Thanks to Norbert Vischer, fixed a bug the caused the Array.findMaxima() macro function to throw an exception when the array length was one.
  • Fixed a bug that caused images with overlays containing black transparent images to not be correctly saved and restored.
  • Thanks to Jan Brocher, fixed a v1.48 regression that caused changes made in the Image>Overlay>Add to Overlay dialog (displayed when you press alt+b) to not be remembered.
  • Thanks to Kees Straatman, fixed a bug that caused the recorder to incorrectly record the Process>Binary>Convert to Mask command.
  • Thanks to Chris Weisiger, fixed a bug in Image>Stacks>Othogonal Views that caused it to fail with extened StackWindows with custom controls.
  • Thanks to Philippe Carl, fixed a v1.48t regression that caused the Plot#drawNormalizedLine() method to not work with log plots.

Version 1.48 19 April 2014

• 1.48v 19 April 2014
  • Plot and Histogram windows are no longer centered on the screen.
  • Added the Overlay.clear and setOption("Add to overlay",boolean) macro functions.
  • Thanks to David Knecht, commands listed in the Plugins>Shortcuts>List Shortcuts and Plugins>Shortcuts>Create Shortcut dialogs are sorted with case ignored.
  • Thanks to Denis Roussel, changed an incorrect Javadoc reference in PlugInFilter.java from SUPPORTS_STACKS to DOES_STACKS.
  • Thanks to Johannes Schindelin, added @link tags to the PlugInFilter.java Javadocs.
  • Fixed a bug that caused the progress bar to not terminate after dragging a jar file to the "ImageJ" window.
  • Fixed a bug that caused the roiManager("add") macro function to unexpectedly set the stack position of the source selection.
• 1.48u 9 April 2014
  • Selections added to overlays by the Measure command when "Add to Overlay" is enabled in Analyze>Set Measurements are labeled with the measurement number.
  • Thanks to Ted Toal, Image>Zoom>Set sets the zoom center based on a point selection and it no longer enlarges the window.
  • Thanks to Norbert Vischer, the macro debugger's Array Inspector now flags array value changes.
  • Added getStringProperty(key) and getNumericProperty(key) methods to the ImagePlus class.
  • Added a TextWindow constructor that accepts an ArrayList.
  • Thanks to Johannes Schindelin, added the GenericDialog#isPreviewActive() method.
  • Thanks to Herbie Gluender, fixed a bug that caused the output of the Plot Profile and Measure commands to be inconsistent with horizontal or vertical one pixel wide straight line selections.
  • Thanks to Gabriel Landini, fixed a bug that could cause the Results table to be displayed very slowly on Java 1.7 and 1.8.
  • Thanks to Burni, fixed a bug that prevented the ImageWindow.setNextLocation() method from working with windows normally centered on the screen, such as plot windows.
  • Fixed a v1.48 regression that caused the run("Add Selection...", options) macro function to not work as expected with text selections.
  • Thanks to Johannes Schindelin, fixed a v1.48r regression that caused the "Fonts" dialog to be displayed multiple times or incorrectly if you double-clicked the text tool icon multiple times.
  • Thanks to Johannes Schindelin, Gabriel Landini and Volker Baecker, fixed a v1.48r regression on Linux that caused ImageJ to freeze when opening a NonBlockingGenericDialog such as the text tool or arrow tool options dialogs.
• 1.48t 28 March 2014
  • Thanks to Ted Toal, holding down the alt key prevents the '+' command (Image>Zoom>In) from enlarging the window.
  • ImageJ remembers the location of the first small image opened.
  • Thanks to Norbert Vischer, Plugins>Utilities>Capture Image hides the zoom indicator.
  • Thanks to Dimiter Proanov, Image>Stacks>Plot Z-axis Profile displays the plot in calibrated units.
  • Thanks to Michael Schmid, added a File>Revert command to the text editor.
  • Fixed the Undo command in the text editor and added the Edit>Balance command, which locates the pair of curly braces or parentheses that surround the insertion point.
  • Thanks to Norbert Vischer, the text editor's Edit>Balance command handles '{' and '}' in comments and quotes, handles '[' and ']' brackets, handles escaped characters and detects errors if nested pairs are not balanced.
  • The Edit>Options>Compiler command now supports Java 1.8.
  • Thanks to Lorenz Maier, the run("Macro...", options) function now works when the options string starts with "v=" instead of "code=v=".
  • Thanks to Nico Stuurman, fixed a bug that caused the GaussianBlur.blurGaussian() method to throw an exception if the image had an ROI.
  • Thanks to Michael Schmid, fixed a bug that could cause the BackgroundSubtracter#rollingBallBackground() method to throw an exception when called with a FloatProcessor.
  • Thanks to Carnë Draug and Johannes Schindelin, fixed a bug that caused the File.directory macro function to not return the expected value after calling open(path).
  • Thanks to Carnë Draug, fixed a bug that precluded running macro files without extensions from the command line.
  • Thanks to Bill Heeschen, fixed a bug that caused Image>Duplicate to shift any non-rectangular selection in the source image to x=0, y=0.
  • Thanks to Jochen Cammin, fixed a bug in File>Import>Raw that caused it to only load the first slice from each file when "Open all files in folder" was checked.
  • Thanks to Julio Buonfigli, fixed a bug that caused the File>Compile and Run command in the text editor to throw an exception if the file name did not end in ".java".
  • Thanks to Philippe Carl, fixed bugs that caused the drawLine(), drawNormalizedLine() and drawDottedLine() methods of the Plot class to not work with log plots.
  • Thanks to Norbert Vischer, fixed a bug in Image>Zoom>Set that caused it to not correctly set the window size of stacks with selections.
  • Thanks to Eric Denarier, fixed a bug that caused Image>Overlay>From ROI Manager to not work in batch mode macros.
  • Thanks to Ted Toal, fixed a bug in the setResult() macro function that caused it to not work as expected when changing a string value in the Results table.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the getProfile() and run("Plot Profile") macro functions to not work as expected.
  • Thanks to Lorenz Maier, fixed a bug that could cause Process>Math>Macro to throw a null pointer exception.
  • Thanks to Michael Schmid, fixed a bug that caused Process>Math>Gamma to not check for invalid gamma values in preview mode.
  • Thanks to Ilan Tal, fixed a regression that caused the "B&C" and "Threshold" windows to not remember their positions when the "ImageJ" window was closed.
• 1.48s 7 March 2014
  • Thanks to Johannes Schindelin, added the Window>Main Window [return] menu command. On Windows, the command is Main Window [enter].
  • Thanks to Philippe Gendre, added a "Marker size:" menu to the Edit>Options>Point Tool dialog box. The choices are "Tiny", "Small" (the default), "Mediam" and "Large".
  • Thanks to Jeremy Sword, added a "Zero transparent" option to the Edit>Selection>Image to Selection and Image>Overlay>Add Image commands.
  • The recorder no longer records default options (e.g., 'size=0-Infinity') when recording Analyze>Analyze Particles, File>Import>Image Sequence and Image>Stacks>Z Project.
  • Image>Show Info displays the image's screen location and, in parentheses, the screen dimensions.
  • Plugins>Utilities>ImageJ Properties displays "Max window bounds" and the bounds of all monitors on systems with multiple monitors.
  • When creating a straight line selection, the angle displayed in the status bar is now calculated using sub-pixel resolution.
  • Added the GenericDialog.setSmartRecording() method, which allows plugins to suppress recording of default dialog box parameters.
  • Thanks to Matt Smith, fixed a bug that could cause a deadlock when using the stack window scrollbar to move through the slices.
  • Thanks to Jiri Janacek, fixed a bug that caused alt-click removal of a point selection to fail if the point was over an overlay element.
  • Thanks to Aaron Schain, fixed a bug that caused Image>Stacks>Tools>Concatenate to sometimes not work as expected with hyperstacks.
  • Thanks to Stoyan Pavlov, fixed a bug in the Roi Manager that caused ROIs to not be updated after changing the position in the More>>Properties dialog box.
  • Thanks to Josh Balsam, fixed a bug in Image>Stacks>Tools>Make Substack that caused it to not work in batch mode macros.
  • Thanks to Ryota Homma, fixed a bug that caused NonBlockingGenericDialogs to not be removed from the Window menu when the dialog was closed.
  • Thanks to Jan Brocher, fixed a bug that caused Edit>Selection>Make Band to fail if "EDM output" was not set to "Overwrite" in Process>Binary>Options.
  • Fixed a bug that could cause the "ImageJ" window to open behind the Windows taskbar.
  • Thanks to Gabriel Landini, fixed a 1.48r regression that caused the Image>Adjust>Threshold dialog to throw an exception if it was activated when already open.
  • Thanks to John Lim, fixed a 1.48q regression that caused the run("RGB Color") macro function to not work as expected with composite color images in batch mode macros.
• 1.48r 18 February 2014
  • Added "Angle", "Color" and "Bkdg" (background color) choices to the dialog displayed when you double click on the text tool or use the Edit>Options>Fonts command.
  • Thanks to Michael Schmid, the Image>Adjust>Threshold dialog displays the percentile of thresholded pixels, along with other improvements (details).
  • With text selections, the Edit>Selection>Properties dialog adds a "Angle:" field and a "Antialiased text" checkbox.
  • Improved text tool recording.
  • NonBlockingGenericDialogs are added to the Window menu.
  • Thanks to Michael Schmid, the Edit>Crop command is undoable.
  • Thanks to Aryeh Weiss, added the RoiEncoder.save() and RoiDecoder.open() methods (example).
  • Thanks to Aryeh Weiss, fixed bugs that caused the recorder to not work as expected when using the ROI Manager to save a single ROI.
  • Thanks to Norbert Vischer, Analyze>Set Scale no longer changes the voxel depth if it is set to a value other than 1.0 (the default value).
  • Thanks to Michael Kummer, fixed a bug that caused ROIs with widths or heights greater than 65535 to not be saved correcty.
  • Fixed a 1.48q reqression that caused CompositeImage unit test errors.
  • Thanks to Norbert Vischer, fixed a bug that caused voxel depths of zero to not be saved in the TIFF header.
  • Thanks to Michael Schmid, fixed bugs that caused the ImageJ menus to disappear on Macs when using the "Threshold", "B&C", "Channels", "CP" (Color Picker) and "Command Finder" dialogs.
  • Fixed a bug that caused the text tool to draw the text outline in the foreground color instead of the selection color.
• 1.48q 1 February 2014
  • Image>Overlay>Flatten now works with non-RGB stacks and hyperstacks.
  • Thanks to Michael Schmid, the Edit>Selection>Specify command adds a "Constrain square/circle" option, supports non-integer numbers and no longer moves the selection when 'Centered' or 'Scaled units' are checked.
  • Thanks to Jerome Mutterer, added a setAngle() method to the TextRoi class (example1, example2, example3).
  • Thanks to Dimiter Prodanov, Image>Stacks>Plot Z-axis Profile, in "Live" mode, draws a vertical line on the plot that corresponds to the current stack position.
  • Thanks to Jean-Olivier Irisson, added setNormalize(boolean), setProcessStack(boolean) and setUseStackHistogram(boolean) methods to the ContrastEnhancer class.
  • Added the Overlay.setFillColor() macro function (example).
  • Thanks to Mark Hiner, the CompositeImage constructor no longer converts stacks to channels when the number of slices is less than eight if the dimensions have been set or if the mode is IJ.GRAYSCALE.
  • Thanks to Marcel Boeglin, added the ImagePlus.flattenStack() method.
  • Fixed a bug that caused horizontal and vertical lines in overlays in to be deleted when duplicating or cropping images.
  • Thanks to Nicolas Brouilly, fixed a bug that caused scales greater than 2,147,483 pixels/unit to be saved incorrectly in the TIFF header.
  • Fixed a bug that caused File>Open Next to not work as expected with TIFF files with overlays.
  • Thanks to Norbert Vischer, fixed a bug that caused the close(wildcard) macro function to sometimes not keep current image active.
  • Fixed a bug that caused the ImagePlus.hide() method to remove overlays.
  • Fixed a bug that caused macro run() calls using the keyword 'stack' in the options string to fail after the "d" (Draw) or "f" (Fill) keyboard shortcuts had been used.
  • Thanks to Marcel Boeglin, fixed bugs that caused Image>Overlay>Flatten to not work correctly with hyperstacks and to not be correctly recorded.
• 1.48p 12 January 2014
  • Added an "Overlay" option to the Analyze>Tools>Calibration Bar dialog box.
  • Image>Color>Split Channels and Image>Hyperstacks>Reduce Dimensionality are faster and preserve slice and frame positions.
  • The Image>Color>Make Composite command no longer displays the "Channels" window or resets the slice position.
  • The Help>Update ImageJ dialog now appends the daily build number, if it exists, to the "You are currently running" version.
  • When processing stacks, a "List thresholds" option is added to the Process>Binary>Make Binary dialog box.
  • The Image>Color>Merge Channels command no longer attempts to auto-fill its dialog unless there are open images created by Image>Color>Split Channels.
  • Added a DEBUG option to the ImageJ constructor. For example, a Java program can run ImageJ invisibly in debug mode using "new ImageJ(ImageJ.NO_SHOW+ImageJ.DEBUG)".
  • Thanks to Philippe Carl, added the GenericDialog.getRadioButtonGroups() method.
  • Added the TextRoi(String,double,double,Font) constructor that can be used as a drop-in replacement for the drawString() macro function and the ImagePlus.drawString() method.
  • Thanks to Jon Nathan, fixed a bug that caused radio buttons in GenericDialogs to not generate dialogItemChanged events (example).
  • Thanks to Ashley Peery, fixed bugs in Image>Color>Merge Channels that caused it to not correctly merge more than three RGB images and to ignore the "Make composite" option when merging RGB images.
  • Fixed a bug that caused Image>Stacks>Z Project to not correctly show progress when processing hyperstacks.
  • Fixed a bug that caused the getSelectionCoordinates() macro function to not work as expected with selections created using makeOval().
  • Thanks to Neil Fazel, fixed a bug that caused File>Import>Text Image to skip the first line of the text image if it consisted of all NaNs.
  • Thanks to Tiago Ferreira, fixed a bug that caused the particle analyzer to sometimes unexpectedly display the Results table if "Stack position" was enabled in Analyze>Set Measurements.
• 1.48o 31 December 2013
  • Fixed a 1.48n regression than caused the "-" (zoom out) command to sometimes display invalid zoom indicators.
• 1.48n 31 December 2013
  • Thanks to Norbert Vischer, Image>Zoom>Set now works with selections (example).
  • Added the Image>Zoom>Scale to Fit command.
  • Fixed a 1.48m regression than caused the "-" (zoom out) command to sometimes not work correctly with images magnified 100% or less.
• 1.48m 29 December 2013
  • Thanks to Dimiter Prodanov, Image>Stacks>Plot Z-axis Profile now supports "Live" profiling.
  • Thanks to "aschain", the channel-slice-frame priority used by the ">" (Next Slice) and "<" (Previous Slice) keyboard shortcuts can be reversed by enabling "Reverse CZT order of ">" and "<" in Edit>Options>Misc. Also, typing ">" or "<" no longer stops animation.
  • Image>Scale and Image>Adjust>Size no longer always use nearest neighbor interpolation when the image width or height is one (example).
  • Thanks to Norbert Vischer, fixed a bug that caused the close(wildcard) macro function to not work with batch mode images.
  • Fixed a bug that caused the active batch mode image to sometimes not remain the active image after setBatchMode("exit and display");
  • Thanks to Michael Schmid, fixed a bug that caused the value unit of 32-bit images to not be saved in the TIFF header.
  • Thanks to Christian Meggle, fixed a bug that caused the ImageProcessor.resize() method to throw an exception when the image width or height was one (test case).
  • Thanks to Norbert Vischer, fixed a bug that cause the close("*") macro function to throw an exception if no images were open.
  • Thanks to Marcel Boeglin, fixed bugs that sometimes caused hyperstacks with overlays to not be correctly duplicated or cropped (test case).
  • Fixed a bug that caused the ImageProcessor.setRoi(Roi) method to sometimes not work as expected with single point selections.
  • Fixed a bug that caused the "List" option in plot windows to sometlimes display duplicate arrays.
  • Thanks to Steffen Decker, fixed a bug that prevented images displayed at 100% from being scrolled after after the window was reduced in size.
  • Thanks to Kees Straatman, fixed a v1.47 regression that caused the getList("window.titles") macro function to not include the Threshold and B&C windows.
  • Thanks to Norbert Vischer, fixed a 1.48a regression that caused filters to not work on virtual stack slices.
• 1.48k 15 December 2013
  • Added a "previous" choice to the Help>Update ImageJ command.
  • Thanks to Marcel Boeglin, the Image>Stacks>Z Project, Image>Type>RGB Color and Image>Color>Stack to RGB commands now support overlays.
  • Added a TextRoi(x,y,width,height,string,font) constructor that is useful for creating centered and right-justified text selections (example).
  • Thanks to Marcel Boeglin, fixed a bug that caused right-justified text selections to not be correctly saved and/or retrieved.
  • Fixed a v1.48h regression that caused TrakEM2 tools to not work as expected.
• The Convert Overlay To Icon macro converts an overlay or selection in a 16x16 image into a tool icon.
• 1.48j 11 December 2013
  • The toolbar is now expandable, with support for up to 15 custom tools.
  • Added the String.show(string) and String.show(title,string) macro functions.
  • Added a 'G' (draw polygon) command to the macro tool icon generation language (example).
  • Thanks to Thomas Suchyna, the Image>Adjust>Threshold window is resizable on Linux and Windows.
  • Thanks to Norbert Vischer, fixed a bug that caused Edit>Selection>Straighten to throw an exception with composite color images with straight line selections.
  • Thanks to Marcel Boeglin, fixed a bug in the Overlay.crop() method that sometimes caused the cropped overlay to be shifted.
  • Thanks to Marcel Boeglin, fixed bugs in Image>Hyperstacks>Reduce Dimensionality that caused it to not work correctly with overlays and with one channel hyperstacks.
  • Thanks to Mats Nilsson, and Johannes Schindelin, fixed a 1.48h regression that caused the getInfo(DICOM-tag) macro function to return empty strings or unexpected values.
  • Thanks to Dietmar Kunz, fixed a v1.48f regression that caused the ImageProcessor.duplicate() method to sometimes not work as expected.
• 1.48i 2 December 2013
  • The "Abort Macro or Plugin" action tool (used by Fiji) is not installed if its installation would result in no free tool slots.
  • Thanks to Michael Cammer, fixed a bug that caused the Overlay.setPosition() macro function to not work as expected with Overlay.drawSting().
  • Thanks to Davide Heller, fixed a bug in Process>Binary>Skeletonize that could result in disconnected segments (test image).
  • Thanks to Pierre, fixed a bug that sometimes caused spline fit segmented lines to shift 0.5 pixels up and to the left after using Edit>Selection>Interpolate.
  • Thanks to Aryeh Weiss and Jay Unruh, fixed a 1.48h regression that could cause Fiji to fail to start if there were AutoRun macros.
• 1.48h 30 November 2013
  • Replaced the blank "Unused Tool" slot in the toolbar with a 9 pixel gap. The toolsets on the ImageJ website without an "Unused Tool" have been updated to use no more than seven tools.
  • Thanks to Jerome Mutterer, added a "List properties" option to the Edit>Selection>Properties dialog box.
  • Thanks to Sebastien Octeau, added a "Skip dialog when opening .raw file" option to the Edit>Options>Input/Output dialog box.
  • Thanks to Norbert Vischer, the information shown in the Help>About ImageJ window is displayed in a text window when you press "i" (Image>Show Info) and is therefore easily copied to the clipboard.
  • Changed the default file extension for tables from ".txt" to ".csv" (comma-separated values).
  • Added "Insert", "Info" and "Close" buttons to the dialog opened by the macro editor's Macros>Function Finder command.
  • Plots created by Analyze>Calibrate always use an x range of 0-255 with 8-bit images.
  • The makeRectangle() and makeOval() macro functions support subpixel resolution.
  • Thanks to Jerome Mutterer, added getProperty(), setProperty() and getProperties() methods to the Roi class and Roi.getProperty(), Roi.setProperty() and Roi.getProperties() macro functions (example).
  • Thanks to Norbert Vischer, added setBatchMode("show") and setBatchMode("hide") macro functions.
  • Added Roi.getBounds(), Roi.getColor, Roi.getFillColor, Roi.getCoordinates(), Roi.getName, Roi.setFillColor(), Roi.setLocation(), Roi.setName(), Roi.setStrokeColor() and setStrokeWidth() macro functions (example).
  • Fixed a bug that caused toolbar icons to sometimes be drawn incorrectly.
  • Thanks to Michael Schmid, fixed a bug in Process>Noise>Salt and Pepper that caused it to omit the last column and row of the image.
  • Thanks to Michael Schmid, fixed bugs in the macro interpreter that caused expressions in the form s+"abc", where 's' is a string variable, to cause macros to abort when used as a function argument or used in a 'return' statement.
  • Thanks to Patrick Page-McCaw, fixed a bug that sometimes caused the particle analyser, when run from a plugin, to display a "No particles were detected..." dialog.
  • Thanks to Norbert Vischer, fixed a bug that caused an exception if the Size or Circularity fields in the particle analyzer dialog box were blank.
  • Fixed a bug that caused the wand tool to not be correctly recorded if the Recorder was not in "Macro" mode.
  • Thanks to Rainer Engel, fixed a bug that caused the particle analyzer to sometimes unexpectedly add selections to overlays.
  • Thanks to Norbert Vischer, fixed a bug that caused the LUT to be incorrect after switching channels in a batch mode macro.
  • Fixed a bug that caused the ROI Manager to sometimes unexpectedly display a "Save n ROIs as an overlay" message.
• Holger Lorenz contributed the Sphere Builder and Ellipsoid Builder, macros that create spheres/ellipsoids as 3D stacks.
• Ved Sharma has released Invadopodia tracker, a plugin for analyzing invadopodia dynamics parameters from fluorescence time-lapse movies.
• 1.48g 14 November 2013
  • Increased the size of toolbar icons from 26x26 to 28x28 pixels, which increased the width of the "ImageJ" window by 42 pixels.
  • Reduced the height of the status bar and increased the font size.
  • Increased the default menu font size on Windows from 14 to 15 points.
  • Added a "Fill with" option of "Random" to the File>New>Image dialog box.
  • Thanks to Michael Schmid, File>Save As>Tiff and File>Save As>ZIP now save the FFT data of FFT windows, except for FFTs of RGB images.
  • The File>New>Hyperstack command now labels using an overlay.
  • The Image>Show Info command displays overlay information.
  • Thanks to Michael Schmid, added the getInfo("window.type") macro function.
  • Thanks to Nico Stuurman, added setPaintPending() and getPaintPending() methods to the ImageCanvas class.
  • Thanks to Marcel Boeglin, added translate(x,y) (JavaScript example) crop(Rectangle), crop(firstSlice,lastSlice) and crop(firstC,lastC,firstZ,lastZ,firstT,lastT) methods to the Overlay class.
  • Thanks to Marcel Boeglin, fixed bugs that caused Image>Crop and Image>Duplicate to sometimes not work correctly with images containing overlays.
  • Fixed a 1.48f regression that caused unexpected Feret's diameter angles to be returned.
  • Fixed a bug that sometimes caused selections to not be correctly restored to the last slice or frame of a hyperstack.
  • Thanks to Barry DeZonia, fixed bugs that could cause the Image>Transform>Bin command to not work correctly on float images with negative pixel values.
  • Fixed a bug that sometimes caused custom tool preferences to not be correctly saved.
• Packt Publishing has released Image Processing with ImageJ, a 140 page introduction to ImageJ available in either e-book or paperback format, written by Javier Pascau and José María Mateos Pérez.
• 1.48f 30 October 2013
  • The Recorder now records File>Import>Import URL as open(url) (macro mode) or imp=IJ.openImage(url) (script or Java mode).
  • Thanks to Michael Schmid and Audrey O'Neill, ImageJ can now open MJPG-encoded files where the size of the JPEG frames differs from the size of the movie frames.
  • Thanks to Jan Eglinger, fixed a bug that caused the Recorder to record duplicate parameters when recording IJ.getFilePath().
  • Thanks to Ivan Micetic, fixed a bug that caused File>Revert to not restore image properties and LUTs.
  • Thanks to Christophe Leterrier, fixed a v1.48a regression that caused selections names longer than 20 characters displayed in the results table to be truncated.
  • Thanks to Bill Heeschen, fixed a v1.48e regression that caused the Process>Filters>Convolve command to fail.
• Jerome Mutterer contributed the LineAndProfileTool macro tool, which creates a line selection while displaying the corresponding profile plot as an overlay.
• 1.48e 19 October 2013
  • Thanks to Michael Schmid, plots now use scientific notation for large numbers and the curve fitter no longer runs on the event queue and can be aborted.
  • Changed the ROI Manager's "Remove Slice Info" command to "Remove Positions...".
  • Line selections are always drawn offset 0.5 pixels down and to the right regardless of the "Sub-pixel resolution" option in Edit>Options>Profile Plot Options.
  • Thanks to Miettinen Arttu, File>Import>Raw now decodes image dimensions embedded in file names (e.g., "name1_512x512.raw", "name2_256x256x256.raw").
  • The default "Fill with:" option in the File>New>Image dialog is now "Black" and the default foreground color is white and the default background color is black.
  • Added a "Help" button to the Analyze>Gels>Gel Analyzer Options dialog box.
  • Fixed a 1.48d regression the caused the "Simplex Fitting Options" dialog in Analyze>Tools>Curve Fitting to throw and exception when performing user-defined fits.
  • Thanks to Michael Schmid, fixed a curve fitting bug which could cause unintended values for the initial parameters (resulting in more iterations than necessary).
  • Thanks to Peter Haub, fixed a bug that caused the CommandListener interface to not work as expected when ImageJ was exited by clicking on the "ImageJ" window's the close box.
  • Thanks to Pavol Bauer, fixed a bug that caused Process>Batch>Macro to not open .lsm files using Bio-Formats when the LSM_Reader plugin was not installed.
  • Fixed a bug in the new File>Open Samples>Cache Sample Images command that caused it to throw an exception.
  • Thanks to Michael Schmid, fixed a bug that caused the spline fitter to sometimes not work as expected (example).
  • Thanks to David Bragason, fixed a bug that made it impossible to subtract from a selection or create a centered oval selection if there was an underlying overlay.
  • Fixed a bug that caused the bounding box of spline fit selections to be incorrect.
• 1.48d 28 September 2013
  • Thanks to Johannes Schindelin, added the File>Open Samples>Cache Sample Images command.
  • Thanks to Stephan Saalfeld, Image>Type>32-bit now supports conversion of RGB stacks to 32-bit float and RGB to float conversions are done directly.
  • Thanks to Michael Schmid, added "Exponential Recovery (no offset)" and "Chapman-Richards" curve fitting options.
  • The File menu and popup menu of non-active results windows now contain "Rename..." and "Duplicate..." commands.
  • The title of a non-active results window changes if it is saved using a different name.
  • Thanks to Norbert Vischer, added the Array Inspector to the macro debugger (test macro).
  • In the macro language, 'break' and 'continue' statements are now supported in 'for' and 'while' loops.
  • Thanks to Norbert Vischer, added the Array.show() macro function (examples).
  • Thanks to Dimiter Prodanov, fixed a bug that caused the Recorder to not generate a plugin that would compile and run after recording Process>Image Calculator.
  • Thanks to Jonas Ogaard, fixed a bug that sometimes caused an exception when drawing ROIs created with the brush selection tool.
  • Thanks to Dimiter Prodanov, fixed bugs that caused Analyze>Plot Profile to not work correctly when the intensity was uniform.
  • Fixed a bug that caused the Recorder to not correctly record the polygon, segmented line and point tools in "JavaScript" mode.
  • Fixed a bug that caused the Recorder, when not in "Macro" mode, to sometimes not correctly record commands in the Edit>Selection menu.
  • Thanks to Eric Denarier, fixed a bug that could cause the Results window to become inconsistent when using the Measure command after running the particle analyzer.
  • Thanks to Guy Lyons, fixed a bug that caused the roiManager("Show All with labels") macro function to not work in batch mode.
  • Thanks to Dimiter Prodanov, fixed a bug that could cause ImageJ to throw an exception on startup.
  • Thanks to Barry DeZonia, fixed a bug that caused the ImageProperties.getUnitIndex() method to not work correctly when passed the string "mile".
  • Thanks to Barry DeZonia, fixed a bug that caused the Image>Properties dialog to not reset the Y and Z units when the "Unit of length" was changed.
  • Thanks to Michael Schmid, fixed a 1.46f regression that caused some user-defined curve fits to fail.
  • Fixed a 1.48 regression that caused the ROI Manager to not correctly associate hyperstack ROIs to CZT positions.
• 1.48c 12 September 2013
  • Thanks to Marcel Boeglin, plugins launched using Plugins>Compile and Run now display a full stack trace if they throw an exception.
  • Thanks to Chris Coulon, the "<" and ">" keyboard shortcuts no longer display "There are no images open" and "Stack required" error messages.
  • Thanks to Norbert Vischer, the output of the Array.print() macro function is better formatted.
  • Thanks to Norbert Vischer, added the Array.findMaxima() and Array.findMinima() macro functions and corresponding MaximumFinder.findMaxima() and MaximumFinder.findMinima() methods (examples).
  • Thanks to Volko Straub, added the Overlay.moveSelection(index,x,y) macro function (example).
  • Thanks to Wilhelm Burger, added convertToByteProcessor(), convertToShortProcessor(), convertToFloatProcessor() and convertToColorProcessor() methods to the ImageProcessor class.
  • Thanks to Arthur Edelstein, added the Prefs.paintDoubleBuffered flag.
  • Thanks to Jose Maria Mateo, fixed a bug that caused run() macro calls using "&" notation to incorrectly pass numeric variables to the GenericDialog's getNextChoice() method.
  • Thanks to Bjoern Thiel, fixed a bug that caused the Analyze>Plot Profile command to not work as expected with spatially calibrated image with non-square pixels.
  • Thanks to Norbert Vischer, fixed a bug that caused the Plot.create() macro function to throw an exception if the y array was shorter than the x array.
  • Thanks to Norbert Vischer, fixed a bug that caused plots created by batch mode macros to not be scaled.
  • Thanks to Ved Sharma, fixed a bug that caused Analyze>Tools>Synchronize Windows to not work as expected with c=1, z=1, t>1 stacks.
  • Thanks to Rainer Engel, fixed bugs that sometimes caused the IJ.redirectErrorMessages() macro function to not prevent file read errors from aborting macros (example).
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Duplicate to throw an exception if there was a selection outside the image.
• 1.48b 25 August 2013
  • Thanks to Michael Doube and Johannes Schindelin, added the "Interpolate ROIs" command to the ROI Manager.
  • Thanks to Norbert Vischer, submenus are now supported in the Plugins>Macros menu (example).
  • Updated the templates generated by the Plugins>New>Plugin and Plugins>New>Plugin Filter commands.
  • Rather than display an error message, the Copy and Cut commands now copy or cut the entire image when there is a line or point selection.
  • Added the ImageProcessor.set(double) method, now used by the Process>Macro>Set command.
  • Thanks to Eric Barnhill, added the HyperStackConverter.toHyperStack() method. A call to this method is generated if the recorder is running in script mode and the Image>Hyperstacks>Stack to Hyperstack command is used.
  • The Plugins>Macros>StartupMacros command works when the startup macros file is names StartupMacros.ijm.
  • The ImageConverter class works with stacks.
  • Thanks to Johannes Schindelin and Hans Wurscht, fixed a bug that sometimes caused memory used by images opened in batch mode macros to not be reclaimed (test macro).
  • Fixed a bug that caused run("Command") macro calls to run in a separate thread if "Command" was a macro installed in the Plugins>Macros submenu.
  • Thanks to Jan Brocher, fixed a bug that caused Image>Overlay>Flatten to sometimes not work as expected with RGB stacks.
  • Thanks to Gilles Carpentier, fixed a bug in the macro interpreter that caused it to incorrectly assign expanded arrays.
  • Thanks to Michael Schmid, fixed a bug that caused the FFT command to incorrectly display power spectra of RGB images.
  • Thanks to Alberto Duina, fixed a 1.48a regression that sometimes caused the ImageJ.updateAndDraw() method to throw an exception.
  • Fixed a bug that caused the IJ.getImage() method to display a "...Macro cancelled" error when using the "Compile and Run" command and no image was open.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused the particle analyzer to display a blank Results table.
  • Thanks to Michael Schmid, fixed a bug that caused ImageJ to not correctly save 16-bit grayscale images in PNG format.
  • Thanks to Alberto Duina, fixed bugs that caused Edit>Selection>Interpolate to create straight line selections shorter than the original and to not work correctly with straight lines selections wider than one.
• 1.48a 22 July 2013
  • Added the Image>Overlay>List Elements command.
  • Thanks to Peter Haub, color LUTs are saved with 16-bit and 32-bit TIFFs.
  • Thanks to Simon Roussel, added Edit>Find and Edit>Find Next commands to text windows, such as those created by Image>Show Info.
  • The Image>Show Info command displays the display range of each channel, up to 7.
  • The "Set stack positions" option in the Image>Overlay>Options dialog is enabled by default.
  • Added a "Position:" field to the Edit>Selection>Properties dialog box.
  • Thanks to Dimiter Prodanov, added duplicate(), crop() and convertToFloat() methods to the ImageStack class.
  • Thanks to Franz Graf, added the ColorProcessor.setRGBWeights() method, a thread-safe (non-static) version of ColorProcessor.setWeightingFactors().
  • Thanks to Michael Doube, fixed a bug that caused plugins in jar files with a plugins.config entry starting or ending in one or more spaces to not be installed correctly.
  • Thanks to Jason Rogers, fixed a bug that caused the Edit>Copy command in "Results" windows to not work with one line tables.
  • Thanks to Vytas Bindokas, fixed bugs that caused 3D filters in Process>Filters to not work correctly with hyperstacks and to sometimes throw exceptions.
  • Thanks to Fabrice Cordelieres, fixed a 1.47v regression that sometimes caused unexpected results from setting the "plugins.dir" Java property.
  • Thanks to Norbert Vischer, fixed a bug that caused some commands in Process>Filters to throw an exception if the selection was outside the image.
  • Thanks to Gilles Carpentier, fixed a bug that caused a corrupted file to be created when using the setMetadata("Info","") macro function on a composite color image with an overlay and saving in TIFF format.
  • Thanks to Dimiter Prodanov, fixed a bug that sometimes caused a displayed stack to become inconsistent after the ImageStack was updated.
  • Thanks to Julien Berro, fixed a bug the caused the ROI Manager "Update" function to sometimes not work as expected with hyperstacks.
  • Thanks to Karsten, fixed a bug that caused Analyze>Measure to add very long selection names (longer than 20 characters), or selection names duplicating the image name, to labels in the Results table "Label" column.
• 1.47v 8 July 2013
  • Thanks to Wilhelm Burger, Plugins>Compile and Run works with plugins in packages that correspond to subfolders of the plugins folder and the PluginClassLoader searches ImageJ/jars for library jar files and classes.
  • Thanks to Gilles Carpentier, the ROI Manager's More>>List command now displays ROI stack and hyperstack positions and Overlay ROIs are always displayed on composite color images regardless of the stack positions of the ROIs.
  • Thanks to Laurent Holtzer, fixed a bug that caused Image>Adjust>Brightness/Contrast to not work correctly with 16-bit virtual stacks opened using the Bio-Formats plugin.
  • Fixed a bug the caused the getBitDepth() method of ImageProcessor subclasses to sometimes return 0
• 1.47u 25 June 2013
  • Thanks to Tiago Ferreira, the Plugins>Utilities>Search command now displays "Double-click on a file name to open it" in the Log window header bar.
  • Added a "Keep after adding to overlay" option to the arrow tool options dialog box.
  • Thanks to Elyse Aurbach, Analyze>Calibrate supports four more calibration functions and displays better calibration plots.
  • Thanks to Norbert Vischer, added the debug("conditional") macro function.
  • Thanks to Ved Sharma, fixed a bug that caused the particle analyzer to always create a new "Summary of ..." table when processing stack slices.
  • Thanks to Tiago Ferreira, fixed a bug in the Overlay.activateSelection() macro function that caused it to ignore stack positions.
  • Thanks to Barry DeZonia, fixed a bug that caused Image>Stacks>Tools>Reverse to not work with virtual stacks defined in Imglib.
  • Thanks to C Heeney, fixed a bug in the PolygonRoi class that caused it to modify the contains of float arrays passed to it in the constructor.
  • Thanks to Sebastien Simard, fixed a bug that caused multi-line arguments passed to user plugins to be displayed in the Log window when ImageJ was in debug mode.
  • Thanks to Jerome Mutterer, fixed a v1.47 regression that caused command line options similar to "-Dplugins.dir=..\ImageJ" to not work as expected.
  • Fixed a bug that caused the paths returned by getDirectory("image") and getDirectory("macros") to be incorrect if the path specified in the "-Dplugins.dir=path" command line option ended in "plugins".
  • Thanks to Andrew York, fixed a bug that caused macros run from the command line to sometimes unexpectedly display dialog boxes.
  • Thanks to Alberto Duina and Gabriel Landini, fixed a v1.47t regression that caused an exception to be thrown if a string with a length less than 3 was entered into a dialog box and the recorder was running.
• 1.47t 7 June 2013
  • The macro intepreter provides a better error message when a macro tries to index an empty array, such as the ones returned by the split() function when no tokens are found.
  • Thanks to Gilles Carpentier, fixed a bug that caused Image>Stacks>Tools>Reverse to not work as expected with composite color images.
  • Fixed a bug that sometimes caused Edit>Options>Memory & Threads to fail when ImageJ was started using the Linux launcher.
  • Thanks to Josef Borkovec, fixed a bug that caused GenericDialogs to not correctly record strings containing Windows file paths with backslashes.
  • Thanks to Barry DeZonia, fixed a bug in Image>Color>Arrange Channels that caused it to throw an exception with stacks with more than 10 channels.
  • Thanks to Gilles Courtand, fixed a v1.47s regression that caused the Process>Batch>Macro and Process>Batch>Virtual Stack commands to throw exceptions.
• Peter Bankhead has made available Analyzing fluorescence microscopy images with ImageJ, a 184 page introduction to image analysis in PDF format.
• 1.47s 3 June 2013
  • Fixed a 1.47r regression that sometimes caused color composite images to not work as expected.
• 1.47r 2 June 2013
  • Added the Image>Color>Display LUTs command.
  • Improved the Plugins>Utilities>Search command, which now uses radio buttons in its dialog box.
  • Philippe Carl extended the Plot class to support log and arrow plots (example1, example2).
  • Thanks to Federico Luzzati, added a "Prepend" option to the Image>Stacks>Add Slice dialog box.
  • Added a "BeanShell" mode to the command recorder (Plugins>Macros>Record).
  • Thanks to Samuel Inverso, the File>Import>Raw dialog is displayed when a .raw file is dragged and dropped on the "ImageJ" window or opened using File>Open.
  • ImageJ now replaces underscores with spaces when adding .lut files in the ImageJ/luts directory to the Image>Lookup Tables menu.
  • Thanks to Ingo Bartholomaeus, several ImageProcessor methods (e.g. copyBits()) no longer display progress bars.
  • Thanks to Norbert Vischer, the setColor() and Plot.setColor() macro functions now accept hex strings such "#ff0000".
  • Added the getList("LUTs") macro function (example) and the IJ.getLuts() method.
  • Added the newImage(title,type,width,height,channels,slices,frames) macro function, which is recorded when using the File>New>Hyperstack command.
  • Added the addRadioButtonGroup() and getRadioButton() macro functions (example).
  • Added the addRadioButtonGroup() and getNextRadioButton() methods to the GenericDialog class (example).
  • Thanks to David Nauen, fixed a bug that caused Analyze>Measure to not calculate and display "Centroid" values of straight line selections.
  • Thanks to Matt Smith, fixed a bug that caused RGBA tiff stacks to not be opened correctly.
  • Thanks to Gilles Carpentier, fixed a bug that caused the Edit>Selection>Restore Selection command to sometimes fail.
  • Thanks to Gilles Carpentier, fixed a bug that caused Edit>Paste to not work as expected with selections that extend beyond the image boundary.
  • Thanks to Johannes Schindelin, fixed ROI Manager bugs that caused key presses to be recorded twice, caused multiple selections to be recorded incorrectly as single selections, and caused macro calls like roiManager("Select",newArray(1,2)) to not update the GUI.
  • Worked aroung a bug in Java 1.7 for OS X that caused the DirectoryChooser, used by File>Import>Image Sequence, to fail.
  • Thanks to Christophe Leterrier, fixed a bug in File>Import>Image Sequence that caused it to not set the slice label when the folder being opened contained a single image.
  • Thanks to Sebastian Rhode, fixed a bug that sometimes caused Analyze>Tools>Synchronize Windows to not work as expected when synchronizing hyperstack positions.
  • Thanks to Gilles Carpentier, fix a bug that sometimes caused ROIs with names containing dashes to not be displayed in a stack overlay.
• 1.47q 6 May 2013
  • Added the Image>Stacks>Tools>Set Label command.
  • Thanks to Stephan Saalfeld, fixed a bug that caused the width and height of selections to be capped at 99999.
  • Thanks to Burri Olivier and Michael Schmid, fixed a bug that caused Analyze>Distribution to not work with ranges containing negative numbers.
  • Thanks to Abed Alnaif, fixed a bug that caused Analyze>Plot Profile to sometimes not work correctly with wide segmented line selections.
  • Thanks to Brian Barford, fixed a v1.47j regression that caused the Chart White Balance plugin to not work correctly.
  • Fixed a v1.47o regression that caused Bio-Formats to throw an exception when opening virtual stacks.
• 1.47p 29 April 2013
  • Added the Edit>Selection>Scale command.
  • The roiManager("Rename",name) macro function adds "-1" to names that duplicate existing names.
  • Fixed a bug that caused the Edit>Selection>Rotate command to not work with composite selections.
  • Fixed a 1.47o regression that caused incorrect display of measurement results if "Stack position" was enabled in Analyze>Set Measurements and also caused the List.setMeasurements() macro function to fail.
• Jan Brocher contributed BioVoxxel Toolbox, which includes these macros: Advanced Particle Analyzer, Feature Extractor, Speckle Inspector, Watershed Irregular Structures, EDM Erosion and Dilation, Auto Binary Masking, Threshold Checker, Contrast Detection, Difference of Gaussian, Difference from Median and Hyperstack Color Coding. Documentation is at www.biovoxxel.de/macros.html.
• 1.47o 26 April 2013
  • Results tables can now contain columns of strings (example).
  • Added the File>Import>Table command.
  • Added an "Open images using Bio-Formats" option to Process>Batch>Convert.
  • Thanks to Norbert Vischer, File>Save As>PNG saves 4-image 8-bit stacks or hyperstacks as PNG with alpha if the label of the fourth image is "Alpha".
  • Thanks to Wilhelm Burger, added the ImagePlus.setAntialiasRendering(boolean) method, which enables/disables use of antialiasing by the ImagePlus.flatten() method and the Image>Overlay>Flatten command.
  • Updated the ColorProcessor.getChannel() and ColorProcessor.setChannel() methods to support the alpha channel (example).
  • Updated the setResult() macro function to work with string values and added the getResultString() function.
  • Updated the ResultsTable addValue() and setStringValue() methods to work with string values and added the getStringValue() method (example).
  • Added the IJ.getFilePath(dialogTitle) method.
  • Added the Opener.openUsingBioFormats(path) and Opener.openTable(path) methods.
  • Johannes Schindelin added missing close() calls that caused Eclipse's resource leak warnings.
  • Johannes Schindelin made the ImageJ source compatible with Java 1.5 again by removing an illegal @override annotation from SubHyperstackMaker.java.
  • Thanks to Tom Kazimiers, fixed a v1.47f regression that caused the saveAs("tif",path) macro function to convert ".tiff" extensions to ".tif".
  • Thanks to Curtis Rueden, fixed a bug the caused Image>Stacks>Make Montage to not work as expected with composite color images.
  • Fixed a bug the caused Edit>Selection>Fit Spline to not work correctly with polygon selections.
  • Thanks to Philippe Carl, fixed a bug that sometimes caused the ImagePlus.setProcessor() method to not work as expected with stacks.
  • Thanks to Fabrice Cordelieres, fixed a bug that caused the Image>Stacks>3D Project command to throw an exception when working with 16 or 32 bit stacks and the "Interpolate" option was enabled.
  • Thanks to Jan Eglinger, fixed a bug that caused the precision of imported results to always be set to 3 decimal places.
• Norbert Vischer released Perspective Stack View, a macro set that creates perspective views of stacks and hyperstacks for use in presentations or publications.
• 1.47n 30 March 2013
  • The Image>Show Info command uses the Exif Reader plugin (version 2013/03/29 or later) to display Exif data of JPEG images.
  • Added a Macros>Show Log Window command to the macro editor.
  • Thanks to Johannes Schindelin, the eval("script",JavaScriptCode) macro function now returns, as a string, the value of the last expression evaluated.
  • The ImageListener interface triggers an image updated event when an image is renamed.
  • The Compile and Run command downloads the Java compiler to the plugins/jars folder as needed.
  • Added the blurGaussian() and applyMacro() methods to the ImageProcessor class (example1, example2).
  • Added the Overlay.setPosition(c,z,t) and Overlay.drawLabels() macro functions.
  • Fixed a bug that caused the Python print statement to not work as expected.
  • Thanks to Julian Cooper, fixed a bug that caused bounding box values displayed in the Results window, when measuring lines selections, to always be in pixel units.
  • Thanks to Curtis Rueden, fixed a bug that caused the ROI Manager to not restore hyperstack ROIs to the current CZT position.
  • Thanks to Julian Cooper, fixed a bug that caused vertical lines selections at the left image edge or horizontal line selections at the top image edge to not be restored correctly.
  • Thanks to Dimiter Prodanov, fixed a bug that could cause the ROI Manager to throw an exception if it contained a zero-point PolygonRoi.
  • Thanks to Michael Epping, fixed bugs that caused the Flip Horizontally, Flip Vertically, Rotate Left and Rotate Right commands to not correctly transform the image origin.
  • Thanks to Rich VanMetter, fixed a bug that caused some DICOM images to open slowly.
  • Thanks to Stephen Cody, fixed a bug that caused the "Select" option in Image>Adjust>Color Threshold to sometimes not work as expected.
• 1.47m 6 March 2013
  • Added the Plugins>Install command.
  • Thanks to John Hayes, added a Macros>Evaluate Python command to the macro editor. The 8MB Jython interpreter is downloaded as needed from the ImageJ website to ImageJ/plugins/jars.
  • Scripts in the plugins folder with ".bsh" and ".py" extensions are added to the Plugins menu.
  • "Exception" windows now display the ImageJ version, Java version, OS version and memory usage.
  • Plugins>Utilities>ImageJ Properties now displays values returned by IJ.getDirectory() and all Java properties.
  • Improved recording of foreground/background color settings and the "Black background" option.
  • Thanks to Wilhelm Burger and Johannes Schindelin, output to System.out and System.err is redirected to the Log window when ImageJ is in the debug mode.
  • Wilhelm Burger's IjLogStream class is built into ImageJ as ij.io.LogStream.
  • Thanks to Christophe Deroulers, added the roiManager("save selected", path) macro function.
  • Added the eval("bsh",script) and eval("python",script) macro functions.
  • Fixed a v1.47d regression that sometimes caused the Process>Binary>Convert to Mask command to change the "Black Background" option.
  • Thanks to Leon Espinosa, fixed a v1.47j regression that caused ROIs added to the ROI Manager by the particle analyzer to have null names.
  • Thanks to Norbert Vischer, fixed a bug that caused the Edit>Selection>Rotate command to not work as expected with rounded rectangle selections.
  • Thanks to Antti Niemisto and Gabriel Landini, fixed a bug that caused the "Minimum" thresholding method to set the wrong threshold for some unusual histograms.
• Gilles Carpentier contributed Sort Selections in Overlays, a macro that sorts selected overlay elements by color (requires v1.47k).
• 1.47k 17 February 2013
  • Thanks to Norbert Vischer, fixed a 1.47j regression that caused the Analyze>Plot Profile command to not work with line selections wider than 1.
• 1.47j 15 February 2013
  • The Edit>Selection>Enlarge command is much faster.
  • Thanks to Norbert Vischer, the macro debugger now flags changed variables.
  • Thanks to Norbert Vischer, Edit>Selection>Line to Area, with straight line selections, now creates 4-corner polygons instead of traced selections.
  • Added the "Enhanced line tool" option to Edit>Options>Misc, which allows straight line selections to be created by clicking at the start and at again the end.
  • The File.openAsString() macro function no longer has a file size limit.
  • Thanks to Rainer Engel, added the File.copy(path1,path2) macro function.
  • Thanks to Norbert Vischer, added the Array.resample(arr,len) macro function.
  • Added the Overlay.addSelection(color), Overlay.addSelection(color, strokeWidth) and Overlay.addSelection("", 0, fillColor) macro functions.
  • Thanks to Miso Mitkovski, fixed a 1.47i regression that caused the command finder to sometimes not work as expected when using the down arrow and enter keys.
  • Thanks to Gilles Carpentier, fixed a bug that could cause the ROI Manager to not work correctly if ROIs with duplicate names were programatically added.
  • Thanks to Norbert Vischer, fixed a bug that caused the split() macro function to not return a zero length array when no tokens were found.
  • Thanks to Ignacio Arganda-Carreras, fixed a bug that caused the SaveDialog class to add the extension twice if it was longer than four characters.
  • Thanks to Sebastien Tosi, fixed a bug that sometimes caused the getHistogram() macro function to not work as expected with 16-bit images.
• Photos from the 2012 ImageJ conference in Luxembourg are available online.
• 1.47i 25 January 2013
  • Thanks to Curtis Rueden, the command finder (Plugins>Utilities>Find Commands) uses a table to display additional information about the commands it finds.
  • Improved the Plugins>Shortcuts>Create Shortcut command.
  • The Image>Stacks>Plot Z-axis Profile command works with hyperstacks.
  • Thanks to Adam Brin, added the IJ.getErrorMessage() method.
  • The "Startup Macros" command in the toolbar's ">>" menu looks for a file named StartupMacros.fiji.ijm if StartupMacros.txt is not found in the macros folder.
  • Added the Overlay.addSelection() and Overlay.activateSelection() macro functions.
  • Michael Schmid fixed a bug that sometimes caused Process>Noise>Remove Outliers and Process>Binary>Erode to not work correctly when processing stacks using multiple threads.
  • Thanks to Alistair MacDougall, fixed a v1.47f regression in the saveAs("tiff",path) macro function that caused it to not update the image title.
  • Fixed a 1.47f regression that caused the saveAs("tiff") macro function to throw an exception.
  • Fixed a bug that caused the String.copyResults() macro function to ignore selections, which is not consistent with the Results window's Edit>Copy command.
  • Thanks to Ved Sharma, fixed a bug that caused the macro language return statement to not correctly return string array values.
  • Thanks to Erik Belanger, fixed a bug the caused Image>Stacks>Delete Slice to not work correctly with hyperstacks.
  • Thanks to Julien Vaubourgeix, fixed a bug in Image>Stacks>Label that caused it to delete any existing overlay when the "Use overlay" option was enabled.
  • Fixed a bug that caused the saveAs(path) macro function to display a "Save As" dialog box.
• 1.47h 23 December 2012
  • Thanks to Denis Meuthen, you can now create a straight line selection by defining the start of the line with one click and the end with another click.
  • Thanks to Curtis Rueden, Image>Stacks>Tools>Make Substack now works with hyperstacks.
  • Thanks to Jerome Mutterer, the arrow, brush, pencil and pixel inspector tools remember the location of their options dialogs.
  • Thanks to Rainer Engel, the "Log" window remembers its dimensions.
  • File>Save As>Image Sequence displays a warning if the first file in the sequence will overwrite an existing file.
  • The File>New>Hyperstack command can be invoked by pressing alt-n.
  • Thanks to Gilles Carpentier, fixed a bug that caused the run("Make Composite") macro function to sometimes not work as expected.
  • Michael Schmid fixed a bug that prevented the AVI Reader from correctly opening as virtual stacks AVI files with blank frames.
  • Thanks to Alex Hughes, fixed a bug that caused the ROI Manager's Multi Plot command to disregard the "Vertical profile" option in the Edit>Options>Profile Plot Options dialog box.
  • Thanks to Kees Straatman, fixed a bug that caused Analyze>Tools>Analyze Line Graph to hang with non-thresholded images.
  • Thanks to John Oreopoulos, fixed a bug that caused File>Import>Image Sequence to sometimes not work as expected when all the images in the sequence were not the same type.
  • Thanks to Jerome Mutterer, fixed a bug that caused an exception when pasting, in a macro, a non-recangular ROI that was partially outside the target image.
  • Thanks to Vanessa Bell, fixed a bug that caused the getSelectionCoordinates() macro function and Roi.getPolygon() method to sometimes unexpectedly return the bounding rectangle of composite selections.
  • Thanks to Aivar Grislis, fixed a v1.47g regression that caused the setLocation() macro function to not work with some non-image windows.
  • Thanks to Michael Schmid, fixed a bug that caused "Cancel" to not work as expected for dialogs in "Preview" mode with commands called from macros.
  • Thanks to Jarek Sacha, fixed a bug that caused ImageListeners to sometimes not be notified when the image was updated.
  • Michael Schmid fixed two PlugInFilterRunner bugs related to Preview and PARALLELIZE_IMAGES.
• 1.47g 2 December 2012
  • Changed the "Brightness/Contrast", "Channels", "Threshold" and "Color Picker" windows to modeless dialogs that do not have the iconize and maximize buttons that are problematic on Windows.
  • Thanks to Bill Christens-Barry, added an "Auto contrast stacks" option to the Edit>Options>Appearance dialog box. Alternatively, hold down the shift key when scrolling stacks.
  • Thanks to Thomas Kuhne, Emil Kesler and Yili Zhao, Plugins>Compile and Run, on Java 1.6 or later, uses javax.tools.JavaCompiler instead of com.sun.tools.javac.Main.
  • Thanks to Norbert Vischer, added the close(pattern) macro function (example) and the ij.util.WildcardMatch class.
  • Thanks to Jerome Mutterer, added the getValue("rgb.foreground") and getValue("rgb.background") macro functions.
  • Thanks to Norbert Vischer, added the setForegroundColor(rgb) and setBackgroundColor(rgb) macro functions.
  • Thanks to Bill Christens-Barry, added the setOption("auto contrast",boolean) macro function.
  • Worked around a bug on Windows 8 that made scrollbar thumbs nearly invisible.
  • Fixed a bug that caused an exception when File>Revert was used on a duplicated image.
  • Thanks to Olivier Cardoso, fixed a bug that could cause an exception when calling an Ext macro function.
• Jerome Mutterer and Edda Zinck have released FigureJ, a plugin that makes it easy to create figures for scientific articles.
• Dimiter Prodanov contributed Mexican Hat Filter, a plugin that convolves a 2D image with a Laplacian of Gaussian filter.
• 1.47f 18 November 2012
  • Added the IJ.saveAsTiff() method.
  • Fixed a v1.46f regression that caused the applet version of ImageJ to not open images specified using HTML parameters.
  • Thanks to Erik Belanger, fixed a bug that caused the setMinAndMax() macro function to not work with batch mode composite color images.
  • Fixed several stack flattening bugs.
  • Fixed several hyperstack related bugs in the Image>Scale command.
  • Fixed a bug that caused the saveAs("tif",path) macro function to not work correctly on consecutive command line macro calls.
  • Thanks to Norbert Vischer, fixed a bug that caused Copy from the "Log" window to not work correctly for lines containing tabs when "Copy row numbers" was not enabled in Edit>Options>Input/Output.
  • Thanks to Jerome Mutterer, fixed a bug that prevented the FigureJ plugin from being able to restore tools.
• 1.47e 9 November 2012
  • Added the Macros>Evaluate BeanShell command to the macro editor. This command requires that a copy of BeanShell.jar be in the plugins folder.
  • Thanks to Michael Kaul, bilinear interpolation works better with float images containg NaNs.
  • Thanks to Michael Schmid, added a "Gaussian (no offset)" curve fitting option.
  • The recorder displays a warning when the options string in run(command,options) calls contain one or more non-ascii characters.
  • Added the Toolbar.restoreTools() method (example).
  • Added the ParticleAnalyzer.setFontColor(String) method and the call("ij.plugin.filter.ParticleAnalyzer.setFontColor","blue") macro function. .
  • Thanks to Thomas Boudier, added a public GaussianBlur3D.blur() method.
  • Thanks to Michael Schmid, fixed a v1.46 regression that could cause curve fitting errors.
  • Simon Bear fixed a bug that caused black pixel data to be ignored when loading CMYK TIFFs.
  • Fixed a bug that caused the source stack to become corrupted when scaling by x=1.0 and y=1.0 in Image>Scale.
  • Thanks to Thorsten Wagner and Michael Schmid, fixed a bug that caused the Analyze>Summarize command to fail if the Results table contained headings with spaces.
  • Thanks to David Gauntt, fixed a bug in the FHT class that caused it to fail when calculating the power spectrum of 1D arrays larger than 32K.
  • Thanks to Jarek Sacha, fixed a bug that cuased File>Import>Image Sequence to sometimes not set the correct slice labels when opening a series as a virtual stack.
• Gilles Carpentier contributed Angiogenesis Analyzer, a macro toolset for analysis of cellular networks, for example the pseudo vascular organization of endothelial cells cultured in a gel medium (documentation).
• 1.47d 5 October 2012
  • Thanks to Norbert Vischer, added the Image>Color>Arrange Channels command.
  • Thanks to Michael Cammer, when processing stacks, added "Method" and "Background" choices to the Process>Binary>Convert to Mask dialog.
  • Thanks to Ved Sharma, the arrow tool draws bolder outlined arrows.
  • Deleted the redundent Image>Hyperstacks>Channels Tool menu command.
  • Thanks to Norbert Vischer, added the getInfo("command.name") macro function (example).
  • Added the setOption("jfilechooser") macro function.
  • Fixed a bug that caused the roiManager("select",n) macro function, and RoiManager.select() method, to display an error message if no images were displayed.
  • Thanks to John Page, fixed a bug that caused CMYK TIFFs to open inverted.
  • Thanks to Birgit Möller, fixed a bug that sometimes caused the ImagePlus.show() method to not work as expected on closed images.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the Edit>Selection>Line to Area command to not work as expected.
  • Thanks to Gilles Carpentier, fixed bugs in Process>Binary>Skeletonize that caused it to sometimes not remove all skeleton pixels.
  • Thanks to Leon Espinosa, fixed a bug that caused "Apply" in the "Threshold" tool to always use the default thresholding method.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording, when the recoder was in "JavaScript" or "Plugin" mode, of plugins that used the run(imp,..) methods of the Duplicator class.
  • Norbert Vischer fixed a bug that caused line numbers in macro error messages to be incorrect with macros containing emptly lines inside SlashStar comments.
  • Thanks to Jiri Janacek, fixed a bug the caused the perimeter of composite ROIs in spatially calibrated images to be incorrect.
  • Thanks to Michael Schmid, fixed a bug that could cause file corruption if the Crop command was used while a stack was being saved.
  • Thanks to Eric Denarier, fixed a bug in Process>Batch>Macro that caused it to somestimes not output the correct images.
• Kota Miura has made available two textbooks ("Basics of Image Processing and Analysis" and "Macro Programming in ImageJ") he uses for the ImageJ classes he teaches.
• 1.47c 8 September 2012
  • Added a "Source" (display source code of selected command) button to Plugins>Utilities>Find Commands.
  • Dorai Iyer added a "Bar" option to the arrow tool.
  • Bill Mohler modified the ROI Manager to use a JList instead of a List, which makes loading and sorting the large (>10,000) ROI sets faster.
  • Added an "Append results" checkbox to the ROI Manager's "Multi Measure" command.
  • When opening images, the transfer rate in MB/sec is displayed in the status bar.
  • Thanks to Sébastien Tosi, opening TIFF files using File>Import>URL is faster and requires less memory.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording of commands implemented in JavaScript when the recorder was in "JavaScript" mode.
  • Thanks to Sébastien Tosi, fixed a bug that caused File>Import>URL to not correctly read TIFF files larger than 2GB.
  • Fixed a bug in the Analyze>Tools>Synchronize Windows command that caused it to not work as expected when changing the channel of composite color images.
  • Thanks to Christoph Deil, fixed a bug in Plugins>Utilities>Find Commands that caused esc and ctrl-w key presses to not close the window after "Show full information" was enabled.
  • Thanks to Christoph Deil, fixed bugs in the "Save changes?" dialog that caused it to not work as expected after the focus was changed (by tabbing) to the "Don't Save" or "Cancel" buttons.
• 1.47b 12 August 2012
  • Added the Image>Stacks>Statistics command.
  • Thanks to Michael Schmid, the built in brush, pencil and overlay brush tools draw using the background color when alt key is down, are constrained to draw horizontally when shift is down, are resized when shift&control are down (shift&cmd on Macs), and "pick up" the foreground color when control is down (cmd on Macs).
  • Added a "16 bit range" choice to the Edit>Options>Appearance dialog box. This is the same as the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog.
  • Thanks to Olivio Donati, File>Import>Image Sequence opens any associated ROIs that are in a file named RoiSet.zip.
  • Thanks to David Knecht, added a "sum" option to Image>Transform>Bin.
  • The getHistogram() macro function no longer limits the number of bins to 256 with 8-bit and RGB images.
  • Added the IJ.createHyperStack(title,width,height,channels,slices,frames,bitdepth) method, where 'bitdepth' is 8, 16, 24 (rgb), or 32 (float).
  • Thanks to Qingzong Tseng, fixed a bug that caused overlays to be lost when converting composite stacks to RGB.
  • Thanks to Jan Eglinger, fixed a bug that caused images created by the particle analyzer's "Show:" option to not use the calibration of the original image.
  • Thanks to Guenter Giese, fixed bugs that caused the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog to not work as expected with multi-channel images.
  • Thanks to Barry DeZonia, fixed a bug that caused the command recorder to not work with Image>Stacks>3D Project when processing 16 and 32 bit images.
  • Thanks to William Edwards, fixed a bug that sometimes caused the median of 32-bit float images to be calculated incorrectly.
  • Thanks to Michael Cammer, worked around a bug that could cause commands in the Image>Type submenu to not work as expected in non-batch-mode macros.
• 1.47a 17 July 2012
  • Thanks to Thomas Boudier, added five new 3D filters (Median, Mean, Minimum, Maximum and Variance) to the Process>Filters submenu.
  • Added the "Restore Startup Tools" command to the toolbar's >> menu.
  • Thanks to Tiago Ferreira, built-in and plugin tools can be added to toolsets and the startup macros (example).
  • Michael Schmid modified the Overlay Brush tool for constrained motion (vertical or horizontal) with shift and resizing with ctrl-shift (cmd-shift on Macs).
  • Thomas Tongue added support for the CDELT and CTYPE headers to the FITS Reader.
  • Added the getinfo("selection.color") and getValue("selection.width") macro functions.
  • Thanks to Simon Roussel, fixed a bug that could cause overlays to not be displayed on virtual stacks.
  • Fixed a bug that caused the brush and pencil tools to activate overlay selections.
  • Michael Schmid fixed a bug that sometimes caused Preview to not work correctly with commands in the Process>Filters submenu.
  • Fixed a 1.46 regression that caused the ROI Manager to generate incorrect ROI labels when the Associate 'Show All" ROIs with Slices" option was not enabled.
  • Thanks to Stephan Semmler, fixed a regression that caused the ImagePlus.getNDimensions() method to sometimes return the wrong value.
  • Thanks to Glen MacDonald, fixed a 1.46 regression that caused the setOption("Show All",boolean) macro function to not work.
• Kevin Eliceiri and Caroline Schneider published the article "NIH Image to ImageJ: 25 years of image analysis" in Nature Methods.
• 1.46r 26 June 2012
  • Thanks to Bob Loushin, fixed a bug that caused dashed line ROIs to only display correctly at 100% zoom.
  • Thanks to Raymond Coory, fixed a v1.46o regression that caused the TurboReg plugin to throw an exception.
  • Fixed a v1.46n regression that caused the ROI Manager's "Associate 'Show All' ROIs with Slices" option to not work as expected.
  • Thanks to Olivier Bardot, fixed a v1.46p16 regression that caused the Image>Hyperstacks>Temporal-Color Code command in Fiji to fail.
• 1.46q 19 June 2012
  • Thanks to Michael Cammer, added the ROI Manager More>>List command.
  • Thanks to Jerome Mutterer, added the Macros>Macro Functions command to the macro editor.
  • On Windows, the preferences file (IJ_Prefs.txt) is now saved in the .imagej directory, in the user's home directory.
  • Thanks to Norbert Vischer, fixed a bug that caused the wrong image window to have focus after another window was closed.
  • Thanks to Kees Straatman, fixed bugs that caused Image>Color>Merge Channels to sometimes lose the scale and to sometimes not work as expected when used in a macro.
  • Thanks to Michael Schmid, worked around a race condition in the run("Make Composite") macro function that could cause non-batch mode macros using it to fail.
  • Thanks to Carlos Becker, fixed a bug that caused File>Open and File>Import>TIFF Virtual Stack to fail when importing TIFF stacks larger than 2GB.
  • Thanks to Michael Schmid, fixed a bug that could cause a 'for' loop, at the end of a macro, containing a single 'if' statement to terminate prematurely.
  • Thanks to Christophe Leterrier, fixed a bug that caused the ResultsTable.open() method to not correctly open results tables with row labels but without row numbers.
• Tiago Ferreira added a "Print list" button to the Built-in Macro Functions page.
• Tiago Ferreira updated and improved the ImageJ User Guide for v1.46p, adding sections on overlays, 3D volumes, sub-pixel selections, curve fitting and interface customization. The User Guide, which contains 200 pages and 270 illustrations, is available online, as a 10 MB PDF, and as US and A4 booklets.
• 1.46p 4 June 2012
  • Added the Edit>Options>Reset command.
  • The line of information at the top of image windows is displayed antialiased.
  • Added the rotate(), setAngle() and setZeroTransparent() methods to the ImageRoi class (example).
  • Fixed a bug that caused an exception when Image>Stacks>Add Slice was used to add a channel to a 7 channel composite color image.
  • Fixed a bug that caused Edit>Selection>Rotate to not work with ImageRois.
  • Thanks to Hiroki Hakoshima, fixed a bug that caused the saveAs() macro function to fail if the file path contained a "]" character.
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Stacks>Add Slice and Image>Stacks>Delete Slice to not set the 'changes' flag.
  • Thanks to Norbert Vischer, fixed a bug that caused the macro interpreter to not correctly parse hex constants larger than 0x7fffffff.
  • Fixed bugs in the Image>Hyperstacks>Stack to Hyperstack and Hyperstack to Stack commands that caused them to not work as expected in batch mode macros.
  • Thanks to Dorai Iyer, fixed a 1.46o regression that caused the ROI Manager "Flatten" command to stop working.
• 1.46o 18 May 2012
  • Set the stroke width to 0 in the Edit>Selection>Properties, Image>Overlay>Overlay Options and ROI ManagerProperties dialogs to have selections drawn using a width of one pixel regardless of the image magnification.
  • Fixed a bug that could cause selections being moved to not be displayed correctly when the "Use ROI names as labels" option in the ROI Manager was enabled.
  • Fixed a bug that caused Analyze>Plot Profile to fail with line selections with widths less than 1.0.
  • Thanks to Franklin Shaffer, fixed a bug that sometimes a caused a stack overflow error when importing large image sequences.
  • Thanks to Tiago Ferreira, fixed a 1.46n regression that caused overlay items to be removed when toggling the ROI Manager "Show All" checkbox.
• 1.46n 11 May 2012
  • In "Show All" mode, the ROI Manager now uses an overlay to display the selections.
  • Added the More>>Labels... command to the ROI Manager, as a shortcut to Image>Overlay>Labels.
  • Add a "Show plot" checkbox to the Analyze>Calibrate dialog box.
  • File>Save As>XY Coordinates now correctly saves subpixel resolution selections, and it works with more kinds of selections.
  • Tiago Ferreira added a list of valid factors to the Image>Stacks>Tools>GroupedZProjector dialog.
  • Made the IJ.runPlugIn(String,String,String) method public.
  • Added the IJ.getFullVersion() method.
  • Thanks to Burri Olivier, fixed a bug that caused Image>Adjust>Threshold, when the "Stack histogram" option was enabled, to use the histogram of all channels instead of only the current channel.
  • Tiago Ferreira fixed a bug that caused stacks binned with Image>Stacks>Tools>GroupedZProjector to loose spatial calibration.
  • Thanks to Burri Olivier, fixed a bug that caused incorrect auto stack thresholds when "Limit to threshold was enabled in Analyze>Set Measurements.
  • Thanks to Thomas Boudier and Michael Schmid, fixed a bug that caused the Analyze>Summarize command to not work correctly on reopened results tables.
  • Thanks to Jim Passmore, fixed a bug that caused NonBlockingDialogs to not handle the yes/no/cancel option.
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Show Info to incorrectly display the selection location when the image origin was not (0,0).
• 1.46m 23 April 2012
  • ROIs in an overlay can be activated by alt-clicking, control-clicking or long-pressing (1/4 second or longer).
  • Thanks to Gabriel Landini, the Brush and Pencil tools installed from the toolbar's >> menu can be resized by shift-dragging.
  • The icons for drawing tools installed from the toolbar's >> menu reflect the foreground color and are updated when the foreground color changes.
  • Commands in the Edit>Selection submenu that modify the selection now support Undo/Redo and transfer color and line width properties.
  • Fiji saves and loads custom tool configurations.
  • Thanks to Ved Sharma, removed the restriction in Image>Stacks>Tools>Insert that the destination must be a stack.
  • Thanks to Richie Mort, fixed a bug that could cause the contents of multiple custom results tables created by plugins to be invalid.
• Dimiter Prodanov has published a chapter summarizing parts of his research with ImageJ.
• 1.46k 11 April 2012
  • Custom tool configurations created using the toolbar's ">>" menu are saved in the preferences file.
  • Process>Filters>Gaussian Blur 3D works with hyperstacks.
  • Thanks to Tiago Ferreira, fixed a bug that caused FIle>Import>Image Sequence to throw an exception of the first file in the folder was a stack and other files were not stacks.
  • Thanks to Norbert Vischer, fixed a bug that caused metadata to be lost when saving and reopening 3-channel composite 16-bit images.
  • Fixed a bug that caused Edit>Selection>Properties to change selection stroke widths less than 1.0 to 1.0.
  • Fixed a bug that caused Edit>Selection>Fit Spline and Edit>Selection>Interpolate to reset stroke colors and widths.
  • Fixed regressions that caused Analyze>Measure to not work with angle selections and to sometimes throw an exception.
• Tiago Ferreira contributed ROI Manager Tools, a macro toolset that renames selections stored in the ROI Manager.
• Gilles Carpentier contributed Multi-Channel Image and Stack Helper, a macro toolset for working with composite color images and stacks.
• The Transparent Image Overlay plugin demonstrates how to draw an image with a transparent background in an overlay.
• 1.46j 27 March 2012
  • Added the Process>Filters>Gaussian Blur 3D command.
  • When the ROI Manager window is closed, a dialog box is displayed that provides the option of moving displayed ROIs to an overlay.
  • File>Import>Image Sequence displays warnings if the folder contains tiff stacks and the "Use virtual stack" option is enabled.
  • Image>Calibrate now uses scientific notation to draw fit parameters, if needed.
  • Thanks to Wilhelm Burger, added a ByteProcessor(ip, scale) constructor.
  • Thanks to Gabriel Landini, fixed a bug that caused an invalid 0.0 to be entered into the Analyze>Calibrate dialog box if "Stack position" was enabled in Analyze>Set Measurements.
  • Thanks to Mark Krebs, fixed a 1.46e regression that could cause Image>Stacks>Tools>Concatenate to fail when called from a macro.
  • Thanks to Michael Cammer, fixed a v1.46g regression that caused the "Use stack histogram" option in Process>Ehance Contrast to not work as expected.
  • Thanks to Norbert Vischer, fixed a v1.46i regression that could cause an exception when using using Analyze>Measure to measure Feret's Diameter.
• Ved Sharma contributed Measure Hyperstack, a macro that runs "Measure" on a hyperstack in a user-selected (c,t,z) order.
• 1.46i 15 March 2012
  • Added the Image>Transform>Bin command, based on Nico Stuurman's Binner plugin.
  • Added the Edit>Selection>Interpolate command. To view the interpolated points, use this command on small selections created on images zoomed 1200% or greater.
  • Added the Image>Transform>Image to Results and Results to Image commands.
  • Added a "Remove Tool" command to the toolbar's >> menu;
  • The Image>Stacks>Add Slice command works with hyperstacks.
  • The Fly Brain and T1 Head sample stacks open displaying the middle slice instead of the first.
  • Added the getChannel(int, ByteProcessor) and setChannel(int, ByteProcessor) methods to the ColorProcessor class (example).
  • Added the getTableAsImage() (example), createTableFromImage() (example) and open2() methods to the the ResultsTable class.
  • Added the ImageProcessor.bin() and Roi.getInterpolatedPolygon() methods.
  • Thanks to Michael Schmid, added the ImageProcessor.isGrayscale() method and the is("grayscale") macro function.
  • Added JavaScript-compatible constructor and methods to the Plot class (examples).
  • Thanks to Jan Eglinger, fixed a bug that caused Image>Transform>Rotate Right and Image>Transform>Rotate Left to not work with square composite color images.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused Image>Stacks>Z Project to not work with 3D composite color images.
  • Fixed a bug that caused overlays to be lost when opening TIFF files using a URL.
  • Fixed a bug that caused an exception when the user canceled the File>Import>Results dialog box.
  • Fixed a bug in Process>Binary>Skeletonize that caused it to sometimes create skeletons that were more than one pixel wide.
  • Fixed a bug that caused the setf() functions to not round when storing values in ByteProcessors and ShortProcessors.
  • Fixed a bug that caused the Sync_Windows plugin to not work with hyperstacks.
  • Fixed bugs that caused an error message, or caused the command to be ignored, when saving results created by some MBF plugin using File>Save As>Results.
  • Thanks to Arttu Miettinen, fixed bugs that sometimes caused histogram bin counts of stacks larger than 2 gigapixels to be incorrect.
  • Thanks to Michael Cammer, fixed a bug in Image>Stacks>Reslice that caused it to not work as expected if there was global calibration and "Avoid interpolation" was not checked in the dialog box.
• 1.46h 28 February 2012
  • Added the Arrow, Overlay Brush, Pixel Inspector, Spray Can and LUT Menu tools to the toolbar's >> menu.
  • Image>Color>Merge Channels now works with up to 7 channels.
  • Added the String.getResultsHeadings() macro function (example).
  • Thanks to Xiao Chen, fixed a bug that caused ImageJ to not correctly open PNG images with alpha.
  • Fixed a bug that caused the Results window to flicker when the ResultsTable.show("Results") method was called repeatedly (example).
  • Thanks to Andrew French, fixed a bug that caused the ImageStack.getVoxel() method to fail with RGB stacks.
  • Fixed a bug that could cause File>Import>Text Image to fail with files containing empty lines.
  • Thanks to Gregory Reneff, fixed a bug that caused the call("ij.plugin.frame.RoiManager.getName", index) macro function to not work in batch mode.
• Vilppu Tuominen and Jorma Isola have released ImmunoMembrane, a plugin for analyzing HER-2 immunohistochemistry.
• 1.46g 16 February 2012
  • The ">>" toolbar menu lists installed plugin tools.
  • Added "Help" buttons to the Image>Stacks>3D Project and Process>Enhance Contrast dialog boxes.
  • Fixed a bug that caused hyperstacks to be converted to interleaved stacks in macros that opened a hyperstack and did a crop or type conversion operation.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused commands in the Image>Lookup Tables submenu to not work as expected with single channel composite images.
  • Thanks to Michael Cammer, fixed a bug that caused Process>Enhance Contrast to not work as expected when the "Equalize histogram", "Process all n slices" and "Stack histogram" options were enabled.
  • Thanks to Rainer Engel, fixed bug that caused Image>Stacks>Z Project to not correctly perform "Median" and "Standard Deviation" projections of RGB stacks.
  • Thanks to Eik Schumann, fixed a bug that caused the run("Merge Channels...","...") macro function to not close source images in batch mode macros.
  • Thanks to Zeljka Maglica, fixed a bug that caused position-dependent overlays to not be saved when using the Image>Overlay>Flatten, File>Save As>AVI and Image>Stacks>QuickTime Movie commands.
  • Thanks to Fabian Svara, fixed a bug that caused an incomplete ROI to be added to the ROI Manager if you pressed "t" (Edit>Selection>Add to Manager) before you finished drawing the ROI.
• 1.46f 5 February 2012
  • Michael Schmid contributed an improved Curve Fitter.
  • Built in Joachim Walter's Sync Windows plugin as the Analyze>Tools>Synchronize Windows command.
  • Thanks to Denny Hugg, ImageJ uses a custom crosshair cursor if there is a GIF image named "crosshair-cursor.gif" in the ImageJ/images folder. There is an example custom cursor at imagej.net/ij/images/crosshair-cursor.gif.
  • With hyperstacks, the Image>Stacks>Delete Slice command can delete the current channel, slice or frame.
  • Michael Schmid added support for I420, YV12 (a.k.a. IYUV), NV12 and NV21 formats to the AVI Reader.
  • The GifWriter now uses ImageIO to save single images.
  • Thanks to Norbert Vischer, fixed a bug that made it impossible to select an image with a duplicate name from the Window menu.
  • Thanks to Michael Schmid, added the IJ.d2s(n,significantDigits,maxDigits) method, which is used by the macro language to convert numbers to strings, by Analyze>Histogram to display values in histogram windows, and by ImageJ to display values in the status bar as the curser is moved over float images.
  • Replaced the SocketListener class with Johannes Schindelin's RMI-based OtherListener class from Fiji, which works on multi-user machines and is more secure.
  • Thanks to David M. Gauntt, added the FHT(ImageProcessor,boolean) constructor to the FHT class.
  • Thanks to Denny Hugg, fixed a bug that caused File>Save As>Gif to create GIF images that would not work as custom cursors.
  • Thanks to Gilles Carpentier, fixed a bug that cuased Image>Stacks>Z Project to throw an exceptions if no image window was open.
  • Thanks to Wilhelm Burger, fixed a bug that caused the Image>Adjust>Canvas Size command to not properly repositioned overlays.
  • Thanks to Christopher Harrison, fixed a bug that caused LUTs to be improperly applied to "Grayscale" mode composite images.
  • Fixed a bug that caused Analyze>Plot Profile to not work with rectangular selections containing NaN values.
• 1.46e 18 January 2012
  • Thorsten Wagner added a "Label" (display slice labels) option to the Image>Stacks>Label dialog box.
  • Changes made to options in the Edit>Options>Appearance dialog box cause the current image to be immediately updated.
  • Upgraded the Image>Stacks>Tools>Concatenate plugin to the Jon Jackson version from the MacBiophotonics distribution and Fiji.
  • Less memory is required to display float images.
  • Thanks to Michel Julier, images zoomed less than 100% are displayed with higher quality.
  • Edit>Selection>Rotate uses floating-point coordinates
  • Added the call("ij.gui.ImageWindow.setNextLocation",x,y) macro call.
  • Added the Roi.getFloatBounds() and FloatPolygon.getFloatBounds() methods.
  • Added the ParticleAnalyzer.setResultsTable() method.
  • Thanks to Jan Eglinger, ImageJ displays an error message when you attempt to apply a threshold or brightness/contrast change to a virtual stack.
  • Thanks to Martin Dressler, fixed bugs in Image>Duplicate and Image>Stacks>Tools>Make Substack that caused image "Info" metadata to be discarded.
  • Thanks to Johannes Schindelin, fixed a 1.46a regression that could cause plugins to fail if they extended the PolygonRoi class, did spline fitting and accessed the protected xp and yp arrays.
  • Thanks to Vytas Bindokas, fixed bugs that could cause Edit>Selection>Rotate to not work as expected with straight line selections.
  • Fixed a bug that caused the makeLine(x1,y1,x2,y2,width) macro function to round non-integer arguments.
  • Fixed a bug that caused thresholds to not be reset when converting from 16-bit to 8-bit.
  • Fixed a v1.45c regression that caused Process>Math>Macro to fail on multiprocessor machines with expressions containing "getPixel".
• Aleksandr Mironov contributed Merz grid, a macro that creates a Merz grid with semicircular lines and points as a non-destructive overlay.
• 1.46d 1 January 2012
  • Added the Plugins>New>Macro Tool and Plugins>New>Plugin Tool commands.
  • Single macro tools are now installed in the first available toolbar slot, or if no slots are free, in the last slot.
  • Added the ij.plugin.tool.PlugInTool class, which was inspired by Johannes Schindelin's AbstractTool class in Fiji (examples).
  • Added the getC(), getZ(), getT(), setC(), setZ() and setT() methods to the ImagePlus class.
  • Thanks to Norbert Vischer, fixed a bug the caused the setZCoordinate() macro function to not work as expected.
  • Thanks to Ian Lim, fixed a bug that prevented some AVI files from opening.
  • Thanks to Cheryl McCreary, fixed a bug that caused the run("Histogram","...") macro function to sometimes not work as expected.
  • Thanks to Jerome Mutterer, fixed bugs in Process>Batch>Macro and Process>Batch>Virtual Stack that caused them to fail with macro code that duplicated or opened images.
  • Thanks to Paul Jurczak, fixed a bug that caused some RGB BMP files to fail to open.
  • Fixed a bug that caused the makeText() macro function to not work if the text was too wide.
  • Fixed a regression, introduced in v1.46a, that caused measurements of spline fit freehand and traced selections to be inconsistent with earlier versions of ImageJ.
  • Wilhelm Burger fixed a bug that caused the Edit>Crop command to not correctly handle overlays.
• Dimiter Prodanov contributed Results Importer, a plugin that imports numeric values from text windows (e.g., histogram or profile plot lists) into the ResultsTable.
• 1.46c 12 December 2011
  • Thanks to Tiago Ferreira, the ColorChooser widget now displays hex values.
  • Thanks to Jesper Pedersen and Michael Schmid, ImageJ opens >2GB AVI 2.0 files, opens AVIs faster as virtual stacks and opens MJPEG encoded AVIs that are missing Huffman tables.
  • Thanks to Jerome Muttere, Process>Find Maxima, when the output type is "Count", respects the Analyze>Set Measurements "Display label" setting.
  • Added the "Sub-pixel resolution" option to the Edit>Options>Profile Plot Options dialog box (documentation).
  • Added the Array.concat(), Array.slice() and Array.print() macro functions (example1, example2).
  • Thanks to Norbert Vischer, fixed a bug that caused the Stack.setActiveChannels() macro function to not update the "Channels" window.
  • Thanks to Balazs Nyiri, fixed a bug that caused the image id of composite color images to change after using the Image>Stacks>Add Slice and Image>Stacks>Delete Slice commands.
  • Fixed a bug that caused the slice selector scrollbar to not be updated after using the Add Slice or Delete Slice commands.
  • Thanks to Jakob Preus, fixed a bug that caused use of "&" to pass directory path variables in macros using the File>Save As>Image Sequence command to fail.
• 1.46b 29 November 2011
  • Added the File>Import>XY Coordinates command.
  • Added a "List coordinates" checkbox to the Edit>Selection>Properties dialog box.
  • "Help" buttons in dialog boxes can display HTML formatted messages (macro, JavaScript).
  • The Edit>Selection>Line to Area command now works with one pixel wide straight lines.
  • The color of the rounded rectangle tool no longer defaults to the foreground color.
  • Thanks to Aryeh Weiss, the ROI Manager's "OR (Combine)" command now works with line selections.
  • Added the ParticleAnalyzer.setRoiManager() method (example).
  • To support sub-pixel positioning, added constructors that accept double arguments to the Roi, OvalRoi and TextRoi classes (example).
  • Thanks to Norbert Vischer, added the ij.util.StringSorter.sortNumerically() method.
  • Thanks to Jose Wojnacki, fixed a bug that could cause a macro to fail if a drawing tool was used during a waitForUser() break.
  • Thanks to Norbert Vischer, fixed a bug that caused the "Sort names numerically" option in the File>Import>Image Sequence dialog to sometimes not work as expected.
  • Fixed a bug that caused the default stroke width and color to change when an arrow was added to an overlay.
  • Fixed a bug that caused lines to be displayed incorrectly in the ROI Manager "Show All" mode after adding a rounded rectangle.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the Plot.show() macro function to return before the plot window was fully displayed.
  • Thanks to Norbert Vischer, fixed a bug that caused macros displaying showMessage() dialogs to not be aborted when the user pressed the esc key.
  • Thanks to Jerome Mutterer, fixed a bug that sometimes caused selections in ROI Manager "Show All" mode and in overlays to be displayed with the wrong stroke width.
  • Thanks to Winfried Wurm, fixed a bug that could cause the run("Restore Selection") and run("Enlarge...") macro functions to fail in batch mode macros.
• 1.46a 12 November 2011
  • The segmented line, freehand line, point and multi-point tools now support sub-pixel resolution.
  • The Plot class constructors generate an X value sequence if the X array argument is null or empty (JavaScript examples).
  • An informative message is displayed when a batch mode macro attempts to open an ROI set using open(path) (which does not work) instead of roiManager("open",path).
  • Thanks to Tiago Ferreira, the ROI Manager "Multi Plot" command no longer ignores "Fixed y-axis scale" in Edit>Options>Profile Plot Options.
  • Thanks to Bob Hamilton, "Area Fraction" (renamed "%Area") in the Analyze Particles Summary window now uses the Set Measurements decimal places.
  • Added the MaximumFinder.getMaxima() method (example).
  • Fixed a bug that caused the length of non-straight line profile plots to be greater that the measured line length.
  • Michael Schmid fixed a bug that could cause the RankFilters (Mean, Minimum, Median, etc.) to hang.
  • Thanks to Jan Eglinger, fixed bugs that could cause the recorder to throw bogus error messages or to record "null" or "nullnull" when opening or saving files.
  • Fixed a bug that caused the elliptical selection tool to always have integer starting coordinates.
  • Thanks to Oliver Bannach, fixed a bug that caused Histograms in batch mode macros to not be properly closed.
  • Thanks to Norbert Vischer, fixed a bug that caused File>Import>TIFF as Virtual Stack to not correctly open c=3, z=1, t=1 16-bit hyperstacks.

Version 1.45, 29 October 2011 (download)

• 1.45s 29 October 2011
  • Added the setOption("ExpandableArrays") macro function (example).
  • The Roi.getFloatPolygon() method works with more selection types.
  • Thanks to Kees Straatman, fixed a bug that caused Edit>Selection>Fit Ellipse to not work with spatially calibrated images.
  • Thanks to Gilles Carpentier, fixed a bug that caused the Overlay.drawString() macro function to display text at the wrong Y location and another bug that caused the run("From ROI Manager") macro function to not work in batch mode.
  • Thanks to Michael Schmid, fixed a bug that caused the CurveFitter.setMaxIterations() method to not work as expected.
  • Thanks to Jamie Robinson, fixed a bug that could cause the mm scale of newly opened hybrid DICOM/TIFF files to not be set.
  • David Gauntt fixed a bug that caused the NonBlockingGenericDialog to not correctly handle esc and enter key presses.
  • Thanks to Bentorey Hernandez Cruz, fixed a bug that caused the Panel Window example plugin to not work with hyperstacks.
  • Thanks to Norbert Vischer, fixed a bug that could cause the Plot.add("error bars", errorBars) macro function to throw an exception.
• Mahdi Rawak contributed Command Bar, a plugin that adds a toolbar with 19 buttons for running ImageJ commands.
• Kris Sheets contributed 3D Convex Hull, a plugin that calculates 3D shape descriptors, solidity and convexity based on a convex hull constructed from a stack.
• The University of Leicester is offereing two ImageJ/FIJI workshops in December.
• 1.45r 15 October 2011
  • Thinks to Norbert Vischer, macro arrays automatically expand as needed (example).
  • Thanks to Gilles Carpentier, image selections created using Edit>Selection>Image to Selection or Image>Overlay>Add Image can now be saved and restored.
  • Thanks to Johannes Schindelin, fixed a bug that caused the status bar to not be updated when scrolling a stack using the mouse wheel.
  • Thanks to Nagananda Gurudev and Johannes Schindelin, fixed a bug that sometimes caused an exception when opening LZW-compressed LSM files.
  • Thanks to Christophe Leterrier, fixed a bug in the newArray() macro function that caused it to not correctly handle array element arguments.
  • Thanks to Gilles Carpentier, fixed a bug that caused Analyze>Tools>Scale Bar to delete pre-existing overlays.
• 1.45q 4 October 2011
  • Added "Live" buttons to histogram and profile plot windows.
  • Added an "RGB" button to RGB histogram windows.
  • The Histogram command displays composite image LUTs.
  • Thanks to Gabriel Landini, fixed bugs that caused TIFF images larger than 2GB to not be correctly saved or opened.
  • Fixed a bug that caused File>New>Image to throw an exception when the user attempted to open an image larger than the maximum supported size (2 gigapixels).
  • Fixed a bug that sometimes caused the cursor coordinates to not be displayed in plot windows.
  • Thanks to Christophe Leterrier, fixed a bug in the newArray() macro function that caused it to sometimes not correctly handle string variable arguments.
  • Thanks to Norbert Vischer, fixed bugs that caused the plot window "List" and "Save" options to sometimes not work as expected if the window contained multiple plots.
  • Fixed a bug that sometimes caused a blank Results table to be displayed after changing "Decimal places" or enabling/disabling "Scientific notation" in the Analyze>Set Measurements dialog box.
  • Thanks to Christophe Leterrier, fixed bugs in Image>Color>Merge Channels that sometimes caused it to fail.
• 1.45p 20 September 2011
  • Image>Stacks>Make Montage works with hyperstacks.
  • Added the roiManager("Remove Slice Info") macro function.
  • Thanks to Daniel Hornung, removed the Toolbar.setBrushSize() lower limit of 5.
  • Worked around bug in the FileDialog class on Mac OS X that could cause files to be overwritten without warning if "Show all filename extensions" was not enabled in Finder Preferences.
  • Thanks to Bill Mohler, fixed a bug that caused File>Import>Image Sequence to not ignore .zip files created by the ROI Manager .
• Make Magazine Vol. 27 has an ImageJ tutorial, written by Bob Goldstein.
• 1.45o 12 September 2011
  • Thanks to Christophe Leterrier, File>Import>Image Sequence loads overlays when opening a folder of TIFFs as a non-virtual stack.
  • Added the ResultsTable.showRowNumbers() method (example) and the setOption("ShowRowNumbers",false) macro function (example).
  • Thanks to Airen Peraza, fixed a bug that caused the setTool() macro function and IJ.setTool(String) method to not work with macro tools.
  • Thanks to Charles Anderson, fixed a bug in the run("Make Composite") macro function that sometimes caused non-batch mode macros to not work as expected.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused images with extra periods in their names to be saved without an extension.
  • Fixed a bug that caused the run("Straighten...") macro function to require user input with line selections wider than one pixel.
  • Thanks to Christophe Leterrier, fixed an ROI Manager "Properties" bug that made it impossible to set the line width to 1 after having set it to greater than 1.
  • Thanks to Bill Mohler, fixed a bug in Analyze>Summarize that caused it to fail if the "Integrated Density" option was enabled.
  • Fixed bugs that caused Analyze>Measure to not calculate perimeter, circularity, feret-x, feret-y, feret angle, aspect ratio, roundness and solidity when there was no selection.
  • Fixed a bug that caused Analyze>Measure to not calculate feret-x, feret-y, feret angle and solidity of edited ROIs.
  • Fixed a v1.45n regression that caused the ROI Manager "Save" command to create corrupted .zip files if ROIs had been updated.
• Norbert Vischer contributed the AdvancedPlots macro set, five macros that demonstrate advanced plotting techniques.
• 1.45n 5 September 2011
  • Added the Image>Overlay>Labels command.
  • Added the Edit>Selection>Image to Selection command, which replaces the "Create image selection" option in the Image>Overlay>Add Image dialog.
  • Added the "Use file chooser to import [/export image] sequences" option to the Edit>Options>Input/Output dialog box.
  • Thanks to Damon Poburko, the ROI Manager "Delete" and "Deselect" commands are much faster on Windows.
  • The Image>Adjust>Brightness/Contrast command records as a comment.
  • The "Propagate to all open images" option in the "B&C" window's "Set" dialog box works with multi-channel images.
  • The run("Brightness/Contrast...") macro function does nothing if the "B&C" window is open and the current image is RGB.
  • Thanks to Norbert Vischer, added the toScaled(x,y), toUnscaled(x,y) and Plot.setFrameSize(width,height) macro functions (examples).
  • Added the getInfo("threshold.method") and getInfo("threshold.mode") macro functions and the ThresholdAdjuster.getMethod() and ThresholdAdjuster.getMode() methods.
  • Added the makeSelection(type,x,y,n) macro function (example).
  • Thanks to Ajay Gopal, fixed a bug that sometimes caused plots created in macros to be displayed twice and plots created in batch mode to not be displayed.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused selections added to the ROI Manager using roiManager("Add") to not be associated with the correct stack slice.
  • Thanks to Norbert Vischer, fixed a bug that caused plot window cursor locations displayed in the status bar to be incorrect if the plot x-origin was not zero.
  • Thanks to Jean-Pierre Clamme, fixed a bug that caused the color thresholder to somethimes not work as expected.
  • Fixed a bug that caused macro tools to be restarted on mouse clicks.
• 1.45m 20 August 2011
  • Added the Image>Overlay>Overlay Options command.
  • Added an "Add to overlay" option to the Analyze>Set Measurements dialog box.
  • The Image>Overlay>Add Selection command only displays a dialog if the alt key is down.
  • Thanks to Ved Sharma, added a "Use text tool font" option to the Image>Stacks>Label dialog box.
  • Improved the appearance of the "Threshold" window on Windows.
  • File>Import>Image Sequence ignores files named "RoiSet.zip".
  • Overlay selection names are preserved when saving in TIFF format.
  • Added the FileSaver.serialize() and Opener.deserialize() methods (example).
  • Thanks to Arttu Miettinen, fixed bugs that caused auto-thresholding of large (>1 gigapixel) stacks to fail and caused the "Threshold" tool to generate unneeded stack histograms.
  • Fixed a bug that sometimes caused the "Threshold" tool to generate incorrect 16-bit image thresholds when enabling/disabling the "Stack histogram" option.
  • Thanks to Ved Sharma, fixed a bug in Image>Stacks>Label that caused it to not work correctly for ranges not starting with 1.
  • Thanks to Michael Cammer, fixed a bug that caused an exception when adding a slice after splitting channels.
  • Fixed a bug that caused Process>Math>Square to not work as expected with 16-bit pixel values greater than 46341.
  • Fixed a bug that caused the run("Make Binary") macro function to display a dialog when the current image was thresholded.
  • Thanks to Steven Green, fixed bugs that caused intensity measurements made with line and point selections to not be redirected.
  • Thanks to Emmanuel Levy, fixed a bug that caused Image>Overlay>To ROI Manager to ignore selection names.
  • Bruno Vellutini fixed a bug that caused the roiManager("show all with labels") macro function to not work as expected.
• Aleksandr Mironov contributed three macros (Multipurpose grid, Multiple Circles grid and Unbiased Frames) for creating stereological grids and unbiased counting frames as non-destructive overlays.
• Tiago Ferreira updated the ImageJ User Guide (PDF) for v1.45m and added several new sectons. He also completely redesigned the HTML version and made available printable booklets in US and A4 versions.
• 1.45l 20 July 2011
  • Thanks to Richard Cole, added a "Use system proxy settings" option to the Edit>Options>Proxy Settings dialog.
  • Thanks to Ved Sharma, added a "Delete slices from original stack" option to Image>Stacks>Tools>Make Substack
  • Added the "Max Dimension" macro snippet, which resizes images to specified maximum dimension, to Process>Batch>Macro.
  • Thanks to Jerome Mutterer, the saveAs("raw",path) macro function no longer requires a ".raw" extension (example).
  • The getFileList() macro function now filters "Thumbs.db" files.
  • Added the ParticleAnalyzer.setFontSize() and ParticleAnalyzer.setLineWidth() methods.
  • Thanks to David McDonald, fixed a bug that caused horizontal and vertical straight line selections to not work with Edit>Selection>Restore Selection.
  • Thanks to John Oreopoulos, fixed bugs that sometimes caused the Plot.getValues() macro function to fail and the run("Distribution...","...") function to throw an exception.
  • Fixed a bug that caused headings of non-displayed results tables to not be saved.
  • Thanks to Ingo Bartholomaeus, fixed a bug that caused drawing tools to not set the image 'changes' flag.
  • Thanks to Gilles Carpentier, fixed a bug that caused an exception when duplicating a stack with a selection extending beyond the image edge.
  • Thanks to Daniel Kalthoff, fixed a bug that caused slice labels to be lost when importing stacks using File>Import>Image Sequence.
• 1.45k 5 July 2011
  • Added the Image>Stacks>Tools>Remove Slice Labels command.
  • The Process>Batch>Convert command averages when downsizing.
  • Thanks to Michael Doube, fixed a bug that could cause an exception when the image window was closed while a stack was being saved in TIFF format.
  • Thanks to Valerio Mussi, fixed bugs that caused the ROI Manager to not work as expected when the image origin was not at the top left corner.
  • Thanks to Tomas Karlsson, fixed a bug that sometimes caused the "+" and "-" keyboard shortcuts (zoom in/zoom out) to not work as expected with non-US keyboards.
  • Fixed bugs that caused run() macro calls with options like "open=&dir", "size=&min-&max" and "range=&first-&last" to fail.
  • Fixed a 1.45j regression that caused the RankFilters.rank() method to fail.
• 1.45j 24 June 2011
  • Added the Plugins>Utilities>Monitor Events command.
  • Thanks to Michael Schmid, the Median, Mean, Minimum, Maximum and Variance filters use less memory when processing non-float images.
  • Added a "Overlay" checkbox to the Analyze>Tools>Scale Bar dialog.
  • Added a "Stack histogram" checkbox to the Image>Adjust>Threshold dialog.
  • Added "Center" and "Right" text justification options to the Edit>Options>Fonts dialog, and, with text selections, to the Edit>Selection>Properties, Image>Overlay>Add Selection and the ROI Manager "Properties" dialog boxes.
  • The default text editor directory for saving is saved in the preferences file.
  • Image>Scale no longer limits the X and Y scale factors to 25.
  • Thanks to Johannes Weissmann, added the ImageProcessor.drawString(String, int, int, Color) method and drawString("text", x, y, background) macro function (example).
  • Added the ImagePlus.setImage(ImagePlus) and PlotWindow.getResultsTable() methods.
  • Thanks to Bruno Vellutini, fixed a bug that caused point selection measurements on single images to include a "Slice" Results table column even when "Stack position" was not checked in Analyze>Set Measurements.
  • Fixed bugs that caused JavaScript and Java code recorded by Image>Color>Stack to RGB and Image>Hyperstacks>Reduce Dimensionality to not work as expected.
• 1.45i 3 June 2011
  • Thanks to Jean-Yves Tinevez and Johannes Schindelin (creators of the Fiji ArrowTool plugin), added an "outline" checkbox to the arrow tool options dialog.
  • Added the Edit>Options>Rounded Rect Tool command.
  • Thanks to Michael Schmid, the popup menu activated by right clicking on an image window now works as expected with non-foreground images.
  • Added an "Ignore source LUTs" option to the Image>Color>Merge Channels dialog box.
  • Added "X center" and "Y center" fields to the Image>Zoom>Set dialog box.
  • The DICOM reader applies the Rescale Slope value when "Open as 32-bit float" is enabled in Edit>Options>DICOM and tag 0028,1053 has a value<>1.0.
  • Added the openFolder(), openAsVirtualStack() and sortFileNames() methods to the FolderOpener class;
  • Added drawRoi() and drawOverlay() methods to the ImageProcessor class (example).
  • Added the roiManager("select",indexes) macro function and RoiManager.setSelectedIndexes() method.
  • Fixed a bug that caused the magnification to be dropped from the title bar when using Image>Stacks>Add Slice on a single image.
  • Thanks to Vytas Bindokas, fixed bugs that caused the wand tool and the getStatistics() macro function to not work with virtual stacks imported using the Bio-Formats plugin.
  • Thanks to Johannes Schindelin, fixed a bug that sometimes caused the "Add [t]" command in the ROI Manager to sometimes save incorrect slice positions.
  • Michael Schmid, fixed bugs that sometimes caused objects to disappear when using Process>Binary>Ultimate Points and sometimes caused Process>Find Maxima to not work correctly on high dynamic range float images.
  • Thanks to Jan Eglinger, fixed a bug that caused transparent arrows to not be displayed correctly.
  • Thanks to Vytas Bindokas, fixed bugs that sometimes caused Edit>Selection>Make Band to fail.
  • Thanks to Jonathan Silver, fixed a regression that caused File>Save As>Text Image to not save float images using scientific notation when "Scientific notation" was checked in the Analyze>Set Measurements dialog box.
  • Thanks to Norbert Vischer, fixed a bug that caused TIFF virtual stacks to not gracefully handle the deletion of the source TIFF file.
• Tseng Qingzong has released PIV, a plugin that performs iterative particle image velocimetry analysis.
• 1.45h 17 May 2011
  • Added a "Use ROI names as labels" checkbox to the ROI Manager's More>>Options dialog box.
  • The ij.util.Java2.setSystemLookAndFeel() method (called by File>Import>Image Sequence) no longer sets the Swing look and feel to the system look and feel on Linux.
  • Added Stack.getFrameInterval(), Stack.setFrameInterval() and Stack.getUnits() macro functions.
  • Added setAntialiased() and getAntialiased() methods to TextRoi class.
  • Worked around a bug in the text tool that sometimes caused Edit>Clear to clear an area narrower than the drawn text.
  • Thanks to Peter Haub, fixed an ROI Manager "Edit Mode" bug that sometimes made selection of ROIs in stacks unreliable.
  • Thanks to Jan Eglinger, fixed a bug that caused mouse wheel scrolling of inactive hyperstack windows to not work.
  • Thanks to Daniel Kalthoff and Michael Schmid, fixed a macro bug that sometimes caused the Image>Crop, Image>Duplicate and Image>Adjust>Size commands to erroneously change the image focus.
  • Thanks to Mat Al-Tamimi, fixed a bug that caused profiles of image-height vertical lines and image-width horizontal lines to contain one extra value.
  • Thanks to Barry DeZonia, fixed a bug that sometimes caused the ImagePlus.setPositionWithoutUpdate() method to not work as expected.
  • Thanks to Andrii Savchenko, fixed a bug that caused the particle analyzer to not corretly summarize zero particle images.
  • Thanks to Jerome Mutterer, fixed a bug that caused IJ.redirectErrorMessages() to not work as expected with IJ.open(URL).
  • Thanks to Andrew French, fixed a bug that caused Image>Overlay>Flatten to always render text antialiased.
• 1.45g 2 May 2011
  • Thanks to Philippe Gendre, added the More>>Multi Plot command to the ROI Manager.
  • Thanks to Jason Newton, ImageJ can now open ZIP-compressed TIFFs.
  • The GenericDialog.getNextNumber() method returns NaN if the user has not entered a valid number (example).
  • The makePoint() macro function can now both add and delete points (example).
  • Fixed v1.45 regression that caused the ROI Manager "Show All" option to not respect slice info.
  • Thanks to Carne Draug, fixed a bug that sometimes caused ImageJ to hang on quitting when running on OpenJDK 6.
• 1.45f 23 April 2011
  • Added the Edit>Selection>Area to Line command.
  • Thanks to Michael Schmid, the Mean and Variance filters no longer propagate NaNs to the end of the line.
  • Thanks to Marcel van Herk, File>Import>Stack from List works with URLs (example).
  • Added the Dialog.addSlider() method (example).
  • Fixed a bug that caused Image>Scale and Image>Adjust>Size to throw an exception when there was a selection and "Average when downsizing" was enabled.
  • Thanks to Simon Roussel, fixed a bug that caused overlays to be lost when converting stacks to hyperstacks and vis versa.
  • Thanks to Kris Sheets, fixed a bug that could cause the ROI Manager to not work as expected on Mac OS X when using the waitForUser() macro function.
  • Thanks to Norbert Vischer, fixed a bug that caused incorrect centroid, major and minor results when using Analyze>Measure on thresholded images with "Fit Ellipse" and "Limit to Threshold" enabled.
  • Fixed a bug that caused the size of JPEG files to not be reduced when re-saving at lower resolution or quality.
  • Thanks to Vytas Bindokas, fixed a bug that caused an exception when an image was listed twice in the Image>Color>Merge Channels dialog box.
• J. Lewis Muir has released CBF Reader, a plugin for reading miniCBF image files produced by DECTRIS PILATUS detectors.
• 1.45e 2 April 2011
  • File>Import>Image Sequence and File>Save As>Image Sequence now use the directory chooser.
  • Thanks to Michael Schmid, added the Process>Noise>Remove NaNs command.
  • Analyze>Plot Profile ignores NaNs.
  • "Feret" and "MinFeret" of selections created using the elliptical tool are calculated more accurately.
  • Added the Overlay.copy and Overlay.paste macro functions.
  • Added the FolderOpener.open() method.
  • Thanks to Gabriel Landini, fixed a bug that sometimes caused the ability to record the selectWindow() macro function to be lost after a macro error.
  • Fixed a bug that caused File>Save As>Image Sequence to record duplicate "save=" keys.
  • Thanks to John Pearl, fixed a bug that caused the "Label points" option in Edit>Options>Point Tool to sometimes not work as expected.
  • Thanks to Michael Schmid, fixed a bug that caused the Dynamic Profiler plugin to flicker and sometimes crash.
  • Thanks to Francis Burton, fixed a bug that caused the Plot.update macro function to throw an exception in batch mode.
  • Thanks to Michael Doube, fixed a 1.45d regression that caused Edit>Selection>Add to Manager to sometimes lose the slice position.
  • Thanks to Karen Collins, fixed several bugs in the directory chooser.
  • Thanks to Norbert Vischer, fixed a bug that caused the run("Add to Manager") macro function to sometimes draw the ROI.
• Dimiter Prodanov contributed nVidia Fix, a plugin that fixes display problems caused by buggy nVidia drivers.
• 1.45d 19 March 2011
  • Thanks to Tiago Ferreira, the Plugins>Utilities menu is now more logically organized and the "Do:" drop down menu in the Process>Binary>Options dialog includes "Outline", "Fill Holes" and "Skeletonize" choices.
  • An ROI Manager selection no longer loses its stack position when its label is changed.
  • The "Update" ROI Manager command now updates the z-position.
  • Thanks to Tseng Qingzong, the particle analyzer respects the Process>Binary>Options "Black background" setting when working with non-thresholded 8-bit binary images.
  • The Image>Duplicate command can duplicate a range of channels in C>1, Z=1, T=1 hyperstacks.
  • Thanks to Frank Sprenger, fixed bugs that caused Image>Color>Split Channels and Image>Hyperstacks>Reduce Dimensionality to sometimes not work correctly in batch mode and to not generate grayscale images when the input image was in "Grayscale" mode.
  • Added the Overlay.setPosition() and IJ.pad() macro functions (example).
  • Added roi.setPosition(), roi.getPosition() and IJ.pad() methods (example).
  • Fixed a bug that could cause Image>Duplicate to fail in non-batch mode macros.
  • Thanks to Jarek Sacha, fixed bugs that caused the coordinate origin to be unchanged after Image>Crop and Image>Duplicate.
  • Thanks to Bill Mohler, fixed a bug that could cause an exception when working with single channel composite images.
  • Fixed a bug that caused overlays stored in the TIFF header to not display on stacks opened using File>Import>TIFF Virtual Stack.
• 1.45c 10 March 2011
  • Process>Filters>Gaussian Blur processes single images much faster on multi-core computers thanks to multi-threading support added by Stephan Saalfeld.
  • The Process>Math>Macro, Convolve, Despeckle, Remove Outliers, Median, Mean, Minimum, Maximum, Variance and Unsharp Mask commands are faster when processing single images on computers with multi-core CPUs.
  • Tiago Ferreira made the Plugins>Utilities>Search command recordable and added support for scripts.
  • Image Selections (ImageRois) created using Image>Overlay>Add Image can be moved beyond the image boundary and their location is displayed in the status bar as they are moved.
  • Removed the broken Help>Search Website command and renamed Help>List Archives to Help>Mailing List.
  • Thanks to Bill Mohler, fixed a bug that caused the Image>Stacks>Tools>Concatenate command to not work as expected in batch mode macros.
  • Fixed a bug the caused the waitForUser() macro function to not work with the brush and pencil tools.
  • Thanks to Alberto Duina, fixed a bug that caused the IJ.redirectErrorMessages macro function to not prevent macros from being aborted when opening DICOM images.
  • Fixed a bug that enabled "Show All" mode in the ROI Manager when unchecking "Edit Mode".
  • Fixed a bug in Image>Stacks>Make Montage that sometimes caused borders to overlap labels.
  • Fixed a bug in File>Import>Image Sequence that could cause the pixel width and height to be incorrect if the value of "Scale images" in the dialog was not 100.
  • Thanks to Daniel Senff, fixed a bug that caused an exception when using the setForeGroundColor() macro function after starting ImageJ using "new ImageJ(ImageJ.NO_SHOW)".
  • Thanks to Stephan Saalfeld, fixed a bug that caused overlays on composite images to sometimes not display correctly.
• Alberto Duina contributed Dicom Sorter, a macro that reorders a directory with a lot of dicom files by moving the files to subdirectories sorted by patient id, study id etc.
• 1.45b 18 February 2011
  • Improved Memory Monitor (Plugins>Utilities>Monitor Memory): it is larger, it displays the number of open images, it remembers its screen position, it is no longer an image window, keyboard shortcuts work when it has focus and clicking on it runs the garbage collector.
  • The "Run single instance listener" option in Edit>Options>Misc is set by default with new Windows installations.
  • Image>Stacks>Add Slice and Delete Slice work with composite images.
  • Fixed a bug that sometimes caused composite images with custom LUTs to not be saved correctly as TIFFs.
  • Thanks to Michael Daube, fixed a bug that could cause the FHT.dfht3() method to throw an exception.
  • Fixed a bug that sometimes caused the DICOM reader to not correctly decode the pixel spacing.
  • Thanks to Michael Schmid, fixed a bug that sometimes caused dynamically updated messages in GenericDialogs to be truncated.
  • Thanks to Michael Schmid, fixed a bug that caused Process>FFT>Inverse FFT to lose the image calibration if the size of the original image was not a power of two.
  • Fixed a bug that made it impossible to open the Color Picker and Fonts windows after they had been closed using File>Close.
  • Fixed a bug that caused the scale of profile plots created using wide line selections on globally calibrated images to be incorrect.
• Tseng Qingzong has released plugins that use the OpenCV library to do template matching and image alignment.
• 1.45a 6 February 2011
  • The Edit>Undo command is, in most cases, undoable.
  • Added the "Keep multiple undo buffers" option to the Edit>Options>Memory dialog box.
  • Image>Stacks>Tools>Concatenate works with composite images and stacks.
  • Keyboard shortcuts now work in all TextWindows (e.g., the Log window).
  • Users are prompted to save changed editor windows when quitting ImageJ.
  • Added a keyboard shortcut to the Editor's Debug>Run To Insertion Point command.
  • The waitForUser macro function uses a default "Click OK to continue" message if called without an argument and without parentheses.
  • Added the ImageProcessor.swapPixelArrays() method, which is used to make Undo undoable.
  • Fixed a bug, introduced in 1.44n, that sometimes caused Image>Color>Merge Channels to not work as expected.
  • Fixed a bug that caused pasting of non-rectangular selections the same size as the target image to not work as expected.
  • Fixed a bug that caused the "Run single instance listener" option in Edit>Options>Misc to not work as expected.

Version 1.44, 31 January 2011

• 1.44o 31 January 2011
  • Process>FFT>Bandpass Filter uses multiple threads when processing stacks.
  • Plugins and scripts can now use IJ.log("\\Close") to close the Log window.
  • Added a constructor to the FileInfoVirtualStack class that allows opening of TIFF stack subsets (example).
  • Added the RGBStackMerge.mergeChannels(ImagePlus[],boolean) method.
  • Fixed bugs that caused incorrect recording of B&C window commands.
  • Fixed a bug that caused incorrect passing of variables using the '&' operator in run() calls within macro functions.
  • Thanks to Norbert Vischer, fixed a bug that caused error messages generated by the selectImage() macro function to be missing the source line number.
  • Fixed a bug that could cause 16-bit LZW compressed TIFFs to fail to open.
• Tiago Ferreira updated the ImageJ User Guide (PDF) for v1.44 and added sections on advanced ImageJ usage, IJ and Fiji Scripting, command line usage and ImageJ interoperability. He also created a greatly improved HTML version, available either online or as a downloadable ZIP file.
• 1.44n 17 January 2011
  • Image>Color>Merge Channels preserves LUTs and display ranges when merging images and stacks to create composite images.
  • Thanks to Michael Schmid, the current image is now only auto-thresholded when the Threshold window is activated via the menu command or by pressing "T".
  • Thanks to Duncan Mak, the "Loop back and forth" option in the Image>Stacks>Tools>Animation Options dialog box is now persistent.
  • Added the setOption("loop", boolean) macro function.
  • Fixed a bug that sometimes caused a DICOM sequence opened as a virtual stack to not be sorted correctly.
  • Fixed a bug that caused Plugins>Macros>Run to record incorrect code.
  • Thanks to Michael Schmid, fixed bugs that caused commands that bring windows to the front, like selecting from the Window menus and Window>Show All, do not de-iconify windows on Windows and Linux.
  • Fixed a bug that sometimes caused the More>>Fill command in the ROI Manager to fail with composite ROIs.
  • Fixed a bug that could cause an out of memory error when opening a DICOM sequence from a folder containing a .xml file.
  • Thans to Barry DeZonia, fixed a bug that caused the Paste command to not work as expected in "Transparent-white" mode with 32-bit images.
  • Thanks to Nico Stuurman, fixed a bug that caused channel and slice position changes in animating hyperstacks to be ignored.
  • Fixed a bug that caused an exception when an empty folder was dragged and dropped on the "ImageJ" window.
  • Fixed a bug that caused the getSelectionCoordinates() macro function to not work as expected with wider than one pixel straight line selections.
• Norbert Vischer contributed Offline Macro Help, a macro that downloads "functions.html" and the files it references, making macro programming documentation locally accessible.
• David Stepensky contributed IntraCell, a plugin for analysis of nanoparticle colocalization with organelles within the cells
• 1.44m, 1 January 2011
  • Thanks to Ved Sharma and Michael Doube, added the Edit>Selection>Fit Circle command, which fits a circle to line and multi-point selections. With area selections, it creates a circle with the same area and centroid.
  • Thanks to Barry DeZonia, fixed a bug that caused Undo of finalized pastes to fail.
  • Thanks to Bill Mohler, Image>Stacks>3D Project now works with hyperstacks, and with 16 and 32 bit images.
  • Thanks to Michael Ellis, added support for single channel CompositeImages.
  • Added the ImagePlus.duplicate() method.
  • Fixed a bug that caused the roiManager("reset") macro function to not not remove the "Show All" overlay.
  • Fixed a bug that caused macros using run("Calibrate...", "...") to fail.
  • Fixed a bug that caused File>Open Next to fail after saving an image.
  • Fixed a bug that caused an exception if a file displayed in a virtual stack was deleted.
  • Fixed a bug that caused a "Save changes?" dialog to be displayed when closing a virtual stack window.
• Jan Bonne Aans contributed Nonlinear Polar Transformer, a plugin that corrects radial and angular distortions in X-ray images.
• 1.44l, 16 December 2010
  • Image>Stacks>Orthogonal Views works with hyperstacks and can be started/stopped using the shift-h keyboard shortcut.
  • Thanks to Bob Dougherty, the color bar in histograms is now scaled to reflect the display range of the image.
  • Thanks to Michael Doube, voxel depth of imported DICOMs is based on the distance between the first and last slices.
  • Thanks to Michael Schmid, zooming in or out no longer causes the position to be lost when the cursor is not over the image.
  • Image>Stacks>Z Project saves the projection method in the preferences file.
  • Added a "Bare Outlines" option to the particle analyzer.
  • Thanks to Christian Moll, added the getInfo("log") macro function and the IJ.getLog() method.
  • Added the DicomTools.getTag() method.
  • Fixed a bug in Image>Stacks>Reslice that caused, with a stright line selections, inconsistent line shifting if "Slice count" was greater than 1 and "Avoid interpolation" was enabled.
  • Fixed several bugs in Image>Stacks>Orthogonal Views.
  • Jan Funke fixed a bug that made it impossible to use the ZProjector class concurrently.
  • Fixed a bug that caused Image>Stacks>Make Montage, when used with signed 16-bit images, to sometimes draw borders using pixel values of -32768.
  • Fixed a bug that caused Image>Transform>Translate to fill with white for non-integer bicubic translations.
  • Thanks to Johannes Schindelen, fixed bugs that sometimes caused Image>Color>Merge Channels to not work as expected when merging four stacks.
• The 2004 ImageJ paper by Michael Abramoff, Paulo Magalhaes and Sunandra Ram, which has over 2000 citations, is now available as a PDF.
• Wilhelm Burger has released Export EPS, a plugin that exports images as Encapsulated PostScript (EPS) files.
• Run the Find 3D Max benchmarks to compare the speed of various dimension and type independent pixel access methods.
• 1.44k, 26 November 2010
  • Thanks to Norbert Vischer, added the ellipse tool, which shares the second slot on the toolbar with the oval and the selection brush tools.
  • Karen Collins contributed an improved FITS_Writer (File>Save As>FITS).
  • Image>Show Info displays the pixel or voxel size.
  • Edit>Selection>Straighten checks to see if the line has already been prepared for straightening by a run("Fit Spline", "straighten") call.
  • The getPixel(x,y) macro function now interpolates if x or y are non-integer.
  • Thanks to Norbert Vischer, added the Array.rankPositions() (example) and makeEllipse() macro functions.
  • Thanks to Jerome Mutterer, added the getDisplayedArea() macro function (example).
  • Ved Sharma fixed a bug that caused Image>Stacks>Label to not correctly display negative times in min:sec and hour:min:sec modes.
  • Fixed a bug that caused selection adjustment handles to be too small on zoomed images.
  • Fixed a bug that sometimes caused batch mode macros that used the particle analyzer with the "Add to Manager" option to fail.
  • Thanks to Michael Schmid, fixed a bug that caused a bogus syntax error when calling a user-defined macro function with an expression similar to a[i]+b.
  • Thanks to Wilhelm Burger, fixed a bug that caused the stroke width of ShapeRois to not scale with the zoom factor.
  • Fixed a bug that caused the pixel width of the output image to be incorrect after using Image>Stacks>Reslice with a line selection on a spatially calibrated image.
  • Fixed a bug in IJ.d2s() that caused it to not correctly convert infinite values.
• Gilles Carpentier contributed the Zoom_in_Images_and_Stacks macro tool (example).
• Samuel Pean has released the Heatmap From Stack, HeatMap Histogram and Image Stack Merger Plus (background remover) plugins.
• The photos from the 2010 ImageJ conference in Luxembourg are now online.
• The Macro Language Reference Guide and example macros from Jerome Mutterer's Macro Tutorial at the ImageJ conference in Luxembourg are now available.
• Norbert Vischer contributed RandomEllipseTool, a macro tool for creating elliptical selections with arbitray orientations and aspect ratios.
• 1.44j, 10 November 2010
  • The Image>Duplicate command now works with hyperstacks.
  • Double click on the angle tool icon to enable measurement of reflex angles.
  • Thanks to Johannes Schindelen, added the More>>XOR command to the ROI Manager.
  • Added a "y" keyboard shortcut to the Edit>Selection>Properties command.
  • Added the ImageJ(ImageJ.NO_SHOW) constructor, which allows other Java applications to open ImageJ invisibly.
  • Fixed a bug that caused ImageCanvases to ignore mousePressed and mouseMoved events when using ImageJ as a library.
  • Fixed a bug that caused the Image>Adjust>Size interpolation setting to be changed to "None" after using Image>Crop.
  • Thanks to Wilhelm Burger, fixed a bug in the ByteBlitter class that caused it to throw an exception if the copyBits() method was passed a ShortProcessor or a FloatProcessor.
  • Fixed a bug that caused saving of Results windows created using IJ.write() calls to fail.
  • Thanks to Norbert Vischer, fixed a bug that caused TIFF files opened as virtual stacks to become corrupted when saved in place.
  • Fixed a bug that caused Process>Binary>Skeletonize to not work as expected for some diagonal objects.
  • Fixed a bug that caused use of the up and down arrow keys in the Control Panel to zoom the image in and out.
  • Fixed bugs that caused the "Control Panel" and "List Commands" commands to fail in the drop down menu that appers when right-clicking on an image.
• Usage statistics for imagej.nih.gov for the month of October are now available. In one month, there were 216,007 visits from 159,623 unique sites and 3029 gigabytes of data were downloaded. ImageJ was downloaded 213,921 times, an average of 6900 times per day.
• Gilles Carpentier contributed the Protein Array Analyzer toolset (online documentation).
• Volker Baecker has made available a comprehensive 93 page ImageJ tutorial (11MB PDF).
• 1.44i, 8 October 2010
  • Added the Edit>Selection>To Bounding Box command.
  • Added the "Run garbage collector on status bar click" checkbox to the Edit>Options>Memory&Threads dialog box.
  • Added "Help" buttons to the FFT dialog boxes.
  • Pressing "+" (Image>Zoom>In) now zooms to the center of the image when the cursor is not over the image window.
  • File>Revert now works with stacks.
  • The particle analyzer now works with virtual stacks and with RGB images thresholded using Image>Adjust>Color Threshold.
  • The state of the Image>Adjust>Threshold and ColorThreshold "Dark background" checkboxes are saved in the preference file.
  • The Array.sort() macro function now does case-insensitive string sorts.
  • Fixed a bug that sometimes caused the magnifying glass tool to zoom the wrong image on Linux.
  • Thanks to Matthew Smith, fixed a bug that caused non-rectangular pastes to fail when switching to another image.
  • Fixed a bug that caused the wrong button to be highlighted in showMessageWithCancel() dialog boxes.
  • Fixed a bug that caused 3D projection of RGB stacks to fail if "Use inverting lookup table" was enabled in Edit>Options>Appearance.
  • Fixed a bug that caused a "Rename as" dialog to be displayed if the alt key was held down while a batch mode macro using the ROI Manager was running.
  • Fixed a bug that caused an FFT window to always be displayed when "Raw power spectrum" was checked in the "FFT Options" dialog box.
  • Fixed a bug with the roiManager("Add") macro function that caused it to set the ROI stroke color to cyan.
  • Fixed a bug that caused duplicate images with names ending in "-xx" do sometimes be renamed incorrectly.
• Timm Weitkamp, David Haas and Alexander Rack contibuted ANKAphase, a plugin that processes X-ray inline phase-contrast radiographs.
• Kristopher Sheets contributed Open Heyex Raw Files, plugins that import Heidelberg Spectralis OCT images.
• Dimitrios Vavylonis has released JFilament, a plugin for segmentation and tracking of 2D and 3D filaments in fluorescenece microscopy images.
• 1.44h, 21 September 2010
  • Added drop down menus to the Image>Adjust>Color Threshold window for selecting any of 16 different automatic thresholding methods and for selecting the threshold color.
  • Fixed a bug that sometimes caused the Image>Adjust>Contrast/Brightness "Apply" option to fail with RGB stacks.
• Erik Meijering released an updated version of TransformJ that works with hyperstacks and includes source code.
• 1.44g, 18 September 2010
  • Plugins>Utilities>Control Panel no longer creates a "PCPanel2.ini" file in the user's home directory.
  • ImageJ can now open zip archives, using a URL, that contain multiple DICOM images.
  • The arrow keys can now be used to vertically scroll the Results window.
  • The getInfo() macro function can now retrieve Bio-Formats metadata values.
  • Added the selectionContains(x,y), is("animated") and debug("dump") macro functions.
  • The TextPanel.setSelection() method now insures that the selection is visible.
  • Added the TextPanel.addMouseListener() method.
  • Thanks to Barry DeZonia, fixed a bug that caused Process>Smooth to not round results with 8-bit images.
  • Fixed a bug that sometimes caused passing of choices in macro run() calls to fail when "item=&varname" notation was used.
  • Fixed a bug that caused virtual stacks backed by a folder containing a script to not open correctly.
  • Fixed a bug that sometimes caused the image count displayed in the dialog box to be incorrect when a folder is dragged and dropped.
  • Barry DeZonia fixed a bug that sometimes caused division of 16-bit images to fail and a bug that could result in Windows directory paths ending in "/\\".
  • Fixed a bug that caused an exception to be thrown when opening LZW compressed 32-bit float TIFFs.
  • Fixed a bug that caused the macro debugger to sometimes fail to work with macro code pasted into the editor on Mac OS X.
  • Thanks to Barry DeZonia, fixed a bug that caused the ImageProcess.convolve3x3() method (used by Process>Sharpen) to not correctly handle edge pixels of 8-bit and RGB images images.
  • Tseng Qingzong fixed a bug in the MaximumFinder.findMaxima() method that caused it to fail when called with outputType List or Count.
  • Andreas Maier fixed an edge handling bug in ImageProcessor.getInterpolatedValue(), which is used by Analyze>Plot Profile.
• Christian Aeberhard contributed GHT, a plugin that uses the General Hough Transformation to recognize rotated and scaled objects.
• Thanks to Evan McCreedy, the ImageJ website has a new, easier to remember, URL (imagej.nih.gov/ij). The old URLs (rsbweb.nih.gov/ij and rsb.info.nih.gov/ij) will continue to work.
• 1.44f, 22 August 2010
  • Added the Image>Stacks>Tools>Grouped Z Project command.
  • Thanks to Michael Schmid, Image>Adjust>Size and Image>Scale have "Average when downsizing" options and Image>Adjust>Size supports Undo.
  • Thanks to Michael Doube, the Ortho Viewer (Image>Stacks>Orthogonal Views) can be controled by clicking and dragging in the XZ and YZ views and the mouse wheel changes the screen plane in all three views..
  • Image>Stacks>Z Project now works with RGB hyperstacks.
  • The headers are now saved when saving a DICOM virtual stack in TIFF format.
  • Thanks to Mark Longair, IJ.getScreenSize() now returns the correct size when the screen size is changed after ImageJ has started.
  • The perimeter of a composite selection is now calculated by decomposing it into individual selections. The composite perimeter and the sum of the individual perimeters may be different due to use of different calculation methods.
  • Thanks to Michael Doube, added getInstance(), getCrossLoc() and setCrossLoc() methods to the Orthogonal_Views class (example).
  • SetStack() calls no longer cause a new ImageWindow to be constructed when adding a slice to a single image or subtracting a slice from a two slice stack.
  • Newly opened macro sets with two or more macros are installed in the Plugins>Macros submenu.
  • Added the getInterpolationMethod() and resize(int,int,boolean) methods to the ImageProcessor class.
  • Fixed a regression than caused the particle analyzer to fail with stacks when "Display labels" was enabled in Analyze>Set Measurements.
  • Fixed bugs in Image>Stacks>Orthogonal Views that caused it to not work correctly with anisotropic voxels.
  • Fixed a bug that caused Edit>Selection>Rotate to fail with thick lines.
• Thanks to Johannes Schindelin, the 16 plugins developed under the supervision of Noël Bonnet were recovered and are now available at plugins/inserm514.
• Sean Parsons contributed MetaData (Line Scan Analysis), a plugin that saves and opens images with metadata and does filtering, normalization and spark detection of confocal line scans of intracellular calcium.
• Jorma Isola has released ImmunoRatio, a plugin for analyzing ER, PR, and Ki-67 immunohistochemistry.
• Ben Corry and Rasha Ruhayel contributed 2D NMR Analysis, a plugin for analysing and integrating peaks in 2D NMR spectra.
• 1.44e, 2 August 2010
  • Added the Image>Stacks>Tools>Make Substack command, based on the Substack Maker plugin by Anthony Padua, Daniel Barboriak and Ved Sharma.
  • Added an "AND" command to the ROI Manager.
  • The Image>Overlay>Add Selection dialog remembers the stroke width and color.
  • The run("Close All") macro function no longer displays a warning message when there are unsaved changes.
  • The particle analyzer now displays a blank image when the count is zero and "Show:" is not "None".
  • Added the Overlay.* macro functions (example).
  • Added the CompositeImage.setChannelsUpdated() and Macro_Runner.runMacroFromJar() methods.
  • Fixed a regression that caused the save() macro function to change the image name.
  • Fixed a regression that caused File>Import>Text Image to fail if the file contained values with a plus sign (e.g., "1.23e+02").
  • Fixed a macro run() call parsing bug that caused "min=234;run("Analyze Particles...", "size=&min");" to fail.
  • Fixed a bug that caused an exception if the newImage() macro function was called with width or height set to zero.
  • Fixed a bug that caused setAutoThreshold("Default") to sometimes not generate the expected threshold with images that had a sharp peak in its histogram.
  • Fixed a bug that caused Plugins>Utilities>Control Panel to not correctly save its preferences.
• 1.44d, 12 July 2010
  • Added the Edit>Selection>Line to Area command.
  • Added "Help" buttons to the File>Import>Image Sequence, File>Import>Raw and Process>Math>Macro dialog boxes.
  • The CurveFitter resolves 6 parameter user-defined equations.
  • Image>Color>Make Composite now opens the new composite color image in place.
  • Removed the "Convert to 8-bit grayscale" option from File>Import>Image Sequence. As a replacement, use the "Use virtual stack" option and then convert to 8-bit using Image>Type>8-bit.
  • Assigned the "U" keyboard shortcut to Plugins>Utilities>Control Panel.
  • ImageJ no longer automatically installs, at startup, plugins in JAR file directories that start with a lower case letter.
  • ImageJ runs "-batch" command line scripts in batch mode.
  • Added setImage(ImagePlus) and setNextLocation(Point) methods to the ImageWindow class.
  • The up and down arrow keys no longer cause the LOCI Data Browser window to zoom in and out.
  • Fixed a bug that sometimes caused an exception when an animating stack window was closed.
  • Fixed a bug that sometimes caused Process>Image Calculator to not work correctly with signed 16-bit stacks.
  • Fixed a bug that caused an exception when using Image>Overlay>Flatten on an image without an overlay.
  • Fixed a bug that sometimes caused the "Ch", "Slice" and "Frame" Results table columns (enabled by checking Stack Position in Set Measurement) to contain incorrect values.
  • Fixed a bug that caused JPEGs smaller than 8x8 pixels to always open as 8-bit grayscale images.
  • File>Save As>AVI no longer caps the frame rate at 60 FPS.
  • Fixed a bug that caused the slice range to be ignored by Image>Stacks>Label when using an overlay.
• Adam Gorlewicz has released Colocalization Colormap, a plugin for quantification and visualization of colocalized fluorescent signals.
• Michael Mohn and Jannik Meyer contributed Asymmetry, a plugin for automated analysis of variations in imaging conditions across the field of view in high resolution TEM images.
• 1.44c, 15 June 2010
  • Raw integrated density (sum of pixel values) is displayed when "Integrated density" is enabled in Analyze>Set Measurements.
  • Added a File>Rename command and Results menu to Results windows.
  • Added "Help" buttons to the Process>Find Maxima, Process>Image Calculator and Process>Subtract Background dialog boxes.
  • Pressing 'esc' aborts macros displaying a "WaitForUser" dialog.
  • Changed the name of the File>Save As>Measurements command to File>Save As>Results and changed Help>Update Menus to Help>Refresh Menus.
  • Plugins>Compile and Run adds the Bio-Formats plugin (loci_tools.jar) to the Java compiler's classpath.
  • The TIFF reader displays information needed to import the file (number of images, offset to first images, gap between images) when ImageJ is in debug mode.
  • The MacClipboard plugin, which opens PICT images from the clipboard using QuickTime for Java, is now included in ij.jar.
  • Added the IJ.renameResults() macro function.
  • Worked around a bug that caused the Image>Stacks>Reslice command to be very slow on some 64-bit versions of Java.
  • Fixed a bug that sometimes caused a "negative seek offset" error when opening TIFF files larger than 2GB.
  • Fixed a bug that caused File>Import>TIFF Virtual Stack to not display the TIFF tags when ImageJ was in the debug mode;
  • Fixed a bug that caused "/" to be added to the FileInfo directories when opening a folder of images using drag and drop on Windows.
  • Fixed a bug in the setAutoThreshold() macro function and ImageProcessor.setAutoThreshold() method that caused the threshold level to be one less than the level set by the "Threshold" widget when "Dark background' was enabled.
• Jerome Mutterer has released Serial Macro Extensions, a plugin that provides macro language functions to talk to a device attached to a serial port.
• 1.44b, 1 June 2010
  • Added the "Unsigned 16-bit range" drop down menu to the Image>Adjust>Contrast/Brightness "Set" dialog.
  • Added show="Overlay Outlines", show="Overlay Masks" and "In situ Show" options to the Analyze>Analyze Particles dialog box.
  • Added "Help" buttons to the Process>Binary>Options, Analyze>Analyze Particles, Analyze>Set Measurements, Analyze>Set Scale and Analyze>Calibrate dialog boxes.
  • Added a "Use overlay" option to Image>Stacks>Label.
  • File>Export>AVI and File>Export>Image Sequence (when saving JPEG or PNG) now preserve overlays.
  • Added the Overlay.setStrokeColor() and Overlay.setfillColor() methods.
  • Fixed a bug that caused the getResult() macro function to return NaN with imported results containing column headers with leading or trailing spaces.
  • Fixed a bug that caused 8 and 16 bit grayscale stacks saved as JPEG-compressed AVIs to not play correctly in the Windows 7 Media Player.
  • Fixed a bug that caused macros to become uninterruptible after doing a custom curve fit.
  • Fixed a bug that caused redirected sampling of non-displayed images to fail.
• Franklin Shaffer, an engineer at the USDOE National Energy Technology Laboratory in Pittsburgh, used ImageJ to help estimate the leak rate from the Gulf oil spill.
• The 3D Viewer plugin, included with imageJ as the Plugins>3D>ImageJ 3D Viewer command, was published in BMC Bioinformatics. Please cite this article when using it for your visualization needs.
• The RGB to CMYK plugin converts an RGB image into a 32-bit CMYK stack.
• 1.44a, 13 May 2010
  • Overlays are preserved when printing and when saving in PNG format.
  • Thanks to Tiago Ferreira, Image>Stacks>Tools>Montage to Stack now takes borders into acount.
  • Added "Rotate YZ" and "Flip XZ" options to Edit>Options>DICOM.
  • Thanks to Juan Grande, added "Save column headers" and "Save row numbers" options to Edit>Options>Input/Output.
  • Constructing a HistogramWindow when using ImageJ as a library no long causes an image to be displayed.
  • Added a GenericDialog.addCheckboxGroup() method that specifies column headings.
  • Fixed a bug that caused "Results" window summary data to not be saved.
  • Fixed a bug that caused Orthogonal Views crosshair lines to be saved as an overlay when saving in TIFF format.
  • Thanks to Barry DeZonia, fixed a bug that sometimes caused an exception when drawing a composite selection (ShapeRoi).
  • Fixed a bug that could cause the Threshold tool to not work correctly after using File>Revert on a 16-bit DICOM image.
  • Fixed a bug that could cause the Image>Overlay>Hide Overlay and Show Overlay commands to not work as expected.
  • Thanks to Johannes Schindelin, fixed a bug in the PluginClassLoader that could cause an exception when running plugins using MIJ (Matlab to ImageJ interface).
  • Fixed a bug that caused DialogListeners to not be called with checkbox groups with fewer than five checkboxes.
  • Worked around a Linux bug that caused labels in GenericDialog checkbox groups to be centered rather than left justified.
  • Fixed bugs in Image>Stacks>Othogonal Views that caused it to not work correctly with zoomed images and with the "+" (Zoom In) and "-" (Zoom Out) commands.
• The MultiColumnDialog plugin demonstrates how to create a dialog box with checkboxes in two or more columns.
• Ben Tupper contributed Graph Demo, a plugin that demonstrates the creation of adjacency lists based on particle separation distances.
• Tiago Ferreira's ImageJ User Guide (PDF) is now also available in HTML format, either online or as a downloadable ZIP file.
• Ricardo Henriques has released QuickPALM, a plugin for real-time acquisition, reconstruction and visualization of 3D PALM (PhotoActivated Light Microscopy) or STORM (STochastic Optical Resolution Microscopy) images.
• Michael Fischer contributed Diameter, a plugin for measuring the diameter of a blood vessels.

Version 1.43, 22 April 2010

• 1.43u, 22 April 2010
  The code for opening PICT images from the clipboard using QuickTime for Java was moved to a separete plugin (MacClipboard.java) distributed with the OS X version of Image.
  • Fixed a bug that caused the setAutoThreshold() macro function, and the IJ.setAutoThreshold() and ImageProcessor.setAutoThreshold() methods, to not work correctly with 16 and 32 bit images that were not using the default display range.
  • Barry DeZonia contributed an improved OvalRoi.contains() method.
• Guanghua Du contributed Foci Picker3D, a multithreaded plugin that finds local maxima in 2D and 3D images.
• 1.43t, 17 April 2010
  • ImageJ now requires Java 1.5 or later.
  • Added the Image>Stacks>Tools>Insert and Image>Stacks>Tools>Montage to Stack commands.
  • Image>Stacks>Label works with hyprestacks and support for 00:00 and 00:00:00 timestamp formats.
  • Edit>Draw now draws to left and below rectangular selections when the line width is one.
  • Add "Timestamp" code generator to Process>Batch>Macro and Process>Batch>Virtual Stack.
  • The "Auto", "Reset" and "Set" buttons of the B&C widget are now recorded correctly when the Recorder is in "Script" or "Plugin" mode.
  • File>Import>Raw opens stacks with the middle slice selected.
  • Changed the initial Log fit 'a' and 'b' parameter values to 1.0.
  • Added the SetOption("black background", boolean) macro function.
  • Added the LutLoader.open(String), LutLoader.open(InputStream) and LutLoader.createImage(IndexColorModel) methods.
  • Thanks to Wilhelm Burger, The AutoThresholder class now uses a compile-time safe enum to specify the method rather than a string that can cause an exception to be thrown.
  • Fixed a bug that caused File>Import>Image Sequence to not create slice labels for images imported from stacks.
  • Fixed a bug that caused the "+" shortcut for zooming in to not work with German keyboards.
  • Fixed a bug that could cause ImageJ to hang when when displaying an error message in debug mode.
• Jonathan Glass contributed Export Point Cloud, a plugin that creates a point cloud viewable in Excel, Matlab or Paraview from a stack of CT scans.
• Tiago Ferreira contributed The ImageJ User Guide, an 8 MB PDF document that contains:
  • 188 pages
  • 198 illustrations
  • 867 internal cross-references
  • 332 external links to the WWW
  • 5 tables
  • 7 macro listings
• Tiago Ferreira contributed SourceCodeRetriever, a macro that searches for a menu entry and tries to retrieve the java source file of the respective plugin.
• The Laboratory of Scientific Image Analysis has released the CDA (Confined Displacement Algorithm for Colocalization) plugin.
• 1.43s, 19 March 2010
  • Moved the Combine, Concatenate, Start Animation, Stop Animation and Animation Options commands from the Image>Stacks submenu to the Image>Stacks>Tools submenu.
  • Moved the Find Maxima command from the Process>Binary submenu to the Process menu.
  • Moved the List Shortcuts command from the Plugins>Utilities submenu to the Plugins>Shortcuts submenu.
  • Moved the Options... command to the bottom of the Process>Binary submenu.
  • Changed the default Find Maxima output type to "Point Selection".
  • Changed the default AVI Writer compression from "Uncompressed" to "JPEG".
  • ImageJ now displays an error message when the user attempts to open a tiled TIFF file.
  • Thanks to Daniel White, Analyze>Tools>Scale Bar is no longer annoyingly slow for image stacks with thousangs of slices.
  • The ROI Manager More>>Options dialog is now recordable.
  • ImageJ now opens 48-bit TIFFs that are missing the required StripByteCounts tag.
  • Added the ResultsTable.getResultsWindow() and TextWindow.close(boolean) methods.
  • Fixed a bug that caused the particle analyzer to sometimes not work as expected when the "Display Results" option was not enabled.
  • Thanks to Barry DeZonia, fixed a bug that caused big-endian, ARGB, uncompressed TIFFs to not open correctly.
  • Thanks to Barry DeZonia, fixed a bug that sometimes caused an exception when IJ.getImage() was called and the "ImageJ" window was not open.
  • Fixed a bug that caused an exception when opening some BioRad Quantity One 16-bit TIFFs.
  • Fixed a bug that caused PackBits-compressed 16-bit TIFFs to not open correctly.
• Tiago Ferreira contributed MathMacroDemo, a macro that demonstrates how to use the Process>Math>Macro command to apply custom formulas to each pixel in an image.
• 1.43r, 4 March 2010
  • Added the Edit>Options>DICOM command.
  • Added a "Headless" style to the arrow tool.
  • Overlays are preserved when saving in JPEG format.
  • Restored the ROI Manager "FIll" and "Draw" commands.
  • Added the getInfo("overlay") macro function (example).
  • Fixed regressions that caused 16-bit composite images to be converted to grayscale when saving in JPEG and PNG format.
  • Fixed a bug that caused the particle analyzer to open the Results window when the "ImageJ" window was not open.
  • Fixed a bug that caused the File>Open Next command to not work correctly with composite images and hyperstacks.
  • Fixed a bug that caused stacks created by importing Analyze format images using File>Import>Image Sequence to contain duplicate images.
  • Fixed a bug that sometimes caused the wrong channel to be selected when clicking on the channel slider.
• Jerome Mutterer contributed MacBook Position, a plugin that uses the JNI library at www.shiffman.net/p5/sms/ to read a MacBook's Sudden Motion Sensor.
• Gabriel Landini has released Dithering, a macro that dithers an image using one of nine available methods, including Floyd-Steinberg, Atkinson, Jarvis-Judice-Ninke, Stucki, Bayer, Clustered and Random.
• 1.43q, 12 February 2010
  • Fixed a bug, introduced in v1.43p, that caused Image5D to crash.
• 1.43p, 11 February 2010
  • Added the File>Close All command.
  • Selections and overlays are saved in the TIFF header.
  • Stack sliders now have a play/pause button, and hyperstack channel sliders have a "c" label, hyperstack slice sliders have a "z" icon and hyperstack frame sliders have a play/pause button.
  • Added "Print actual size" checkbox and "Print" button to the File>Page Setup dialog box.
  • Most of the Process>Math commands are now faster when operating on 16-bit and float images.
  • ShortProcessor constructors no longer call the time-consumming findMinAndMax() method.
  • Fixed a bug in Analyze>Calibrate that caused it to ignore minus signs.
  • Fixed a bug that caused incorrect histograms of stacks larger than two gigapixels.
  • Thanks to Barry DeZonia, fixed a bug that caused big-endian, ARGB, LZW-compressed TIFFs to not open correctly.
  • Michael Schmid fixed a bug that caused Process>Binary>Find Maxima to not display zero counts in the Results window.
  • Julian Cooper fixed a bug that caused resizing of rectangular and oval selections from the center (by holding down Control and Shift) to fail when moving handles on the top and left.
  • Fixed a bug that caused the run("Next Slice [>]") macro function to fail in batch mode macros.
• David Entenberg contributed a tutorial on how to use the Eclipse IDE to develop ImageJ plugins.
• The Floyd_Steinberg_Dithering plugin converts an image to binary using the Floyd Steinberg algorithm.
• Mark Chopping has released CANAPI (CANopy Analysis with Panchromatic Imagery), a macro for analysis of forest/shrub canopies.
• Emerson Ferreira de Lucen contributed Fractal Surface Measurement, a plugin that estimates the fractal dimension of fracture surfaces.
• Damon Poburko contributed the Mulitple Thresholds macro, which segments locally bright puncta in images with varying background intensity.
• Emerson Ferreira de Lucena and Luis Rogerio de Oliveira Hein contributed Depth From Focus, a plugin for improving the focal depth of light microscopy z-series stacks.
• 1.43o, 27 January 2010
  • Added a "Double headed" option to the Edit>Options>Arrow Tool dialog box.
  • The Edit>Options>Arrow Tool options are saved in the preferences file.
  • Thanks to Matt Smith, the "List" and "Save..." buttons in plot windows now list and save all the data that has been plotted.
  • Added the IJEventListener interface (example).
  • Added the "-debug" command line option.
  • The ThresholdAdjuster now records the default thresholding method as setAutoThreshold("Default") or setAutoThreshold("Default dark");
  • ImageJ now opens TIFF files with invalid compression tag values of 0 created by the PerkinElmer Acapella system.
  • The macro language "+=" operator can now be used for string concatenation.
  • Added the open(path,n) macro function and the IJ.open(path,n) and IJ.openImage(path,n) methods, which open the nth image in a tiff stack.
  • Added the random("seed", seed) macro function.
  • FloatProcessor() constructors no longer call findMinAndMax().
  • Fixed a bug that caused some "-batch" mode command line macros to fail.
  • Fixed a bug that caused the line width adjuster slider to sometimes not be set correctly.
  • Fixed a bug that caused the run() and doCommand() macro functions, and the IJ.run() and IJ.doCommand() methods, to fail to run commands in the File>Open Recent menu.
  • Fixed a bug that sometimes caused Analyze>Calibrate to not correctly calibrate 16-bit images with straight line functions.
  • Matt Smith fixed a bug that caused a "nullnull" file to be created when a plot window file save was canceled.
  • Fixed a bug that caused ImageJ64 on Mac OS X to fail to start if the memory limit was set to less that 256MB.
  • Fixed the FloatProcessor(int[][]) constructor.
  • Thanks to Barry DeZonia, fixed a bug that caused odd-width 12-bit TIFFs to not open correctly.
• The FlipSelection macro flips a selection either vertically or horizontally.
• Pablo Manuel Jais contributed the SetScaleFromTiffTag macro, which uses the TIFF Tags plugin to set the scale of SEM images taken with the Carl Zeiss SmartSEM program.
• 1.43n, 28 December 2009
  • Added the rounded rectangle and arrow tools, which share space on the toolbar with the rectangle and line tools. The arrow tool was inspired by the Fiji arrow tool written by Jean-Yves Tinevez and Johannes Schindelin.
  • Selections (e.g., arrows) can be added to a non-destructive overlay by pressing "b", the new keyboard shortcut for the Image>Overlay>Add Selection command.
  • Added the Edit>Options>Arrow Tool command.
  • Added support for saving results tables as .csv (comma-separated values) files and for opening them using drag and drop.
  • The color picker is no longer an ImageWindow, and it remembers its location.
  • Removed the "JPEG Quality" option (which wasn't working) from the File>Save As>AVI dialog box.
  • The ROI Manager works with stacks that have more than 9999 images.
  • The Command Finder (Plugins>Utilities>Find Commands) remembers the state of the "Close when running" checkbox.
  • The 'changes' flag is now reset after saving an image in PNG, BMP, PGM or FITS format.
  • The "Antialiased tool icons" setting in Edit>Options>Appearance is enabled by default.
  • Fixed a bug in the Command Finder that caused it to fail to run macros installed in the Plugins>Macros submenu.
  • Fixed a bug that caused File>Revert to vertically flip FITS images.
  • Fixed a bug that caused ImageJ to not correctly open some 16-bit TIFFs.
  • Fixed bugs that caused the lineTo() and drawLine() macro functions to not correctly draw lines with negative starting coordinates.
• Vincent Dorcet et al. have contributed EXTRAX, a plugin for electron diffraction intensity extraction.
• Ben Tupper contributed the RATS (Robust Automatic Threshold Selection) plugin.
• 1.43m, 7 December 2009
  • Virtual stacks can now be saved in TIFF, "raw", Analyze and NIfTI format.
  • Thanks to Michael Schmid, "MinFeret" calculations are now more accurate and correctly handle pixel aspect ratios not equal to 1.
  • Results tables (in tab-delimited text format) with an ".xls" extension can be opened using File>Open and drag and drop.
  • When using the particle analyzer in a macro, the default values (0-Infinity, 0-1 and "Nothing") are assumed if the 'size', 'circularity' or 'show' options are omitted.
  • The updateResults() macro function and ResultsTable.show() method, when creating a new table, scroll to the top of the window (example).
  • Added the Overlay.getSize() and Overlay.removeSelection() macro functions.
  • Added the ImagePlus.setOverlay(Overlay) method (JavaScript example).
  • Added the ImagePlus.setOverlay(Roi,Color,int,Color) method (JavaScript example).
  • Added open(path) and saveAs(path) methods to the ResultsTable class (JavaScript example).
  • Fixed a bug that caused Analyze>Summarize to somethimes fail if "Stack Position" was enabled in Analyze>Set Measurements.
  • Volker Backer fixed a bug that sometimes caused the B&C adjuster to work with the wrong channel of a composite color image after having changed the channel by dragging the channel selection slider.
• Tiago Ferreira has released ROI Color Coder, a macro that labels segmented particles by matching measured parameters to indexes of a chosen LUT.
• Gilles Carpentier contributed Object_Color_Sorting, a macro that demonstrates how to segment objects based on their color.
• Eugen Labun has released ImageJ SURF, a plugin that does feature detection and image comparison.
• The ToothRootToCrownRatio macros use a non-destructive overlay to allow easy measurement of tooth dimensions in dental radiographs.
• 1.43l, 24 November 2009
  • Gabriel Landini's Threshold_Colour plugin is now built in as the Image>Adjust>Color Threshold command.
  • Added the Image>Overlay>Remove Overlay command.
  • Added a "New Overlay" option to the Image>Overlay>Add Selection dialog box (example).
  • Added "Opacity" and "Create image selection" options to the Image>Overlay>Add Image dialog box.
  • The Recorder, in "JavaScipt" and "Plugin" mode, correctly records ROI Manager commands.
  • Added the IJ.getToolName() macro function and method.
  • Added the Analyzer.setRedirectImage() method.
  • The AVI Writer displays an error message if the user attempt to overwrite a virtual stack
  • Fixed a bug that caused Image>Color>Merge Channels to always create a composite image when merging four channels.
  • Fixed a bug related to passing path variables to export plugins by macros using "&varname" notation (example).
  • Gabriel Landini fixed a bug in Image>Adjust>Threshold that caused the mask created when "Dark Background" was enabled to not be identical to an inverted version of the mask created when "Dark Background" was not enabled.
  • Fixed a bug in Analyze>Calibrate that could cause values copied into the dialog box from a webpage to be converted to zeros.
  • Fixed a bug that caused 8-bit images with pseudo-color LUTs to be incorrectly classified as type "8-bit Color" (ImagePlus.Color_256).
• Ignacio Arganda-Carreras has released SIOX (Simple Interactive Object Extraction), a plugin for segmenting color images.
• Stephan Saalfeld has released CLAHE, a plugin that implements Contrast Limited Adaptive Histogram Equalization.
• 1.43k, 10 November 2009
  • Added the multi-point tool, which is enabled by right-clicking on the point tool.
  • Added a "Record:" drop down menu, with three choices ("Macro", "JavaScript" and "Plugin"), to the Recorder.
  • The Recorder generates thread safe JavaScript and Java code.
  • Thanks to Michael Schmid, Process>Binary>Find Maxima has a "List" output option, and is faster.
  • File>Import>Image Sequence sets the voxel depth equal to the pixel width.
  • Image>Stacks>Reslice displays the voxel size in its dialog box.
  • Spline fit selections and Text selections can now be saved (using File>Save As>Selection) and restored (using File>Open or drag and drop).
  • The Edit>Clear command in the "Results" table is now recorded.
  • Added the IJ.deleteRows() macro function and method.
  • Added the getInfo(DicomTag) macro function.
  • Michael Schmid worked around a Java bug on Windows and Linux that prevented selection of mutltiple ROIs in the ROI Manager with a single shift click.
  • Michael Schmid fixed a bug in Process>Binary>Find Maxima, with "Segmented" output, that caused it to create extra invalid features.
  • Fixed a bug that could cause 8-bit DICOMs to not open correctly.
  • Fixed a bug that could cause headings in empty custom results tables to not be displayed.
  • Fixed a bug in Image>Stacks>Images to Stack that caused it do not work properly with 8-bit color images.
  • Fixed a bug in Image>Hyperstacks>Stack to Hyperstack that caused it to not shuffle the slice labels of stacks not in CZT order.
• Yugo Sakamoto & Adilson Zacaro contributed Levan, an ROI Manager-like plugin for chromosome morphology.
• Roberto Sotto-Maior contributed HanningWindow and DirectionalFilterWindow, macros that generate 32-bit images useful for Fourier filtering applications.
• 1.43j, 28 October 2009
  • Added the Image>Overlay submenu with Add Selection, Add Image, Hide Overlay, Show Overlay, From ROI Manager, To ROI Manager and Flatten commands (example1, example2).
  • Added the ImageRoi class (JavaScript example).
• Bruno Vieira contributed Colony Counter, a plugin for counting bacteria colonies in agar plates.
• Marcel Austenfeld contributed Twain Scan, a plugin that uses the open source library from www.mms-computing.co.uk to capture images from Twain campatible scanners and cameras.
• 1.43i, 22 October 2009
  • Added the Edit>Selection>Properties command.
  • Added the Plugins>Macros>Record Script command.
  • Thanks to Jay Unruh, File>Import>Text Image opens images in comma-delimited text format.
  • Thanks to Gabriel Landini, the Thresholding tool's "B&W" mode now respects the "Black background" flag in Process>Binary>Options.
  • Added the "Flatten" button to the ROI Manager and removed the "Draw", "Fill" and "Label" commands from the "More>>" drop down menu.
  • The aspect ratio of rectangular and elliptical selections is displayed in the status bar as they are created and resized.
  • The "Transparent-zero" mode in Edit>Paste Control and Process>Image Calculator now works with 16-bit and 32-bit images.
  • Assigned the shift-f keyboard shortcut to Image>Flatten and the "]" (close bracket) shortcut to Window>Show All.
  • Worked around a bug with Java 1.6 on Mac OS X that caused multiple selection in the ROI Manager to not work.
• Jerome Mutterer has released Droplet, a drag and drop file processor that uses customizable macros.
• Thanks to Johannes Schindelin, ImageJ now has a Git version control repository, which is updated daily.
• Niels Jensen contributed PlateMontage, a macro that creates a labeled plate montage image from BD Pathway 855 / AttoVision 1.6 data sets.
• 1.43h, 9 October 2009
  • ROI Manager selections can be assigned colors and line widths using the "Properties..." button and selection labels can be disabled/enabled using the "Edit Mode" checkbox. (example).
  • Added the Image>Flatten command.
  • Changed the name of the Image>Rotate submenu to Image>Transform.
  • Removed the "Double buffer selections" option from Edit>Options>Appearance. ROIs and display lists (overlays) are now always double buffered on Linux and Windows.
  • Dialogs can be dismissed by pressing ctrl+w.
  • Added the Image>Transform>Flip Z command.
  • Added the makeText(), Array.invert(), getInfo("image.directory" ), getInfo("image.filename" ), roiManager("Set Color", color) and roiManager("Set Line Width", width) macro functions.
  • Added the setStrokeColor(), setFillColor(), setStrokeWidth() and setNonScalable() methods to the Roi class (example1, example2, example3).
  • Fixed a bug that could cause an exception if the "l" key (Plugins>Utilities>Find Commands) was pressed immediately after launching Fiji.
  • Fixed bugs that could cause commands to be recorded when a macro was running.
• Jan Eglinger contributed ThreeColorPlot, a macro that creates profile plots of each channel of a color image and overlays the plots in composite image.
• 1.43g, 18 September 2009
  • Added the Process>Batch>Virtual Stack command.
  • Added the "Draw As Overlay" (display ROIs using a display list) and "Remove Overlay" commands to the ROI Manager.
  • Multi-point and text selectons are now properly displayed in the ROI Manager "Show All" mode.
  • Tiff stacks with a .tif extension open as virtual stacks when dragged and dropped on the ">>" toolbar icon.
  • The Image>Show Info command and the getMetadata() macro function retrieve the "DateTime" and "Software" TIFF tags.
  • Plugins>Compile and Run defaults to the plugins directory instead of the ImageJ directory.
  • Added the IJ.handleException() and IJ.setExceptionHandler() methods.
  • Fixed a bug that could cause an exception when using the Measure command with segmented line selections wider than 1 pixel.
  • Fixed a bug that caused commands that opened a web page to fail on Mac OS X 10.6 when running the 32-bit version of Java 1.6.
  • Fixed a bug that caused "[aborted]" to be displayed in the Log window when a macro called using runMacro() was canceled.
  • Fixed a bug that could cause macro files containing 100 or more functions to fail to install.
  • Fixed a bug in Analyze>Measure that cause it to incorrectly calculate the area of line selections on spatially calibrated images and to incorrectly calculate the mean of straight line selections wider than one pixel on spatially calibrated images.
• Jacqui Ross has written four ImageJ Tutorials (in PDF format), Introduction to ImageJ, Color Analysis Tools, Colocalization Tools and Using and Writing Macros.
• Joachim Wesner contributed TIFF Tags, a plugin that displays the tags of a specified TIFF file.
• Curtis Rueden contributed TIFF Dumper, a plugin that uses the Bio-Formats plugin to display the TIFF tags of the current image.
• Marco Righi has released Vessel_Distribution, a macro that compares the space-filling properties of microvessels networks.
• 1.43f, 24 August 2009
  • The Image>Scale and Image>Adjust>Size commands now scale stacks and hyperstacks in the Z dimension.
  • The Image>Color>Merge Channels command now works with hyperstacks.
  • Added the File>New>Hyperstack command, an alias for Image>Hyperstacks>New Hyperstack.
  • Analyze>Tools>Fractal Box Counter writes results that can be read by macros.
  • Added the List.setCommands, setFont("user"), getInfo("font.name"), getValue("font.size") and getValue("font.height") macro functions.
  • Thanks to Johannes Schindelin, added the NonBlockingGenericDialog class, now used by the Process>Batch>Process command.
  • Fixed a bug that sometimes caused the Image>Adjust>Brightness/Contrast "Apply" function to fail with RGB stacks.
  • Fixed a bug that sometimes caused Image>Color>Split Channels to display a "save changes?" dialog box.
  • Fixed a bug that caused File>Save As>Image Sequence to throw an exception if the window was closed before all the images in the stack were saved.
• Jerome Mutterer has released PDF Macro Ext, a plugin that uses the iText library to add PDF creation functions to the ImageJ macro language.
• 1.43e, 6 August 2009
  • Added the Process>Batch> submenu, containing Measure, Convert and Process commands.
  • Thanks to Norbert Vischer, it is now much easier to outline circular objects using the constrained (shift key down) elliptical selection tool.
  • Added an "Export" button to Plugins>Utilities>Command Finder.
  • Added the selectWindow("ImageJ") macro function.
  • Fixed a bug that caused image zooming to fail on secondary monitors.
  • Fixed bugs that caused the particle analyzer to sometimes not work as expected when "Black Background" was enabled in Process>Binary>Options.
  • Fixed a bug that caused the Plugins>Utilities>Memory Monitor tool to not work correctly when the line width was greater than one.
• Robert Clements contributed Demontager, a plugin that converts an image montage into a stack.
• 1.43d, 21 July 2009
  • Thanks to Dimiter Prodanov, plugins (.jar and .class files) dragged from a browser window and dropped on the "ImageJ" window are installed and the menus are updated.
  • Text files (.txt, .ijm, .js and .java) can be opened in ImageJ by dragging from a browser window and dropping on the "ImageJ" window.
  • Thanks to Julian Cooper, the alt key constrains resizing to the current aspect ratio for rectangle and oval selections, and keeps the same length for line selections.
  • Added a "32-bit ABGR" option to the File>Import>Raw dialog box.
  • The ImageJ and Java version numbers are displayed when you click in the status bar.
  • Added the getInfo("micrometer.abbreviation") macro function.
  • Added the IJ.openUrlAsString() method.
  • Fixed a bug that sometimes caused the micron symbol (µ) to not be displayed correctly on Linux.
  • Fixed a bug that caused big-endian ARGB TIFFs to open incorrectly.
  • Fixed a bug that caused LUTs in the ImageJ/luts folder to not be added to the Image>Lookup Tables menu when running Fiji on OS X.
  • Fixed a bug that could cause Metamorph .stk files to open with an all zero LUT.
  • Fixed a bug that could cause ImageJ to generate an exception or fail to start if there was a corrupted jar file in the plugins folder.
  • Fixed a bug in the TIFF reader that could cause a "Strip offsets are not in order" error.
• Gilles Carpentier contributed an enhanced LUTs, Macros and Tools Updater toolset.
• Janos Roszik et al. have released RiFRET, a plugin for the evaluation of intensity-based ratiometric FRET images.
• 1.43c, 8 July 2009
  • Thanks to Olaf Freyer, ImageJ can now open 48-bit LZW compressed TIFFs.
  • Thanks to Michael Schmid, the Process>Binary>Options dialog box now has a "Preview" option.
  • Roi Manager "Show All" mode selections can again be moved by clicking on the selection's label and dragging.
  • Images can be opened by dragging from a browser window and dropping on the ImageJ window.
  • When dragging and dropping, "<<Drag and Drop>>" is displayed in the status bar when the cursor is over the drop site.
  • Increased the size of toolbar icons from 24x24 to 26x26 pixels, which increased the width of the ImageJ window by 42 pixels.
  • With composite images, Image>Show Info adds a "Composite mode: mode" line to its output.
  • Added the GenericDialog.enableYesNoCancel(yesLabel,noLabel) method (example).
  • The setVoxelSize() macro function converts "um" units "µm".
  • Worked around a "feature" in the latest Mac OS X Java update that caused the getDirectory("temp") macro function to return paths like "/var/folders/C-/C-bqCJHiFxOuNwlNmBmRG1UNxXY/-Tmp-/" instead of the expected "/tmp/".
  • Fixed a bug, introduced in v1.43a, that caused the XStart and YStart values saved by the particle analyzer to be incorrect.
  • Fixed a bug that caused Image>Show Info to not display metadata of stacks opened using File>Import>Stack from List.
  • Fixed a bug that sometimes caused Image>Hyperstacks>Stack to Hyperstack to not correctly set the active image.
  • Fixed a bug that caused the File.directory() macro function and the OpenDialog.getLastDirectory() method to return a path to the luts directory after a LUT had been loaded from the Image>Lookup Tables submenu.
• Julian Cooper contributed the CT Window Level and Anonymize IJ DICOM plugins.
• Romain Francois has released a package that embeds ImageJ in R.
• Andrew Weitz contributed SomaRoiTool, a tool macro for labeling somas (cell bodies) or other elliptical structures.
• 1.43b, 23 June 2009
  • Added the "Use Titles as Labels" checkbox to the Image>Stacks>Images to Stack dialog box.
  • Kevin Moll contributed an enhanced and simplified PluginClassLoader that extends URLClassLoader (example).
  • Fixed a bug, introduced in v1.43a, that caused Help>Update ImageJ to fail if the path to ij.jar contained a space.
  • Fixed a bug that caused Image>Show Info to not display metadata of stacks opened using File>Import>TIFF Virtual Stack.
  • Fixed a bug that sometimes caused the threshold limits to not be passed to PlugInFilters using the CONVERT_TO_FLOAT flag.
• 1.43a, 19 June 2009
  • Thanks to Michael Schmid, the wand tool now supports 4-connected and 8-connected tracing, and a tolerance can be specified. Double click on the tool icon to configure.
  • The Image>Stacks>Delete Slice command works with hyperstacks.
  • Added a "Name" field to the Image>Stacks>Images to Stack dialog box.
  • Thanks to Johannes Schindelin, Help>Update ImageJ updates ij.jar files in non-standard locations, and those embedded in ImageJ64 on OS X.
  • ImageJ can now be compiled with OpenJDK, thanks to Johannes Schindelin and Mark Longair.
  • Added the doWand(x,y,tolerance,mode) macro function and IJ.doWand(x,y,tolerance,mode) method.
  • Fixed a bug that caused plugins in packages with names starting with "ij" to sometimes not be found.
  • Fixed a bug that caused the Threshold tool "Apply" option to not be recorded for 32-bit images with "Set Background Pixels to NaN" enabled.
  • Fixed a bug that caused uncompressed TIFF stacks larger than 2GB to not open correctly.

Version 1.42, 8 June 2009

• Michael Schmid contributed Smallest Enclosing Circle, a macro that creates a circular selection that is the smallest circle enclosing the current selection.
• 1.42q, 8 June 2009
  • Fixed bugs, introduced in v1.42p, that caused an exception when opening a virtual stack or when closing an Image5D stack.
  • Fixed a bug that caused bicubic intepolation edge artifacts.
• David Marso contributed StackBlaster, a macro that allows an image or stack to superimposed upon a background image or stack.
• Gilles Carpentier contributed List Online Macros, a macro that generates a list of all the macros, tools and toolsets available on the ImageJ website.
• Michael Schmid has released Versatile Wand, a wand tool with selectable tolerance, gradient detection, 4-connected or 8-connected operation and preview.
• 1.42p, 4 June 2009 (release candidate)
  • Thanks to Gabriel Landini, the Image>Adjust>Threshold tool now has a drop down menu for selecting any of 16 different thresholding methods.
  • Thanks to Julian Cooper, rectangular and elliptical selections can now be created and resized from their centers by holding down the control key (command key on Macs).
  • Added the Label (Time Stamper), Combine and Concatenate commands to the Image>Stacks submenu.
  • The Stack Reducer plugin replaces the Image>Stacks>Reduce Size command.
  • Added the "Run socket listener" option to the Edit>Options>Misc dialog. Enabling this option prevents multiple copies of ImageJ from starting but it can cause a security alert when ImageJ starts.
  • Added the setAutoThreshold(string) and getList("threshold.methods") macro functions (example).
  • Added the ImageProcessor.setAutoThreshold(String) method.
  • Added the Dialog.addHelp(string) macro function and the GenericDialog.addHelp(String) method. The new Image>Stacks>Label command uses the addHelp() method.
  • The ImagePlus.flush() method not longer runs System.gc() and no longer nulls the ImageProcessor pixel array.
  • Bicubic interpolation edge artifacts are reduced.
  • Michael Schmid fxed a bug in Edit>Selection>Straighten that caused it to not work well for very wide selections.
  • Fixed a bug that caused the x values to be deleted in the Analyze>Calibrate dialog box.
  • Fixed a bug that caused the Plot.getValues() macro function, when retrieving values from plot windows, to not work in batch mode macros.
• Steffen Schmidt contributed the TIA Reader plugin, which opens .ser files created by the TIA software (FEI/Emispec).
• Julian Cooper contributed the Make Isotropic and Untilt Stack plugins.
• Michael Schmid contributed Erode Demo, a plugin that demonstrates how to do binary erosion using the EDM, how to provide a "Preview" option, how to process stacks using parallel threads, and how to add a "Help" button to a dialog box.
• Michael Schmid has released Radially Averaged Autocorrelation, a macro that calculates the radial average of the autocorrelation of a (binary) image, and Radial Distribution Function, macro that calculates the radial distribution function (RDF) of particle centers.
• Gilles Carpentier contributed the Scale Bar Tools for Microscopes toolset (online documentation).
• 1.42o, 14 May 2009
  • Added the Image>Stacks>Orthogonal Views command, which is based on Dimiter Prodanov's StackSlicer plugin and Albert Codona's Updater class.
  • Thanks to Julian Cooper, a straight line selection can now be rotated about its center by holding down the control key (command key on Macs).
  • File>Save As>AVI now works correctly with 5D hyperstacks (e.g., the Mitosis sample image).
  • Thanks to Michael Schmid, the EDM algorithm is more accurate, there are options for 16-bit and float output, stacks are processed using multiple threads, and Voronoi diagrams can be generated.
  • Thanks to Michael Schmid, Process>Binary>Find Maxima works with images>32768 pixels in width or height.
  • Gabriel Landini added the "Pad edges when eroding" option to Process>Binary>Options.
  • With hyperstacks, Image>Stacks>Make Montage displays instructions that explain how to create C, Z or T montages.
  • Added the Mitosis (26MB, 5D Stack) sample image, courtesy of Eric Griffis and Nico Stuurman.
  • Fixed a bug that caused images with a width or height greater than 65,535 to not be correctly saved in TIFF format.
  • Fixed a bug in the File.openAsRawString() macro function that caused it to not correctly read bytes with values greater than 127.
  • Fixed a bug that caused an error message to be displayed when a URL stack download was aborted by pressing 'esc'.
  • Fixed a bug that caused Process>Filters>Convolve to sometimes record an extra "\".
  • Fixed a bug that caused TIFF and RAW virtual stacks greater than 2GB to not open correctly.
  • Fixed a bug that could cause the measurent length of rapidly drawn freehand line selections to be incorrect.
  • Fixed a bug that could cause the newImage() macro function to display a bogus "out of memory" error.
  • Fixed a bug that caused the TIFF reader to not correctly decode metadata containing non-ASCII characters.
  • Fixed a bug that caused Image>Color>Merge Channels to throw an exception of the source images were not all the save type.
• Philippe Thevenaz has released SheppLogan, a plugin that generates a sampled version of the Shepp-Logan phantom.
• Tiago Ferreira contributed Filename_Randomizer, a macro that randomize the names of files in a folder.
• 1.42n, 26 April 2009
  • Added the is("binary") macro function and ImageProcessor.isBinary() method.
  • Fixed bugs, introduced in v1.42m, that caused LSM images to open with incorrect channel colors and sometimes caused the Image>Color>Merge Channels command to fail.
  • Fixed a bug that caused the saveAs() macro function to sometimes truncate file names containing periods and no extension
• Jerome Mutterer has released IJ Ed, a jEdit-based code editor plugin for ImageJ.
• Jean-Yves Tinevez and Albert Cardona have released the Dynamic Reslice plugin, a dynamic version of the built in Image>Stacks>Reslice command.
• Gabriel Landini has released Auto Threshold, a plugin that converts 8-bit images to binary using any of 15 global thresholding methods, and Auto Local Threshold, that converts to binary using any of 5 local thresholding methods.
• 1.42m, 22 April 2009
  • The Image>Stacks>Reslice command works with hyperstacks.
  • The up and down arrow keys now substitute for the "+" and "-" shortcuts when zooming in and out. This only works if the shift or control key is down when there is a selection.
  • When there is no selection, or the shift key is down, the arrow keys can substitute for "<" and ">" when navigating stacks and hyperstacks.
  • The More>>Multi Threshold command in the ROI Manager is much faster.
  • When previewing point selections, Process>Binary>Find Maxima does not label the points regardless of the "Label Shift-Click Points" setting.
  • The Adjust>Threshold tool saves the LUT mode ("Red", "B&W" or "Over/Under") in the preferences file.
  • Added the Stack.getStatistics(), is("changes"), getInfo("selection.name") and File.nameWithoutExtension macro functions.
  • Added the ImageProcessor.setOverColor() and setUnderColor() methods, which can be called from a macro to set the Over/Under threshold colors (example).
  • Norbert Vischer fixed a bug that caused the macro debugger to not work, and error message line numbers to be invalid, with macros containing multiple line /*...*/ comments.
  • Michael Schmid fixed a bug in the public RankFilters.rank() method that caused it to only process the red channel of RGB images.
  • Sylvain Mainguy fixed a bug that caused the cursor to change to a hand at the corners of the bounding box of composite selections.
  • Fixed a bug that caused FL and FD DICOM VRs to not be correctly decoded.
  • Fixed a bug in Image>Hyperstacks>Reduce Dimensionality that caused it to not preserve image labels.
  • Fixed a bug that caused jar files containing class files with "_" in the name in subfolders and no plugins.config file (e.g., ImageJ_3D_Viewer.jar) to generate startup error messages.
  • Fixed a bug, introduced in 1.42i, that could cause ImageJ to hang when using the Measure command if "Shape Descriptors" or "Feret's Diameter" were enabled in Set Measurements.
  • Fixed bugs that caused the Image>Type>RGB Color, Image>Color>Stack to RGB and File>Save As>AVI commands to not work correctly with hyperstacks when called from batch mode macros.
  • Fixed bugs that caused Image>Hyperstacks>Reduce Dimensionality to not be macro compatible.
  • Fixed a bug that caused Image>Hyperstacks>Stack to Hyperstack to throw an exception when converting one channel Image5D stacks.
  • Fixed a bug that caused the Image>Adjust>>Threshold tool to sometimes override existing threshold settings of 16 and 32 bit images.
• Fanny Serman contributed Smart Projector, a plugin that optimizes, for each time point, the projection of time-lapse stacks.
• Dimiter Prodanov contributed the StackSlicer plugin.
• 1.42l, 24 March 2009
  • Added keyboard shortcuts for hyperstacks:
    • > - next channel
    • < - previous channel
    • ctrl+> - next slice
    • ctrl+< - previous slice
    • alt+> - next frame
    • alt+< - previous frame
  • Added bicubic interpolation option to Image>Rotate>Arbitrarily, Image>Scale and Image>Adjust>Size. The bicubic interpolation method is from Chapter 16 of Digital Image Processing: An Algorithmic Introduction Using Java by Wilhelm Burger and Mark Burge, with the 'a' control parameter set to 0.5 (Catmull-Rom interpolation).
  • The range of images to be copied can be specified when duplicating a stack using Image>Duplicate.
  • Image>Stacks>Images to Stack no longer requires that all images be the same type and size.
  • The Image>Translate command works with sub-pixel offsets (example).
  • Image>Stacks>Make Montage draws antialiased labels and allows the font size to be set in the dialog box.
  • File>Import>URL replaces spaces in URLs with "%20".
  • Thanks to code contributed by Mark Longair, Image>Type>HSB Stack now converts RGB stacks to a 3 channel (Hue, Saturation and Brightness) hyperstacks.
  • Image>Type>RGB Stack now converts RGB stacks to a 3 channel (Red, Green and Blue) hyperstacks.
  • Mark Longair made usability improvements to Plugins>Utilities>Command Finder: 1) double-click to run a command; 2) press backspace to switch focus to prompt; 3) press escape to close.
  • Added the Edit>Copy to Image Info command to the text editor.
  • The search command in the text editor remembers the "Case Sensitive" setting.
  • Added the fill(Roi), fileOutside(Roi) and draw(Roi) methods to the ImageProcessor class (example).
  • Fixed a bug in Image>Stacks>Plot Z-axis Profile that caused it to not work correctly in batch mode macros.
  • Fixed a bug that prevented the selection from being resized after using Edit>Selection>Select All.
  • Fixed a bug that could cause an exception when opening 24-bit BMP images.
  • Fixed a bug that caused Process>Binary>Find Maxima to not work with composite color images.
• The Multiple LUT Stack plugin demonstrates how to display a stack using a lookup table for each image.
• Gabriel Landini contributed Colorize, a macro which adds hue and saturation to user defined regions in a greyscale image, while leaving the brightness constant.
• Gilles Carpentier contributed PlotSigmoidDerivatives, macros that demonstrate how to do curve fitting and how to calculate and plot first and second derivatives.
• 1.42k, 6 March 2009
  • Added the Image>Zoom>Set command, which is based on Albert Cardona's ZoomExact plugin.
  • Process>Math> commands now support "Preview" and use parallel threads when processing stacks.
  • Image>Type>RGB Color will convert the channels in a multichannel composite color stack to an RGB stack if the number of channels is the same as the number of images in the stack and the display mode, set with the "Channels" tool, is "Color" or "Grayscale".
  • Scripts can be passed a string argument when called from the command line (using the -macro or -batch options) or using the IJ.runMacroFile() method. Scripts can use the getArgument() function to retrieve the argument.
  • Removed the "Input Slice Spacing" field from the Image>Stacks>Reslice dialog box.
  • File>Import>URL opens JPEG, PNG and GIF images from URLs based on either the extension or the content type.
  • Added the Plot.drawLine(x1,y1,x2,y2) macro function (example).
  • Added the Stack.setTUnit(string) and Stack.setZUnit(string) macro functions.
  • Julian Cooper fixed a bug in Image>Stacks>Reslice that somethimes caused the preview rectangle did not accurately show the extent when starting with a line selection.
  • Berthold Daum fixed a bug that caused ImageJ to fail to open 48-bit TIFFs created by the RawTherapee program.
  • Fixed a bug that caused run("Measure") to not work as expected when used in "-batch" command line macros.
  • Fixed a bug that sometimes caused the cursor X and Y coordinates to not be displayed in plot windows.
  • Fixed a bug that caused scripts called from the command line using the "-batch" option to fail to run.
  • Fixed a bug that caused IJ.getDirecory() calls to not be recorded on Linux and Windows.
  • Fixed a bug that caused Image>Stacks>Reslice to not work correctly with signed 16-bit stacks.
  • Fixed bugs the caused batch mode macros that used Process>Math>Macro or did user-defined curve fitting to fail.
  • Fixed a bug on Windows that sometimes caused paste operations in the macro editor to not insert the text in the correct location.
• Winnok de Vos contributed the RegisterStackUsingTranslation macro, which registers a stack based on the center of mass of each image.
• Daniel Senff and Kai Uwe Barthel have released ImageFlow, a plugin that provides a node-based graphical user interface for macro-creation and image editing.
• Jerome Mutterer contributed the GammaCorrectionTool macro, which allows the Gamma curve to be adjusted by dragging on the image.
• Julian Cooper contributed Radial Reslice, a plugin that reslices a stack by rotating the sliced plane around the z-axis, and RC Montage, an enhanced version of the Image>Stacks>Make Montage command.
• 1.42j, 23 February 2009
  • Analyze>Analyze Particles is faster because results are no longer continuosly displayed.
  • With 32-bit (float) images, Process>Math>Divide creates Infinity, -Infinity or NaN pixels when the source pixels are positive, negative or zero.
  • Added the Array.copy(), Array.getStatistics(), Array.sort() and Array.trim() macro functions (example).
  • Values passed to the makeRectangle() and makeOval() macro functions are rounded.
  • JavaScript scripts import more packages (ij.util, ij.plugin, ij.plugin.filter and ij.plugin.frame).
  • The addResults() and updateResults() methods in the ResultsTable class allow values to be added to the "Results" window more quickly.
  • Fixed a bug, introduced in 1.42i, that caused the Smooth, Sharpen and Find Edges commands to invert16-bit stacks.
  • Fixed a bug that caused the Stack.setSlice() macro function to sometimes not work correctly in batch mode macros.
• Peter Stierlen has released Scan Calculator, a plugin that calculates 3D data from 2D scanline data captured with a laserscanner.
• Added a Windows version of ImageJ bundled with 64-bit Java to the Download page.
• 1.42i, 17 February 2009
  • Circularity (4pi*area/perimeter^2) , aspect ratio (major axis/minor axis), roundness (4*area/pi*major axis²) and solidarity (area/convex area) are calculated and displayed when "Shape Descriptors" is enabled in Analyze>Set Measurements.
  • The angle of the Feret's diameter is displayed when "Feret's Diameter" is enabled in Analyze>Set Measurements.
  • Histograms of 16-bit stacks are generated much faster.
  • Edit>Invert inverts 16-bit stacks based on the stack min and max.
  • File>Save As>Selection now saves only the base coordinates of spline fit selections.
  • The frame interval and unit set in Image>Properties are now saved with both single images and stacks.
  • Added "(32-bit)" or "(64-bit)" to the Java version displayed in the Help>About ImageJ window and in the status bar on startup and when the cursor is over an unused toolbar slot.
  • Added the List.setMeasurements() and List.getValue() macro functions (example).
  • The getCursorLoc() macro function sets a flag bit when the cursor is inside an area selection (example).
  • Added the setOption("ShowMin", boolean) macro function.
  • Added the getNonSplineCoordinates() and getUncalibratedLength() methods to the PolygonRoi class.
  • Fixed a bug that caused the "(V)" in the title bar to remain after type converting a virtual stack.
  • Fixed a bug in Analyze>Measure that caused the bounding rectangle to not be calculated correctly for line selections.
  • Fixed a bug on Windows Vista that caused the first few characters of the image subtitle to be cut off.
  • Rob Lewis Fixed a bug that caused File>Import>URL to throw an exception when opening DICOMs with headers larger than 200,000 bytes.
  • Berthold Daum fixed a bug that sometimes caused an exception when opening 48-bit RGB TIFFs.
  • Greg Joss fixed a bug that sometimes caused Edit>Selection>Straighten to not work correctly.
• Jerome Mutterer contributed the DrawParticleEllipseAxis macro, which demonstrates how to add axis to the ellipses drawn by the particle analyzer.
• Michael Doube contributed the CheckDICOMSlicePositions macro, which verifies that the slice positions in a DICOM stack agree with the voxel depth.
• Jerome Mutterer contributed the Fixed Angle Line Tool and L-Shape Tool macros.
• 1.42h, 30 January 2009
  • Added the Process>Math>Macro command, which is modeled after Ulf Dittmer's Expression plugin.
  • A pasted image no longer needs to be the same type as the receiving image.
  • Minimum Feret diameter (minimum rotatating calipers width) is calculated when "Feret's Diameter" is checked in Analyze>Set Measurements
  • Tweaked the default settings in the curve fitter (Analyze>Tools>Curve Fitting) so that it is more likely to converge (example).
  • Selected lines in the Results and Log windows can be deleted by pressing the backspace key.
  • An updated Menus class, contributed by Johannes Schindelin, provides better Fiji compatibility and allows plugins to be installed in more menus.
  • Added the centerDialogMethod() to the GenericDialog class (example).
  • Fixed a bug that caused the Macro>Run Macro and Debug>Debug Macro commands in the macro editor to not run the first macro in a macro set with global variables (example).
  • Fixed a bug on the Mac that caused the macro debugger to fail to work with macros pasted from the system clipboard using File>New>System Clipboard.
  • Fixed a bug with the Convolver.convolve() method that caused it to throw an exception if it passed a non-float image.
  • Fixed a bug with the Fit.doFit() macro function that caused to throw an exception of the arrays were not the same length.
• Gabriel Prieto Renieblas contributed MS_SSIM_index, a plugin that calculates the MS-SSIM (multi-scale structural similarity) and MS-SSIM* Indexes.
• 1.42g, 12 January 2009
  • ImageJ now checks for, and deletes, duplicate plugins on startup, when running Help>Update Menus and when running Plugins>Compile and Run.
  • Fixed a bug, introduced in v1.42f, that caused commands in the Plugins>Macros submenu to fail to work and caused extra commands to be added to the Plugins>Utilities submenu.
• Use Benjamin Schmid's 3D Viewer plugin for hardware-accelerated 3D visualization of image stacks as volumes, surfaces and orthoslices.
• 1.42f, 9 January 2009
  • Added the Plugins>Utilities>Capture Image command.
  • Added a "Show 'Debug' Window" option to macro error messages.
  • Added a "*User-defined*" fit option to Analyze>Tools>CurveFitting.
  • The LUT Editor (Image>Color>Edit LUT) displays the ending index in the status bar as the user drags to select a range and it no longer moves the green and blue sliders when the red slider is moved.
  • The Fit.doFit() macro function will now fit a user-defined equation to a set of data points (example).
  • Added the Fit.showDialog and Fit.logResults macro functions.
  • Reported UnsupportedClassVersion exceptions now include the line "This plugin requires Java 1.x or later."
  • ImageJ no longer throws an exception when opening DICOMs with UT (unlimited text) tags.
  • Fixed a bug on Windows, introduced in v1.42e, that made it impossible to enter into editor windows some characters (e.g., "{") accessed using the AltGr key.
  • Fixed a bug in the particle analyzer that caused it to sometimes not correctly add particles to the ROI Manager.
  • Fixed a bug in the saveAs() macro function that sometimes caused it to fail if the path contained a period and the file name did not have an extension.
• Luke Miller has written a tutorial on how to quantify western blots using ImageJ.
• 1.42e, 17 December 2008
  • Added a "Debug" menu to the macro editor.
  • Histograms of 8-bit and RGB stacks are created much faster.
  • "Convert RGB to Composite" option added to Image>Hyperstacks>Stack to Hyperstack dialog when image is in RGB format.
  • Added the is("Caps Lock Set") macro function.
  • The save() and saveAs() macro functions work with text editor windows.
  • Fixed a rounding error with histograms of RGB stacks.
  • Fixed a bug that sometimes caused ImageJ to create TIFF stacks that caused Matlab to crash.
  • Fixed a bug in File>Save As>FITS that could cause an error when resaving a FITS image.
• Gabriel Landini created a macro you can run to evaluate your system's performance and compare results with 36 other systems.
• The Open Source Paleontologist blog has an article about ImageJ.
• Dimiter Prodanov contributed the Image Moments plugin.
• Gabriel Prieto Renieblas contributed SSIM Index, a plugin that calculates the structural similarity index.
• 1.42d, 5 December 2008
  • The Image>Colors>Channels Tool is recorded.
  • Added the setMinAndMax(min,max,channels) macro function.
  • Fixed a bug, introduced in v1.42c, that caused the run("Set Scale...", options) macro function to fail.
  • Fixed a bug, introduced in v1.38, that caused the threshold to be reset when clearing or filling a stack slice.
• 1.42c, 2 December 2008
  • Added a "Scaled Units" checkbox to the Edit>Selection>Specify dialog and "Pixel Units" checkboxes to the Analyze>Analyze Particles and Edit>Selection>Enlarge dialogs. These checkboxes are only displayed if the image is spatially calibrated.
  • The ROI Manager "Multi Measure" command adds the ROI name to the column headers if the name does not start with a digit or if its length is less than nine characters.
  • The length of the current straight line selection is now displayed in the Analyze>Set Scale dialog even when the image is spatially calibrated.
  • The getDirectory("image") macro function is more likely to work with an image loaded by an external plugin.
  • Worked around a bug on Mac OS X that required pressing the "Remove Scale" button twice in the Analyze>Set Scale dialog box.
• Jeffrey Woodward contibuted the QTVirtualStack class, which has been incorporated into the QuickTime Opener plugin.
• Michael Schmid has released Fast Filters, a collection of filters (mean, min, max, median, background, ...) that are up to 40 times faster than the filters in the Process>Filters submenu.
• Ignazio Gallo contributed Poisson Noise, a plugin that adds Poisson distributed noise to all ImageJ data types (8-bit, 16-bit, float and RGB), to stacks and to non-rectangular selections.
• 1.42b, 20 November 2008
  • Edit>Selection>Straighten works with stacks.
  • Added an "Add to ROI Manager" option to the Edit>Options>Point Tool dialog box.
  • The File>Import>Image Sequence "Convert to RGB" option now works with the "Use Virtual Stack" option.
  • Added a "Convert to RGB" option to the dialog box displayed when a folder is dragged and dropped onto the "ImageJ" window.
  • Edit>Draw displays a "Process Stack" dialog when operating on a stack. Use the "d" shortcut to avoid this dialog.
  • Image>Show Info now displays the display range of 8-bit images.
  • Process>FFT>Custom Filter now mirrors the image around its edges to avoid wrap around artifacts.
  • The ROI Manager "Multi Measure" function now works with line and (single) point selections.
  • Renamed the "Reset" button in the Analyze>Set Scale dialog to "Remove Scale" and changed the unit displayed with unscaled images from "cm" to "pixel".
  • Image window activations are recorded.
  • 16-bit composite color images are now correctly converted to 8-bits.
  • Fixed a bug, introduced in 1.41n, that caused Process>Math>NaN Background to fail with stacks.
  • Fixed a bug that caused Analyze>Tools>Calibration Bar to throw an exception on Windows if the default calibration bar was taller than the image.
  • Fixed a bug that caused virtual stacks to hang if the backing folder contained images that were not all the same size and type.
  • Fixed a bug that caused indexed 8-bit grayscale images to not be correctly converted to 16 and 32 bits.
• Photos from the ImageJ Conference have been posted to the Wiki.
• 1.42a, 31 October 2008
  • Added the 4200x4200 "NileBend" image and the "Confocal Series" 4D stack to the File>Open Samples menu.
  • The Image>Color>Stack to RGB command is faster.
  • The Help>Update ImageJ drop down menu no longer displays the letter suffix except for the prerelease version at the top of the list.
  • The IJ.openImage(path) method displays a file open dialog if the 'path' argument is omitted or it is an empty string.
  • Fixed bugs that caused Image>Adjust>Color Balance to not work correctly with composite color images.
  • Fixed a bug that caused the Adjust>Brightness/Contrast "Set" option to not work as expected with composite color images.
  • Fixed a bug that caused the first slice and frame to always be displayed after using Image>Hyperstack>Channels Tool to switch a hyperstack to "Composite" mode.

Version 1.41, 24 October 2008

• 1.41o, 24 October 2008
  • Added the Process>Math>Set command.
  • Help>Update ImageJ, except when updating to the "daily build", deletes "functions.html" in the macros folder, which forces the macro editor's Macros>Function Finder command to download a fresh copy.
  • The call() macro function can now call static methods with integer arguments.
  • Added the getOutputImage() and setHideOutputImage(boolean) methods to the ParticleAnalyzer class.
  • Added the Toolbar.setBrushSize() method.
  • Fixed a bug, introduced in v1.41k, that caused macro functions not in an installed macro set to not be able to write to global (var) variables.
  • Fixed a bug that caused plugins using the ImagePlus.getImage() method to not work as expected when called from a stack-processing batch mode macro.
• Michael Schmid contributed a new Accurate Gaussian Blur plugin.
• 1.41n, 17 October 2008
  • Added the Edit>Options>Compiler command.
  • Added support for opening PackBits compressed TIFFs and ARGB TIFFs.
  • Added a "Scientific Notation" option to the Analyze>Set Options dialog box.
  • Files in the plugins folder with ".ijm" and ".js" extensions no longer require an "_" in the name to be installed in the Plugins menu.
  • JPEGs are saved using ImageIO if the JpegWriter class is removed, allowing ImageJ to be compiled with the OpenJDK.
  • Added "Exponential Recovery" [y=a*(1-exp(-b*x))+c] fitting to the CurveFitter class. This function is used by the FRAP_Profiler plugin included with the MBF package.
  • The d2s() macro function uses scientific notation if the second argument is negative.
  • Help>Update Menus resets the plugin class loader.
  • Added the ImageProcessor.getPixelInterpolated(double,double) method, which was contributed by Stephan Saalfeld.
  • Fixed bugs that caused the setThreshold(), getThreshold() and setMinAndMax() macro functions to not work correctly with intensity calibrated 8-bit images.
  • Fixed a bug, introduced in v1.41l, that caused File>Save As>FITS to create FITS files that could not be opened by some other FITS readers.
  • Fixed a bug that caused the calibration plot to be displayed when running the Analyze>Calibrate command in a macro.
  • Fixed a bug that caused run("Command", "stack") macro statements to not process the entire stack if "Hide 'Process Stack?' Dialog" was enabled in Edit>Options>Misc.
• Tiago Ferreira contributed Toolset Creator, a macro that creates toolbar menus for running plugins, macros and scripts.
• Janos Roszik, Janos Szollosi and Gyorgy Vereb have released AccPbFRET, a plugin for analysis of acceptor photobleaching FRET images.
• Jenoptik has released an ImageJ driver for their ProgRes microscope cameras.
• 1.41m, 19 September 2008
  • File>Save no longer displays a "Save As" dialog when resaving a TIFF stack.
  • A more informative error message is displayed when attempting to process a virtual stack.
  • Analyze>Plot Profile now uses the full file name, minus the extension, in plot window titles.
  • Added the eval("script", javascipt) macro function.
  • Fixed a bug, introduced in v1.41l, that caused infinite numbers to be displayed as "∞" instead of as "Infinity".
• 1.41l, 16 September 2008
  • Added the Help>Update Menus command, which allows plugins to be installed and/or removed without restarting ImageJ.
  • Area, line, angle and point measurements can be recorded in the same Results window.
  • The Roi Manager "Measure" function no longer requires that all selections be areas or all selections be lines.
  • Making a change in the Analyze>Set Measurements dialog box no longer caused the Results window to be reset.
  • The Particle Analyzer's "Summarize" option displays the average mean, mode, perimeter, major axis, minor axis, angle, circularity, Feret diameter, integrated density, median, skewness and kurtosis if the corresponding option is enabled in Analyze>Set Measurements.
  • Frederic Hessman contributed an improved version of File>Save As>FITS that preserves any existing FITS header.
  • Image>Stacks>Stack to Images no longer discards slice labels (e.g., DICOM headers).
  • Numbers displayed using scientific notation in plots, histograms, and in the Results window, now use a maximum of 3 decimal places.
  • The angle tool is now correctly recorded.
  • File>Save As>AVI now accepts frame rates as low as 0.5 (2 seconds per frame).
  • Fixed a bug that caused the Process>Binary>Erode and Dilate commands to throw an exception with one pixel wide images.
• Sebastian Rhode contributed Calc_Objective, a plugin that calculates parameters of interest for an objective lens.
• Gilles Carpentier contributed the Dot Blot Analyzer toolset (online documentation).
• 1.41k, 2 September 2008
  • The "Line Width", "Fonts", "Log" and "ROI Manager" windows remember their locations.
  • The Edit>Adjust>Adjust Line tool updates all images with lines selections and has increased slider range of 1-300.
  • The Measure command and getStatistics() macro function calculate area statistics of line selections wider than one.
  • Process>FFT>Inverse FFT improvements (courtesy of Michael Schmid):
    • Areas marked as "pass" or "filter" in the power spectrum are made symmetric.
    • The smoothing algorithm uses periodic boundary conditions.
    • Inverse FFT on a cropped power spectrum does not cause an exception.
    • The filter created after symmetrizing and smoothing is shown in debug mode or if the alt key is down.
  • The particle analyzer assumes the size is in pixels if it is followed by a "p", for example run("Analyze Particles...", "size=100p display clear").
  • Added a "Close when running" checkbox to the Plugins>Utilities>Find Command window and changed the "Cancel" button to "Close".
  • Added curve fitting functions (Fit.*) to the macro language (example).
  • Added the Plot.getValues() macro function.
  • The open() macro function now works with image URLs.
  • Gzip compressed FITS images on network drives open up to 10 times faster.
  • Fixed a bug, introduced in v1.41b, that caused the ImageJ applet to fail to load DICOM images on startup (example).
  • Fixed a bug in File>Import>AVI, introduced in 1.41h, that caused some color video formats to open as 16-bit grayscale.
  • Fixed a bug that caused the slider in the Image>Adjust>Line Width window to blink on Windows.
  • Fixed a bug that caused the setForegroundColor() macro function to reset the line width.
  • Reduced the likelyhood of a bug that caused the Image>Adjust>Threshold "Set" option to sometimes enter incorrect values on Linux.
  • Fixed a bug that caused upper case shortcuts created using Plugins>Shortcuts>Create Shotcut to open macros instead of running them.
• Jerome Mutterer contributed TiltedRectangleTool, a macro tool that creates tilted rectangular selections.
• Joel Sheffield has made available an ImageJ tutorial in PowerPoint format he gave at a recent Microscopy & Microanalysis meeting and the images and stacks used in the tutorial.
• David Webb contributed Toe_Indexer, a macro set for measuring footprints and calculating the toe index.
• 1.41j, 8 August 2008
  • Profile plots of segmented and freehand lines wider than 1 are averaged across the line.
  • File>Save As>Image Sequence exports hyperstacks as C/Z/T labeled files (e.g., "name_t01_z01_c01").
  • Added the Image>Adjust>Line Width command (or double click on the line tool).
  • Added a "Spline Fit" checkbox to the Image>Adjust>Line Width tool.
  • Added a "Background Value" field, and "Invert Y Coordinates" and "Suppress Log Output" options, to the Analyze>Tools>Save XY Coordinates dialog box.
  • The ROI Manager "Deselect" option is recorded.
  • Added the File.saveString(string,path) and File.append(string,path) macro functions, and corresponding IJ.saveString() and IJ.append() methods.
  • Fixed a bug, introduced in v1.41f, that could cause batch mode macros to fail.
  • Fixed a bug that could cause LZW-compressed TIFFs to be incorrectly decoded.
  • Fixed a bug in Image>Stacks>Reslice the caused the spatial calibration to not be correctly transformed if the voxel width and height were not the same.
  • Fixed a bug that sometimes caused the wrong selection to be copied when duplicating stacks with non-rectangular selections.
  • Fixed a bug that caused a "Data chunk size too short" error when opening uncompressed RGB AVI files.
  • Fixed a bug that caused .flex files to fail to open if the Bio-Formats plugin was not installed.
  • Fixed a bug that caused an exception when opening PGM images less than 20 pixels in size.
  • Fixed a bug that caused the LUT to not be correctly copied when duplicating a single image in hyperstack in a batch mode macro.
• 1.41i, 25 July 2008
  • Added the Edit>Selection>Straighten command.
  • An extension is added to file names in File>Save As dialogs that do not have one.
  • Added the substring(string,index) macro function.
  • Fixed a bug that caused the Analyze>Summarize command to not work with "IntDen" results.
• 1.41h, 18 July 2008
  • Added the Plugins>Macros>Edit command, which replaces the Plugins>Edit command removed in v1.41g. There is also a plugin version of this command at imagej.net/ij/plugins/download/jars/Edit_.jar.
  • JavaScript programs in the plugins folder with an underscore in the name and a ".js" extension are installed in the Plugins menu at startup.
  • Virtual stacks imported using File>Import>Image Sequence now include slice label metadata.
  • ImageJ opens 16-bit grayscale AVIs created by MIL (Matrox Imaging Library), thanks to a patch by Reinhard Mayr.
  • Added the run("Fit Spline", "straighten") macro function, which converts a line selection to one defined by points spaced one pixel apart (example).
  • The point selection tool is now recordable.
  • The ROI Manager "Combine" function works with point selections.
  • Added the makePoint(x,y) macro function and IJ.makePoint(x,y) method.
  • Fixed a bug that caused selections extending beyond the image boundary to not be correctly copied to the clipboard.
  • Fixed a bug that caused the round() macro function to not work correctly with NaN and infinite arguments.
  • Fixed a bug that caused images to no longer be displayed after aborting a batch mode macro by pressing Esc.
  • Fixed a bug that caused the setOption("QueueMacros",true) macro function to not work as expected with macros using a function key shortcut.
  • Fixed a bug that caused the ROI Manager "Update" option to hold a reference to the image, preventing it from being garbage collected.
• Johannes Schindelin contributed Thread Killer, a plugin that aborts plugins that do not quit when the escape key is pressed.
• The Dodge Burn and Smooth macros demonstrate how to use the "QueueMacros" option to avoid "Image is Locked" errors caused by overlapping macro execution.
• Wilhelm Burger has released MovieIO, a library that can be used to read and write video files frame-by-frame.
• Albert Cardona has written a tutorial on how to use JavaScript with ImageJ. ImageJ 1.41g, which adds the Macros>Evaluate JavaScript (in the editor) and Plugins>New>JavaScript commands, is required to run the examples. More JavaScript examples are available at imagej.net/ij/macros/js/.
• 1.41g, 3 July 2008
  • Dialogs can now be canceled by clicking on the close box.
  • Added Merge Channels, Edit LUT, Red, Green, Blue, Cyan, Magenta, Yellow and Grays command to the More» menu in the "Channels" tool.
  • Split the Plugins>New command into a submenu with Macro, JavaScript, Plugin, Plugin Filter, Plugin Frame, Text Window and Table commands.
  • Removed the Plugins>Edit command. In its place, use File>Open or drag and drop.
  • Thanks to a patch by Ulf Dittmer, the File>Open Recent menu no longer lists files multiple times.
  • The "The calibration of this image conflicts with the current global calibration." warning message is not displayed for images opened in macros.
  • The waitForUser() macro function remembers the dialog box location.
  • The PlugInClassLoader loads classes faster from JAR files.
• Norbert Vischer has released Wrap AppleScript, a macro that allows you to run AppleScript in ImageJ, and AliasResolver, a macro for resolving aliases. Both macros require Mac OS X 10.4 or later.
• Ulf Dittmer has released Animated PNG Writer, a plugin that creates APNG files from stacks of images.
• 1.41f, 24 June 2008
  • The File>Import>URL command now opens Java (.java) and JavaScript (.js) programs.
  • Renamed the Image>Color>RGB Split and RGB Merge to Split Channels and Merge Channels.
  • Added a redundant Image>Color>Channels Tool command.
  • Added a Split Channels command to the More» menu in the "Channels" tool, replacing the Open HeLa Cells command.
  • Added a "JavaScript" type to the Plugins>New dialog.
  • To run JavaScript on Java 1.5 and earlier, and on Mac OS X, download JavaScript.jar to the plugins folder.
  • Added the List.set(key,value), List.get(key), List.size, List.clear, List.setList(string) and List.getList macro functions.
  • Added the IJ.run(ImagePlus, command, options), IJ.save(ImagePlus, path) and IJ.saveAs(ImagePlus, format, path) methods.
  • Fixed bug that could cause Image>Color>RGB Merge to throw an exception if one of the input images was a hyperstack.
  • Fixed a bug that caused an extra tab at the end of Results window lines copied to the clipboard or saved as a text file.
• 1.41e, 10 June 2008
  • Michael Schmid added the ability to save using Motion JPEG and PNG compression to the File>Save As>AVI command and the ability to read JPEG and PNG compressed AVIs to the File>Open command.
  • Added the Macros>Evaluate JavaScript command to the macro editor (example). This command requires Java 1.6, which has the Mozilla Rhino JavaScript interpreter built in.
  • Added the Help>Update ImageJ command, which duplicates the Plugins>Utilities>Update ImageJ command.
  • Added the "Move Isolated Plugins to Misc. Submenu" option to the Edit>Options>Misc dialog. Enable this option and single .class plugins in a directory are installed in the Plugins>MIscellaneous submenu instead of in submenus with only one command.
  • Jerome Mutterer contributed the macro editor's new Macros>Find Functions command.
  • Edit>Selection>Rotate works with composite selections.
  • Edit>Selection>Restore Selection works with non-rectangular selections that extend beyond the boundary of the destination image.
  • The getStatistics() and getRawStatistics() macro functions now work with line selections.
  • The File.delete() macro function now returns true (1) if the file or directory was successfully deleted. "1" will be displayed in the Log window if File.delete() is not called in an assignment or 'if' statement.
  • Fixed a bug that sometimes caused 16-bit signed stacks to not be correctly converted to 32-bits.
• The OpenTextImagesAsStack macro opens a sequence of text images as a stack.
• Michael Schmid contributed Video Capture Tool, a macro for capturing video on Windows via VirtualDub.
• 1.41d, 28 May 2008
  • Mark Longair contributed the Plugins>Utilities>Find Commands command, which provides a dialog for interactively finding ImageJ commands by typing a substring of the command name. Type "l" (launch), a few letters for disambiguation and then 'enter' to run the matching command.
  • Gabriel Landini contributed an improved version of Process>Binary>File Holes that is up to 100 times faster.
  • The Image>Stacks>Make Montage command now works with composite color images.
  • Enable "Save TIFF and Raw in Intel Byte Order" in Edit>Options>Input/Output and File>Save As>Tiff will save in little-endian format.
  • File>Save As>PNG saves 8, 16 and 32 bit images as 8-bit PNGs, and now works with composite color images.
  • Changed the "GIF Transparent Index (0-255)" field in Edit>Options>Input/Output to "GIF and PNG Transparent Index".
  • The "<" and ">" keys and the mouse wheel now change hyperstack channels.
  • Added a "Copy Row Numbers" option to the Edit>Options>Input/Output dialog box.
  • Changed the Results window File>Set File Extension menu item to File>Options.
  • Right-clicking on a macro tool runs a macro with the name <tool name>+" Options".
  • DICOM IMPLICIT_VR tags with a length less than 4 are now displayed in the Image>Show Info window.
  • Added the Neuron (1.6M, 5 channels) sample image, which was contributed by John Alexander. Press "i" (Image>Show Info) to get a description.
  • Added the getStringWidth(string) macro function.
  • Added getBufferedImage() methods to the ImagePlus and ImageProcessor classes.
  • Added a get16BitBufferedImage() method to the ShortProcessor class.
  • Fixed a bug that caused Image>Crop to fail with merged composite images when using Java 1.6.
  • Fixed bugs in the Plot class and Plot.* macro functions that caused incorrect axis labeling if setLimits() was not called first and caused lines and shapes wider than three pixels to sometimes be drawn outside the plot frame.
  • Fixed a bug in the imageCalculator() macro function that sometimes caused the result image to not be the currently selected image.
  • Fixed a bug in the setColor() macro function that caused it to always convert the argument to an integer.
  • Fixed a bug in the Image>Adjust>Threshold tool that caused the "Auto" feature to not work correctly on images with line selections.
• Brade Busse has released MultiStackReg, an extenson of the StackReg plugin that supports saving and loading of alignment parameters and multi-stack alignment (requires TurboReg).
• 1.41c, 16 May 2008
  • Added the Plugins>Utilities>Proxy Settings command, based on the NetSetup plugin contributed by Dimiter Prodanov.
  • With merged composite color images, the "Preview" check box is not added to dialog boxes and the "Process all n images?" dialog is not displayed.
  • Added 13 tags to the built in DICOM dictionary.
  • ImageJ calls system.gc() when a stack and/or the last image is closed.
  • Added the Dialog.addCheckboxGroup() macro function.
  • Added the GenericDialog.setEchoChar() method, which is used to implement the password field in the Edit>Options>Proxy Settings "Authentication" dialog.
  • Fixed a bug that sometimes caused the Image>Adjust>Brightness/Contrast "Auto" option to fail on images with non-rectangular selections.
  • Fixed a bug, introduced in v1.40b, that caused the labels in images created by the particle analyzer Show:Outlines option to be black instead or red.
  • Fixed a bug that caused 8-bit PNGs to open in RGB format.
  • Fixed a bug that caused ImageJ to not correctly read ImageJ TIFF stacks modified by LibTIFF.
  • Fixed a bug that sometimes caused 90 degree rotated large composite color images to not be correctly displayed.
  • Fixed a bug that caused an "out of memory" error when opening DICOM files with a UT (Unlimited Text) tag.
  • Fixed a bug that caused the "Show All" feature of the ROI Manager to not work as expected with more than 10,000 slice-associated ROIs.
• The Virtual Stack From List macro demonstrates how to generate a list of images and then use that list to open the images as a virtual stack.
• 1.41b, 6 May 2008
  • Michael Schmid's AVI Reader plugin is now built in. AVI files can be opened using File>Open, File>Import>AVI and drag and drop.
  • To reduce the size of the Plugins menu, JAR files that implement fewer than four Plugins submenu commands are installed in the submenu corresponding to the folder containing the JAR file. In addition, single plugins distributed as ZIP archives are installed in the "Miscellaneous" submenu.
  • Johannes Hermen and Christian Mol added the ability to parse float header values to the DICOM reader and also contributed a 2652 tag dictionary (DICOM_Dictionary.txt) that the DICOM reader will use if it is copied to the ImageJ folder.
  • The DICOM reader uses the value of the "Slice Thickness" tag for voxel depth if the "Slice Spacing" tag is missing.
  • The particle analyzer, when run from a batch mode macro, no longer opens the ROI Manager window when "Add to Manager" is enabled, resulting in faster and more reliable operation.
  • Process>Enhance Contrast works with composite color images.
  • The minimum plot size that can be set in Edit>Options>Profile Plot Options was reduced from 300x100 to 100x50.
  • Added a "Restore ROIs Centered" option to the ROI Manager's More»Options command.
  • Added the Stack.setActiveChannels() macro function.
  • Fixed a bug that could cause an exception when saving composite color images.
  • Fixed a bug that caused composite color images with custom LUTs to revert to the default LUTs after resaving.
  • Fixed a bug that caused Z projection of hyperstacks to fail in batch mode macros.
  • Fixed a bug that caused ImageJ to not correctly read ImageJ TIFF stacks modified by LibTIFF.
  • Fixed a bug that caused macros using the Analyze>Surface Plot plot command, with both the "Draw Wireframe" and "Draw Axis" options enabled, to fail.
• Michael Schmid contributed a new AVI Reader plugin that adds support for YUV formats, the ability to specify the starting and ending frame, an option to convert to 8-bit grayscale and an option to open the movie as a virtual stack.
• Jerome Mutterer has released Magic Montage, a macro toolset for easy montage and overlay creation.
• 1.41a, 21 April 2008
  • The Duplicate, Scale, Adjust>Size, Z Project, Reduce Dimensionality and Image Calculator commands now work correctly with hyperstacks that have custom channel LUTs.
  • The Copy to System, Make Binary and Convert to Mask commands now work with composite color images.
  • Added the setAutoThreshold() method to the ImageProcessor class.
  • Fixed bugs that caused the setAutoThreshold() macro function, and the Make Binary and Convert to Mask commands, to sometimes not produce the same result as the "Auto" button in the "Threshold" window.
  • Fixed a bug that caused the getLut() macro function to throw an exception when attempting to retrieve a LUT from a composite image in batch mode

Version 1.40, 18 April 2008

• 1.40g, 18 April 2008
  • The Java version is displayed in the status bar on startup.
  • Fixed a bug that caused images saved in TIFF format to have their contents shifted left if the "Info" property was set to an empty string.
  • Fixed a bug, introduced in v1.40c, that caused stacks saved in TIFF format to have their contents shifted left if any slice had a blank label and all other slice labels where null.
• 1.40f, 18 April 2008
  • Increased the maximum frame rate accepted by Image>Stacks>Animation Options to 1000.
  • When animating stacks, the frame rate is displayed in the ImageJ status bar.
  • Drag and Drop exceptions are now displayed in an ImageJ window.
  • Fixed a bug that caused some Bruker "fid" files to fail to open.
• Jerome Mutterer contributed two macro tools (Macro Sliders Demo and RGB Color Picker) that demonstrate how to create customizable sliders for entering macro parameters.
• Albert Cardona has written a tutorial on how to create image file reader and writer plugins, and how to integrate them with the rest of ImageJ.
• 1.40e, 15 April 2008
  • While creating a straight line selection, hold down the alt key to force the two points that define the line to have integer coordinate values.
  • Results table labels now include the file name extension.
  • Set the JPEG Quality in Edit>Options>Input/Output to 100% to disable color sub-sampling, reducing the likelihood of artifacts.
  • The DPI of images saved in JPEG format is set to the scale defined in Analyze>Set Scale if the unit of length is "inch".
  • Added the setOption("Display Labels", boolean) and setOption("Limit to Threshold", boolean) macro functions.
  • Added the Analyzer.setMeasurement(int, boolean) method.
  • Worked around a OSX Leopard/Java 1.5 bug that caused dialogs boxes to return default field values when the return key was pressed.
  • Fixed a bug that caused the LSM Reader to not correctly open 16-bit files using LZW compression with differencing.
  • Fixed a bug that caused saving in BMP format to fail with 16-bit and 32-bit images.
• Dimiter Prodanov contributed the RSS Feed Reader plugin, which uses RSS to download the pictures of the day from the NASA website.
• Bob Dougherty contributed macros that add a calibration bar to a stack or to all the images and stacks in a folder.
• The search box on the ImageJ home page now uses the ht://Dig search engine, which is better at seaching the contents of source files. For example, seach for "waitForUser" and it quickly finds a description of this macro function, a macro that demonstrates how to use it, the method that implements it in Functions.java, the WaitForUserDialog class the method uses, and a plugin that uses WaitForUserDialog.
• 1.40d, 9 April 2008
  • Converted the FluorescentCells sample image into a three channel composite color image.
  • The Image Calculator now creates a hyperstack when the input is a hyperstack.
  • Fixed a bug that could cause macros (not in batch mode) running the particle anlyzer on a stack to not run reliably.
  • Fixed a bug that caused reading of LZW compressed TIFF stacks to fail.
  • Fixed a bug that caused Image>Color>RGB Merge, when creating a composite image, to sometimes not use expected the channel colors.
• 1.40c, 2 April 2008
  • Image>Stacks>Z Project now works with t-series hyperstacks.
  • Image>Hyperstacks>Stack to Hyperstack will now convert an Image5D to a hyperstack.
  • Added the File>Open Samples>Organ of Corti sample hyperstack, courtesy of Glen MacDonald.
  • Made the "Channels" window wider on Windows and Linux.
  • Added the Stack.swap(n1,n2) macro function.
  • Fixed a bug, introduced in v1.40b, that caused decimal points to be replaced with commas on European systems.
  • Fixed a bug that causedImage>Color>Stack to RGB to fail to work with 32-bit composite images.
  • Fixed a bug that caused an incorrect z value to be displayed in the status bar as the cursor was moved over a hyperstack.
  • Fixed a bug that caused stack slice labels after the first null label to not be saved.
  • Fixed a bug that made it impossible to open the "Channels" window after it had been closed by WindowManager.closeAllWindows().
• Sebastian Rhode contributed Calc_TIRF, a plugin that does TIRF microscopy calculations and plots the results.
• Sebastian Rhode contributed Calc_CCD_SNR, a plugin that calculates and compares the SNR of two CCD cameras.
• 1.40b, 28 March 2008
  • Added the Image>Hyperstacks>Reduce Dimensionality command, based on Jerome Mutterer's Reduce HyperStack macro.
  • Thanks to Alden Dima, added the "Count Mask" option to the particle analyzer, which generates masks filled with a pixel value corresponding to the particle count.
  • Removed the Image>Hyperstacks>Split Channels command. Instead, use Image>Color>RGB Split.
  • The Image>Color>RGB Split command, when working with composite images, is faster and uses less memory, and it no longer displays a dialog box.
  • Added the setMetadata("Info", string), getMetadata("Info"), setMetadata("Label", string) and getMetadata("Label") macro functions.
  • Fixed a bug, introduced in v1.39s, that could cause ImageJ to deadlock (hang) when opening a dialog box, especially on Java 1.5.0.
  • Fixed a bug that caused some 48-bit interleaved RGB TIFFs to not display correctly.
• The Make Slice Binary macro converts the current stack slice to binary and advances to the next when you press a key.
• Jerome Mutterer contributed the Reduce HyperStack macro, which reduces the dimensionality hyperstacks (requires v1.40a).
• 1.40a, 21 March 2008
  • Added the Stack.setDisplayMode(string) and Stack.getDisplayMode(string) macro functions.
  • Added the setSelection(start, end) method to the TextPanel class.
  • Fixed numerous hyperstack and composite image bugs.
• Joachim Wesner contributed ImpProps, a plugin that allows macros to set and get image properties using the call function.

Version 1.39, 13 March 2008

• 1.39u, 13 March 2008
  • Image>Stacks>Start Animation now works with hyperstacks.
  • Added a "Use Virtual Stack" option to the dialog displayed when a folder is dragged and dropped on the ImageJ window.
  • The Gel Analyzer displays an error message if the user clicks with the wand tool and the shift key is down.
  • The command recorder now records blank string fields as "key=[]".
  • Fixed several composite image and hyperstack bugs.
  • Fixed a bug that could cause incorrect centroid calculation on an 8-bit image with a non-rectangular selection larger than ~4 megapixels.
  • Worked around a bug that could cause a thread deadlock in macros attempting to open a non-existant file.
• 1.39t, 3 March 2008
  • The Image>Adjust>Brightness/Contrast histogram is now updated when the B&C window is brought to the front.
  • The Analyze>Gels>Select First Lane command displays a "Are the lanes really horizontal?" dialog when the selection is more than twice as wide as it is tall.
  • An error message is displayed when a calibrated image is opened and "Global" calibration is enabled.
  • PNGs are again opened using ImageIO, which fixes several bugs (introduced in v1.39i) that caused 16-bit and RGB PNGs to not open or to not open correctly.
  • Added the getInfo("image.description") macro function.
  • Added the ImportDialog.getLastFileInfo() method.
  • Fixed a bug that caused File>Import>URL to fail to open GIF, JPEG, PNG and DICOM files with uppercase extensions.
  • Fixed several bugs in Edit>Selection>Specify, thanks to patches contributed by Joachim Wesner.
  • Fixed a bug in Image>Scale that could cause a blank result if the source was RGB, the x scale was less than 0.25 and the y scale was greater than 0.5.
• 1.39s, 15 February 2008
  • Added the Plugins>Utilities>Update ImageJ command, which is also available for earlier versions of ImageJ as the ImageJ Updater plugin.
  • File>Import>URL now correctly opens 16-bit PNGs.
  • Added the DirectoryChooser.setDefaultDirectory() method.
  • Fixed a bug, introduced in v1.39i, that sometimes caused an exception when opening 16-bit PNGs.
  • Fixed a bug that caused the B&C and W&L tools to record incorrect setMinAndMax() calls with signed 16-bit images.
  • Fixed a thread synchronization bug that sometimes caused the IJ.d2s() method to return numbers with the wrong number of decimal places.
• Paolo Ariano added ImageJ 1.39q to the official Debian repository at packages.debian.org/sid/imagej.
• Jerome Mutterer contributed the Dynamic Stats and Histo macro tools, which dynamically calculate and display statistics and histograms as a selection is moved around.
• Kang Li contributed Image Stabilizer, a plugin that stabilizes jittery image stacks using the Lucas-Kanade algorithm.
• The ImageJ Updater plugin updates ImageJ to the latest version.
• Dwight Bartholomew contributed Calculate 3D Noise, a plugin for analyzing 3D noise in videos.
• 1.39r, 8 February 2008
  • Added the "or Enter Pattern [regular expression]" text field to the File>Import>Image Sequence dialog box.
  • Plugins>Compile and Run adds .jar files without an underscore in the name to the compiler's classpath.
  • The Image>Stacks>Set Slice command, the ROI Manager and the setSlice() macro function were updated to work with hyperstacks.
  • Image>Show Info displays the image ID.
  • Added the waitForUser(string), waitForUser(title, string), matches(string, regex) and is("composite") macro functions.
  • Added an optional second argument (decimal places) to the toString() macro function.
  • Fixed a bug that resulted in incorrect measured median values for thresholded images with "Limit to Threshold" enabled.
  • Fixed a bug that caused the information displayed by Image>Show Info (e.g., DICOM tags) to be incorrect for images opened with File>Open Next.
  • Thanks to Stefan Starke, fixed a bug the caused the call() macro function to fail when ImageJ was running as a signed applet.
• Carles Mitj and Raquel Revuelta contributed Slanted Edge MTF, a plugin that calculates the Modulation Transfer Function from an image containing an edge.
• Piotr Wendykier has released Parallel Iterative Deconvolution 2D, a multithreaded plugin that does iterative deblurring using MRNSD, CGLS or HyBR.
• Bob Dougherty has released Label Image, a plugin that adds x and y scales and labels to an image.
• A Practical Approach to Medical Image Processing [Using ImageJ] by Elizabeth Berry is now available. The book includes a CD with example images and the Windows version of ImageJ 1.37.
• 1.39q, 26 January 2008
  • When using the Image>Adjust>Brightness/Contrast tool, hold the shift key down to simultaneously adjust all channels of a composite image (e.g., File>Open Samples>HeLa Cells).
  • Clicking "Apply" in Image>Adjust>Brightness/Contrast propagates the current composite image display range to the other channels.
  • Image>Adjust>Color Balance works with composite images.
  • The text tool is recorded.
  • ImageJ now opens LZW-compressed RGB planar TIFFs.
  • Stefan Woerz added Gaussian fitting to the CurveFitter class.
  • Albert Cardona added HandleExtraFileTypes support for File>Import>URL.
  • Added the is("Virtual Stack") macro function.
  • Fixed a bug that caused hyperstacks and images with panels to not be displayed correctly when the window was maximized.
  • Fixed a bug that caused files in folders dropped onto ImageJ to not be sorted in numeric order.
  • Fixed a bug in File>Import>Raw (ImageReader class) that caused it to not correctly handle EOF errors with data types other than 8-bit.
  • Fixed a bug in the PGM_Reader that caused pixel intensities of imported 48-bit images to differ slightly from the expected values.
• Digital Image Processing: An Algorithmic Introduction Using Java [and ImageJ] by Wilhelm Burger and Mark Burge is now available. The ImageJ Short Reference (Appendix C of the book) and the source code for the example plugins are available on the book's website.
• Gilles Carpentier contributed the Time-Lapse Video Macros, which can be used to capture a video sequence using the QuickTime Capture plugin.
• 1.39p, 15 January 2008
  • Image>Stacks>Z Project works with hyperstacks.
  • Image>Hyperstacks>New Hyperstack settings are saved in the preferences file.
  • Added a "Sliding Paraboloid" option to Process>Subtract Background. ImageJ uses the original rolling ball algorithm when this option is not enabled.
  • Added a "Create Composite" option to Image>Color>RGB Merge.
  • Image>Color>RGB Split works with composite images.
  • Process>Smooth, Process>Sharpen and Process>Find Edges now process edge pixels of 16-bit and 32-bit images thanks to code contributed by Michael Schmid.
  • Composite images (e.g., File>Open Samples>HeLa Cells) use less memory.
  • 48 bit PPM files open as 16 bits per channel composite images.
  • 16-bit images use less memory when running Java 1.6 or later.
  • The getInfo("window.contents") macro function works with the Recorder.
  • Added the is("batch mode") macro function.
  • Fixed a bug with Image>Rotate>Arbitrarily that caused it to sometimes clip the image when "Enlarge Image to Fit Result" was enabled.
  • Fixed a bug that caused Image>Hyperstacks>New Hyperstack to fail when ImageJ was running as an applet.
  • Fixed a memory leak in ByteProcessor.resetMinAndMax() when not running on Java 1.6 or later.
• 1.39o, 7 January 2008
  • Image>Stacks>Z project works with hyperstacks.
  • Custom channel LUTs are saved in the TIFF header.
  • Added the "Copy Column Headers" option to Edit>Options>Input/Output.
  • The Image>Adjust>Brightness/Contrast "Auto" option no longer deletes the selection.
  • Image windows open at the top of the screen on systems with a screen height of 600 pixels or less (e.g., the Eee PC).
  • Increased the maximum radius in Median, Mean, Minimum, Maximum and Variance filters from 100 to 1000 pixels.
  • Increased the width of the "Maximum Memory" field in Edit>Options>Memory & Threads from 4 to 5 digits to allow easy entry of values greater than 9999 (9.8GB).
  • Removed the System.gc() call, which sometimes caused long pauses when closing images, from ImagePlus.flush().
  • Fixed a bug that could cause a bogus "Selection required" message when closing the Results window or using the Analyze>Clear Results command.
• The National Resource For Imaging Mass Spectrometry contributed OpenMIMS, a plugin that that opens, displays and processes MIMS (Multi Isotope Mass Spectrometry) data.
• 1.39n, 21 December 2007
  • Custom channel LUTs are saved in the TIFF header.
  • The Image>Adjust>Brightness/Contrast "Auto" option no longer deletes the selection.
  • Increased the width of the "Maximum Memory" field in Edit>Options>Memory & Threads from 4 to 5 digits, which allows easier entry of values greater than 9999 (9.8GB).
  • Removed the System.gc() call from ImagePlus.flush().
• Jerome Mutterer contributed the Workspaces macro set, which allows the user to save his or her current 'workspace' (images, results and text windows) and restore it later.
• 1.39m, 17 December 2007
  • The Image>Hyperstacks>Stack to Hyperstack command converts an RGB stack into a 3 channel hyperstack.
  • For stacks larger than 1GB, memory usage displayed in the image subtitle is in gigabytes.
  • The title of the Edit>Options>Memory and Threads dialog is "Memory (32-bit)" on 32-bit systems and "Memory (64-bit)" on 64-bit systems.
  • Added the IJ.is64Bit() method.
  • Big-endian TIFF files with names ending in .flex are passed to the Bio-Formats plugin.
  • Fixed a bug, introduced in 1.39l, that caused the Stack to Hyperstack command to not appear in the Image>Hyperstacks> submenu.
  • Fixed a bug that sometimes caused the maximize button in stack windows to not work as expected.
  • Worked around a bug with 64-bit Java on OS X that caused ImageJ to crash when opening a Web page.
  • Fixed a bug with Plugins>Utilities>Memory Monitor that caused an exception of a batch mode macro was running.
• David Marso contributed Kaleidoscope, a macro for computationally intensive artistic endeavors. For an example of what this macro does, view this QuickTime movie.
• Kai Uwe Barthel contributed Mean Shift Filter, a plugin that that can be used for edge-preserving smoothing or for color segmentation.
• 1.39l, 7 December 2007
  • Added the Image>Translate, Image>Hyperstacks>Split Channels and File>Import>Stack From List commands.
  • Added a "Use Virtual Stack" option to File>Import>Raw.
  • The File>Import>TIFF Virtual Stack command now works with hyperstacks.
  • B&C settings for each channel in hyperstacks and CompositeImages are saved in the TIFF header.
  • Changed the Histogram x-axis label from 0-256 to 0-255 for 8-bit and RGB images.
  • Added the setTool(name) and roiManager("Multi Measure") macro functions.
  • Added the Stack.isHyperstack(), Stack.getDimensions(), Stack.setDimensions(), Stack.getPosition(), Stack.setPosition(), Stack.setChannel(), Stack.setSlice() and Stack.setFrame() macro functions (example).
  • Added the getSelectedRoisAsArray() method to the RoiManager class and made the getSliceNumber() method public.
  • ImageListeners are now notified when the Revert command is used.
  • Fixed a bug that caused the ROI Manager More>>Fill, More>>Draw and More>>Label commands to sometimes not work correctly with selected ROIs.
  • Fixed a bug that could cause an invalid error message when opening gzip compressed FITS and raw images.
• Michael Schmid has released Pixel Inspector, a plugin that displays pixel values at the cursor and its surroundings, and Wait For User, a plugin that asks for user intervention while a macro is running.
• Nikon Instruments contributed ND2 Reader (Windows only), a plugin that opens Nikon ND2 images and displays them in six dimensions.
• Michael Schmid has created a plugin version of the Subtract Background command used in ImageJ 1.39e and earlier, with added support for "Preview" and multiple processors.
• 1.39k, 21 November 2007
  • Added the File>Import>TIFF Virtual Stack command.
  • When calculating the background, Process>Subtract Background now uses a 3x3 maximum filter to remove outliers.
  • Added a "Display Mode" popup menu to the Image>Hyperstacks>New Hyperstack and Stack to Hyperstack dialogs.
  • A better error message is displayed when the user attempts to open a JPEG compressed TIFF.
  • Added the is("Hyperstack") macro function.
• Gilles Carpentier contributed CustomTabStatFromResults, a macro set that demonstrates how to create, modify, open and save custom results tables.
• 1.39j, 14 November 2007
  • Image>Duplicate preserves non-rectangular area selections.
  • Thanks to a patch by Johannes Schindelin, the macro language now accepts numbers in scientific notation.
  • Plugins>Compile and Run uses the -Xlint:unchecked option on Java 1.5 and later.
  • Fixed a bug that prevented Image>Adjust>Brightness/Contrast, Window/Level and Color Balance from opening if any of these tools was already open.
  • Fixed a bug that caused the Roi Manager to sometimes not work as expected when more than 9999 ROIs were added to it by the particle analyzer.
  • Fixed several bugs related to hyperstacks and composite color images.
  • Fixed several ImageListener interface problems.
  • Fixed a bug that caused File>New>Image to display an invalid message in the status bar when opening stacks larger than 2GB.
  • Fixed a bug that caused Plugins>Utilities>Memory Monitor to not work correctly when using more than 2GB.
• 1.39i, 8 November 2007
  • Updated to support ImageJ64, a launcher for Mac OS X Leopard that runs ImageJ in 64-bit mode. ImageJ64 requires a Mac with a 64-bit Intel processor and at least 2.5 GB of memory.
  • Column headers are now included when copying data from the Results window.
  • Tables created by Analyze>Gels are now compatible with the nResults() and getResult() macro functions.
  • Reverted to reading PNGs using Toolkit.createImage(), rather than ImageIO, which is much slower and does not correctly read some 8-bit PNGs.
• Maria Barilla contributed Color Transformer, a plugin that converts an RGB image into XYZ, Yxy, YUV, YIQ, Luv, Lab, AC1C2, I1I2I3, Yuv, YQ1Q2, HSI, HSV, HSL, LCHLuv, LSHLuv or LSHLab color space.
• 1.39h, 5 November 2007
  • Updated the setLut() macro function to work with composite color images.
  • Fixed a bug, introduced in 1.39g, that caused Plugins>Compile and Run to fail when using Java 1.6.
• 1.39g, 2 November 2007
  • Added the Image>Hyperstacks submenu, containing New Hyperstack..., Stack to Hyperstack..., Hyperstack to Stack and Channels... commands.
  • Added a "Transparent Zero" (zero pixels are transparent) operator to Process>Image Calculator and Edit>Paste Control.
  • The "List", "Save" and "Copy" options in profile plot windows use 9 decimal places for y values if "Decimal Places" in the Analyze>Set Measurements dialog is less than 6.
  • Multi-image 48-bit RGB TIFF files open as a single composite color stack.
  • Maximizing a zoomed image causes it, if needed, to fill the screen.
  • "(G)" is displayed in all image title bars if the "Global" flag is set in Analyze>Set Scale, Analyze>Calibrate or Image>Properties.
  • Custom tables now use the "File Extension for Tables" default extension specified in Edit>Options>Input/Output.
  • Changed Image>Color>Convert to Composite to Make Composite
  • Use the -port0 command line option and ImageJ will not start the SocketListener used to check for other ImageJ instances.
  • Fixed a bug that caused the memory size displayed in the sub-title of stacks larger than 2GB to be incorrect.
  • Fixed a bug that caused File>Import>Text Image to leave the progress bar in an invalid state if there was an error.
• Philippe Thévenaz has released MosaicJ, a plugin for building a larger image (a mosaic) out of a collection of overlapping partial images.
• Edwin Donnelly contributed Polar Transformer, a plugin that converts images to and from polar coordinates.
• Gilles Carpentier contributed AutoThresholdAndSegment, a macro set that detects bright and dark areas using autothresholding.
• Michael Schmid contributed an enhanced version of Tony Collins' Sigma Filter, a noise reduction filter that preserves edges.
• Tiago Ferreira contributed the Rename and Save ROI Sets, a macro toolset that allows fast renaming and saving of multiple ROIs.
• Sebastien Huart contributed the Slow Fourier Transform macro, which does forward and inverse 1D discrete Fourier transforms.
• Bruno Vellutini contributed QuickSetScale, an easily customizable macro tool for setting the scale of images aquired from specific microscope and camera setups.
• 1.39f, 12 October 2007
  • Michiel Schmid contributed an improved Process>Subtract Background command with new "Create Background", "Disable Smoothing" and "Preview" options.
  • Maximized windows use more of the screen on OS X and Windows.
  • When shrinking selections, Edit>Selection>Enlarge now works with selections touching the image edge.
  • File>Revert no longer deletes the selection.
  • Plugins>Compile and Run now runs compiled plugins (.class files) without the Java compiler (usually in tools.jar) being present, and, thanks to Johannes Schindelin, it uses com.sun.tools.javac instead of the deprecated sun.tools.javac.
  • On Linux, the preferences file (IJ_Prefs.txt) is saved in the .imagej directory and the menu font size is no longer set to 14 points.
  • The ImageCanvas.setDisplayList(Vector) method now accepts a list of ShapeRois with differing colors and line widths (example).
  • Added the File.openAsRawString(path) macro function. Refer to the First10Bytes and ZapGremlins macros for examples.
  • Added the COPY_ZERO_TRANSPARENT constant to the Blitter class.
  • Added the IJ.isMacro() method, which returns true if a macro is running or an IJ.run() method is executing.
  • Added the getInstanceColor() and setStroke() methods to the Roi class.
  • Fixed a bug that could cause the imageCalculator() macro function to return before the output window had opened.
  • Fixed a bug that could cause a boolean variable in a macro run() call to trigger the inclusion of other boolean variables.
  • Fixed a bug that caused an exception if showProgress() was called in a macro run from the command line using the -batch option.
  • Fixed a bug that could cause the image count to increase by one if the setBatchMode(true) macro function was called twice in succession.
• Nichole Jonas contributed the new search box on the ImageJ home page.
• The ImageJ home page has a new logo, created using the this macro.
• Piotr Wendykier has released Parallel Spectral Deconvolution, a multithreaded plugin that does 2D and 3D Tikhonov and TSVD image deblurring.
• 1.39e, 21 September 2007
  • Toolbar menu commands are now recorded.
  • The setLocation(x,y) macro function now moves non-image windows.
  • Added the getValue("foreground.color") and getValue("background.color") macro functions.
  • Added the setOption("OpenAsHyperVolume", boolean) macro function.
  • As a work around for a problem on Linux where dialog boxes are sometimes slow to open, run ImageJ using the Motif toolkit with
       java -Dawt.toolkit=sun.awt.motif.MToolkit -jar ij.jar
  • Fixed a bug, introduced in v1.38, that caused the threshold color to not be taken into account when saving in AVI format.
  • Fixed a bug that sometimes caused toolbar menus to not display currectly on Linux.
• Francois Aguet has created tutorial on how to use Apple's Xcode to develop ImageJ plugins.
• 1.39d, 23 August 2007
  • Added the "Gif Transparent Index" field to Edit>Options>Input-Output, which allows the user to specify the transparent color used for images saved in GIF format.
  • The File>Save As>Gif command now saves stacks as animated Gifs.
  • RoiManager calls in batch mode macros are faster, especially on Windows. The RoiManagerSpeedTest macro, for example, runs 10 times faster.
  • Edit>Selection>Rotate and the makeLine() macro function no longer convert coordinate values to integers.
  • Added seek(long) and getLongFilePointer() methods to the RandomAccessStream class.
  • Fixed bugs in Image>Stacks>Reslice
  • Fixed a bug that caused incorrect interpolated line profiles along image edges.
  • Worked around a JIT compiler bug that could cause Process>Filters>Convolve to throw exceptions on multi-processor Linux systems.
• Eckard Picht has released SparkMaster, a plugin for calcium spark analysis in confocal line-scan images.
• 1.39c, 9 August 2007
  • Added a "Set Color" button to the ROI Manager's More>>Options dialog that sets the color used in "Show All" mode.
  • The selection brush tool now adds to the selection when you click in it and subtracts from it when you click outside it. Or hold down the shift key to always add to the selection and the alt key to always subtract from it.
  • The MacroExtension interface, contributed by Shannon Stewman, allows plugins to add functions to the macro language. As an example, the Image5D_Extensions plugin adds functions to the macro language that deal with the Image5D plugin (querying and setting the channel, frame, display mode), and the Image5dMacros use these functions.
  • Added the exec() macro function for executing native commands and opening documents in other applications (examples). Credit to Curtis Rueden for the idea.
  • Fixed a bug, introduced in 1.38q, that caused TIFF stacks saved by the Image5D plugin to be corrupted.
  • Fixed a bug that caused an exception when an Image5D stack was duplicated.
  • Johannes Schindelin contributed a patch that provides a better error message when a method called by the call() macro function throws an exception and a patch that fixes bugs in the Roi Manager "Split" command.
  • Fixed a bug that caused 48-bit RGB TIFFs created by ImageJ to not open correctly in other applications.
  • Michael Schmid fixed a bug in Process>Binary>Watershed, introduced in v1.38c, that could cause particles to disappear. A test image is available.
• Gamaliel Isaac and Larry Dougherty contributed the ROI Adjust Tool, a plugin which allows the user to adjust the shape of a selection.
• The HyperVolume Maker macro creates a stack with labeled slices useful for testing 4D and 5D viewers and reconstructors such as Image5D, HyperVolume Browser, LOCI 4D Browser, TransformJ and Hypervolume Shuffler.
• XLi Digital Imaging has released a plugin (Windows only) for their megapixel USB 2.0 cameras.
• The Batch GLCM Measure macro is a wrapper for the GLCM_Texture plugin that allows batch processing of all the images in a directory.
• 1.39b, 23 July 2007
  • With FFT images, Analyze>Measure records the polar coordinates of point selections.
  • Added the More>>Options dialog to the Roi Manager, which contains an "Associate ROIs with Slices in 'Show All' Mode" checkbox.
  • Added a clone() method to the ImagePlus class.
  • Fixed a bug, introduced in v1.39a, that caused the drawString() function to fail on Windows when drawing non-antialiased text.
• The MeasureCumulativeDistances macro measures cumulative distances along a segmented line selection or between the points of a point selection.
• 1.39a, 20 July 2007
  • Added the "Avoid Interpolation" option to Image>Stacks>Reslice, based on a patch contributed by Adrian Daerr.
  • The setLocation() macro function now accepts optional width and height arguments.
  • ImageProcessor.drawString() no longer instantiates a java.awt.Frame, which caused an exception when running in "headless" mode.
  • Fixed a bug that caused missing semicolons in if-else statements to not be detected.
  • Fixed a bug, introduced in v1.38, that caused the makeLine() macro function to fail when the line length was zero.
  • Fixed a bug that caused table updates using print("[Table]", "\\Updaten:"+values) to fail when n was greater than 25.
• The Process Virtual Stack macro demonstrates how to process the images in a virtual stack opened using File>Import>Image Sequence.
• Christophe Klopp has released MAI Simulator, a plugin that generates simulated DNA microarray images.
• The Stack Moving Average macro does a 3, 5 or 7 slice moving average in the z direction of a stack.
• Readers of Scientific Computing magazine voted to gave ImageJ a Bronze Award in the imaging software catagory.
• Johannes Schindelin contributed the TypeTheSky macro, which types a message using Lisa Rienermann's "Type The Sky" alphabet.

Version 1.38, 9 July 2007

• 1.38x, 9 July 2007
  • Fixed a bug, introduced in v1.38u, that caused the Analyze>Calibrate command to fail.
  • Fixed a bug that caused a macro error if the File>Import>Results dialog was canceled.
  • Fixed a bug that caused image names to be truncated when saving if the name contained a period followed by a digit or more than four characters.
  • Fixed a bug that caused stack metadata to be lost after use of the Image>Adjust>Canvas Size command.
• Philippe Carl contributed the Azimuthal Average plugin.
• 1.38w, 2 July 2007
  • Fixed a bug, introduced in v1.38u, that caused the particle analyzer to fail to work on stacks.
  • Fixed bugs, introduced in v1.38u, that caused the TransformJ plugins and the Dynamic Threshold plugin to throw exceptions.
• 1.38v, 29 June 2007
  • Added preview and grid options to Image>Rotate>Arbitrarily.
  • Added the Help>Installation command.
  • Added the get(int), set(int,int), getf(int), setf(int,float) and getPixelCount() ImageProcessor methods for reading and writing pixels using a pixel array index instead of x and y coordinates.
  • Fixed bugs in Image>Adjust>Threshold, and the setThreshold() and setAutoThreshold() macro functions, that caused the threshold to not be set correctly on blank 16-bit and 32-bit images.
  • Fixed bugs that could cause Process>Binary>Convert to Mask to fail on 16-bit and 32-bit stacks with blank slices, or with high dynamic range 16 and 32 bit images.
• 1.38u, 15 June 2007
  • Michael Schmid added previewing and multiprocessor support (when processing stacks) to the Gaussian Blur, Median, Mean, Minimum, Unsharp Mask and Variance filters, and increased the speed of these filters by up to 100 times.
  • Changed the name of the Edit>Options>Memory command to Memory and Threads and added the "Parallel Threads for Stacks" field, which defaults to the number of available processors.
  • Michael Schmid contributed the new Process>Noise>Remove Outliers filter.
  • Added a preview option and multi-processor support to Process>Filter>Convolve and removed the square kernel restriction.
  • Results tables are no longer limited to 150 columns.
  • The makeLine() macro function now accepts a 5th argument that specifies the line width.
  • Fixed a bug that caused entries in the File>Open Recent submenu to not be stored correctly in the preferences file if they contained non-ascii characters.
  • Fixed a bug that could cause an exception when using the Edit>Selection>Create Selection command.
  • Ulf Dittmer fixed a bug on Mac OS X that could cause the same image to be opened repeatedly when several images were dragged onto the ImageJ icon.
  • Fixed a bug, introduced in v1.38s, that caused a delay when running a command for the first time.
  • Fixed a bug on Windows that caused the Prefs.getHomeDir(), Menus.getPlugInsPath(), Menus.getMacrosPath() methods and the getDirectory() macro function to sometimes return paths containing double path separators.
  • Fixed a bug that caused File>Export>Image Sequence to fail when "Use Slice Labels as File Names" was enabled and the file names contained multiple periods.
  • Fixed a bug that sometimes caused text files containing the word "macro" to not open.
  • Fixed a bug that could cause the ROI Manager "Multi Measure" function, and the Multi_Measure plugin, to fail when the were a large number of ROIs.
• 1.38t, 25 May 2007
  • Fixed a bug, introduced in v1.38s, that caused newly created horizontal or vertical straight line selections to disappear.
  • Fixed a bug that caused File>Revert to fail on images that had been re-saved in TIFF format.
• 1.38s, 24 May 2007
  • The Gaussian Blur and Unsharp Mask filters now display a single progress bar instead of two or six.
  • When saving in JPEG format, the current quality setting (0-100) is displayed in the title bar of the "Save As" dialog.
  • Added the ROI Manager More>>Remove Slice Info and More>>Specify commands.
  • The ROI Manager Measure command no longer displays a "Process Stack?" dialog.
  • ImageJ now opens gzipped FITS (".fits.gz") and raw (".gz") images.
  • The File.directory and File.name macro functions now return the path to the last file dragged and dropped on the ImageJ window.
  • Added the getDimensions(width,height,channels,slices,frames) macro function.
  • Added the IJ.getScreenSize() method.
  • Added a getBounds() method to the Line class.
  • Added the OpenDialog.setLastDirectory() and OpenDialog.setLastName() methods.
  • Added the setInitialParameters(double[]) method to the CurveFitter class.
  • Fixed bugs that could cause ImageJ to hang, especially when using the Sync_Windows plugin or when quitting.
  • Fixed a bug that sometimes caused File>New>Image and File>Open to display duplicate dialog boxes when invoked by typing ctrl-n or ctrl-o.
  • Fixed a bug that caused dialog boxes to be incorrectly positioned on multi-monitor Linux systems.
  • Fixed a bug that caused the standard deviation calculated by Analyze>Tools>Curve Fitting to be incorrect.
  • Fixed a bug that could cause an exception when opening 16-bit grayscale PNGs.
  • Fixed a bug that caused directories with spaces in the path to fail to open when dragged and dropped on the ImageJ window.
  • Fixed a bug that could cause an exception in the particle analyzer when processing a stack with more than 10,000 particles and "Add to Manager" was checked in the dialog box.
  • Fixed a bug, introduced in v1.38q, that caused stacks with blank slice labels to not be correctly saved in TIFF format.
  • Fixed a bug, introduced in v1.38n, that could cause an exception when opening multiple 48-bit tiff images and stacks using JFileChooser.
• The Concentric Circles plugin displays concentric rings in a non-destructive overlay.
• The Save Virtual Stack As 8-bit TIFFs macro demonstrates how to process and save a virtual (disk resident) stack.
• 1.38r, 11 May 2007
  • Michael Schmid contributed a faster and more accurate Gaussian Blur filter (description) and an improved Unsharp Mask filter (source code) that shows how easy it is to write a plugin that processes all ImageJ data types (8-bit, 16-bit, float and RGB) by using the new CONVERT_TO_FLOAT flag.
  • Added the File>Import>Results command, which opens an ImageJ Results table, or any tab or comma-delimited text file. This command is based on Jerome Mutterer's Import_Results_Table macro.
  • Thanks to Johannes Schindelin, the Edit>Selection>Create Selection and Enlarge commands create selections that are displayed, analyzed and processed faster because they consist of fewer line segments.
  • Added a "Smooth" checkbox to the "Fonts" window, which is opened by double clicking on the text tool.
  • Added an "Unscale" button to the Analyze>Set Scale dialog box.
  • Added a "No Image Border" option to the Edit>Options>Appearance dialog box.
  • In theAnalyze>Analyze Particles dialog box, the "Size" parameter is in pixels if the image's unit of lengh is "inch".
  • ImageJ switches to the rectangle tool when the user clicks in the CP (Color Picker) window and the current tool is the eye dropper.
  • When creating polygon and line selections, the length and angle of the current segment are based on uncalibrated coordinates when the alt key is down.
  • Added an Image>Show Info description (press "i") to the "HeLa Cells" sample image.
  • File>Save As>FITS now saves 8-bit (by converting to 16-bit) and signed 16-bit (by converting to float) images.
  • Added the String.resetBuffer, String.append, String.copy and String.paste macro functions (documentation).
  • The PointRoi.contains(x,y) method now returns true when (x,y) is one of the points in the current point selection.
  • Added the non-static setInstanceColor() method to the Roi class. This color overrides the global color set by the static Roi.SetColor() method.
  • Added the ImageJ.getArgs() method, which returns the command line arguments passed to ImageJ.
  • Fixed a bug that caused re-opened composite selections to not work correctly with the ROI Manager on Java 1.6.
  • Fixed bugs that caused the "Set" option in Image>Adjust>Contrast/Brightness and Image>Adjust>Threshold to not be recorded correctly with 32-bit (float) images.
  • Fixed a bug that sometimes caused the progress bar to not be display when opening slow to load images.
• Peng Xi contributed the X Shifter plugin, which corrects the pixel mismatch of confocal spot scanning images or stacks.
• Gilles Carpentier contributed the Image, Stack and Timelapse Arrow Labelling toolset (online documentation), which allows the user to draw arrows on images and stacks. Requires ImageJ 1.38p or later.
• 1.38q, 27 April 2007
  • Added the "Use Virtual Stack" option to the File>Import>Image Sequence dialog box.
  • Double click on (the point tool) to change the selection color.
  • Added First Frame and Last Frame fields to the Image>Stacks>Animation Options dialog box, and also the alt+\ keyboard shortcut for opening this dialog.
  • The backslash ("\") keyboard shortcut for starting/stopping animation now works with European keyboards.
  • ZIP-compressed TIFF and DICOM images open faster.
  • File>Save As>Tiff now stores metadata and lookup tables before the image data, resulting in faster loads when opening TIFFs from a URL or ZIP archive.
  • Press "i" (Image>Show Info) to get a description of the File>Open Samples>T1 Head and T1 Head Renderings sample images.
  • The roiManager("Open", path) macro function displays a file open dialog if the second argument is "".
  • Added the File.name and File.directory macro functions, which provide the name and directory path of the last file opened using open(), saveAs(), File.open() or File.openAsString().
  • Added the OpenDialog.getLastName() and OpenDialog.getLastDirectory() methods.
  • Added the openZip(path) method to the Opener class and removed the ij.plugin.Zip_Reader class.
  • Added the getCount() and getRoisAsArray() methods to the RoiManager class.
  • Increased the maximum number of vertices a polygonal selection saved using File>Save As>Selection can have from 32,767 to ~60,000.
  • Fixed a bug that could cause particle analyzer measured areas to be slightly larger than expected with particles with holes, or a composite selection with holes, and "Include Holes" was not checked in the dialog box.
  • Fixed a bug, introduced in 1.38a, that sometimes prevented selection from being added to the ROI Manager.
  • Fixed a bug that caused the ImageJ applet to not work correctly when restarted after being terminated by closing the browser window.
  • Fixed a bug that could cause an exception when opening BMP files with names not ending in ".bmp".
  • Fixed a bug that caused ImageJ, when running as an applet, to not load StartupMacros.txt if the URL did not end in "index.html".
• Ignacio Arganda-Carreras has released SplineDeformationGenerator, a plugin that generates deformations (fisheye, elastic, barrel/pincushion, perspective, etc.) based on cubic B-splines.
• James Norman has released the RoiPushTool, a macro/plugin that allows users to "push" an area of an established selection in any direction, and the WindowlevelTool, a macro/plugin that allows users to adjust the window/level by dragging the mouse over the image.
• 1.38p, 13 April 2007
  • Hold down the alt key when moving through the slices in a stack and the B&C histogram is automatically updated.
  • Process>Binary>Make Binary no longer ignores the "Black Background" flag in the Process>Binary>Options dialog box.
  • Added "Bat Cochlea Renderings" to the File>Open Samples menu. These are 3D renderings of "Bat Cochlea Volume", one created using Image>Stack>3D Project and the other using the VolumeJ plugin.
  • Added "T1 Head Rendering" to the File>Open Samples menu, an animation of the "T1 Head" dataset created using VolumeJ.
  • Fixed a bug that caused the histogram in the B&C window to not be updated after switching to a different stack slice.
• 1.38o, 12 April 2007
  • Added mouse wheel support for TextWindows ("Results", "Log", etc.).
  • Added "Calculate Threshold for Each Image" and "Black Background" checkboxes to the dialog displayed by Process>Binary>Make Binary and Convert to Mask when processing stacks.
  • Analyze>Analyze Particles now appends summaries for single images to a table similar to the table used for stack summaries.
  • Added a "None" choice to "Output Types" in the Process>Binary>Find Maxima dialog.
  • ZIP compressed TIFF and DICOM images open faster and use less memory when downloaded from a URL.
  • Added "T1 Head" to the File>Open Samples menu, a 256x256x129 T1 weighted MRI dataset courtesy of Jeff Orchard (www.cs.uwaterloo.ca/~jorchard/mri/).
  • Thanks to a patch submitted by Shannon Stewman, the roiManager("Save", path) macro function displays a file save dialog if the second argument is "".
  • Fixed a bug that could cause an exception when using Analyze>Tools>Calibration Bar on Mac OS X.
  • Fixed a bug, introduced in v1.37, that caused the flood fill tool to not work correctly on floating-point images.
  • Fixed a bug that caused the flood fill tool to sometimes fail when doing 4-connected filling of objects with holes.
  • Fixed a bug that could cause some TIFF stacks with "white is zero" photometic interpretation tags to not open correctly.
  • Worked around a bug that sometimes caused the roiManager("select",i) macro function to fail on Mac OS X.
  • Fixed a bug in Process>Binary>Find Maxima that caused it to not work as expected if the image had non-area selection (e.g., points) .
  • Fixed a bug that caused File>Save As>BMP to write an incorrect bfSize value to the file header when saving RGB images.
• Gilles Carpentier contributed the SelectionColorMenuTool macro, which adds a toolbar menu for changing the selection color.
• Michael Schmid contributed Blend Images, a sample plugin that blends one image with another. This verbosely commented plugin works with all image types because it uses the ip.toFloat(i,fp), ip.setPixels(i,fp) and ip.getNChannels() methods added in ImageJ 1.38n.
• Jerome Mutterer contributed the RGB Profiles Tool macro, which draws red, green and blue line profiles on the same plot.
• 1.38n, 30 March 2007
  • Added the Image>Color>Convert to Composite command, which converts an RGB image, or stack with 2-7 slices, into a composite color stack. Use Edit>Adjust>Brightness/Contrast (shift-c) to adjust the brightness/contrast of each channel of the composite stack. Use Image>Color>Convert Stack to RGB to convert to RGB. Use Image>Color>Show LUT to plot the current channel's LUT, or Image>Color>Edit LUT to edit it. Use Image>Duplicate to extract a single channel or to convert to an ordinary stack. 48-bit RGB TIFFs open as 16-bit composite color stacks and File>Save As>Tiff saves 3-slice, 16-bit composite stacks as 48-bit RGB TIFFs.
  • Added the File>Open Samples>HeLa (1.3M 48-bit RGB) sample image, a 16-bits/channel composite color image of HeLa cells with red lysosomes, green mitochondria and red nucleus, contributed by Tony Collins.
  • Added the File>Open Samples>Cardio (768K RGB DICOM) sample image, a 3D heart reconstruction from a Siemens Sensation CT scanner, contributed by Oliver Lazar.
  • Added the "Sort Names Numerically" checkbox to the File>Import>Image Sequence dialog box.
  • Downloading of ZIP files using File>Import>URL can be aborted by pressing the esc key.
  • Added the Analyze>Gels>Re-plot Lanes and Draw Lane Outlines commands, and enabled "Invert Peaks" in Gel Analyze Options by default.
  • The gel analyzer automatically draws lane outlines in a non-destructive graphics overlay.
  • Macro functions defined in ImageJ/macros/Library.txt are appended to macro files when they are run or installed.
  • The setColor macro function accepts the same string constants as Plot.setColor ("black", "blue", "cyan", "darkGray", "gray", "green", "lightGray", "magenta", "orange", "pink", "red", "white" or "yellow").
  • File>Import>URL can now open ZIP compressed DICOMs (e.g., https://imagej.net/ij/images/ct.dcm.zip).
  • Added the toFloat(i,fp), setPixels(i,fp) and getNChannels() methods to the ImageProcessor class, courtesy of Michael Schmid (example).
  • Added a constructor to the DICOM class that accepts an InputStream.
  • Johannes Schindelin contributed a patch that allows ImageJ to work with .class plugins that have the main class in a package as long as the package name and subdirectory name are the same.
  • Fixed a bug that caused File>Import>URL to not correctly open planar RGB TIFFs and DICOMs (e.g., https://imagej.net/ij/images/cardio.dcm).
  • Fixed a bug that caused Image>Show Info to not display the URL of images loaded using File>Import>URL.
  • Joachim Walter fixed a bug in the FFT_Filter plugin (Process>FFT>Custom Filter) that caused incorrect calculation of the filter from structure sizes.
• Jerome Mutterer contributed the SinglePanelGelAnalyzer macro, which uses the Plot functions and the Roi Manager to plot multiple gel lanes in a single window.
• The SampleImagesMenu macro adds a menu to the tool bar with all the images, LUTs and macros in a specified directory.
• Uwe Walschus created a PDF version of the ImageJ macro language documentation.
• 1.38m, 16 March 2007
  • Added a "Multi Measure" function to the ROI Manager, based on a similar function in Bob Dougherty's Multi_Measure plugin.
  • The selection brush tool is faster and uses fewer CPU resources thanks to code contributed by Albert Cardona.
  • Added "Width" and "Height" fields and "Menu Bar" and "Monospaced Font" checkboxes to the Plugins>New... dialog, which are used by macros when opening text windows and tables.
  • The print() macro function outputs to a text window (example1, example2) or to a table (example3, example4) if the first argument is a window title in brackets.
  • Added the getInfo("image.subtitle"), getInfo("slice.label"), getInfo(key), getList("window.titles") (example) and getList("java.properties") (example) macro functions.
  • Added the ImageWindow.createSubtitle() and ImageProcessor.getSnapshotPixels() methods.
  • Added a constructor to the DICOM class that accepts a BufferedInputStream.
  • Fixed a bug in Image>Stacks>3D Project that caused "Brightest Point" projections with "X-Axis" rotation to not work correctly.
  • Fixed a bug the caused the selection brush tool to fail with non-area selections.
  • Fixed a bug that sometimes caused "setThreshold(min,max)" to be recorded when Convert to Mask was run from a macro.
• Michael Schmid contributed FilterTester, a macro that tests whether ImageJ commands produce the same results as previously and that they work correctly with stacks.
• Michael Doube released Volume Slicer, a macro for setting up batch-mode rendering jobs that run Kai Uwe Barthel's Volume Viewer plugin.
• Michael Schmid contributed the FindStackMaxima macro, which runs Process>Binary>Find Maxima on all the images in a stack, creating a second stack for the output images.
• 1.38l, 5 March 2007
  • Histogram and Plot windows are ignored when tabbing through open images.
  • The maximize button works better with zoomed images.
  • On Linux, the ImageJ window, menus and dialog boxes consistently use a light gray background.
  • Added the ImageJ(Applet, int) constructor to the ImageJ class, where the second argument can be ImageJ.STANDALONE or ImageJ.EMBEDDED.
  • Added the ImageJ.exitWhenQuitting(boolean) method.
  • Added the ContrastAdjuster.update() method, which is used by File>Revert to update the "B&C" window when the user restores the original image.
  • Added the ImageProcessor.setSnapshotCopyMode(boolean) method. ImageProcessor.getPixelsCopy() no longer returns a reference to the snapshot buffer unless this method has been called.
  • Fixed a bug, introduced in v1.38k, that caused most filters in the Process>Filters submenu to fail when applied to a stack.
• 1.38k, 1 March 2007
  • The ability to cycle through the open images by pressing the tab key is working again.
  • Commands that open a Web page, such as Help>ImageJ Website, now work on Linux systems that have any of the following commands: netscape, firefox, konqueror, mozilla, opera, epiphany or lynx.
  • The slider buttons in the Image>Adjust>Brightness/Contrast tool use smaller increments with 16 and 32 bit images.
  • The "Auto" option in Image>Adjust>Brightness/Contrast works better with images that have a solid background.
  • File>Revert updates the Image>Adjust>Brightness/Contrast tool.
  • The "Use JFileChooser to Open/Save" option in Edit>Options>Input/Output is no longer saved in the preferences file on OS X.
  • Changed the name of Edit>Options>Display to Edit>Options>Appearance.
  • Added the "Menu Font Size" field to Edit>Options>Appearance. Set the size to "0" to use the Java default menu font size.
  • The directory path, returned by the getDirectory("image") macro function, is now retained by Image>Stacks>Convert Stack to Images.
  • Fixed a bug in Image>Stacks>Reslice that caused a black first slice when starting at the bottom or right.
  • Fixed a bug that could cause an exception when using the roiManager() macro functions.
  • Fixed a bug that sometimes caused the sliders in the "B & C" and "Threshold" windows to blink on Windows.
  • Fixed a bug that caused Edit>Selection>Create Mask to fail if "Black Background" in Process>Binary>Options and "Use Inverting LUT" in Edit>Options>Appearance were both enabled.
  • Fixed a bug that caused Edit>Selection>Restore Selection to sometimes fail if the size of the selection was the same as the size of the image.
  • Fixed a bug that caused Edit>Selection>Restore Selection to fail in batch mode macros.
• Rainer Heintzmann has released View5D, an ImageJ plugin, Matlab plugin and Java applet that interactively displays of up to 5 dimensional volumetric datasets.
• Nenad Amodaj and Nico Stuurman have released Micro-Manager, an open source software package for microscope image acquisition that runs as an ImageJ plugin. Micro-Manager controls a number of cameras, shutters, filter wheels, stages and other devices, enabling acquisition of time-lapses, z-stacks and multi-channel images.
• The Save As JPEG macro creates a command that allows the user to press "j' to set the compression level and save in JPEG format.
• 1.38j, 12 February 2007
  • Replaced the Window/ImageJ[enter] command with Show All. Press shift-f, the shortcut for Show All, to make all windows associated with ImageJ visible.
  • Clicking with the angle or segmented line tool deletes the current selection. Click a second time to start creating an angle or line selection.
  • The Image/Type/16-bit and Image/Type/32-bit conversion commands work with RGB images.
  • File/Import/Image Sequence skips files with names ending in ".lut", ".roi" or ".pty".
  • Thanks to Robert Dougherty, worked around a bug that sometimes caused the first numeric field in a dialog box to not be editable on Intel Macs.
• 1.38i, 31 January 2007
  • When running on Java 1.6, ImageJ opens RGB images using half as much memory.
  • The Roi Manager restores selections located outside the image boundary to the center of the image.
  • Fixed a bug that caused filter plugins that set the NO_CHANGES flag, but not NO_UNDO, to use extra memory.
  • Fixed a bug in Image/Color/RGB Split that could cause it to leak memory.
  • Fixed a bug that coused the roiManager("reset") macro function to not work correctly.
• 1.38h, 25 January 2007
  • Process/Filters/Gaussian Blur now works with non-integer radii thanks to code contributed by Kai Uwe Barthel.
  • When running on Java 1.6, ImageJ opens 8-bit images using half as much memory.
  • Added the setOption("DisableUndo", true) macro function. On Java 1.6, with this option enabled, ImageJ can open and process an 8-bit image using one third as much memory.
  • Added the Plugins/Utilities/Reset command, which replaces Plugins/Utilities/Unlock Image.
  • Added eight links to the ImageJ website to the Help menu.
  • The "B&C", "Threshold" and "Results" windows remember their screen locations.
  • If no images are open, images less than one half the width of the screen open centered on the screen.
  • Added a Duplicate command to the Edit menu of the "Results" window and to the drop down menu that appears when you right click on the "Results" window.
  • Added the shift-x keyboard shortcut for the Image/Crop command.
  • Edit/Paste displays text on the system clipboard in a text window if the internal clipboard is empty and there is not an image on the system clipboard (example).
  • Image windows no longer move to the left edge of the screen after being cropped or resized.
  • The Plugins/Utilities/ImageJ Properties command displays more information.
  • Added a constructor to the ParticleAnalyser class that accepts minCircularity and maxCircularity arguments.
  • Fixed bugs that sometimes caused scroll bars in stack windows, in the "Results" window and in the "Log" window to blink on machines running Windows.
  • Fixed a bug that could cause negative calculated mean values with 8-bit images larger than 8MB.
  • Fixed a bug that could cause an exception when the ParticleAnalzer class was called from a plugin.
• FCLab released a plugin for their FC1000 and FC2000 USB 2.0 cameras.
• Grant Harris released CamAcqJ, a plugin that works with QImaging Retiga cameras on Windows, and a tutorial that explains how to use the NetBeans IDE for plugin development.
• 1.38g, 12 January 2007
  • Michael Schmid contributed an enhanced Plot class (used by Analyze/Plot Profile) that adds grid lines to plots. This feature can be turned off using the "Draw Grid Lines" checkbox in the Edit/Options/Profile Plot Options dialog box.
  • Added support for mouse wheel scrolling in image windows. Hold the space bar down to scroll horizontally.
  • Added the "Label Points" checkbox to the Edit>Options>Point Tool dialog.
  • Image/Stacks/Reslice is faster and now works with single images (e.g., you can turn an image on its side).
  • On Windows Vista/Java 1.6, tool icons are always drawn using antialiasing.
  • Added the setAdditionalFunctions() method to the Interpreter class, which allows plugins to add functions and global variables to the macro language.
  • A ResultsTable displayed in a window not named "Results" can now be edited using Edit/Cut and Edit/Clear.
  • ImageJ displays an error message in the "Log" window if the system ResultsTable is displayed in a window not named "Results".
  • Added the setOption("QueueMacros", boolean) macro function (example).
  • Fixed a bug that caused values written to the "Results" window by a macro or plugin to be lost without warning if the window was closed or the Analyze/Measure command was used.
  • Fixed bugs that caused the getImageID and getTitle macro functions to not be aware of images opened by plugins and menu commands.
  • Fixed a bug that caused the d2s() macro function to not work as expected if the resulting string was longer than 12 characters.
  • Fixed a bug that sometimes caused the progress bar to be left in an invalid state by batch mode macros.
• The AnimatedGaussianBlur macro demonstrates how to create an animation that shows how an image changes with different filter parameters.
• Ibidi (www.ibidi.de) released Chemotaxis and Migration Tool, a plugin for analyzing chemotactical or migration data obtained by video microscopy.
• Added a "Search ImageJ Website Using Google" option and a "Search Mailing List Archives" link to the to the Search page at rsb.info.nih.gov/ij/search.html.
• Michael Doube released Umis_Array, a macro designed to correlate mineralisation density information from an SEM image of bone and cartilage to nanoindentation modulus from a UMIS nanoindentation array.
• 1.38f, 22 December 2006
  • Added the File/Save As/FITS command, which is a stripped-down version Jennifer West's SaveAs FITS plugin.
  • Added support for FITS, PGM and PNG to the File/Save As/Image Sequence command.
  • Files opened using drag and drop are now added to the File/Open Recent menu.
  • Added the setOption("OpenUsingPlugins", boolean) macro function (example).
  • Fixed a bug that caused the isOpen() macro function to fail with images opened in batch mode.
• Johannes Schindelin released an alpha version of ImageJA (the 'A' standing for 'Applet'), an applet version of ImageJ that can be embedded into a web page. The ImageJA website is at imageja.sourceforge.net.
• Gilles Carpentier contributed the LSM Transmission Deblurring toolset (online documentation), which requires ImageJ 1.38e or later.
• The Calculate Mean plugin demonstrates how to use a mask to tally the values and number of pixels within a non-rectangular selection.
• 1.38e, 15 December 2006
  • As a shortcut for Image/Zoom/View 100%, press "+" with the alt key down.
  • Menus in the ImageJ window use a larger font (14 pt.).
  • Edit/Selection/Enlarge attempts to convert a composite selection into a polygon selection when a value of zero is specified.
  • Added the setCTable(float[],String) method to the Calibration class.
  • Added the setKeyDown("esc") macro function (example).
  • Added the setSelectionLocation(x,y) macro function (example).
  • The saveAs("Measuremens",filepath) macro function now works in batch mode.
  • Fixed a bug that could cause a plugin to fail if it called IJ.setTempCurrentImage() and IJ.run("Enlarge"), or any another command that is implemented using macro code.
  • Fixed a bug that caused the Edit/Selection/Enlarge command to fail if an image with the name "Mask" was open.
  • Fixed a bug that could cause macros that called run("Add Slice") to fail when not running in batch mode.
• Jennifer West and Ian Cameron published the paper Using the medical image processing package, ImageJ, for astronomy in the Journal of the Royal Astronomical Society of Canada.
• The PlotRadialMeanVersusAngle macro generates a plot of mean radial pixel value versus angle.
• 1.38d, 1 December 2006
  • Added a "Light Background" option to Process/Binary/Find Maxima.
  • Changed the "White Background" option in Process/Subtract Background to "Light Background". Macros that use the "white" keyword will continue to work.
  • Added the Prefs.setImageURL() method, which can be called from the "AutoRun" macro in the StartupMacros to specify the directory used to load the sample images.
  • Fixed a bug, introduced in 1.38c, that caused the Image5D plugin to generate a NoSuchMethodError exception.
• v1.38c, 28 November 2006
  • Added the Process/Binary/Find Maxima command, which is based on a plugin contributed by Michael Schmid.
  • The menu that pops up when you right click on an image can now be customized (example).
  • Michael Schmid contributed improved versions of the Process/Binary/Distance Map, Ultimate Points and Watershed commands.
  • Improved support for the maximize/minimize button in image windows.
  • Fixed a bug on Mac OS X and Linux, introduced in 1.38a, that sometimes prevented a window displaying a zoomed image from being enlarged.
• Dimiter Prodanov contributed the Float Morphology plugin, which does mathematical morphology operations (erode, dilate, open, close) on 32 bit float images.
• Volker Lohweg has made available the Inhomogen Isotropic Diffusion 2D plugin, designed as a discrete version of the Perona-Malik PDE.
• Gilles Carpentier contributed the LUTs, Macros and Tools Updater macro toolset.
• v1.38b, 16 November 2006
  • Added macro language support for toolbar menus (example).
  • Albert Cardona added Linux support for opening files dragged and dropped onto the ImageJ window and an option to open a dragged and dropped folder as a stack.
  • Added "Sort" and "Help" options to the ROI Manager.
  • File/Import/URL opens URLs that end in ".html#name" in the default browser.
  • The beginning control point of line selections is drawn using the selection color instead of white.
  • Image/Stacks/Convert Stack to Images now uses image names in the form "stack-0001", "stack-0002", etc., where "stack" is the name of the stack.
  • Image/Stacks/Z Project creates image names in the form "XXX_stack", where XXX is "AVG", "MAX", "MIN", "SUM", "STD" and "MED" and "stack" is the name of the stack.
  • Added the File.rename() macro function.
  • Increased the maximum number of macros that can be installed from 60 to 75.
  • Edit/Selection/Create Selection creates, if possible, a non-composite selection. The "Issue with ROI closing" workaround on the Documentation Wiki is no longer needed.
  • Fixed a bug that caused a delay on Mac OS X when dragging and dropping files onto the ImageJ window.
  • Fixed several bugs in Edit/Selection/Enlarge.
  • Fixed a bug that caused color 16-bit ASCII PPM/PGM images to not open correctly.
  • Fixed a bug that sometimes caused the "AutoRun" macro to be added to the Plugins/Macros menu.
  • Fixed a bug that caused Image/Stacks/3D Project to fail when called from a batch mode macro.
• The Convert Stack To Binary macro converts a stack to binary using thresholds calculated locally for each image.
• Michael Schmid contributed the Click Coordinates Tool macro.
• David Zachmeyer contributed the Close All Windows macro, which closes all open image windows.
• Michael Doube contributed the RadialScattergraph macro, which draws a radial scattergraph from a CSV (comma-separated values) list of angles and radii.
• v1.38a, 27 October 2006
  • ImageJ 1.38a requires Java 1.4.2 or later due to the addition of mouse wheel and maximize/minimize support.
  • Added support for the maximize/minimize button in the title bar of image windows.
  • Added scroll wheel support to stack windows and the ROI Manager.
  • When the the shift is key down, clicking and dragging with the zoom tool zooms to the selection.
  • Edit/Paste improvements: pastes from system clipboard if internal clipboard is empty; if no images are open, opens one and displays internal clipboard; improved Mac system clipboard support.
  • Analyze/Calibrate has better support for 16-bit images.
  • The ImageJ window is better positioned at startup when the preferences file is not found.
  • Newly opened images are better sized and positioned.
  • Alt key presses are recorded when using File/Open Next (Open previous) and Analyze/Plot Profile (Plot vertical profile).
  • The Image/Stacks/Z Project command uses shorter names for generated images.
  • Added the setOption("changes", boolean) macro function, which sets/resets the 'changes' flag of the current image.
  • The drawString() macro function supports multiple lines (example).
  • Underscores in Choice control labels in GenericDialogs are converted to spaces.
  • Fixed a bug in the selectImage(n) macro function that caused it to be very slow when n was greater than 1.
  • Fixed a bug in the ROI Manager that prevented a selection from being added to more than one stack slice.
  • Fixed a bug that sometimes caused File/Import/Image Sequence to not sort files in numeric order.
  • Fixed bugs in File/Import/Image Sequence that sometimes caused the estimated stack size to be incorrect.
  • Fixed a bug in the IJ.getDirectory() method that caused it to not return null when the user canceled the dialog.

Version 1.37, 13 October 2006

• Patrick Pirrotte released IJProxy, a plugin for setting the HTTP proxy settings used by ImageJ
• v1.37u, 6 October 2006
  • Lookup tables in the ImageJ/luts folder are added to the Image/Lookup Tables menu.
  • Added the "Add to Manager" option to Analyze/Analyze Particles.
  • Added the setOption("Show All", boolean) macro function.
  • Added the IJ.suppressPluginNotFoundError() method, used by HandleExtraFileTypes to better support the LOCI Bio-Formats plugin.
• v1.37t, 2 October 2006
  • Added the ">>" tool, a drop down menu for installing alternate macro tool sets or for reverting to the default StartupMacros set.
  • In the ROI Manager's "Show All" mode, click on label (selection number) to activate the corresponding selection.
  • Macros with names ending in "Action Tool" define tools that execute when the user clicks on the tool icon (examples).
  • Version information is displayed in the status bar when the mouse is over an unused tool.
  • Added the "Label" command to the ROI Manager.
  • The "AutoRun" macro now only runs when the macros in StartupMacros.txt are installed at start up.
  • A default StartupMacros set is loaded from ij.jar if it is not found in the macros folder.
  • "Thumbs.db" files are ignored when opening images.
  • Fixed a bug that caused the "Use Pointer Cursor" option in Edit/Options/Misc to be ignored when a macro tool was being used.
  • Fixed a bug that sometimes caused incorrect Plugins menu entries when using the -Dplugins.dir command line option.
• Erik Meijering has released MTrackJ, a plugin for manual tracking of moving objects and measurement of traveled distances and instant velocities.
• Guy Levy has released ParticleTracker, a plugin for multiple particle detection and tracking from digital videos.
• 24 plugins are now available on the ImageJ Documentation Wiki.
• The Tool Demo plugin demonstates how a plugin can add a tool to the ImageJ toolbar..
• Arne Seitz released a collection of Plugins for importing PerkinElmer UltraViewERS data into ImageJ.
• v1.37s, 19 September 2006
  • Added Analyze/Tools/ROI Manager "Show All" and "Fill" options. Click "Show All" to display all selections on the ROI Manager list. Click "Show All" again to stop displaying them. To move a selection, choose it from the list, click "Update", then move it.
  • Added the Plugins/Utilities/Search command.
  • Fixed a bug that could cause the "Record Starts" option to not work as expected when the particle analyzer was called from a plugin
• v1.37r, 7 September 2006
  • The three line selection tools now share a single toolbar slot. Right click on the tool icon to switch to a different tool.
  • Point selections are now displayed as white crosses.
  • The center of the point selection tool icon is drawn using the current selection color.
  • Uncompressed 1-bit TIFF stacks open correctly.
  • Clicking on "Open" or "Save" in the Process/Filters/Convolve dialog no longer causes the file-path to be recorded.
  • Double clicking on the freehand selection tool icon no longer displays the Set Measurements dialog.
  • Added the setOption() macro function.
  • Added the ImageCanvas.disablePopupMenu() method.
  • Added the PointRoi(x,y) constructor to the PointRoi class.
  • Fixed a macro bug that caused the precision of numeric variables passed to run() functions to be limited to four decimal places.
  • Fixed a bug that sometimes caused the rename() macro function to not work as expected.
• Patrick Pirrotte and Jerome Mutterer released LSMToolbox, a plugin for working with images acquired using Zeiss confocal microscopes.
• Patrick Pirrotte released IJUpdate, a plugin that supports upgrading/downgrading to different versions of ImageJ.
• Johannes Schindelin released the Scrollable StackWindow plugin, which adds mouse wheel support to stack windows.
• Gilles Carpentier contributed the Macros And Tools Updater tool, which looks for new and updated macros and tools, and installs them.
• Jerome Mutterer contributed the Version Checker macro, which uses the File.openUrlAsString() function added in 1.37q to verify that you are running the latest version of ImageJ.
• v1.37q, 30 August 2006
  • Added the Edit>Selection>Add to Manager command. Press 't', the shortcut for this command, to open the ROI Manager or to add a selection to it.
  • Added the "More>>" drop down menu to the ROI Manager with Combine, Split and Add Particles commands.
  • Messages displayed in the status bar are not overwritten until the cursor moves at least 12 screen pixels away from its location at the time the message was displayed.
  • The unit of time ("sec", "msec", etc.) can be entered into the "Frame Interval" field of the Image/Properties dialog box.
  • Added the "Interpolate Line Profiles" checkbox to the Edit/Options/Profile Plot Options dialog box.
  • Added the roiManager("Select All"), roiManager("index") and File.openUrlAsString() macro functions.
  • Added getTimeUnit() and setTimeUnit() methods to the Calibration class.
  • The Calibration class implements the Cloneable interface.
  • File/Save As/Image Sequence not longer saves the file name in the TIFF header as an "Info" property.
  • Fixed a bug that could cause File/Import/Image Sequence to fail on Windows XP systems with directories containing hidden "Thumbs.db" files.
  • Fixed bugs in the ImageWindow class that caused incorrect behavior when it was used to replace an existing window containing a zoomed image or an image with a selection.
  • Fixed a bug that could result in a blank, non-functional image when the close() macro function was called in batch mode. (1.37p)
• Jerome Mutterer contributed the Snake macro set, which demonstrates advanced macro programming techniques.
• Johannes Schindelin contributed the 3D Angle Tool.
• Philippe Carl contributed the Radial Profile Extended plugin.
• Dimiter Prodanov contributed the JCalc plugin, a simple calculator that demonstrates how to write a PlugInFrame.
• v1.37o, 15 August 2006
  • Added a "Background" and "Serif Font" options to Analyze/Tools/Scale Bar, based on code contributed by Divakar Ramachandran.
  • Fixed a bug, introduced in v1.37n, that caused the particle analyzer's "Record Starts" option to fail.
• Johannes Schindelin contributed a JNLP file (rsb.info.nih.gov/ij/ImageJ.jnlp) that runs ImageJ using Java Web Start and patches that allow plugins to run. (The plugins and macros folders are assumed to be in the ImageJ folder in the users home directory.) Another link for running ImageJ using Web Start is available at rsb.info.nih.gov/ij/applets.html.
• v1.37n, 11 August 2006
  • The "zoom indicator", in the upper left corner of magnified images, shows what portion of the image is currently displayed.
  • The spatial scale of profile plots is now set and the cursor coordinates are displayed in the status bar.
  • Histogram and profile plot windows are centered on the screen and no longer have the line of information above the image.
  • Image/Stacks/Plot Z-axis Profile now correctly displays the "Slice" value in the Results window.
  • The "plugins.dir" property, used to specify the parent of the plugins and macros directories, is now recognized when there is no "ImageJ" window.
  • Drawing text on images is faster on some Linux systems.
  • The default headings are no longer assigned to a ResultsTable when it is created or reset.
  • Added the ResultsTable.setDefaultHeadings() method.
  • Fixed a bug that could cause incorrect text display on some Linux systems.
  • Fixed bugs that could cause an exception when importing a DICOM series, especially one with more than 10,000 images.
  • Fixed a bug that could cause the selectImage(id) macro function to fail if there was another open image with the same title as the one being selected.
  • Fixed a bug that could cause columns added to the Results table using setResult() or rt.setValue() to not appear in the correct order.
• Balaji contributed the Time Series Analyzer plugin.
• Jonas Wilson-Leedy and Rolf Ingermann contributed the Computer Assisted Sperm Analyzer plugin.
• v1.37m, 28 July 2006
  • Histogram and plot windows are centered on the screen and no longer have the information line above the image.
  • The pixel value unit of 32-bit images can be set in the Analyze/Calibrate dialog box.
  • Drawing of text on images on Linux is much faster.
  • Fixed a bug that could cause the selectImage() and selectWindow() macro functions to fail if the image being selected and another image had the same name.
  • Fixed a bug that could cause an exception when opening a DICOM series using File/Import/Image Sequence
  • Fixed a bug that caused the "Slice" parameter to not be displayed correctly by Image/Stacks/Plot Z-axis Profile.
• Ignacio Arganda-Carreras has made available bUnwarpJ, a plugin for bidirectional elastic registration of two images.
• Jerome Mutterer contributed the Calculator Tool macro.
• v1.37l, 20 July 2006
  • Image/Selection/Create Mask and Process/Binary/Convert to Mask create black background masks if "Black Background" is checked in the Process/Binary/Options dialog box.
  • "Reset" in Image/Adjust/Threshold resets the histogram and threshold limits to the current slice. If the alt key is down, it resets based on the histogram of the entire stack.
  • Plugins/Edit opens macro files with ".ijm" extensions.
  • Plugins in jar files that use the package statement are installed on startup.
  • IJ.getDirectory() calls are recorded.
  • Fixed a bug that caused "Save" of a single selection in the ROI Manager to fail if no image was open.
  • Fixed a bug, introduced in v1.37i, that caused Image/Color/Convert Stack to RGB to fail with 8-bit stacks.
  • Fixed a bug, introduced in v1.37k, that caused the setKeyDown macro function to not work as expected with makeRectangle, makeOval, makePolygon and makeSelection.
• Gilles Carpentier contributed the Macro Plugin Shortcuts Tool, which makes plugin shortcuts for macros and tools.
• Discovering Image Processing for ImageJ is now available from the Center for Image Processing in Education.
• Patrick Pirrotte has written a guide that explains how to develop plugins using Eclipse.
• v1.37k, 14 July 2006
  • Added the selection brush tool, based on Johannes Schindelin and Tom Larkworthy's ROI Brush Tool. It shares a toolbar slot with the oval selection tool, so you have to double click, or right click, on that tool to activate it.
  • Renamed the Process/Binary/Threshold command to Make Binary and removed the option to apply the threshold to only one slice in a stack.
  • Added the Process/Binary/Convert to Mask command, which is similar to Make Binary but always creates images with white (0) backgrounds and inverting LUTs.
  • Renamed Edit/Options/Images to Edit/Options/Display.
  • Added the "Double Buffer Selections" option to the Edit/Options/Display dialog, based on code contributed by Erik Meijering. This option reduces flicker when working with complex selections but it also increases memory usage and slows screen updates. It is not needed on Mac OS X, which has built in double buffering.
  • Added the "CT" sample image.
  • ImageJ opens a DICOM (.dcm) image contained in a ZIP archive.
  • Windows and Linux users can select multiple items in the ROI Manager by holding down the shift key.
  • File/Import/URL opens files ending in .html or .htm in the default browser.
  • Image/Stacks/Make Montage saves the number of rows and columns as an image property that can be retrieved by macros using the getMetadata function.
  • The ImagePlus.setRoi() method no longer erases the previous selection, so macros like CircularSelectionTool that continuously draw selections are less likely to flicker.
  • The run() macro function does the equivalent of setKeyDown("none") before returning.
  • Calling setBatchMode("exit & display") in a macro displays all open batch mode images and exits batch mode.
  • Calling roiManager("Split") in a macro splits a composite selection into its components.
  • ImageJ, when running on Mac OS X, is less likely to hang while quitting.
  • A better message is displayed when an class not found error occurs while a plugin is being loaded.
  • Fixed a bug in the getDirectory() function that could cause it to fail when selecting a root directory on Windows (e.g., "D:\").
  • Fixed a bug that caused Edit/Draw to incorrectly draw composite selections.
• The Sine/Cosine Table plugin demonstrates how to add values to the ImageJ Results Table.
• Johannes Schindelin contributed the Topolines macro, which creates a selection whose outlines are topographic lines.
• Jerome Mutterer contributed the HDR Explorer Tool macro for viewing High Dynamic Range Images. It adjusts the display range to local min and max, a little like what the eye does when scanning a scene.
• The SelectionIntersection macro creates the intersection of two ROI Manager selections.
• Cyndy Erickson and Janet Campbell at the University of New Hampshire Coastal Ocean Observing Center have written a 37 page PDF tutorial with the title "Hands-on Tutorial on How to Access and Work with Remote Sensing Images Using ImageJ".
• Gilles Carpentier contributed the URLtools macro set, which adds online resources to the ImageJ tool bar.
• Jerome Mutterer contributed the HueRotation macro, which rotates the hue values of an RGB image by a specified angle.
• v1.37j, 29 June 2006
  • Added the Edit/Selection/Create Selection command, based on the Threshold_To_Selection plugin contributed by Johannes Schindelin. This command creates a composite selection from a thresholded image or a binary mask.
  • Send commands like "\\Clear" and "\\Update:text" to the Log window to clear it or update its contents. Refer to the LogWindowTricks macro for an example.
  • Error and message dialogs use a larger font.
  • Added the get(x,y), set(x,y,value), getf(x,y) and setf(x,y,value) methods to the ImageProcessor class. The get() and set() methods read/write pixels as integers, and getf() and setf() read/write pixels as floats. Refer to the Image Inverter plugin for an example.
  • Added the TextPanel.clear() method.
  • Added the "CT" sample image (signed 16-bits with DICOM tags).
  • Fixed a bug that caused File/New/Image to sometimes create incorrect 8-bit and RGB "Ramp" images.
  • Fixed a bug that caused macros with braceless if-else statements containing calls to built in string functions that returned null to fail.
  • Fixed a bug, introduced in 1.35p, that caused macro calls to Image/Properties to fail to set the voxel depth.
• Jonathan Jackson contributed the Concatenate plugin, which concatenates two or more images or stacks.
• Johannes Schindelin and Tom Larkworthy contributed the ROI Brush plugin.
• Frank Rogge has made available QA-Distri, a package of 11 plugins for QA in digital radiology.
• Olivier Marchal and Noel Converset contributed the FRET and Colocalization Analyzer plugin.
• Jerome Mutterer contributed the Montage Shuffler tool macro for reording images in a montage created using Image/Stacks/Make Montage. Also includes a bonus puzzle to practice with.
• Gilles Carpentier created an improved AppleScript application for updating ImageJ on Mac OS X.
• Mikulas Stencel and Jiri Janacek contributed the Lipschitz Filter plugin.
• v1.37i, 16 June 2006
  • Images with inverting LUTs have "(inverting LUT)" added to the information at the top of the window.
  • Zoom level is maintained when converting between RGB and RGB (HSV) Stack.
  • The Gaussian Blur and Unsharp Mask filters are faster.
  • Edit/Cut and Edit/Copy in TextWindows ("Results", "Log", etc.) no longer require a selection.
  • Added the Plugins/Macros/Open Startup Macros command.
  • Added "Black Background" checkbox to Analyze/Tools/Fractal Box Count.
  • File/Import/URL can now open text files.
  • A repeated Edit/Select All in a TextWindow is equivalent to "select none".
  • Double click on a line containing a file path in a TextWindow to open the file.
  • "Apply"in the B&C window is recorded.
  • "Update" and "Delete" in the ROI Manager are recorded.
  • Added RoiManager.getName() method, which can be called from a macro using call("ij.plugin.frame.RoiManager.getName", index).
  • The "plugins.dir" property (set from the command line using -Dplugins.dir=<path>) can now be either a path to the plugins directory or the parent directory.
  • ImageJ is less likely to hang when quitting.
  • Fixed a bug that caused an exception when using Image/Scale with "Interpolate" checked on a one pixel high or one pixel wide image.
  • Fixed a bug that caused an exception when Process/Binary/Erode, Dilate etc. were used on an RGB image.
  • Fixed a bug that caused Image Calculator AND, OR and XOR operations to fail with float images.
  • Fixed a bug in the ROI Manager that caused saving of selections in directories with an apostrophe in the name to fail.
  • Fixed a bug that caused an exception when using the Unsharp Mask filter on some Linux systems.
• Jerome Mutterer contributed the Action Bar plugin, which creates an easy to use and customizable tool bar.
• The PerimeterAndCircularityTest macro displays measured and theoretical area, perimeter and circularity of circles with radii between 0.5 and 100.
• Ben Tupper adding an alphabetical index to the top of the Built-in Macro Functions list.
• v1.37h, 2 June 2006
  • The brush tool and drawing of wide lines are faster.
  • Commands in menus containing both plugins and macros are now sorted.
  • In "Save changes?" dialogs, press return to save the changes, "n" to not save the changes or esc to cancel.
  • Close message dialogs (e.g., "Are you sure you want to quit ImageJ?") by pressing return or cancel by pressing esc.
  • Macros installed in the Plugins/Macros folder now appear in the Plugins/Utilities/Control Panel.
  • When using a macro tool, the cursor no longer changes from a cross to a pointer when it moves over a selection.
  • Added the roiManager("rename", "new name") macro function.
  • Added the TextPanel.setLine(int, String) method.
  • Fixed a bug that caused Edit/Adjust/Brightness/Contrast, and the autoSetThreshold macro function, to not correctly set the threshold for images with symmetrical bimodal histograms.
  • Fixed a bug, introduced in 1.37d, that caused the RunMacro program to fail if files were not specified using a full path.
  • Fixed a bug in the ROI Manager that caused the name to be lost when saving and restoring a composite selection.
  • Fixed a bug that caused Edit/Selection/Enlarge to fail if the enlargement factor was negative and the selection touched the image edge.
  • Fixed a bug that caused ImageJ to crash on startup on Linux systems using IceWM.
• Fabrice Cordelieres and Susanne Bolte contributed JACoP (Just Another Co-localization Plugin).
• Johannes Schindelin has developed plugins that read/write Amira Mesh files and display Amira Surface files.
• Pictures from the first ImageJ User and Developer Conference are available at imagejconf.tudor.lu.
• Jerome Mutterer contributed the WeatherOverFrance macro, which downloads weather maps and animates them.
• The macros from the "Extending ImageJ with Macros" workshop at the ImageJ Conference are now available. Copy them to the plugins folder, restart ImageJ, and run them using commands in the Plugins/Conference Macros menu (requires ImageJ 1.37g or later).
• David Stepensky contributed the FRETcalc (FRET by acceptor photobleaching) plugin.
• Hidenobu Tachibana has created a Japanese language version of the ImageJ website.
• BioArts has created a Japanese language version of ImageJ for Windows and Mac OS X.
• v1.37g, 15 May 2006
  • Macros in the plugins folder with an ".ijm" extension (ImageJ Macro), and an underscore in the name, are installed in the Plugins menu at startup. (added 15 May)
  • Added Font menu to TextWindows ("Results", "Log", etc.).
  • The Edit/Options/Font window (or double click on text tool) now lists all available fonts.
  • On Mac OS X, opening images using drag and drop is faster.
  • Added the Macros/Evaluate Line command to the editor.
  • In the "Log" window, double click on paths to open Java and macro source files (Use with Find and Search_Macros macros).
  • Single lines copied from TextWindows ("Results", "Log", etc.) no longer have \n at the end.
  • The maximum size of the macro symbol table increased from 32K to 512K.
  • Fixed a bug that could cause calculated centroid coordinates to be incorrect with large images.
  • Fixed a bug in the image calculator that caused ANDing of an RGB image and an 8-bit mask to not work correctly if the mask had an inverting LUT.
• Jerome Mutterer contributed the Fonts macro, which demonstrates how to use the new getFontList() macro function.
• v1.37f, 5 May 2006
  • Fixed a bug, introduced in 1.37e, that sometimes caused the particle analyzer to fail if "Include Holes" was not checked.
  • Added getFontList() macro function (example).
  • Hold the shift key down to open a macro installed in the Plugins menu instead of running it.
  • Keyboard shortcuts are no longer ignored when the Plugins/Utilities/Control Panel is in front.
  • Control Panel windows are centered on the screen.
• v1.37e, 4 May 2006
  • Thanks to Joachim Wesner, added a "Complex Fourier Transform" option to the Process/FFT/FFT Options dialog.
  • The call() macro function extended to call methods() that do not return a string (examples).
  • Added an "Export Raw in Intel Byte Order" option to Edit/Options/Input/Output.
  • The "Redirect To:" feature of the Measure command works with binary masks (8-bit images with the name "mask").
  • ImageJ no longer displays an error if the plugins folder is missing.
  • Added the drawRect(), drawOval() and fillOval macro functions.
  • Made all the fields in ImageJCanvas protected for easier subclassing.
  • Added setInsets() method to GenericDialog class.
  • Used setInsets() to improve the layout of the Properties, Set Measurements, Scale and FFT Options dialogs.
  • The IJ.runUserPlugIn() method no longer requires that the plugins folder be present.
  • Added the recordString() method to the Recorder class.
  • Added the getCanvas() method to the ImagePlus class.
  • Fixed a bug that caused the setColor() macro function to not work correctly with signed 16-bit images.
  • Fixed a bug that sometimes caused the JFileChooser to not be used even when "Use JFileChooser to Open/Save" was checked.
  • Fixed a bug that caused incorrect titles to be used in JFileChooser dialogs.
  • Fixed a bug that caused ImageJ to fail to start if a 'var' declaration in StartupMacros generated an error.
  • Fixed a bug that could cause Analyze Particles to fail on images with a width or height of more than 32,000 pixels if "Include Holes" was not checked.
  • Fixed a bug that caused the name to be lost if a selection in the ROI Manager was edited and updated.
• Johannes Schindelin contributed the EPS Writer (Encapsulated PostScript) plugin.
• v1.37d, 20 April 2006
  • Added "Enlarge Image to Fit Result" option to Image/Rotate/Arbitrarily.
  • Added "Case Sensitive" and "Whole Words" options to the text editor's Edit/Find command.
  • Added "Rodbard (NIH Image)" to the list of functions in Analyze/Calibrate.
  • The flood fill (paint bucket) macro tool is now recorded.
  • Global variables can now be defined anywhere in a macro file outside of macro and function blocks.
  • The drawString() macro function uses antialiasing.
  • Macros with names ending in "Tool Selected" are not installed in the menu bar.
  • Added constructors to the ImagePlus and ShortProcessor classes that support 16-bit BufferedImages.
  • Fixed a bug that caused File/Save As/Image Sequence to not transfer calibration and DICOM tags to files saved in TIFF format.
  • Fixed a bug that sometimes caused incorrect histograms of calibrated 8-bit images and signed 16-bit images.
  • Fixed a bug that caused incorrect histograms of images containing line, point or angle selections.
  • Fixed a bug that caused histograms of images with more than 16 million pixels with the same value to be drawn incorrectly.
  • Fixed a bug that sometimes caused Image/Stacks/Z Project to produce incorrect "Standard Deviation" output with 16 and 32 bit images.
  • Fixed bug that caused text to be drawn incorrectly on contrast enhanced 8-bit images.
  • Fixed a bug in File/Import/Image Sequence that caused a bogus "ZVI Reader plugin not found" error message when opening files from a directory containing a "Thumbs.db" file.
  • Fixed a bug that caused opening of images from the command line to fail after use of the "cd" command.
  • Fixed a bug, introduced in 1.37b, that caused null characters in Image/Show Info output of DICOM images.
• Seth Gammon contributed a plugin for spectral unmixing of bioluminescence signals.
• Yasunari Tosa contributed the Multi Otsu Threshold plugin.
• Nikos Katsikanis contributed the Cairn Image Splitter plugin.
• Jan Palenicek has developed an ImageJ launcher for Psion PDAs running the Epoc OS.
• Jonathon Jackson contributed a wrapper script for launching ImageJ from the Unix command line.
• Jerome Mutterer contributed the Show All LUTs macro, which displays a montage of all the LUTs in the luts folder.
• Gabriel Landini contributed the LUTFileTool macro, which loads LUT files from the 'ImageJ/luts' directory. He also contributed a collection of 68 LUT files (luts.zip, LUT_Montage.jpg).
• v1.37c, 4 April 2006
  • Improved Image/Scale command.
  • The ImageJ window is slightly larger.
  • Added "Antialiased Tool Icons" option to Edit/Options/Misc.
  • Restored selections that extend past the image boundary are no longer centered.
  • Image screen updates are faster on OS X/Java 1.4.2 and on Linux.
  • Added the call() macro function, contributed by Johannes Schindelin, that allows macros to call static Java methods.
  • Call getDirectory("luts") in a macro or plugin to get the path to the ImageJ luts folder.
  • Moved the Run Macro command in the editor from the File menu to the Macros menu.
  • Fixed bug that caused excessive memory consumption on Windows when changing LUTs or thresholding.
  • Fixed a bug that sometimes caused thresholding of 16 and 32 bit images to not work correctly on OS X.
  • Fixed a bug that caused Image/Crop to fail with non-rectangular selections that extended beyond the image boundary.
  • Fixed a bug, introduced in v1.37a, that prevented running macros installed in the editor's Macros menu
• Jerome Mutterer contributed the Image To Tool Icon macro, which converts a 16x16 image (e.g., a favicon) into a macro tool icon string.
• The Wikipedia has an article about ImageJ.
• Forrest Mims III has written a review of ImageJ in The Citizen Scientist, the journal of the Society for Amateur Scientists
• Gilles Carpentier has created a web page that explains how to send commands to ImageJ from AppleScript.
• v1.37b, 24 March 2006
  • Added the File/New/ submenu with four command: "Image..." (replaces File/New), "Text Window" (opens a text editor), "Internal Clipboard" (displays internal clipboard) and "System Clipboard" (displays system clipboard; requires Java 1.4 or later).
  • Added the Edit/Copy to System and File/Save As>PNG commands (requires Java 1.4 or later).
  • Added a "Propagate to all open images" checkbox to the "Set" dialog in Image/Adjust/Brightness-Contrast and Image/Adjust/Window-Level.
  • Analyze/Tools/Save XY Coordinates works with stacks.
  • Image/Adjust/Size and Image/Scale now average source pixels when reducing RGB image by more than 4:1 (e.g., when creating thumbnails).
  • Peak areas displayed by the gel analyzer, when the image is calibrated, now use three decimal places.
  • Fixed a bug that caused the Measure and Label macro, and similar macros, to delete results without warning when switching between measuring lines and measuring areas.
  • Fixed a bug that sometimes caused selections moved by a macro from one slice to another in a stack to not have the slice number portion of the name updated.
  • Tabs written to the "Log" window are no longer converted to spaces.
  • Fixed a bug that sometimes caused incorrect display of selected lines in the "Log" window.
• Aurelien Stalder and Daniel Sage have developed the DropSnake and LB_ADSA plugins for high-accuracy measurement of contact angles of sessile drops.
• The CompositeSelections macro demonstrates how to create discountinuous selections and selections with holes in them.
• v1.37a, 17 March 2006
  • Added Font menu to the text editor.
  • Added "Min" and "Max" transfer modes to Edit/Paste Control.
  • The makeOval(), makeRectangle() and makePolygon() macro functions add to the current selection if preceded by setKeyDown("shift"), and subtract if preceded by setKeyDown("alt").
  • Fixed a bug in Process/Image Calculator that caused it to fail when processing single images in two unequal length stacks.
  • Fixed a bug that could cause ImageJ to hang when saving when "Use JFileChooser to Open/Save" was enabled in Edit/Options/Input-Output.
  • Fixed a bug that caused opening of images with pathnames starting with "\\" to fail.
  • Fixed a bug that could cause the run() macro function to fail if the keyword for a checkbox in the options string was contained in a bracketed literal (e.g., "xx=[aa bb cc] bb").
• Ann Arbor Sensor Systems has developed a plugin for their AXT100 thermal imaging camera.
• Maria Barilla contributed plugins for converting RGB images into Luv or Lab float stacks.

  Version 1.36, 13 March 2006

  • v1.36b, 13 March 2006
    • Fixed a bug that caused ImageJ to hang if an infinite number was passed to the Plot.add() macro function.
    • Fixed a bug that caused histograms to be plotted incorrectly if "Y Max" was set and the "Log" button was pressed.
    • In macros, use "setKeyDown('shift'); run('Histogram');" to display a log scaled histogram.
    • Fixed a bug that sometimes caused images opened with the Jimi Reader plugin to be displayed incorrectly.
  • v1.36a, 10 March 2006
    • Added the File>Save As>PGM command, based on a plugin contributed by Johannes Schindelin.
    • File>Revert displays a "Revert to saved?" message if the current image has changes.
    • The default title used by Image>Scale is now the title of the current image + "-1", "-2", etc.
    • Fixed a bug, introduced in 1.35p, that generated an exception when opening PGM files.
    • Fixed a bug on Windows that caused Edit/Options/Memory to fail and the "user.dir" property to change when files were dropped on the ImageJ icon.
  • The Editor Demo plugin demonstrates how to open an editor window containing text.
  • Johannes Schindelin contributed the PNM/PGM/PPM Writer plugin.
  • The Display Pixel Values macro displays pixels values in the "Results" window.
  • The Shift RGB Channel macro shifts the red, green or blue channel in an RGB image by a specified number of pixels.
  • Thomas Kuo and Jiyun Byun contributed the ITCN (Image-based Tool for Counting Nuclei) plugin.
  • The PlotProfileWithSD macro creates profile plots with standard deviation error bars.

  Version 1.35, 6 March 2006

  • v1.35s, 6 March 2006
    • The split() macro function no longer ignores blank lines when using "\n" to split lines.
    • Fixed a bug that caused the "Use Inverting Lookup Table" flag in Edit/Options/Image to be ignored when converting to 8-bits.
  • Tony Collins contributed the Leica TIFF Sequence plugin.
  • Yannick Krempp contributed Correct X Shift plugin.
  • v1.35r, 1 March 2006
    • ImageJ now opens 64-bit (double) FITS images.
    • Added a "64-bit Real" image type to File/Import/Raw.
    • The "java.io.tmpdir" is used when opening ZIP files.
    • Added the getResultLabel(), File.open(), File.openAsString() and File.close() macro functions.
    • The 'flags' variable returned by the getCursorLoc() macro function is updated when the mouse is released.
    • Fixed a bug that sometimes caused incorrect unit conversions in the Image/Properties dialog.
    • Fixed a bug that caused Process/Math/Min (or Max) to sometimes not work correctly with float images.
    • Fixed a bug that caused an exception if the IJ.getDirectory() method was called from the event dispatch thread.
    • Fixed a bug that caused the "Info" image property to not be saved with ZIP files.
    • Fixed a bug that prevented stacks >2GB from being saved as TIFF files. Note that to work with >2GB stacks you need a 64-bit CPU (e.g., AMD64), a 64-bit OS (e.g., Fedora x86_64) and a 64-bit JVM (e.g., J2SE for AMD64).
  • Kai Uwe Barthel contributed the Pong macro, which demonstrates how to do interactive graphics using the ImageJ macro language.
  • The Signed 16-bit Image plugin demonstrates how to create a signed 16-bit image from an array.
  • v1.35q, 16 February 2006
    • Added Process/Math>Exp command and corresponding ImageProcessor.exp() method.
    • Image/Zoom/To Selection command improved, thanks to code contributed by Jon Harman.
    • File/Save As in TextWindows ("Log", "Info for xxx", etc.) is now recordable.
    • The newImage macro function now defaults to "black" for 16 and 32 bit images.
    • Fixed a bug that could cause ImageJ to "hang" when quitting with open modified images.
    • Fixed a bug that caused the Image/Adjust/Brightness/Contrast tool to not work correctly with 32-bit images containing negative values.
    • Fixed a bug, introduced in 1.35o, that caused the Multi_Measure plugin to fail.
  • Duane Schwartzwald contributed Color Space Converter plugin.
  • The CreateImageFromFunction macro demonstrates how to use a math function to generate an image.
  • Added a signed version of the ImageJ applet to the ImageJ website that allows use of the File/Open and File/Save As/ commands.
  • v1.35p, 31 January 2006
    • Added the "Origin" field to Image>Properties for setting the origin of the coordinate system used by Measure, Analyze Particles and the ROI Manager.
    • Thanks to Jarek Sacha, ImageJ now opens 16 bit/channel color (i.e., 48 bit RGB) images in PGM format.
    • Added the getLocalCalibration() method to the ImagePlus class.
    • The 208x222 "Lena" sample image was replaced by a 512x512 RGB version.
    • Fixed bugs that could cause incorrect display of 16 bit signed pixel values if "Global" calibration was enabled.
    • Fixed a bug that sometimes caused an exception when opening LZW compressed 8-bit tiff files.
    • Fixed a bug in the applet version of ImageJ that sometimes caused an exception after a restart.
  • Damien Farrell contributed Radon Transform, a plugin that does back projection of images.
  • George Silva contributed a new Windows launcher (ImageJ.exe) that supports file-associations, drag and drop, auto-configuration and command line operation. If the ImageJ\jre directory is missing, it detects the latest installed Java, generates the configuration file (ImageJ.cfg) and sets the memory limit to 2/3 of installed memory or 640MB, whichever is lower. It is included with a new ImageJ 1.35p installer available on the Downloads page, or separately as a ZIP archive. Refer to the Readme for more information.
  • Remi Cathelin contributed Auto Gamma, a plugin that gamma corrects images, and Linearize GelData, a plugin that linearizes square-root encoded 16-bit .gel images.
  • Andreas Jahnen and Johannes Hermen are organizing the ImageJ User & Developer Conference, which will take place in May at the Public Research Centre Henri Tudor in Luxembourg.
  • v1.35n, 20 January 2006
    • Fixed a bug, introduced in v1.35m, which could cause ImageJ to crash on dual processor Macs.
  • v1.35m, 19 January 2006
    • Added the Edit/Options/Input/Ouput menu and moved the JPEG Quality and Open/Save Using JFileChooser options to it.
    • The default extension in the "Results" window File/Save As command, and in File/Save As/Measurements, is now ".xls". This can be changed in the Edit/Options/Input/Ouput dialog.
    • The algorithm used by Process/Binary/Ultimate Points and Watershed was improved.
    • File/Revert works with PGM files.
    • Added a "Use Foreground Color" option to Image/Stacks/Make Montage.
    • In the "Results" window, added ctrl-s keyboard shortcut for Save As.
    • The "Results" window File/Save As command is recordable.
    • Added "M51 Galaxy (116K, RGB)" (www.noao.edu/outreach/aop/observers/m51.html) to the File>Open Samples menu.
    • Added the getVersion() macro function.
    • The roiManager("select", index) function is faster.
    • Added the close() method to the ImagePlus class.
    • Fixed a bug in the selectImage(id) macro function that caused it to fail when id was greater than zero.
    • Fixed a bug that caused the run("RGB Merge...") macro function to not correctly delete the source images in batch mode.
    • Fixed bugs in Image/Color/Edit LUT that caused "Open" and "Save" exceptions.
    • Fixed a bug on Mac OS X that could cause a thread deadlock (the dreaded spinning beach ball) when switching windows.
  • Jerome Mutterer contibuted the Import Results Table macro.
  • v1.35l, 9 January 2006
    • Added the ImageListener interface, which enables plugins to be called when images are opened, closed or updated. The Image Listener plugin demonstrates how to use this interface.
    • Added the IJ.openImage() method.
    • Fixed a bug that caused the wand tool and particle analyzer to fail with some 32-bit images.
    • Fixed a bug in the particle analyzer that caused it to fail with 32-bit images when "Flood Fill" was checked.
    • Fixed a bug, introduced in v1.33, that caused scrolling (by holding down the space bar) while creating a polygon selection to fail.
    • Fixed a bug in IJ.selectWindow() that caused a 2 second delay when it was called from the event dispatch thread.
  • v1.35k, 23 December 2005
    • Added the File/Open Next command, which is based on a plugin contribute by Jon Harmon. To open the next image in a directory, press shift-o. To open the previous image, press alt-shift-o.
    • The straight line tool supports sub-pixel addressing. To try this out, zoom in 3200% and create a straight line selection.
    • Changed "Flood File" in Analyze/Analyze Particles to "Include Holes", and changed the default maximum particle size from 999999 to Infinity.
    • The ImagePlus.getShortTitle() method removes file name extensions.
    • To support sub-pixel addressing, added the screenXD(), screenYD(), offScreenXD() and offScreenYD() methods to the ImageCanvas class.
    • Fixed a bug in File>Save As/Image Sequence that could cause it to fail when saving DICOMs and "Use Labels as File Names" was checked in the dialog.
    • Fixed bugs that could cause the "Divide by Zero Value" and "Scale When Converting" options to sometimes reset on Mac OS 9.
  • v1.35j, 8 December 2005
    • Added -ijpath, -port, -macro, -batch, -eval and -run command line options. These options are described at the beginning of ImageJ.java.
    • Dialog boxes are no longer resizable, which removes the ugly "grow box" on Mac OS X.
    • Keyboard shortcuts are now more likely to work when the "Threshold" and "B & C" windows are in front.
    • Added a BARG image type (used by MCID) to the FileInfo class.
    • Little-endian ARGB images are now imported correctly.
    • Fixed a bug in Process>Subtract Background that generated errors along the right and bottom edges of the background corrected image.
    • Fixed a bug that caused a bogus dialog box on startup with Java 1.3.1 on OS X.
    • Fixed a bug on Mac OS X that sometimes caused more than one "save changes?" dialog to be open at a time.
    • Fixed a bug in the getProfile() macro function that caused it to return incorrect data if the line selection started or ended on or outside the image boundary.
  • Vladimir Pilny and Jiri Janacek contributed the Anisotropic Diffusion 2D plugin, a filter that reduces noise while preserving edges.
  • Jerome Mutterer contributed the PDF Writer plugin.
  • The OpenGL Example plugin by Ulf Dittmer shows how to use JOGL/OpenGL graphics.
  • Gilles Carpentier contributed the Magnifying Glass Tool macro, which is documented at image.bio.methods.free.fr/magtooldoc.html.
  • v1.35i, 18 November 2005
    • The Analyze/Tools/Curve Fitting tool now accepts comma-delimited data, ignores invalid invisible characters, and displays R^2.
    • The R^2 value displayed by Analyze/Calibrate is now calculated correctly.
    • Added "Duplicate" to the drop down menu displayed when right-clicking on an image.
    • Image/Duplicate creates unique image names by appending "-1", "-2". etc. to the name of the image being duplicated.
    • Thanks to code contributed by Ulrik Stervbo, "Open" in the Roi Manager no longer clears the list and reads only .roi files in ZIP archives.
    • Added sanity checks to the TIFF decoder.
    • Added the selectionName, setSelectionName and toolID macro functions.
    • Fixed bugs in File/Import/Text Image that caused it to sometimes fail with files containing invalid invisible characters and to sometimes not read the last line.
  • Audrey Karperien contributed the Fractal Growth Models plugin.
  • Audrey Karperien contributed a plugin that draws diffusion limited aggregate (fractal growth) models.
  • v1.35h, 10 November 2005
    • Added "24-bit Integer" image type to File/Import/Raw.
    • Fixed a bug, introduced in 1.35g, that sometimes caused a bogus error message when launching ImageJ on Windows.
    • Fixed a bug that could caused an extra error message when attempting to open a LUT.
  • Jon and Jeff Hardin contributed the QuickTime Stack Writer plugin.
  • v1.35g, 3 November 2005
    • On Windows, dropping an image on the ImageJ icon, when ImageJ is already running, no longer launches another copy of ImageJ. ImageJ uses sockets to detect if it is already running, a technique suggested by Curtis Rueden.
    • On Mac OS X, images dropped on the ImageJ icon now open when ImageJ is not already running.
    • Added the Analyze/Distribution command, based on a plugin by Gabriel Landini, and removed the particle analyzer "Bins" and "Area Distribution" options.
    • Pressing Esc cancels a dialog box.
    • The particle analyzer supports redirected sampling of RGB images. Note that redirected sampling is enabled using the "Redirect To:" option in Analyze/Set Measurements.
    • Added an "Update All When Normalizing" option to Process/Enhance Contrast that appears with images that have a selection.
    • Changed the "Interpolate Images <100%" option in Edit>Options>Image to "Interpolate Zoomed Images".
    • Process/Binary/Threshold and "Auto" in the thresholding tool set the threshold levels of the binary images they create.
    • Newly created elliptical selections are allowed to extend beyond the image boundary.
    • The toolbar double click threshold was changed from 500 to 650 milliseconds.
    • The macro interpreter displays an "Arrays of arrays not supported" message when a macro tries to assign an array to an array element.
    • The X axis range (histMin and histMax) of 16-bit images can be be set in the getHistogram() macro function.
    • Added the File.exists(), File.getName(), File.getParent(), File.getAbsolutePath(), File.isDirectory(), File.length(), File.makeDirectory(), File.dateLastModified(), File.lastModified(), File.delete() and File.separator() macro functions.
    • Fixed a bug that could cause an exception when using the setupUndo() macro function.
    • Fixed a bug that caused Process/Enhance Contrast to not work correctly with non-rectangular selections.
    • Fixed a recently introduced bug that caused attempts to add/subtract a polygon selection to/from an existing selection to fail.
    • Worked around a Mac OS X/Java 5.0 bug that caused X, Y coordinates displayed in plot windows to be truncated.
    • Fixed bugs in the setThreshold(), setAutoThreshold(), resetThreshold(), setMinAndMax() and getMinAndMax() macro functions that caused them to sometimes fail with 16-bit images, especially signed 16-bit images.
  • Jerome Mutterer contibuted the Tiff Comments Editor macro set, which lets you edit the TIFF comments field of the active image.
  • Kunito Yoshida contributed the Windowed-Sinc Filter plugin, which does low pass filtering of time series stacks.
  • Jon Harmon developed DStretch, a plugin for digital enhancement of pictographs. He also created a customized ImageJ applet that includes DStretch and 7 sample pictographs.
  • Dimiter Prodanov contributed a plugin that does granulometric filtering.
  • v1.35f, 24 October 2005
    • Fixed a bug, introduced in 1.35e, that sometimes caused "-1", "-2", etc. to be appended to the image name after using a type conversion command.
    • On Mac OS X, the getDirectory() macro function uses the native file open dialog instead of JFileChooser.
  • Daniel Sage et al. have finished a revamped version of the Extended Depth of Field plugin, which merges a stack of microscopic images taken at different focal lengths into a single focused composite image. This version is faster, uses less memory, has a better user interface, and does 3D surface plotting.
  • José G. Conde and Nathaniel Gonzalez have made available the Visible Human Preprocessing Toolkit and Multiple Image Processor plugins.
  • v1.35e, 18 October 2005
    • Added the Process/FFT/FFT Options... command.
    • Newly opened images with duplicate names have "-1", "-2", etc. added to the name.
    • Added the "Circularity" field to Analyze/Analyze Particles dialog. Particles outside the specified circularity range are excluded from the analysis.
    • Min and max values entered into the particle analyzer dialog box are now scaled values (e.g., mm^2) when the image is spatially calibrated.
    • Added the split() method to the Tools class.
    • Fixed a bug in Process/Enhance Contrast that caused it to fail when "Normalize" was checked in the dialog box, or with RGB images, and there was a selection.
    • Fixed a bug that caused histograms of 8-bit and RGB stacks to not use a bin width of 1.
    • Fixed a bug that caused imported DICOM sequences to sometimes not be sorted correctly by image number.
    • Fixed a bug that could sometimes cause ImageJ to hang on Mac OS X when opening files if "Open/Save Using JFileChooser" was checked in Edit/Options/Misc.
    • Fixed a bug that caused TIFFs to be saved incorrectly when using File/Save with renamed images.
    • Fixed a bug that sometimes caused a syntax error when running a macro containing invisible characters.
  • Gilles Carpentier contributed the Change Color Tool macro.
  • The QuickTime Movie Writer plugin now works with Java 1.4 and later on Mac OS X and is packaged with three other QuickTime plugins (Capture, Open and Play).
  • The Batch RGB Merge macro converts a set of images consisting of separate color channels into an RGB Stack.
  • Jonathan Jackson contributed plugins for opening and saving UNC (University of North Carolina) format images.
  • Sandro Morganella contributed the IMT Snake plugin, used for extracting the intima-media thickness (IMT) of the carotid artery in ultrasound images.
  • v1.35d, 22 September 2005
    • The "Redirect To" option in Analyze>Set Measurements now works with stacks.
    • Fixed a bug that caused the Measure and Fill commands to fail after use of Edit/Selection/Fit Spline.
    • Fixed a bug that sometimes caused an incorrect paste of non-rectangular selections.
    • Fixed bugs that sometimes caused LZW compressed TIFF files to open incorrectly.
    • Fixed a macro interpreter bug that caused an error when 'a.length' was used in a print() statement, where 'a' is an array.
  • Kai Uwe Barthel has created a stand-alone version of his Color Inspector 3D plugin.
  • Jerome Mutterer contibuted the LSM Batch With Colors macro, which uses the LSM Reader to batch convert LSM files, keeping the original channel colors.
  • v1.35c, 7 September 2005
    Added "Rename" and "Deselect" buttons to the ROI Manager and removed "Add and Draw" and "Open All", which have been replaced by macros in the ROIManagerMacros macro set.
    • Macros file names can can now use either ".ijm" or ".txt" extensions.
    • File/Revert works with ZIP compressed TIFF images.
    • Fixed a bug with the way the ROI Manager handles duplicate names.
  • Daniel Sage has made available the SpotTracker plugin, which tracks a single particle over a sequence of noisy images.
  • George Silva contributed the Packard InstantImager Reader plugin.
  • The RGB Histogram macro generates red, green and blue channel histograms and saves them in a stack.
  • The MeasureRGB macro separately measures the red, green and blue channels of an RGB image.
  • The ExtractRGBChannels macro demonstrates how to extract the red, green and blue channels from an RGB image.
  • v1.35b, 26 August 2005
    • Added Rotate, Enlarge and Make Band commands to the Image/Selection submenu. These commands are the first ones to have been written in the ImageJ macro language.
    • The polygon and polyline tools are now recordable.
    • Added the setRGBWeights() and makePolygon() macro functions and extended the makeLine() function so it can be used to create polyline selections.
    • Added the Dialog.addNumber(label, default, decimalPlaces, columns, units) macro function.
    • Added a constructor to the FloatProcessor that accepts a float[][] argument.
    • Fixed a bug, introduced in v1.34, that caused the "save changes" dialog to not be displayed when closing image windows.
  • Chris Davies contibuted the AzimuthalProfile macro, which saves profile plots at different azimuthal angles.
  • Jonathon Jackson contributed the Convert to 16-bit Signed, a plugin that converts images and stacks to signed 16-bit.
  • The Kuwahara Filter plugin smooths images while preserving edges.
  • Guy Williams contributed the NIfTI Input/Output plugins.
  • Camillo Bosco and Sebastiano Battiato have made available plugins for performing power and log transforms, contrast stretching and spatial filtering.
  • Vilppu Tuominen has made available the LargeMontage, an plugin that creates a montage/mosaic out of a set of image file.
  • Audrey Karperien contributed the Fractal Generator plugin, which draws fractal contours using adjustable size and iteration settings.
  • Jim Hull contributed three plugins that open Molecular Imaging and Nanoscope AFM files.
  • v1.35a, 9 August 2005
    • Display a histogram by pressing alt-h and a dialog box will be presented that allows the bin count and x and y ranges to be specified.
    • Analyze/Measure calculates area fractions of 32-bit images.
    • TIFF files that specify 72 pixels/inch in the header now open without spatial calibration.
    • Images opened using the JFileChooser are added to the File>Open>Recent list.
    • Analyze/Set Measurements settings are now saved and restored by the saveSettings() and restoreSettings() macro functions.
    • Added the getSelectionStart() and getSelectionEnd() methods to the TextPanel class.
    • Fixed a bug that caused macro statements of the form v=a[i] to fail if the first element of the array was a string and the element being assigned was a number.
    • Fixed a bug that caused the setBatchMode(false) macro call to not work correctly if the active image was a histogram.

  Version 1.34, 12 July 2005

  • John Lydon has made available a 44 page PDF document with the title "The measurement of the modal mineralogy of rocks from SEM imagery: the use of Multispec and ImageJ freeware".
  • Laurent Gelman et al. have made available PixFRET, a plugin for FRET (Fluorescence Resonance Energy Transfer) calculations.
  • v1.34r, 8 July 2005
    • Added the imageCalculator() macro function.
    • Added a "Text File" type to Plugins/New.
    • Plugins/New now uses "My_Plugin", "Filter_Plugin" and "Plugin_Frame" as the default plugin names.
    • Fixed a bug that could cause bogus "There are no images open" errors in batch mode macros.
    • Fixed a bug in Plugins/New that caused the generated plugin frame to use a tiny window.
  • v1.34q, 1 July 2005
    • The Measure and Histogram commands now use scientific notation to display very small and very large values.
    • File/Import/Text Image opens text format images that use scientific notation.
    • Add a "Global" checkbox to Image/Properties.
    • Added the setMetadata() and getMetadata() macro functions.
    • Clicking outside a selection with the polygon tool no longer starts the creation of a polygon selection.
    • Opening a signed 16-bit image disables global calibration.
    • The "zeroClip" calibration flag is saved in the TIFF header.
    • The File/New "Fill With:" Clipboard option now works correctly with non-rectangular selections.
    • Fixed a bug related to pasting non-rectangular selections into same-sized rectangular selections.
    • Fixed several BMP read/write bugs thanks to sample images and code contributed by Yasunari Tosa.
    • Fixed a bug that could cause Process>Noise>Add Noise and Add Specified Noise to generate biased noise.
    • Fixed a bug that could cause the wand tool to fail with 32-bit images containing NaN pixels.
    • Fixed a bug that could cause 32-bit images containing NaNs to be saved incorrectly.
  • Leo Durosemont contributed the Telecran (Etch-a-sketch) macro set, which demonstrates interactive numeric keypad control of macros.
  • The ButtonBar example macro set adds six buttons to the ImageJ tool bar.
  • Walter O'Dell contributed a plugin that performs template matching for detection of objects in an image
  • Sonia Choubrac, Jean-Nicolas Dacher, Michael Dolores and Sylvain Payrouse contributed the MR Urography plugin.
  • Pierre Besson has made available a 3D deconvolution plugin.
  • Christian Kreutzfeldt has written a collection of macros that allow estimation of molecular weights in electrophoresis gels.
  • Fabrice Cordelieres contributed the 3D Objects Counter, Metamorph nd Stack Builder and DeltaVision Opener plugins.
  • Gilles Carpentier contributed the Three Channel Fluorescence Image Exploration Tools macro set. Documentation and a sample image are available.
  • Gali Baler contributed the PointsToStack macro, which creates a stack of sub-images based on a set of user-adjustable points.
  • v1.34p, 10 June 2005
    • Added "Fill with Background Color" options to the Image/Scale and Image/Rotate/Arbitrarily dialogs.
    • Holding down the alt key forces text files to be opened in a TextWindow instead of an Editor window.
    • Holding down alt or shift causes Plugins/Compile and Run to compile using the -g option, which adds debugging information required by symbolic debuggers.
    • The "Exclude on Edges" option in the particle analyzer now works correctly with non-rectangular selections.
    • The getDirectory() macro function returns the path the the users home directory or to the ImageJ directory when called with "home" or "startup".
    • The ColorProcessor.putPixel() method no longer sets the alpha bits.
    • Fixed a bug that could cause BMP images opened in ImageJ to become locked.
    • Fixed a bug with the getDirectory() macro function that could cause ImageJ to hang on Mac OS X 10.4 dual processor systems.
  • Joachim Walter contributed a 5D data set (w=256, h=256, ch=2, z=24, t=7) that can be used to test his Image5D plugins.
  • Gilles Carpentier contributed the Arrow Maker Tool macro. Examples are at image.bio.methods.free.fr/Arrowsdoc.html.
  • Gali Baler has written detailed instructions on how to debug plugins using the NetBeans IDE.
  • Ronald Petie contributed the Anaglyph plugin, which uses two photographs, made at different angles, to make a stereo image.
  • Joachim Walter contributed the Image5D plugins, which display images that have up to 5 dimensions: x, y, channel (color), slice (z) and frame (t).
  • Federico Viel and Vincenzo Della Mea have made available a Microscope Stage Controller plugin.
  • The ArrowTool tool draws arrows.
  • The Translate macro does image translation.
  • Gilles Carpentier contributed the MultiCursorTool macro, which displays multiple synchronized cursors.
  • Audrey Karperien and Thomas Roy contibuted the Hull and Circle plugin for finding the convex hull and bounding circle of patterns in binary images.
  • v1.34n, 17 May 2005
    • Non-rectangular selections can now be dragged paste the edges of the image.
    • Added the getDateAndTime() macro function.
    • The command recorder correctly records threshold levels of signed 16-bit images.
    • Fixed a bug that prevented filtering of images using the "3-3-2 RGB" LUT.
    • Fixed a bug that caused "Standard Deviation" projections using Image/Stacks/Z Project to fail with some 16-bit stacks.
    • Fixed a bug with Process/Binary/Threshold that caused all slice labels of the output stack to be set to the first slice label of the input stack.
    • Fixed a bug that caused drawn lines to be the same width when the line width was set to both w and w+1.
    • Fixed a bug that caused drawn lines to be positioned incorrectly when the starting coordinates were negative.
    • Fixed a bug that caused batch mode macros doing 90 degree rotations to fail.
    • Fixed a bug that caused the lengthOf() macro function to fail when called with a string array element.
    • Fixed a bug that caused the exit() macro function to fail when called with a variable as an argument.
  • The GetDateAndTime macro, contibuted by Bill Heeschen, demonstrates how to display the date and time.
  • The ChangeColors macro replaces foreground colors in an image with the background color.
  • Jerome Mutterer contibuted the 3Dflight macro, which demonstrates scripting of Kai Barthel's Volume Viewer plugin.
  • The BigCursorTool macro simulates a full window cross-hair cursor using a polygon selection.
  • The Windows version of ImageJ is now available bundled with Java 5.0, Update 3.
  • v1.34m, 29 April 2005
    • Added the Dialog.* macro functions. The DialogDemo macro provides an example.
    • File>Import>Image Sequence opens files without leading zeros in the names in the correct order.
    • The applet version of ImageJ closes non-image windows when quitting.
    • The WindowManager.closeAllWindows() method closes non-image windows.
    • Fixed a bug that sometimes caused signed DICOM images opened using File>Import>Image Sequence to not open correctly.
    • Fixed a bug that caused some filters to fail on images with a paste operation in progress.
    • Fixed a bug that caused Process/Filters/Gaussian Blur to not work correctly if "Normalize Kernel" was not checked in the Process/Filters/Convolve dialog.
    • Fixed a bug that caused Image/Zoom/To Selection to sometimes fail with small selections.
    • Fixed a bug that sometimes caused Image/Type/ commands to fail in batch mode macros.
    • Fixed a bug in Process/FFT/FD Math that caused an exception when "Do Inverse Transform" was not selected in the dialog.
    • Fixed a bug that could cause a syntax error when comparing strings in a macro function.
    • Fixed a bug that caused batch mode macros calling runMacro() or eval() to fail.
  • The CalculateMean macro demonstrates how one macro can call another macro and pass it a variable number of numeric values.
  • The DeconvolutionDemo macro demonstrates how to use a point spread function (PSF) and frequency domain convolution and deconvolution to blur and de-blur an image.
  • On Mac OS X, ImageJ may not run after the 10.3.9 upgrade but a new software update ("Java Update for Mac OS X v10.3.9") is supposed to fix the problem.
  • v1.34l, 15 April 2005
    • The "Flood Fill" particle analyzer option enables measurement of nested particles and causes interior holes to be ignored.
    • Added "Skewness" and "Kurtosis" options to the Analyze/Set Measurements dialog.
    • The results table can now contain up to 150 columns.
    • Results table values are stored as doubles (15 digit precision) instead of floats (7 digit precision).
    • Analyze/Measure will display the bounding rectangle of line selections.
    • Faster image display on Java 1.5 (aka 5.0).
    • Images with up to five dimensions (width*height*channels*depth*time) can be defined in the Image/Properties dialog but the rest of ImageJ has not yet been updated to support 4D and 5D images.
    • Thanks to Ulf Dittmer, ImageJ now opens PBM (Portable BitMap) images, where before it would only open PGM (Portable GreyMap) and PPM (Portable PixMap).
    • The applet version of Image will auto-load images. There is an example at rsb.info.nih.gov/ij/applet2/.
    • "Hello World" is no longer automatically added to macro files created using Plugins>New.
    • Fixed a bug that caused incorrect line profile plots of images with non-square pixels.
    • Fixed a bug that caused incorrect wide line profile plots of density calibrated images.
    • Fixed a bug in Image/Stacks/3D Project that caused it to fail if "Rotation Angle Increment" was negative.
    • Fixed a bug that caused File/Save As/AVI to fail when using Java 1.1.
    • Fixed a bug that could cause an exception if there was an error while opening an image in a macro.
    • Fixed a bug in the getDirectory() macro function that resulted in double back slashes with root directories on Windows.
  • v1.34k, 1 April 2005
    • Slices labels (e.g., DICOM tags) are saved in the TIFF header.
    • File/Import/Image Sequence improvements: DICOM images are sorted by image number, the folder name is used as the title of the stack, better error messages, and dialog box error messages are redirected to the "Log" window.
    • Image/Image Calculator now names output stacks "Result of <image1>".
    • The print dialog box is not displayed when File/Print is called from a macro.
    • The screen is not updated when setSlice() is used in batch mode macros.
    • The saveAs() macro function displays a file save dialog if the second argument is omitted.
    • Added "count", "select", "deselect" and "reset" options to the roiManager() macro function. For an example, see the ROI Manager Stack Demo macro.
    • Added the setVoxelSize() and getLocationAndSize() macro functions.
    • Added the IJ.redirectErrorMessages() method.
    • Fixed a bug that caused the fill() macro function to fail with non-rectangular selections extending past the image bounds.
  • The SortDemo macro demonstrates how to sort an array of numbers or an array of strings.
  • Andreas Schleifenbaum contributed the PlotStack macro, which draws a graph in a stack.
  • Remi Cathelin and Christophe Klopp contributed plugins for opening/saving images in the ISAC format used by Fuji BAS scanners.
  • Ron DeSpain contributed the Max Value Segmentation macro, which demonstrates pixel-by-pixel processing of multiple images.
  • The Rotate Image macro rotates images based on the orientation of a straight line selection.
  • Dimiter Prodanov contributed the RGB Measure Plus plugin.
  • Martin Schlüter contributed the XYZ2DEM Importer plugin, which imports XYZ coordinates from a text file and interpolates a Digital Elevation Model (DEM) image using Delaunay triangulation.
  • Michael Doube contributed the VolumeFractionOfBone macro, which measures the volume fraction and mineral density of bone in mineralised tissues.
  • v1.34j, 16 March 2005
    • The tool bar can now contain one more tool.
    • Analyze/Histogram works better with float images containing NaNs and +/-Infinity.
    • Thanks to Curtis Rueden, ImageJ opens 16-bit LZW compressed TIFFs.
    • File/Import/Image Sequence no longer displays "Opening: xxx" messages in the status bar.
    • The Mac OS X menu bar is less likely to disappear.
    • Added a flood fill (paint bucket) tool to the DrawingTools macro set.
    • Added the floodFill() macro function.
    • Added the restorePreviousTool() macro function, which allows creation of tools that perform an action when they are clicked or double-clicked. The AboutTool macro is an example of a single-click action tool and the Flood Fill Tool is an example of a double-click action tool.
    • Image/Duplicate no longer deletes the source image's selection.
    • A "plugins.config" file is automatically generated for JAR files that do not contain one.
    • Fixed a bug that caused an exception when using the Plot.show() macro function in batch mode.
    • Fixed a bug in Process/Binary/Threshold that sometimes caused a non-functional scroll bar to appear below the image.
    • Fixed a bug in the doWand() macro function that sometimes caused the previous selection to be restored.
    • Fixed bugs that prevented .zip files and files using HandleExtraFileTypes from opening from the command line.
    • Fixed a bug that caused the median to be calculated incorrectly for float images containing NaNs.
  • Per Christian Henden has written Fractal Count, Map Fractal Count, Susan Filtering, Extrude Map and Gaussian Noise plugins.
  • David Bright has created tutorial exercises for ImageJ and NIH Image.
  • The OpenImagesFromList macro demonstrates how to open images using a text file list.
  • Paul Werten contributed the BackgroundCorrectedDensity macro, which calculates background-corrected integrated density.
  • The QuickTime Capture plugin now capture multiple frames to a stack and works with Java 1.4.2 on Mac OS X.
  • Gilles Carpentier contributed the DisplayTiffInfo macro, which displays the Image Description tag of TIFFs created by programs such MetaMorph.
  • Philippe Thévenaz has made available StackReg, a plugin for the recursive alignment of a stack of images.
  • Curtis Rueden contributed the Zeiss ZVI Reader plugin.
  • Kai Uwe Barthel contributed the Volume Viewer plugin, which interactively displays a stack as volume within a 3D space.
  • Olivier Marchal and Jerome Mutterer contibuted the 'A trous' Wavelet Filter noise reducing plugin.
  • v1.34i, 15 February 2005
    • JPEG, GIF and PNG images are no longer cached, which reduces the amount of memory required to open and process these images.
    • Added a "Median" option to Analyze/Set Measurements.
    • Added an "Auto-Next Slice" option to Edit/Options/Point Tool.
    • Image/Show Info adds ">" to the description of DICOM tags that are part of a sequence.
    • The default directory used by Plugins/Edit is the ImageJ folder instead of the plugins folder.
    • Added the getStatistics(), getRawStatistics(), calibrate(), replace(), asin() and acos() macro functions.
    • The area fraction displayed by the "Summarize" option in Analyze/Analyze Particles no longer ignores selections.
    • Worked around a Java 5.0/Linux bug that caused exceptions when opening windows.
    • Fixed a bug that could cause macro paste operations to fail if the transfer mode was not "Copy".
    • Fixed a bug that caused an exception when opening some Metamorph TIFFs.
    • Fixed a bug that caused the getImageID() and getTitle() macro functions to fail after an open() call.
  • Jerome Mutterer contibuted a macro that changes an image's display gamma by remapping the LUT, which preserves the pixel values, unlike the built-in Process/Math/Gamma command.
  • v1.34g, 1 February 2005
    • The "Auto" option in Image/Adjust/Threshold is recordable.
    • File/New now sets the initial display range of 16-bit images to 0-65535 and of 32-bit images to 0-1.
    • ImageJ opens 48-bit RGB TIFF stacks.
    • The angle in the Image/Rotate/Arbitrarily dialog is displayed using two decimal places.
    • The TIFF ImageDescription field is now available as the description field returned by ImagePlus.getOriginalFileInfo().
    • Added getSelectionBounds(), getSliceNumber(), fillRect(), screenWidth(), screenHeight(), eval(), runMacro() and toString() macro functions.
    • Second argument of getResult() macro function is optional and it now returns NaN if the specified column is not found.
    • Added an optional third "mode" argument to the setThreshold() macro function.
    • Plugins/Macros/Install displays an error message if the file contains more than 60 macros.
    • In the macro language, user functions now override built in functions.
    • Fixed a bug in the DICOM reader that caused files with a thumbnail in an indefinite length sequence (e.g., GE Senographe 2000 D) to not open correctly.
    • Fixed a bug that sometimes caused macro keyboard shortcuts to fail.
    • Fixed a bug that caused a macro to fail if a boolean expression contained line breaks.
    • Fixed a bug that could cause ImageJ to crash if a macro with a name duplicating an ImageJ menu command was copied to the plugins folder.
    • Fixed stack related problems in the setFont() and setColor() macro functions.
    • Fixed a bug that caused Image/Adjust/Brightness/Contrast to sometimes fail if used after a paste operation.
    • Fixed a bug that caused user a function call at the beginning of a macro file to fail.
    • Fixed a bug that caused Image/Adjust/Brightness/Contrast "Apply" operations on stacks with non-rectangular selections to fail.
    • Fixed a bug that could cause ImageJ to hang when quitting on Mac OS X.
  • The MeasureAreaFraction macro measures area percentages in thresholded images or 8-bit binary images.
  • The RecordProfile macro saves profile plot data in the "Results" table.
  • The Artillery macro demonstrates macro programming techniques, and also provides a little relaxation.
  • Olivier Marchal and Jerome Mutterer contibuted the Haar Wavelet noise reducing filter.
  • The OpenSeriesUsingFilter macro opens an image series as a stack using a customizable file name filter.
  • Bo de Lange contributed the MeasurePieSegmentsTool macro, which measures and labels predefined pie shaped selections.
  • Sergio Caballero has made available the Colocalize RGB and Area Calculator plugins.
  • Greg Jefferis has made available the Biorad Writer plugin.
  • v1.34f, 13 January 2005
    • Added the "Y Max" option to the dialog box displayed when Analyze/Histogram is used on a 32-bit image.
    • Batch mode macros that switch between on-screen images run much faster.
    • Fixed several batch mode macro bugs.
  • The CustomHistogram macro displays a histogram of the active image or stack using a specified number of bins and fixed X and Y axis.
  • v1.34e, 10 January 2005
    • Image/Show Info displays additional tags from the headers of DICOM images.
    • File/Save As/Raw Data now works correctly with signed 16-bit images and stacks.
    • Added the keyDown() macro function. (c)
    • Fixed a bug in the setLocation() macro function that could cause it to fail in batch mode macros.
    • Fixed a bug in the newImage() macro function that caused it to return before the newly created image was activated. (d)
    • Fixed bugs in the SelectImage() and selectWindow() macro functions that could cause them to fail in batch mode macros (d).
  • The ConvertDicomDictionary macro converts the DICOM dictionary to the format used by ImageJ.
  • The CircularQuadrantMeasure tool creates an oval (or circular) selection centered around where you click and measures and labels its four quadrants.
  • The MakeMontage macro demonstrates several macro coding techniques.
  • v1.34b, 5 January 2005
    • Angles displayed by the straight line, polygon and polyline tools are in the range -180 to 180 degrees instead of 0 to 360 degrees.
    • The print() macro function accepsts multiple arguments.
    • Added the toLowerCase() and toUpperCase() macro functions.
    • Fixed a recording bug in Image/Color/Edit LUT.
    • Fixed a bug that caused an error when an "AutoRun" macro used a global variable.
    • Fixed a bug that caused run("Close") to sometimes fail in batch mode macros.
    • Fixed bugs that caused saving in JPEG and BMP formats to fail in batch mode macros.
    • Fixed a bug in the macro interpreter that caused an error with assignments in the form x = f()*y, where f() is a user-defined function.
    • Fixed a minor bug in the MedianCut class (Image/Type/8-bit Color).
    • Fixed a bug, introduced in 1.33s, that caused the DICOM reader to attempt to open thumbnail images stored in private sequence tags.
  • Gary Chinga developed Image CorrelationJ, a plugin that calculating the correlation of two images or stacks.
  • The BatchConvert macros convert a folder of images to a different format.
  • v1.34a, 21 December 2004
    • Thanks to code contributed by Curtis Rueden, ImageJ now opens LZW compressed 8-bit and RGB TIFFs.
    • The "Save changes to..." dialog is no longer displayed when a text window is closed by a macro.
    • Fixed a bug, introduced in 1.33s, that caused the DICOM reader to open a thumbnail of the image.

  Version 1.33u, 15 December 2004

  • v1.33u, 15 December 2004
    • Image/Stacks/Plot Z-axis Profile uses the "Minimum Y" and "Maximum Y" values set in Edit/Options/Profile Plot Options, and it no longer requires a selection.
    • Added the parseInt() and parseFloat() macro functions.
    • Fixed a bug that caused 16-bit signed images imported using File/Import/Raw to open incorrectly if "Open All Files in Folder" was checked.
  • v1.33t, 13 December 2004
    • In the Image/Adjust/Size dialog, when "Constrain" is checked, the width is calculated when the height is changed, and vis versa.
    • In the Image/Scale dialog, when the x scale is changed, the y scale is set to the same value.
    • Process/FFT/Custom Filter works better with non-float images.
    • Added the setAutoThreshold() and rename() macro functions.
    • Fixed bugs in Image/Stacks/Convert Images to Stack and ImagePlus.getStack() that caused them to not carry over the DICOM and FITS header information.
  • Added an example that shows how to analyze a dot blot.
  • v1.33s, 7 December 2004
    • All DICOM tags are now displayed by Image/Show Info, not just the ones in ImageJ's DICOM dictionary.
    • Added the newImage(), save(), saveAs() and getZoom() macro functions, and updated the recorder to generate calls to newImage() and saveAs().
    • The saveSettings() macro function saves more Edit/Options settings.
    • Fixed a bug that caused shortcuts created with Plugins/Shortcuts/Install Plugin to fail if the argument contained one or more back slashes.
  • The Cooke Corporation released a Windows 2000/XP plugin for their pco.1200hs, pco.1600, pco.2000 and pco.4000 14-bit CCD cameras.
  • Gilles Carpentier contributed the GaussianConvolution macro, which does image smoothing using a custom Gaussian matrix.
  • The StackProfilePlot macro generates profile plots of all the images in a stack and stores then in another stack.
  • Jerome Mutterer contibuted a macro that extracts the original name and acquisition mode of JPEG images taken with a Nikon DXM 1200 camera and ACT-1 software.
  • Gabriel Landini contributed the ResizeImagesAndStack macro which creates a stack from images that differ in size.
  • v1.33r, 26 November 2004
    • Analyze/Plot Profile works with straight lines wider than one pixel.
    • Double-clicking on any line tool opens a slider widget for setting the line width.
    • Added "Use Inverting LUT" option to Edit/Options/Image, which causes, with 8-bit images, zero to be displayed as white and 255 as black.
    • Added "Integrated Density" option to Analyze/Set Measurements. Integrated density is the product of the area and mean.
    • Hold down alt when using Image/Color/RGB Split to keep original image.
    • Process/Binary/Erode and Dilate are faster and use less memory.
    • Added a "Count" field to Process/Binary/Options.
    • Added the 0018,0073, 0018,0074 and 0018,0075 tags to the DICOM dictionary.
    • File/Run Macro in the text editor runs the first macro in a macro set.
    • Added the setSlice(), getImageInfo() and isNaN() macro functions and the NaN predefined constant.
    • The open() macro function now aborts the macro if there is an error or if the file is not found.
    • Macros that open windows run more reliably, especially on Mac OS 9.
    • Fixed a bug that caused an exception if an invalid value was entered in the ColorChooser used by Image/Color/Edit LUT and Color Picker.
    • Fixed an edge handling bug in Process/Binary/Erode and Dilate.
    • Fixed an array element argument passing bug in the macro language.
  • Kai Uwe Barthel contributed an interactive 3D surface plot plugin.
  • Michael Schmid contributed the MaskToSelectionMacros macro set.
  • The OpenMacIPLab macro opens 16-bit images created by the Mac version of IPLab.
  • The ListSelectionCoordinates macro displays the coordinates of the points that define the current selection, the length of the segments connecting the points and the average segment length.
  • Gabriel Landini contributed the RandomSampleAndMeasure macro which creates random selections, then measures and labels them.
  • Philippe Thévenaz et al. have made available the UnwarpJ plugin that performs spline-based elastic registration of two images.
  • Gabriel Landini contributed the EDM_16bits macro which extends Process/Binary/Distance Map to support objects with a radius greater than 255.
  • The RadialIntegratedIntensity macro plots integrated radial intensity from 0-360 degrees.
  • The ListDicomTags macro displays the values of selected DICOM tags.
  • Joel Sheffield contributed the ReplaceRedWithMagenta macro that replaces the red channel in an RGB by magenta to allow easier viewing by color blind viewers.
  • v1.33p, 10 November 2004
    • A node can be added to a polygon or polyline selection by shift-clicking on an existing node. A node can be deleted by alt-clicking on it.
    • A point in a point selection can be deleted by alt-clicking on it. (Use shift-click to add points.)
    • The "+", "-", ">" and "<" shortcuts (without control key) are more likely to work with European keyboards.
    • Compiler errors are display using a monospaced font so the "^" error pointer is correctly positioned.
    • The IJ.runMacro() method is up to 30 times faster.
    • On Mac OS X, text windows use a larger font.
    • Worked around a Mac OS X bug that caused the end of newly opened text files to be displayed instead of the beginning.
    • Worked around a Mac OS X bug that caused lines in a text windows to be displayed incorrectly after a 'return' was entered.
  • v1.33o, 4 November 2004
    • Added the Image/Zoom submenu, with commands for zooming in, zooming out, reverting to original magnification and for zooming to a selection.
    • Added the File/Open Recent submenu.
    • Added an option to Analyze/Histogram to generate stack histograms.
    • Added the "Use Stack Histogram" option to Process/Enhance Contrast and renamed the "Process Entire Stack" option to "Normalize All n Slices".
    • File/Save re-saves TIFF files without a file save dialog.
    • Added the "Require Control Key" option to Edit/Options/Misc.
    • Plugins/Macros/Install is now recordable.
    • "[" and "]" can be used instead of single quotes to delimit parameters that may contain spaces in run() calls (e.g., run("Tiff...", "save=["+path+"]")).
    • Added the atan2() macro function.
    • Fixed a bug that caused an exception when opening 48-bit TIFF stacks.
    • Fixed a bug in File/Save As/AVI that caused it to sometimes not correctly set the file length when replacing an existing file.
    • Fixed a bug in the macro interpreter that caused statements in the form print(n+s) to fail, where n is a numeric variable and s is a string variable.
    • Fixed a bug that sometimes caused bogus "No windows Open" errors when running a macro.
    • Fixed a bug that could cause the roiManager() macro function to sometimes fail if the Roi Manager was opened and then closed.
  • Joachim Walter contributed the Spectral Unmixing plugins, which correct for spectral bleedthrough between color channels of fluorescence images.
  • Gilles Carpentier contributed the FFTRemoveStreaks macro for removing interference streaks from confocal images. Before and after images are provided.
  • Jarek Sacha has made available a plugin for texture synthesis using image quilting.
  • Dimiter Prodanov contributed the Color Profiler plugin.
  • v1.33n, 22 October 2004
    • Added the setBatchMode() macro function. Five example macros are available: BatchModeTest, BatchModeCalculator, BatchMeasure, BatchSetScale and BatchRGBMeasure.
    • The getFileList() macro function removes files whose names start with ".".
    • The selectImage() macro function accepts a string argument.
    • Added the close() macro function.
    • Added the addResult("Label", row, string) macro function. The BatchRGBMeasure macro demonstrates how to use this new function.
    • Edit/Selection/Fit Ellipse and Edit/Selection/Convex Hull work with multi-point selections.
    • The "Summarize" option in Analyze/Analyze Particles summarizes stacks.
    • The "Area" parameter is automatically enabled when "Summarize" or "Size Distribution" is selected in the Analyze/Analyze Particles dialog.
    • Press 'Esc' to abort commands in the Process/Filters submenu.
    • Added the IJ.getImageCount() method.
    • Fixed bugs that caused Process/Filters commands, Copy, Paste and the Image Calculator to abort macros run from the command line.
    • Fixed a bug in Process/Filters/Unsharp Mask when used with RGB images with Rectangular selections.
    • Fixed a bug the caused the "Summarize" option in Analyze/Analyze Particles to note work correctly when analyzing a single image in a stack.
    • Fixed a bug in the addResult() macro function that sometimes caused leftover row labels.
    • Fixed a bug in Analyze/Tools/Scale Bar that caused it to fail when run from a macro.
  • v1.33m, 8 October 2004
    • Process/Image Calculator result images inherit the spatial calibration of the first source image.
    • The Image Calculator generates a 32-bit result if either input image is signed 16-bit.
    • Analyze/Label uses larger font sizes with images displayed using less than 100% magnification.
    • Printing works better, especially for large images.
    • Added "Rotate 90 degrees" option to File/Page Setup
    • File/Import/Image Sequence, File/New, Image/Stacks/3D Project and Image/Stacks/Reslice can be abort by pressing 'Esc'.
    • On Mac OS X, the status bar uses a smaller font.
    • Image/Stacks/Reslice shows required and available memory in the dialog, preallocates the output stack, and, with line selections, shows the area to sliced.
    • The DICOM reader now attempts to open all files with a ".dcm" extension.
    • File/New opens stacks faster when "Fill With:" is set to "Black" and it displays the elapsed time in the status bar.
    • Fixed a bug in Image/Stacks/Reslice that caused it to sometimes use the wrong display range for the output stack.
    • Fixed a bug that caused Analyze/Tools/Calibration Bar to not work correctly with nonlinear calibration functions.
    • Fixed a bug that caused the Mac OS X menu bar to disappear when the "B&C" window was active.
    • Worked around a Mac OS X bug that caused invalid text editor "Save Changes" dialogs.
  • Jérôme Mutterer contributed the Subtstack Select plugin.
  • v1.33l, 24 September 2004
    • Process/Subtract Background works with 16-bit images.
    • Rows in the "Results" table are renumbered after a Cut or Clear.
    • Analyze/Summarize works correctly after rows have been Cut or Cleared from the "Results" table.
    • Analyze/Summarize works correctly with line measurements.
    • Fixed a bug that could cause macros run from the command line to abort.
  • The ApplyDicomRescaleSlope macro multiplies images in a stack by the DICOM Rescale Slope value.
  • The JTwain plugin uses the Asprise JTwain library to acquire images from TWAIN sources.
  • Fabrice Cordelieres contributed the Manual Tracking plugin.
  • Noel Bonnet has made available plugins for anisotropic diffusion, shading correction, contrast enhancement, image gradients, segmentation and generating a toolbar.
  • v1.33k, 7 September 2004
    • The getProfile() macro function averages horizontally if preceded by setKeyDown("alt").
    • Added the getMinAndMax() macro function. See the DisplayRangeMacros for examples.
    • Added the ResultsTable.setLabel(String, row) method.
    • The "Interpolate" option in Image/Stacks/3D Project is ignored if the slice spacing (in pixels) is less than or equal to 1.0.
    • Fixed a bug that caused 0.5 to be added to 32-bit images rotated using Image/Rotate/Arbitrarily when "Interpolate" was selected.
    • Fixed a bug that could cause a "too many files open" error when attempting to open TIFF files.
    • Fixed a bug, when using ImageJ as a library, that prevented memory from being released when an image window was closed.
    • Fixed a bug in Image/Stacks/3D Project that caused color LUTs to not carry over to the projections stack if "Interpolate" was selected.
    • Worked around a Windows/Java 1.5 bug that caused Cntrl+V to fail in the editor (Plugins/Edit).
  • v1.33j, 18 August 2004
    • Analyze/Analyze Particles now works with 16-bit signed images.
    • For 16 and 32-bit images, Image/Adjust/Threshold now does a B&C "Reset" to work around a display range not equal to pixel value range thresholding bug.
    • File/Open opens the ZIP archives saved by the ROI Manager.
    • File/Save As/AVI and File/Import/Image Sequence now always display a progress bar.
    • Operations on stacks now always display a progress bar.
    • Added the setFont() macro function. See the TextDemo macro for examples.
    • Added the roiManager("Open", path) and roiManager("Save", path) macro functions.
    • Removed the "Thresh." and "Update" buttons from the Image>Adjust>Brightness/Contrast window. The DisplayRangeMacros replace the "Update" button.
  • v1.33i, 11 August 2004
    • Added the Edit/Selection/Specify command.
    • Macro shortcuts can override built in shortcuts. The KeyboardShortcuts macro file contains examples.
    • Ctrl-x, ctrl-v and ctrl-a (Cut, Copy and Select All) keyboard shortcuts work in the "Results" window.
    • Fixed a bug that prevented status bar display of calibrated frequency values as the cursor is moved over FFT images. The FFT Measurements example shows how to use this feature to measure distances between atomic planes in a TEM image.
    • Fixed a bug that caused Image/Stacks/3D Project to ignore selections when "Interpolate" was checked.
    • Fixed a bug (introduced in 1.33a) that sometimes caused DICOM images to be displayed incorrectly if the RescaleSlope tag was not 1.
    • Fixed a bug that sometimes caused DICOM window and level to be set incorrectly.
  • Michael Abramoff, Paulo Magalhaes and Sunanda Ram wrote an article about ImageJ:
          Abramoff, M.D., Magalhaes, P.J., Ram, S.J. "Image Processing
          with ImageJ". Biophotonics International, July 2004, pp. 36-42.
  • The ParticleCircularityHistogram macro calculates and displays a particle circularity distribution histogram.
  • Dirk Scheffler contributed the DICOM Directory Analyser plugin.
  • Scion released Windows and Mac OS X plugins for their Firewire cameras.
  • David Dunlap and Marco Caimi contributed the AVI Splitter plugin that opens an AVI file for viewing and allows the user to export one or more segments of the file to an ImageJ stack.
  • The Convert to 16-bit Signed plugin converts an unsigned 16-bit image into a signed 16-bit image.
  • v1.33h, 30 July 2004
    • Run a macro or plugin by clicking on an icon in the tool bar (example).
    • The "Fill With: White" option in Edit/New now works with 16-bit and 32-bit images.
    • The "Fill With: Clipboard" option in Edit/New displays a more helpful message when the internal clipboard is empty.
    • Added Edit/Select All command to text editor (Edit/New).
    • Message dialogs use anti-aliased text.
    • The command recorder displays an error message if it encounters a duplicate keyword.
    • Added the IJ.error(title, message) method.
    • Fixed a bug that caused macros to continue running after an error.
    • Fixed a bug that caused the command recorder to insert extra spaces in the options string.
  • Bertram Manz contributed the Bruker Opener plugin.
  • Gilles Carpentier created an AppleScript application for updating ImageJ on Mac OS X using drag and drop.
  • Christopher Philip Mauer contributed the 2D Hybrid Median Filter, 3D Hybrid Median Filter, RG2B Colocalization and RGB Zprojector plugins.
  • v1.33g, 15 July 2004
    • Extended the cross hair tool and renamed it "point selection tool". Shift-click to add a point. Double-click on the tool icon to configure. Use the getPolygon() method or getSelectionCoordinates() function to retrieve the points.
    • Analyze/Measure records point tool Z coordinates.
    • ROI Manager improvements:
      • ROIs added to the list are now bound to the stack slice.
      • List items are in the form YYYY-XXXX or SSSS-YYYY-XXXX, where SSSS is the slice number, YYYY is the y-center and XXXX is the x-center.
      • ROI modifications do not alter an ROI on the list unless "Update" is clicked.
      • Removed the "Rename" option. Use "Save" instead.
      • ImageJ keyboard shortcuts work when the ROI Manager is the active window.
    • Added support for numeric keypad macro shortcuts in the form "[n0]".."[n0]", "[n/]", "[n*]", "[n-]", "[n+]" and "[n.]"
    • Fixed a bug that generated redundant coordinates when using the freehand and freeline tools on magnified images.
    • Fixed a bug that caused the Prefs.set() method to fail with strings containing a backslash.
  • Gilles Carpentier created another example AppleScript application that opens an image in ImageJ and processes it. Requires Mac OS X 10.3
  • Marco Brugnara contributed the Contact Angle plugin.
  • The RoiManagerAddParticles macro demonstrates how to add particle analyzer outlines to the ROI Manager.
  • The LabelParticlesWithArea macro demonstrates how to label particles with the "Area" value.
  • v1.33f, 7 July 2004
    • Macros in "StartupMacros.txt" with the name "AutoRun" run when ImageJ starts up.
    • Added "Rename" to menu that pops up when you right click on an image.
    • Center of mass of RGB images is now calculated.
    • ROI Manager improvements:
      • "Add", "Add & Draw", "Measure", "Draw" and "Combine" are recordable.
      • "Select All" removed. Most functions now operate on all ROIs if no items on the list are selected.
      • "Open All" removed. "Save" now saves ROIs as a ZIP archive and "Open" opens ZIP archives.
      • "Fill" removed. Instead, use "Combine" and the Edit/Fill command.
      • List items are now in the form "TXXXX-YYYY", where T is the selection type, XXXX is the x-center and YYYY is the y-center.
    • Added the roiManager() macro function.
    • Worked around a Mac OS X pop-up menu bug.
  • v1.33e, 28 June 2004
    • With straight line selections, Analyze/Measure now records the angle.
    • Fixed several bugs that caused composite selections to be mistaken for line selections.
    • Fixed a bug that caused recording of "Apply" in Image/Adjust/Threshold to fail.
    • Fixed a bug that could cause File/Import/Image Sequence to fail if the number of images and a file name filter were specified in the dialog.
    • Fixed a bug that caused Edit/Clear Outside to not work with stacks.
    • Fixed a bug that caused some operations on stacks to fail with selections inverted using Edit/Selection/Make Inverse.
    • Fixed a bug that caused the getMask() method to sometimes return a mask with a null pixel array.
    • Fixed a bug that caused Help/About ImageJ to generate an exception when ImageJ was running as an applet.
  • Gilles Carpentier created an example AppleScript application that opens an image in ImageJ and processes it. Requires Mac OS X 10.3
  • Kai Uwe Barthel contributed the 3D Color Inspector plugin.
  • v1.33d, 18 June 2004
    • Added the open() macro function and IJ.open() method.
    • When using File/Open, the command recorder generates a call to open() instead of run().
    • The command recorder records Image/Adjust/Threshold as a comment.
    • Image/Stacks/3D Project of RGB images now works with rectangular selections.
    • Fixed a bug that caused ImageProcessor.setColor() to fail with thresholded images.
    • Fixed a bug that caused Image/Stacks/3D Project to fail when used from command line programs and macros.
    • Fixed a bug that caused plot windows to "popup" in command line programs and macros.
    • Fixed a bug that sometimes caused commands to abort if the user clicked on the active image.
    • Fixed a bug that caused Plot.setLimits() to sometimes fail.
  • The 3D-Distance-Tool macro measures the 3D distance between two points in a stack.
  • The LineAngleTool macro draws a line and measures the angle between that line and the vertical axis.
  • RunMacro program runs ImageJ macros from the command line.
  • v1.33c, 3 June 2004
    • The maximum number of decimal places that can be specified in Analyze/Set Measurements was increased from 8 to 9.
    • Added the IJ.runMacro(macro, arg) and IJ.runMacroFile(path, arg) methods.
    • The return statement, when not called in a function, now exits the macro. If the macro was called using IJ.runMacro() or IJ.runMacroFile(), it can also return a string value.
    • Added the getArgument() and setKeyDown() macro functions.
    • Fixed several bugs that caused exceptions or incorrect operation when processing images with non-rectangular selections extending beyond the edges of the image.
    • Fixed a bug that caused an exception if the ByteProcessor.putPixel() method was called with coordinates that were not inside the image.
    • Fixed a bug that caused Process/Filters/Mean to not work correctly with non-rectangular images if "Separable Square Mask" was checked.
  • v1.33b, 26 May 2004
    • Opens uncompressed 12-bit TIFFs, including TIFF stacks.
    • Pasted non-rectangular selections can be dragged beyond edge of image.
    • Copied selections larger than target image can now be pasted.
    • Fixed a bug that caused the "Results" window to be opened when using ImageJ as a library. The Command Line Example demonstrates how a Java program can use ImageJ as a library.
    • Fixed a bug that caused an exception when using Edit/Cut or Edit/Clear Outside with non-rectangular selections extending beyond the image boundary.
  • v1.33a, 19 May 2004
    • Adds the Rescale Intercept value (usually -1024 for CT) to DICOM images.
    • Calibration data in TIFF and DICOM images imported by File/Import/Image Sequence is now used.
    • Fixed a bug that caused most Process/Math commands to fail with 16-bit signed images.
    • Added the saveSettings() and restoreSettings() macro functions.
    • Image/Color/RGB merge works with 16 and 32 bit images and stacks.
    • With 16-bit signed images, the ImageProcessor putPixelValue() method now works symmetrically with getPixelValue().

  Version 1.32j, 12 May 2004

  • Tony Collins has assembled 98 plugins useful for microscopy and written an accompanying 45 page manual. The software and manual are available at http://www.uhnresearch.ca/facilities/wcif/download.php, or online at http://www.uhnresearch.ca/facilities/wcif/imagej/.
  • Pedro Ramos-Cabrer contributed the Slice Labeler plugin.
  • Thomas Stamm contributed the DICOM Sort plugin.
  • A Windows installer is now available that creates desktop and Start menu shortcuts, an uninstaller, and is 1.7MB smaller than the ZIP distribution. It was created using the Marner Java Launcher (ImageJ.exe) and the Inno Setup installer generator.
  • Fixed bugs in Image/Lookup Tables/Apply LUT and extended it to work with thresholded images. (j)
  • Fixed a bug Analyze/Analyze Particles that sometimes caused the "Summarize" option to fail if "Clear Results Table" was not checked. (j)
  • Dimiter Prodanov contributed the Color Histogram plugin.
  • Edoardo "Dado" Marcora wrote a small tutorial on how to use Jython with ImageJ.
  • Jeff hardin contributed the JMF Movie Player plugin.
  • Added the Edit/Options/Memory command for setting the Java heap size, which is the maximum amount of memory available to ImageJ. Requires Mac OS X or a version of ImageJ that was installed by the new Windows installer. (i)
  • The IJ.showMessage() method and the showMessage() macro function now display HTML formatted text. For examples, run the HtmlDialogDemo macro.
  • Plugins/Compile and Run now runs pre-compiled plugins (.class files). This allows running externally compiled plugins without having to restart ImageJ. (i)
  • Removed the "Create Plugin" button from Plugins/Macros/Record and added a "Name:" field and "?" button. Use the editor's Edit/Convert to Plugin command to convert a macro generated by the recorder into a plugin. (i)
  • Renamed Edit/Options/Miscellaneous as Edit/Options/Misc. (i)
  • Fixed a macro bug that caused run() commands to fail if the ending of a keyword in the options string was the same as another keyword. (i)
  • Fixed a bug in the PluginClassLoader that could case loading of resources from JAR files to fail. (i)
  • When running Java 1.4.1 or later, or a version of ImageJ installed by the new Windows installer, ImageJ can display the maximum available memory and the percent memory used. The Window/About ImageJ and Plugins/Utilities/ImageJ Properties commands, and the status bar when it is clicked, display a string in the form "22MB of 600MB (4%)". The Plugins/Utilities/Memory Monitor tool displays the percent memory used. (h)
  • The "Out of memory" error message now displays the amount of memory available to ImageJ, which is approximately equal to the amound set by the -Xmx command line option. (h)
  • Added the "Black Canvas" option to the Edit/Options/Image dialog. (h)
  • Moved the "Interpolate Images<100%" and "Open Images at 100%" options from Edit/Options/Misc to Edit/Options/Image. (h)
  • Fixed a bug in Process/FFT/Inverse FFT that could cause it to fail if there was a selection. (h)
  • Fixed a bug that could cause a blank error dialog box to be displayed when opeing a TIFF. (h)
  • Added the Edit/Options/Conversions command, which displays a dialog with "Scale When Converting" and "Unweighted Color To Grayscale Conversions" options. (g)
  • On Windows, the Help/ImageJ Web Site and Help/Online Docs commands no longer cause the DOS window to open. (g)
  • File/Import/URL will open a Web page in the default browser if the specified URL ends in "/". (g)
  • Analyze/Calibrate now displays the correct Rodbard equation. (g)
  • Macros located in the plugins folder or sub-folder, with at least one underscore in the name, are installed when ImageJ starts up. (g)
  • Added the Plugins/Macros/Run command. (g)
  • Added the setupUndo() macro function. For an example, see the DrawingTools macros. (g)
  • The makeSelection() macro function now accepts a numeric selection type. See the ScaleSelection macro for an example. (g) macros. (g)
  • Added the "D" (draw dot) command to the tool macro icon description language. (g)
  • Speeded up the macro language return statement. (g)
  • Fixed a macro language bug that caused comparisons of strings longer than eight characters to fail. (g)
  • Fixed a bug that prevented macro language calculator mode statements from starting with "(". (g)
  • Fixed a bug that caused Process/Binay/Threshold to fail with contrast enhanced images. (g)
  • Fixed a bug that caused Process/Enhance Contrast to not work as expected when the "Saturated Pixels" parameter was zero. (g)
  • Fixed a bug in the fromCharCode() macro function that caused it to return extra characters. (g)
  • Fixed a bug that caused Help/ImageJ Web Site and Help/Online Docs to fail on Windows Me. (g)
  • Fixed a bug that caused text file larger than 60K to fail to open on Windows Me. (g)

  • Added the getDirectory(), getFileList(), getPixelSize(), startsWith() and endsWith() macro functions. The ListFilesRecursively and ShowImageInfo demonstrate how to use these functions. (f)
  • Image/Stacks/Make Montage displays slice labels, if available, instead of slice numbers. (f)
  • Fixed a bug that caused incorrect display of results table row labels with DICOM and FITS images. (f)
  • Fixed a bug in Image/Stacks/Plot Z-axis Profile that caused incorrect display of results table row labels. (f)
  • Added the Open() method to the DICOM class. (f)
  • Added the setNormalize() method to the DICOM class. (f)
  • Gali Baler contributed the Exif_Reader plugin for extracting EXIF metadata from digital camera images.
  • Cezar M. Tigaret contributed the ShapeRoi class that gives ImageJ the ability to add/subtract selections and to invert selections. (e)
  • Hold down the shift key to add to a selection and the alt key to subtract from it. Requires Java 1.2 or later. (e)
  • Added the Edit/Selection/Invert Selection command. Requires Java 1.2 or later. (e)
  • Added the Plugins/Utilities/Capture Screen command, which was written by Gali Baler. Requires Java 1.3 or later. (e)
  • Added a "Combine" option to the ROI Manager. (e)
  • Added a "Convert to RGB" option to Import/Image Sequence. (e)
  • Added the getThreshold(lower, upper) macro function. (e)
  • The number of decimal places used for scale (resolution) values displayed by Analyze/Set Scale and Image/Show Info are increased as needed. (e)
  • The selectWindow("title") macro function now waits up to four seconds. (e)
  • Fixed a bug in the isOpen() macro function that caused it to fail when the argument was a string variable. (e)
  • Fixed a bug that caused Roi Manager's "Save" function to corrupt the ROI list if the user canceled the save. (e)
  • Dimiter Prodanov contributed an example that shows how to link ImageJ to a RDBMS engine like MySQL.
  • Tony Collins and Tony parker have made available an enhanced version of the Dispose All Windows plugin that allows the user to select windows to be closed.
  • Analyze/Label now works with the particle analyzer. (d)
  • Fixed a bug in v1.32c that sometimes caused the ColorProcessor.fill(mask) method to fail. (d)
  • Fixed a bug in v1.32c that caused Image/Adjust/Canvas Size to fail on Mac OS 9. (d)
  • Ulf Dittmer enhanced the Prefs class to allow plugins access to the ImageJ preference file ("IJ_Prefs.txt") and contributed the Preference Demo plugin that demonstrates how to save and restore user preferences. (c)
  • Added the Image/Color/Edit LUT command, written by Gali Baler. (c)
  • Added the Analyze/Label command. As a shortcut, press alt-d. Press alt-m, alt-d to measure and label. (c)
  • Edit/Draw labels the selection with the current measurement number if the alt key is down. (c)
  • Added a "Zero Fill" option to Image/Adjust/Canvas Size. (c)
  • Moved Analyze/Show LUT to Image/Color/Show LUT. (c)
  • Masks are now 8-bits. Roi.getMask(), ImagePlus.getMask() and ImageProcessor.getMask() return a ByteProcessor instead of int[]. ImageProcessor.setMask(), ImageProcessor.getHistogram(), ImageProcessor.fill() and ImageProcessor.reset() now expect a ByteProcessor argument. Added the ImageProcessor.getMaskArray() method which returns a byte array. The background pixels in a byte mask are zero. Plugins resident on the ImageJ Web site that use masks (e.g., Stack Histogram, Stack Normalizer and Color Comparison) and have been updated to use byte masks. (c)
  • Filling and drawing of ellipses is faster and the rendering is exactly the same way on all platforms. (c)
  • Fixed a bug that caused importing of 1 bit stacks to fail. (c)
  • Fixed a bug that caused an invalid error message when opening 1 bit TIFFs. (c)
  • Fixed a bug that caused histogram bin start values of 16 bit signed images to be truncated. (c)
  • Fixed a bug that caused the "Apply" option in Image/Adjust/Contrast/Brightness to fail with non-rectangular selections. (c)
  • Fixed a bug that prevented the command execution time from being displayed in the status bar if there was a selection. (c)
  • The length of freehand lines used by Image/Stacks/Reslice is now the same as that reported by the Measure command. (c)
  • File name extensions ending in a digit are no longer hidden when "Show Label" is checked in Analyze/Set Measurements. (c)
  • Worked around an OS X/Java 1.4 bug that caused particle labeling to fail. (c)
  • Worked around an OS X/Java 1.4 bug that sometimes caused the text tool to enter an extra "d". (c)
  • Worked around an OS X/Java 1.4 bug that caused interactive thresolding of 16 and 32 bit images to fail. (c)
  • Matt Daniels contributed the Spectrum Extractor plugin.
  • Brigitte Forster et al. of the Swiss Federal Institute of Technology Lausanne have made available the Extended Depth of Focus plugin.
  • The PNG Writer plugin saves images in PNG format on systems running Java 1.4 or later.
  • Moved the Image/Benchmarks commands to a package of plugins and added the Plugins/Utilities/Benchmark command. (b)
  • Multiple files can be selected (by shift-clicking) and opened using File/Open if "Use JFileChooser" is enabled in Edit/Options/Miscelleaneous. (b)
  • Plugins packaged in a JAR file are installed in submenus corresponding to the folder that contains the JAR file if the *'plugins.config' in the JAR file does not specify a menu. (b)
  • Plugins>Utilities>ImageJ Properties displays a few more properties and, if the alt key is down, displays all Java properties. (b)
  • Keyboard shortcuts now work when the "Results" window is active. (b)
  • Added a "Start At" option to File/Save As/Image Sequence. (b)
  • Added a "Border Width" option to Image/Stacks/Make Montage. (b)
  • XOR mode rubber banding no longer used by the polygon, polyline and angle tools, working around XOR drawing bugs on Mac OS X. (b)
  • Trevor Croft contributed an improved File/Open FITS reader. (b)
  • Fixed a bug that caused the '<' and '>' shortcuts to fail to work after using the slice selector scroll bar. (b)
  • Fixed a bug that caused the angle tool to fail for angles of 0 and 180 degrees. (b)
  • Clones of the Roi classes are serializable. (b)
  • Added the the getPolygon() method to the Roi class and the SetRoi(Polygon), setRoi(Roi), drawPolgon() and fillPolygon() methods to the ImageProcessor class. (b)
  • ResultsTable.getValue() throws an exception i f the column name is not valid. (b)
  • Adam Baker contributed the Quicktime Still Extractor plugin.
  • Stirling Churchman contributed a plugin that opens Andor .SIF files.
  • Erik Meijering has made available NeuronJ, a plugin for neurite tracing and quantification.
  • Jerek Sacha contributed the Maximum Entropy Threshold plugin.
  • Plots generated by Analyze/Gels/Plot Lanes are now normalized when plotting OD calibrated images. (a)
  • Selecting a line in the "Results" window no longer requires dragging the mouse. (a)
  • Tool descriptions displayed in status bar as cursor moves over tool bar. (a)
  • Fixed a bug in File/Save As/AVI that caused it to create AVI files that could not be opened by the Windows Media Player if the stack's frame rate was less than 1.0. (a)
  • Fixed a bug that caused plugins to fail to load if a folder in the plugins folder was not readable. (a)
  • Worked around a Mac OS X/Java 1.4 bug that caused labeling done by the Analyze/Gels commands to fail. (a)
  • Fixed a bug that caused Process/Binary/Skeletonize to sometimes reduce 45 degree lines to a single pixel. (a)
  • Fixed a bug that caused Process/Smooth, Process/Sharpen and Process/Find Edges to throw an exception with one pixel wide images. (a)

  Version 1.31v, 4 February 2004

  • The OS X version of ImageJ has a new icon based on a photograph by Tom Grill of a Hartnack microscope, circa 1870's, at www.arsmachina.com.
  • Albert Cardona has made available a 3D Editing plugin.
  • Jerome Mutterer and Christophe Laummonerie contributed the RGB Profiler and Colocalization Finder plugins.
  • Cezar M. Tigaret contributed a greatly improved Plugins/Utilities/Control Panel command that displays all ImageJ commands in a hierarchical tree structure. (v)
  • Process/Binary/Erode, Dilate, Open, Close and Skeletonize now process edge pixels. (v)
  • Added the Process/Math/Abs command. (v)
  • Added the Edit/Zap Gremlins command to the text editor. (v)
  • Menu keyboard shortcuts, when used with the control key held down, no longer sometimes run commands twice. Note that, except when using the text tool, there is no need to hold down the control or command key when using keyboard shortcuts. (v)
  • Attempts to do 16-bit to 16-bit and 32-bit to 32-bit conversions no longer generate an error message. (v)
  • Fixed a bug that sometimes caused the alt key to appear to be stuck down. (v)
  • Double-clicking in the Color Picker (Image/Color/Color Picker) brings up a dialog with sliders for selecting RGB values. (u)
  • For 32-bit images, Analyze/Histogram displays a dialog that allows the user to specify the number of bins and the range of values to be included in the histogram. (u)
  • Removed the "Real Histogram Bins" option from the Edit/Options/Miscelleaneous dialog. (u)
  • For 16 and 32 bit images, the column label in files created by the Histogram window "List" option changed from "value" to "bin start". (u)
  • The mode of 16-bit images is now the most frequently occuring pixel value rather than the start of the histogram bin with the largest count. (u)
  • Process/Binary/Watershed now uses the Process/Binary/Options dialog. (u)
  • Fixed bugs in Process/Noise/Despeckle that caused it to fail with 8-bit stacks and to not process pixels along the edges of 8-bit images. (u)
  • Spatial calibration of images with pixelWidth=1, pixelHeight=1 and pixelDepth!=1 now works as expected. (u)
  • Fixed a bug in Analyze/Analyze Particles that erased outside the ROI if "Cancel" was selected in the "Save?" (Results) dialog. (u)
  • Shanrong Zhang contributed plugins that open multiple image files from Varian MRI imaging systems and EVS 900 micro-CT systems.
  • Ulf Dittmer added ICO support to the Jimi Writer plugin.
  • Eric Kischell (keesh) contributed the Grid Cycloid Arc plugin.
  • Added the Image/Color/Color Picker tool, written by Gali Baler, and retired Image/Colors. Press shift-k to activate the new color picker. (t)
  • Fixed a bug that caused the dynamically updated X and Y values in plot windows to sometimes be invalid. (t)
  • Dimiter Prodanov contributed the GrayMorphology plugin.
  • Jerome Mutterer contributed a macro that draws the Mandelbrot set.
  • Christopher Mei contributed the Anisotropic Diffusion, Mixture Modeling, Otsu Thresholding and Watershed Algorithm plugins.
  • The text editor's Save As command is better at choosing the initial directory. (s)
  • The Roi clone() method, used by Edit/Selection/Restore Selection, now correctly duplicates polygon and poly-line selections. (s)
  • Worked around a bug that could cause some of the Image/Lookup Tables commands to fail with some JVMs. (s)
  • Fixed a bug in Image/Adjust/Canvas Size that caused it to fail with non-displayed images. (s)
  • Fixed a bug that caused the macro recorder to fail with dialogs containing a single checkbox. (s)
  • When using ImageJ as a library, the "Results" window can be displayed without the "ImageJ" window being open. (s)
  • Added the "Use JFileChooser" option to Edit/Options/Miscelleaneous. Upgrading to the OS X/Java 1.4.1 version of ImageJ and enabling this option may reduce the likelihood of ImageJ crashing on Panther (Mac OS X 10.3). (r)
  • Hold down the control key to create centered rectangular and oval selections. This feature, which currently does not work on the Mac, is based on code contributed by Richard Bonnaire. (q)
  • The image size at the top of image windows is in megabytes for image >= 1024K. (q)
  • The "Black Background" option in Process/Binary/Options is saved in the preferences file. (q)
  • Image/Stacks/Reslice, with RGB stacks, is faster and uses less memory. (q)
  • Replaced the "1/2 Size" option in File/Import/Image Sequence with a more flexible "Scale" option and fixed a bug that caused memory sizes greater than 2GB to not display correctly. (q)
  • Fixed a bug that caused run() macro functions to fail if an option keyword was repeated in the options string. (q)
  • The Virtual Stack Opener opens an image sequence as a "virtual" (disk-resident) stack.
  • Paulo Magalh�es contributed the Ratio Plus plugin, which calculates the ratio between two images or stacks, as used in Fura-2 experiments.
  • The JAR Plugin demonstrates how a plugin can be packaged in a JAR file and installed in multiple menus.
  • Kurt De Vos contributed the Excel Writer plugin. This is the first plugin packaged as a JAR file. It requires ImageJ 1.31p or later.
  • Adam Baker contributed the Radial Grid plugin.
  • The PolygonArea macro calculates the area of a selection and compares it to the area calculated by the Measure command.
  • ImageJ can install plugins packaged in a JAR file. There is an example. (p)
  • Added the getBoolean() macro function. (p)
  • The "List" option in Analyze/Histogram, with calibrated 8-bit images, now displays both calibrated and uncalibrated values. (p)
  • A macro error is displayed when the options string in a run() call contains an invalid numeric value. (p)
  • Plugins/Edit displays an error message when the user attempts to overwrite a write-protected file. (p)
  • Worked around OS X/Java 1.4 bugs in Analyze/Surface Plot, Plugins/Utilities/Monitor Memory and the freehand selection tools. (p)
  • Jeff Hardin updated the QuickTime Movie Opener and Movie Player plugins to work with Java 1.4.x on OS X.
  • Joachim Walter contributed the HyperVolume Opener plugin.
  • Added an example plugin that demonstrates how to display a grid of numeric fields in a dialog box.
  • A Java 1.4.x version of the OS X ImageJ application that may run more reliably on Panther is available on the Download page.
  • Kevin (Gali) Baler contributed a plugin for drawing dotted and dashed lines.
  • Added Process/Binary/Fill Holes, based on code contributed by Gabriel Landini. (o)
  • Process/Binary/Options allows the user to specify the background color (black or white) of binary images. (o)
  • Daniel Tyreus rewrote the PluginClassLoader so it can read jar files and non .class resources (images, config files, etc) from the plugins folder. Everything except the actual class that extends PlugIn can now be placed in a jar file anywhere in the plugins folder or immediate subfolders. JavaDocs are available. (n)
  • Polygon filling is now done using Java code instead of java.awt.Graphics.fillPolygon(). The new fill routine is faster, uses less memory, and works the same way on all platforms. Since Analyze/Measure does polygon filling, this means that measurement results are exactly the same on all platforms. (n)
  • Analyze/Analyze Particles is faster due to the new polygon filler. (n)
  • Worked around several Java 1.4.1 on Mac OS X problems. (n)
  • Fixed a bug that could cause ImageJ to hang when quitting on Mac OS X. (m)
  • Added the Edit/Selection/Create Mask command. (m)
  • Added a "Redirect To" option in Analyze/Set Measurements. (m)
  • Changed the "Filled" option in Analyze/Analyze Particles to "Masks". (m)
  • The Cooke Corporation released Windows plugins for their SensiCam and PixelFly cameras. Plugins for Mac and Linux are under development.
  • Kevin (Gali) Baler contributed the Z Profiler plugin.
  • Added the drawPlot() method to the PlotWindow class. See the Z Profiler plugin for an example.
  • Fixed a bug, introduced in v1.31j, that caused the substring(), lastIndexOf(), charCodeAt(), split(), makeSelection() and indexOf() macro functions to fail. (l)
  • Added "Open..." and "Save..." buttons to the Process/Convolve and Analyze/Calibrate dialog boxes. (l)
  • Added new calibration function, y = a+b*ln(x-c), useful for calibrating to OD standards. (l)
  • The Invert, Smooth, Sharpen, Find Edges, Add Noise and Despeckle commands no longer attempt to process 8-bit true color images. (l)
  • Plugins/Edit now opens files with upper case extensions. (l)
  • Image/Stacks/Convert Images to Stack now ignores any open stacks. (l)
  • Added the setZCoordinate() macro function. For an example, check out the Z Profile Plotting Tool. (l)
  • Added the addPanel() method to the GenericDialog class. (l)
  • Erik Meijering has made available RandomJ, a collection of plugins (Binomial, Exponential, Gamma, Gaussian, Poisson and Uniform) for image randomization.
  • Added a collection of macro plotting functions. Refer to the ExamplePlots macro file for examples. (k)
  • Plots created using the Plot class are clipped to the frame. (j);
  • Image/Adjust/Threshold auto-adjusts the threshold when it first "sees" a new image. (j)
  • The mean, min, max, mode or stddev of the pixels along a line selection are measured if the parameter is selected in Analyze/Set Measurements.
  • Added the "List Values" checkbox to Edit/Options/Profile Plot Options. (j)
  • Added the Dynamic Profiler plugin.
  • Walter O'Dell contributed the DICOM Rewriter plugin for anonymizing DICOM files.
  • Fixed a bug in v1.31h that caused images opened by macros to not be refreshed. (i)
  • Added a "Median" options to Image/Stacks/Z Project. (h)
  • File/Import/URL "remembers" the URL. (h)
  • Added a "White Background" checkbox to Process/Binary/Distance Map, Ultimate Points and Watershed. (h)
  • Worked around a bug that caused the Brightness/Contrast and Threshold windows to not display correctly with Java 1.4.1 on Mac OS X. (h)
  • Added a "Selection Only" option to the File>Page Setup dialog. (h)
  • Fixed a bug that caused File/Import/Image Sequence to fail to work with PGM files. (h)
  • Added the Animated Sine Wave plugin.
  • Added the Edit>Selection>Convex Hull command. (g)
  • Added the Edit>Selection>Fit Ellipse command. (g)
  • Added a "Normalize" option to Process>Enhance Contrast. (g)
  • Added the Process>Math/NaN Background command which sets non-thresholded pixels in float images to the NaN (Not a Number) value. For float images, the "Apply" option in Image/Adjust Threshold runs this command. (g)
  • Added the setResult() and updateResults() macro functions. Refer to the Convexity and Solidarity macro for an example. (g)
  • Audrey Karperien contributed the Named Measurement plugin.
  • Added the "Process Entire Stack" checkbox to the Image/Scale dialog box. (f)
  • The commands in the Process/FFT submenu work with RGB images and images that are not a power of 2 size. (f)
  • Process/Filters/Unsharp Mask is faster and uses less memory. (f)
  • Fixed a bug that caused ImageJ to crash when it was run from the command line while in the plugins directory. (f)
  • Added the Process/FFT/FD Math command, which does frequency domain auto-correlation, cross-correlation, convolution and deconvolution. (e)
  • Fixed bugs in and enhanced the commands in the Process/FFT submenu. (e)
  • Fixed a bug that caused the run("Paste") macro function to not work reliably. (e)
  • Gabriel Landini has made available a collection of macros, including Laplacian, Prewitt, Roberts and Sobel filters, and John Conway's game of life.
  • Fixed a bug in File/Save As/BMP that caused it do save 8-bit images incorrectly. (d)
  • Added a "32-bit Result" option to Process/Image Calculator. (d)
  • The default divide-by-zero value used when dividing 32-bit (float) images is infinity. (d)
  • On Mac OSX, the preferences file (IJ_Prefs.txt) is saved in [home]/Library/Preferences. (d)
  • Interpolation is disabled when "One Polygon Per Line" is checked in Analyze/Surface Plot.
  • Added the getResultsTable() static method and the getValue(String, int) instance method to the ResultsTable class. (d)
  • Kunito Yoshida contributed a plugin for acquiring images using the SensiCam long exposure Camera.
  • The HandleExtraFileTypes plugin upgraded to work with images that have text headers. (c)
  • The main ImageJ window, except on the Mac, is now resizable. (c)
  • The standard deviation used by Process/Noise/Add Specified Noise is saved in the preference file.
  • The URL of the images in the File/Open Samples submenu is displayed by Plugins/Utilities/ImageJ Properties. (c)
  • 48-bit RGB TIFFs are opened as 16-bit stacks. (c)
  • Fixed a bug that caused ImageJ to hang when opening an image with a height more than about 20 time higher than the height of the screen. (c)
  • Selections can now have names. The File/Open, File/Save As Selection, Image/Show Info, Analyze/Measure and Analyze/Tools/ROI Manager commands were extended to support this feature. (c)
  • Made several improvements to Analyze/Tools/ROI Manager, including a new "Rename" option. (c)
  • Jeffrey Kuhn's Resize Canvas plugin is now built in as the Image/Adjust/Canvas Size command. (c)
  • Added the Process/Filters/Variance command. (c)
  • Added the Process/Filters/Show Circular Masks command. (c)
  • Fixed a macro image open synchronization bug on Mac OS X. A test case is available. (c)
  • Added the setValueUnit() method to the Calibration class. (c)
  • Added the getXValues() method to the PlotWindow class. (c)
  • Added the WandAutoMeasure tool macro.
  • Fixed a bug that could cause ImageJ running on OS X to hang when quitting. (b)
  • File/Import/LUT opens lookup tables in text format. (b)
  • Added the Process/Binary/Watershed command. (b)
  • Added "List" option to the Analyze/Show LUT widow. (b)
  • Plugins that call IJ.run() are now recorded correctly. (b)
  • 1.5 and 2.5 radius circular masks used by Process/Filters commands are no longer identical to 1.0 and 2.0 radius masks. (b)
  • Added the makeSelection() macro function. (b)
  • The segment length and angle are displayed in the status bar as polygon and segmented line selections are being created. (b)
  • File/New settings are saved in the preferences file. (b)
  • The frame rate in Image/Stacks/Animation Options can now be set as low as 0.1 fps. (b)
  • Process/Filters/Mean is much faster for large kernels. (b)
  • Added the Graphic Overlay plugin.
  • Fixed a bug that caused the run("Image Sequence...", "open=...") macro function to fail when importing DICOM images. (a)
  • Fixed a bug with the getInfo() macro function that caused an exception when the active image contained a selection. (a)
  • The makeRectangle() and makeOval() macro functions delete the current selection if the width or height argument is less than one. (a)

  Version 1.30v, 3 July 2003

  • Added the IPLab Reader plugin.
  • Gregory Jefferis contributed the HandleExtraFileTypes plugin.
  • Added support for the HandleExtraFileTypes plugin. (u)
  • Image/Adjust/Brightness/Contrast now works with 8-bit images with Java 1.4. (u)
  • Added "Label All Slices" option to Analyze/Tools/Scale Bar. (u)
  • Renamed File/Save As/ROI as File/Save As/Selection and extended it to support all selection types. (u)
  • Fixed setLocation() macro function. (u)
  • File/Save As/Image Sequence displays an error if the number of digits used to generate file names is insufficient. (t)
  • The "Apply" function closes the Image/Adjust/Thresold window. (t)
  • Image/Duplicate preserves DICOM header information. (t)
  • 16-bit to 8-bit scaling improved. (t)
  • Anthony Padua and Daniel Barboria contributed the Substack Maker plugin.
  • Angelo Taibi contributed the Dual-Energy plugin.
  • Gregory Jefferis has written a plugin to import DM3 transmission electron microscope images.
  • Replaced Process/Equalize with Process/Enhance Contrast. (s)
  • File/Import/URL opens DICOMs. (s)
  • Plugins/Edit and Plugins/Compile and Run are recordable. (s)
  • The first <<out of memory>> message refers to rsb.info.nih.gov/ij/docs/install/. (s)
  • Joachim Walter's FFT Filter plugin is now built in as the Process/FFT/Band-pass Filter command. (r)
  • Added the addNumericField(label, default, digits, columns, units) method to the GenericDialog class. See the Process/FFT/Band-pass Filter dialog for an example of how it can be used. (r)
  • The path keyword recorded by file open and save dialogs is now the first word of the dialog title instead of "path". (r)
  • Plugins/Utilities/ImageJ Properties works when ImageJ is running as an applet. (r)
  • Sonia Choubrac et al. contributed the Renal Function and Urinary Excretion plugins.
  • Julio Cabrera contributed a texture analysis plugin.
  • Dimiter Prodanov contributed the Granulometry plugin.
  • Fixed a bug that caused incorrect histograms of non-rectangular selections that extended beyound the image boundary. (q)
  • Plot window coordinates are displayed with more precision and the "List", "Copy" and "Save" options use the decimal places specified in Analyze/Set Measurements. (q)
  • The y-value interactively displayed in plot windows is now the graph y-value instead of the cursor y-value. (q)
  • Changing "Decimal Places" in Analyze/Set Measurements no longer opens an empty "Results" window. (q)
  • Image/Color/RGB Split (Merge) now maintain spatial calibration. (q)
  • Plugins/Utilities/Commands renamed List Commands and Plugins/Utilities/Shortcuts renamed List Shortcuts. (q)
  • Image/Stacks/Z Project works with RGB stacks. (q)
  • Fixed Analyze/Tools/Scale Bar Undo bug. (q)
  • Pasted rectangular selections can be dragged beyond the image edge. (q)
  • The ImagePlus getOriginalFileInfo() method works with stacks opened using File/Import/Image Sequence. (q)
  • Updated the example servlet to use Sun's JPEGImageEncoder.
  • Jarek Sacha created a packaged version ImageJ 1.30q that can easily be installed on the Sharp Zaurus PDA.
  • Daniel Sage et al. of the Swiss Federal Institute of Technology Lausanne have written fractional splines and wavelets plugins.
  • Christopher Philip Mauer contributed the Kalman Filter plugin, which removes noise from time lapse image streams.
  • The ImageProcessor putPixel() method now clips values outside the range 0-255 (8 bit images) and 0-65535 (16 bit images). (p)
  • ImageJ now executes macros passed on the command line. For example,
        java -cp ij.jar ij.ImageJ script.txt
    causes ImageJ to run the macro script.txt on startup. (p)
  • The ReturnStatements.txt macro demonstrates the use of return statements to return arrays and strings. (p)
  • ShowPath.txt macro demonstrates how to retrieve the path. (p)
  • The message "1 macro installed" no longer displayed when opening text files. (p)
  • Kurt DE Vos contributed the Image Viewer plugin.
  • Jerome Mutterer contributed the Guess RAW plugin.
  • Improved macro run-time error checking. (o)
  • Added the split() macro function. (o)
  • Copying the contents of text windows such as "Results" to the clipboard is now faster and more reliable. (o)
  • Analyze/Tools/ROI Manager and Edit/Options/Fonts are now listed in the Window menu. (o)
  • Walter O'Dell contributed the Contour Plotter plugin.
  • Added Process/FFT submenu. (n)
  • Added the indexOf(s1,s2,fromIndex) macro function. (n)
  • Image/Type/8-bit Color is now always check if the active image's LUT has any color entries. (n)
  • Fixed a bug in File/Import/Image Sequence that caused an exception if ImageJ was not able to open any images in the specified folder. (n)
  • Anthony Padua contributed the Query DICOM Header plugin.
  • Pierre Bourdoncle and Christophe Chamot contributed the Colocalization plugin.
  • File/Import/Image Sequence saves DICOM and FITS header information in the stack so Image/Show Info can display header information for each image. (m)
  • Added the File/Save As/Text command for saving the contents of TextWindows such as "Log" and "Info for XXX". (m)
  • The selectWindow() macro function and the File/Close command now work with non-image windows. (m)
  • Added the getInfo() macro function. (m)
  • Moved the Select All, Select None and Restore Selection commands to the new Edit/Selection submenu. (m)
  • Added the Edit/Selection/Fit Spline command, which is based on code contributed by Eric Kischell and John Bradley (author of XV). (m)
  • Added BMP option to File/Save As/Image Sequence. (m)
  • File/Import/Image Sequence no longer display "Unable to open" messages for files with names starting with a period. (m)
  • Image/Stacks/Z project now carries over calibration to the projection image. (m)
  • Tony Parker created a plugin that extends and improves the Stacks/3D Project command.
  • Fixed a bug that caused the setPasteMode("Multiply") macro function to fail. There is a test case at PasteControlDemo.txt. (l)
  • Rectangular, oval, polygon, straight line, segmented line and angle selections can now be edited by dragging "handles". The cursor changes to a hand when the mouse is over a handle. (l)
  • Tool macro options can be set by double-clicking on the tool icon. For examples, see LineTool.txt and SprayCanTool.txt. (l)
  • Tool macros now draw using the current foreground color. (l)
  • Patrick Pirrotte & Jerome Mutterer contributed the HyperVolume Browser plugin.
  • Added support for tool macros. For examples, see Tools.txt, PencilTool.txt and CircularSelectionTool.txt. (k)
  • Added the getSelectionCoordinates() macro function and removed the nCoordinates function and the xCoordinates and yCoordinates built in arrays. See SelectionCoordinates.txt, ConvexHull.txt and FeretsDiameter.txt for examples. (k)
  • The "Auto" function in Image/Adjust/Threshold now works with 16-bit images. (j)
  • Fixed a bug in Analyze/Analyze Particles that could cause invalid results when working with a selection. As a result of the fix, particles are now clipped at the selection boundary. (j)
  • Fixed a bug in The ROI Manager that could cause the "Measure" function to not work correctly when measuring a single slice in a stack. (j)
  • Added the getLut() and setLut() macro functions. See LookupTables.txt for examples. (j)
  • Eric Kischell contributed the Joel Time Stamper plugin which adds time annotation to images opened from a list.
  • Patrick Pirrotte & Jerome Mutterer contributed the LUT Panel plugin which provides fast access to LUT functions and a LUT editor.
  • When using the text tool, alt-m or alt-u displays the micron symbol and alt-shift-a displays the Anstrom symbol.
  • Enter "A" as the unit of length in Analyze/Set Scale or Image/Properties and it will be converted to the Angstrom symbol. Enter "um" and it will be converted to "�m".
  • Added "Open Images at 100%" option to Edit/Options/Miscellaneous. (i)
  • Added "Hide Text" option to Analyze/Tools/Scale Bar. (i)
  • The "Auto" option in Image/Adjust/Threshold works with 16-bit images. (i)
  • Added getBoundingRect(), indexOf(), lastIndexOf(), substring(), fromCharCode() and charCodeAt() functions to the macro language. (i)
  • Analyze/Histogram no longer ignores the "Limit to Threshold" measurement option. (h)
  • File/New uses a progress bar when creating stacks. (h)
  • "Out of memory" errors now displayed in "Log" window. (h)
  • Added getHistogram(), getLine() and getVoxelSize() functions to the macro language. (h)
  • Moved Plugins/Record to Plugins/Macros/Record. (h)
  • PixelSmart released an ImageJ plugin for their line of video frame grabbers cards (Windows only).
  • Added the Plugins/Macros/Install Macros command. (g)
  • Macros in the file ImageJ/macros/StartupMacros.txt are automatically installed in the Plugins->Macros submenu at startup. (g)
  • Added the File/Save As/BMP command. (g)
  • ImageJ now opens 32-bit (BGR0) BMP images. (g)
  • The "Limit to Threshold" option in Analyze/Set Measurements now works with 32-bit floating-point images. (g)
  • Pixels with a value of Float.NaN (0f/0f), Float.POSITIVE_INFINITY (1f/0f) or Float.NEGATIVE_INFINITY (-1f/0f) are ignored when making measurements on 32-bit images. (g)
  • Added support for macro keyboard shortcuts. For examples, see Shortcuts.txt. (e)
  • User-defined macro arrays are now typeless. For an example, see Arrays.txt. (d)
  • Added the getCursorLoc(x,y,z,flags), getImageID(), selectImage(id), isOpen(id), isActive(id) and atan(angle) macro functions. (e)
  • Added the Angle tool. (d)
  • Process/Noise/Add Noise and Process/Noise/Add Specified Noise work with 16 bit images. (d)
  • Process/Noise/Despeckle works with 16 and 32 bit images. (d)
  • Displays an error if the "Width", "Height" and "Offset" fields in the File/Import/Raw dialog are not consistant with the file size. (d)
  • ImageJ opens 3D FITS data sets and opens FITS files more reliably thanks to code contributed by Alex Cabello. (c)
  • Fixed a bug that caused the "Global" option in Analyze/Set Scale and Analyze/Calibrate to not work as expected. (c)
  • Added the newArray(size), getProfile() and setLocation(x,y) macro functions. (c)
  • Added the Image/Lookup Tables/Apply LUT command. (c)
  • Added "Flip Vertically" and "Rotate 90 Degrees" options to the Image/Stacks/Reslice command. (c)
  • The offset field in the File/Import/Raw dialog can now be greater than 2,147,483,648 (2GB). (c)
  • Added the changeFont() and setLineWidth() methods to the PlotWindow class. The Example Plot plugin demonstrates how to use these methods. (c)
  • Fixed a bug in Image/Adjust/Threshold that sometimes caused incorrect display and plotting of the threshold levels of 16 and 32 bit images. (c)
  • The "Set" option in Image/Adjust/Threshold, when used with 32-bit images, is now recorded correctly. (c)
  • Processing of entire stacks in Image/Scale is now optional. (b)
  • Fixed a bug, introduced in 1.29d, that caused Image/Scale to work incorrectly if the Y Scale was less than one and "Create New Window" was not checked. (b)
  • Fixed a bug that caused "wand error" messages when using Analyze/Analyze Particles with a non-rectangular selection and a lower threshold of zero. (b)
  • Added the IJ.showProgress(currentIndex,lastIndex) method. (b)
  • Revert now works with FITS images. (b)
  • 32-bit DICOMS now open correctly. (b)
  • Fixed a bug that caused the "Delete" function in the ROI Manager to sometimes fail if more than one ROI was selected. (b)
  • Added the selectionType(), bitDepth(), setColor(value) and exit() functions to the macro language. (a)
  • Fixed a bug in Image/Scale that could cause the source image to have incorrect spatial calibration. (a)

  Version 1.29, 19 December 2002

  • Worked around a printing bug with Java 1.3.1 on Windows. (x)
  • Added an example that shows how to write command line utilities that use ij.jar as a library. (v)
  • Added an example that shows how to calibrate using an OD step tablet.
  • The IJ.run() methods now work when the ImageJ window is not open. (u)
  • The Image/Rotate/90 Degrees commands now preserve calibartion settings. (u)
  • Image/Stacks/3D Project now works with RGB stacks and has an option to interpolate in the Z-dimension. (t)
  • Image/Stacks/Reslice now works with RGB stacks. (t)
  • The RGB Stack Splitter and RGB Stack Merge plugins are now built into ImageJ as the Image/Color/RGB Split and Image/Color/RGB Merge commands. (t)
  • Added the Image/Color submenu and moved the Image/Stacks/Convert Stack to RGB command to it. (t)
  • Added "Outline Lanes" and "Invert Peaks" options to Analyze/Gels/Gel Analyzer Options, and options are now saved in the preferences file. (s)
  • Added the Image/Adjust/Window/Level and Image/Adjust/Color Balance commands. (r)
  • Added sliders to Image/Adjust/Brightness/Contrast for adjusting the display range min and max. (q)
  • Eric Kischell's Drag And Drop plugin is now built into ImageJ, allowing images, ROIs, LUTs, and text files to be opened by dragging and dropping them on the main ImageJ window. This plugin appears to only work on Windows but Mac users can open files by dragging and dropping on the ImageJ icon. (o)
  • Fixed a bug that could cause the Image/Adjust/Brightness/Contrast tool to fail when used with RGB stacks. (o)
  • The length() macro function was renamed lengthOf(). (o)
  • Walter O'Dell contributed the Window/Level Adjuster plugin.
  • The FeretsDiameter, ConvexHull and BouncingBar macros demonstrate ROI coordinate caculations and animation. (n)
  • Added a "Feret's Diameter" option to Analyze/Set Measurements. (n)
  • The InvertImage and BullsEye macros demonstrate pixel-by-pixel processing. (h)
  • Thanks to Alexei Stapinski, ImageJ can now open 16 bit ASCII PGM files. (m)
  • Anthony Padua updated the Specify ROI plugin and created a spreadsheet that generates macros that use it.
  • Added a "32-bit Unsigned" type to File/Import/Raw. (l)
  • The text editor File/Save command reverts to File/Save As if the text has not been previously saved. (l)
  • Fixed a bug that would sometimes prevent the "Log" window from closing. (l)
  • Added the Image/Stacks/Set Slice command. (k)
  • The Edit/Paste Control tool can be recorded. (k)
  • Fixed a bug with the way Process/Binary/Threshold supports undo. (k)
  • Process/Binary/Distance Map and Ultimate Points work with stacks. (k)
  • On JDK 1.4, the Compile and Run command suppresses the "javac.Main deprecated" warning. (k)
  • Fixed a bug that sometimes caused duplicate paths when recording File/Open. (k)
  • Erik Meijering finished a new package, FeatureJ, containing plugins for the extraction of features such as Gaussian-scaled derivatives, Canny edges, Laplacian zero-crossings, eigenvalues of the Hessian, global statistics, and eigenvalues of the structure tensor, from up to 3D gray-scale image sequences.
  • Rick Turner has added some filter plugins (Prewitt, Roberts, Sobel, etc.) to his home page.
  • Michael Umorin contributed the Stack Focuser plugin.
  • The Process/Filters/Convolve and Analyze/Calibrate commands are now recordable. (j)
  • Fixed a bug that could cause an exception when removing a slice from a two-slice stack and adding another. (j)
  • Added a "Record Starts" option to Analyze/Analyze Particles. The CircularParticles macro demonstrates how to use this feature. (i)
  • Added the Macros/Install Macros command to the text editor. The updated Polygon and MacroSet macros (https://rsb.info.nih.gov/ij/macros/) contain installable macros. (i)
  • Added a "Circularity" option to Analyze/Set Measurements. (i)
  • Fixed a bug that sometimes made it impossible to activate an Image from the Window menu if the start of the image name was the same as the name of another image. (i)
  • The Polygon macro demonstrates user-defined functions and control of screen updates. (h)
  • The text tool uses a larger default font size for images magnified less than 100%. (h)
  • Added a "Circularity" option to Analyze/Set Measurements. (h)
  • Updated the Plasma benchmark.
  • A few example macros are now available at rsb.info.nih.gov/ij/macros/.
  • Fixed minor labeling problems in Analyze/Gels. (f)
  • Image/Rotate/Arbitrarily and Image/Stacks/Make Montage work better with signed 16 bit images. (e)
  • 16 and 32 bit stacks with blank first slices now display correctly when first opened. (e)
  • Fixed a bug in Analyze/Gels (introduced in v1.28) that caused inverted peaks and disabled OD calibration. (d)
  • Fixed a bug in Image/Scale that caused the image to be slightly shifted up and to the left. (d)
  • Analyze/Tools/XY Coordinates now saves in tab-delimited format. (d)
  • Kavagiou Zaharoula contributed a plugin that combines images to create a mosaic.
  • Fixed command recording problems in Image/Stacks/Reslice and Edit/Options/Profile Plot Options. (b)
  • Added a "Create Macro" option to Plugins/Record. (b)
  • Added an option to create a sample macro in Plugins/New. (b)
  • Worked around text window cut and paste problems on Mac OS 10.2. (b)
  • The "Convert to 8-bit Grayscale" option in File/Import/Image Sequence normalizes 8-bit images with color LUTs or with nonstandard grayscale LUTs. (a)
  • Worked around a problem with truncated text on Mac OS 10.2. (a)

  Version 1.28, 22 August 2002

  • Several Mac OS X 10.2 related problems are fixed in the latest OS X version of ImageJ.
  • Audrey Karperien contributed a plugin that encloses an image in a convex hull then calculates circularity and roundness and a plugin that records data for fractal dimension and lacunarity using a box counting algorithm.
  • Added the "Antialiased Text" option to Edit/Options/Miscellaneous (requires Java 2). (u)
  • Added the "Interpolate Images <100%" option to Edit/Options/Miscellaneous (requires Java 2). This option may improve the display quality of large images magnified less than 100% but images will take longer to display. (u)
  • Added the "Smooth" option to Analyze/Surface Plot. (t)
  • Updated Image/Stacks/Reslice. (s)
  • Fixed a bug in Analyze/Surface Plot that could result in incorrect plots of 32-bit float images with color LUTs. (s)
  • Image/Stacks/Convert Images to Stack, Convert Stack to Images and Make Montage now work correctly with calibrated images. (r)
  • Daniel Marsh created the BMP Writer a plugin.
  • Marcus Lamer created the Sequenzer plugin for generating intermediate images between two reference images.
  • Jarek Sacha created the 3D Toolkit, a package of plugins for reading and writing 3D images in MetaImage and VTK formats.
  • Added the "One Polygon per Line" option to Analyze/Surface Plot. (p)
  • The Analyze/Gels commands work with vertical lanes. (p)
  • Hemerson Pistori and Eduardo Rocha Costa contributed the Hough Transform for Circles plugin.
  • Bill O'Connell updated his Oval Profile Plot and Color Comparison plugins.
  • Gary Chinga contributed a plugin that uses Gaussian filtering to decompose an image surface into waveness and roughness.
  • Added the Analyze/Tools/Calibration Bar command, written by Bob Dougherty and Daniel Marsh. (o)
  • On Mac OS X, the layout of the threshold and brightness/contrast tools is better due to the use Daniel Marsh's new TrimmedButton class. (o)
  • Gary Chinga and Oeyvind Eriksen contributed a plugin that performs erosion, dilation, opening and closing of binary images.
  • Improved Analyze/Tools/Scale Bar. (n)
  • Analyze/Analyze Particles works with thresholded 16-bit and 32-bit images. (n)
  • The wand tool works with 16-bit and 32-bit images. (n)
  • File/Revert works with DICOM and BMP images. (n)
  • Closing the "Log" windows exits debugging mode. (n)
  • With stacks, the Z-coordinate of the cursor is displayed in the status bar. (n)
  • The pixel value in the status bar is updated when using "<" and ">" to step through a stack. (n)
  • Yannick Krempp and Jerome Mutterer contributed LSM Reader, a plugin that opens files produced by Zeiss LSM 510 confocal microscopes.
  • Daniel Marsh has written the Color Chooser a plugin.
  • ImageJ is now compiled without debugging information, which reduces the size of ij.jar from 615k to 484k. (m)
  • The ImageJ source now includes an Ant build file ("build.xml") that can generate ij.jar, src.zip and the API documentation.
  • Daniel Marsh has written AVI Reader, a plugin that opens uncompressed 8-bit and 24-bit AVI movies.
  • Adrian Daerr has written JNIAkiz, a plugin and JNI library for full-frame-rate capture using Scion frame grabber cards.
  • Added the File/Save As/AVI command. (l)
  • The ImageProcessor convertToShort() and convertToFloat() methods now work with RGB images. (l)
  • Analyze/Analyze Particles displays a summary that includes total area and area fraction if "Display Results" is not checked in the dialog and "Clear Results Table" is. (i)
  • The animation speed specified in Image/Stacks/Animation Options is saved in the preferences file (IJ_Prefs.txt). (l)
  • Gary Chinga contributed the Shape Descriptors plugin.
  • Analyze/Surface Plot draws axis with labels. (k)
  • Commands in the Process/Filters submenu work with non-rectangular selections. (k)
  • The "OK" button is displayed to the left of the "Cancel" button in most dialogs except on the Macintosh. (k)
  • Right-clicking finalizes polygon and polyline selections. (k)
  • Fixed a bug that caused 3x3 convolution filtes to not work correctly on 16-bit images. (k)
  • Analyze/Clear Results no longer displays an empty "Results" window. (k)
  • Added the Analyze/Surface Plot command, which was created by Daniel Marsh. (j)
  • The "Limit to Threshold" option in Analyze/Set Measurements works with 16-bit images. (j)
  • Commands in the Process/Filters submenu work with rectangular selections. (j)
  • Joachim Walter contributed the Sync Measure 3D plugin.
  • Karl Schmidt contributed the MRI Analysis Calculator and Image Layering Toolbox plugins.
  • Paul Baggethun contributed the Microscope Scale plugin that spatially calibrates images using hard-coded magnifications and length units.
  • Fixed a bug, introduced in 1.28g, that prevented user plugins from being loaded from ij.jar when ImageJ is running as an applet. (i)
  • Added Analyze/Tools/Scale Bar. (h)
  • In the Analyze/Set Scale and Image/Properties dialogs, "um" is automatically converted to "�m". (h)
  • Added the Help/Online Docs command. (h)
  • Plugins/Utilities/Memory Monitor now opens centered on the screen. (h)
  • There is a new About Box (Help/About ImageJ). (h)
  • Perimeter measurements of rectangular and oval selections no longer ignore spatial calibration. (g)
  • When using Java 2, saving in JPEG format is about 10 times faster. (g)
  • Fixed a bug that could cause File/Import> and other submenus to not appear when running ImageJ in countries other than the USA. (g)
  • Image/Adjust/Threshold "remembers" the thresholding mode during an ImageJ session. (g)
  • Bob Dougherty has written the Live Histogram plugin that continuously generates histograms as you step through a stack or move a selection.
  • QImaging released an ImageJ plugin (Windows only) for their Firewire cameras.
  • Joachim Walter contributed an over/under thresholding mode for Image/Adjust/Threshold. (f)
  • Improved the Gel Analyzer (Analyze/Gels). (f)
  • Process/Binary/Threshold uses any threshold settings defined by Image/Adjust/Threshold and also works with 16 and 32 bit stacks. (f)
  • The "Apply" option in Image/Adjust/Threshold works with 16 and 32 bit stacks and is recordable. (f)
  • The "Reset" option in Image/Adjust/Brightness/Contrast is recordable. (f)
  • Commands that process 16 and 32 bit stacks now reset the display range. (f)
  • Added getInstance(), getROIs() and getList() methods to the RoiManager class. (f)
  • Added methods to the ImageProcessor class that get and set pixels using an int array, making it easier to write plugins that process both grayscale and RGB images. The Deinterlace and Averaging Reducer plugins demonstrate how to use these methods.
  • Added the convolve(float[] kernel, int width, int height) method to the ImageProcessor class. (e)
  • Process/Binary/Threshold now uses threshold levels defined by the Image/Adjust/Threshold tool. (e)
  • Updated and expanded (from 72 to 85 plugins) the Plugin Collection.
  • Tony parker has posted two ImageJ applets. One preloads a couple of images, runs the benchmark, starts a cine, and has a customized Plugins menu. The other sets up some buttons that load images.
  • Added "Add & Draw" and "Select All" buttons to the ROI manager. (d)
  • Improved text quality on Mac OS X. (d)
  • Tony Parker has added two new plugins to his collection of 12 plugins for medical image processing.
  • The applet version of ImageJ now runs user plugins added to ij.jar and listed in IJ_Props.txt. (c)
  • Gary Chinga contributed a plugin that calculates surface roughness statistics.
  • Eric Kischell contributed the Drag And Drop plugin.
  • Added support for RGB stack to 8-bit color stack conversions. (b)
  • ROIs saved to a file are no longer limited to 5000 bytes. (b)
  • Fixed a bug, introduced in 1.27, that caused pasting of non-rectangular selections to sometime fail. (b)
  • Fixed a bug that caused pasted image selections to not be initially displayed. (b)
  • Fixed a bug in Image/Adjust/Threshold that caused an exception with 16 or 32 bit images with non-rectangular ROIs. (b)
  • Paul Baggethun contributed the Radial profile Plot plugin.
  • Mark Barclay and Grant Harris contributed a UML class diagram of ImageJ as a 320KB Jpeg.
  • Added the "Increment" field to File/Import/Image Sequence. (a)
  • Added "Plot Width" and "Plot Height" fields to Edit/Options/Profile Plot Options. (a)
  • Increased the font size used by Plugins/Edit when running Mac OS X. (a)
  • Process/Filters/Gaussian Blur now works with density calibrated images. (a)

  Version 1.27, 24-April-2002

  • Improved the error checking in File/Import/Text Image. (z)
  • The Applet version of ImageJ now restarts as expected. (x)
  • File/Open opens 16-bit binary PGM files. (x)
  • The Java 2D Demo plugin uses Java 2D to draw 3D text on an image.
  • Bob Dougherty has written a plugin to open and play QuickTime movies and to grab frames into a stack.
  • There is a new Mac OS X release that opens images dragged onto the ImageJ icon as long as ImageJ is already running.
  • Added the "Invert Y Coordinates" option to Analyze/Set Measurements. (x)
  • Bob Dougherty has written a plugin to divide a stack of RGB images from an NTSC DVersion camera into separate 32 bit red, green and blue stacks.
  • Eric Kischell added a "Create New Window" option to the MRI t2 plugin.
  • Kas Thomas contributed the JavaScript Editor plugin that allows real-time evaluation of JavaScript code.
  • Bob Dougherty has written a plugin to derive surface orientation from a topographical image acquired with a profilometer.
  • Tony Parker has written a plugin that displays orthoganal views (axial, coronal and sagital) of a stack.
  • Fixed rounding problems with ramps and RGB histograms. (v)
  • Contrast/brightness settings are saved in the TIFF header. (u)
  • Angle measurements take the pixel aspect ratio into account. (u)
  • Hold down the shift key to constain line selections to 0 and 90 degrees. (t)
  • Fixed a bug that would sometimes cause ellipse fitting to fail with spatially calibrated images. (t)
  • Added a setColor() method to the PlotWindow class and updated the Example Plot plugin. (t)
  • Updated the Windows distribution to JRE 1.3.1_03, which fixes a printing problem.
  • ImageJ now opens big-endian DICOM files. (s)
  • Histograms and plots are displayed as 8-bit images instead of RGB images. (s)
  • Added drawLine, drawRect and getFontMetrics methods to the ImageProcessor class. (s)
  • Worked around text bugs in Microsoft Java. (s)
  • For 16 and 32-bit images, values displayed by the Histogram window "List" and "Copy" functions no longer have (bin width)/2 added. (q)
  • The ImagePlus.show() and Roi.getMask() methods no longer require that the "ImageJ" window be open. (q)
  • Fixed a bug in Image/Rename that caused the magnification to not be displayed in the title bar. (q)
  • Mike Miller has written a plugin that helps segment images.
  • The histogram window "List" and "Copy" options now use calibrated values. (p)
  • Fixed a bug that caused 16-bit signed DICOM images with no pixels values less than zero to be displayed incorrectly. (o)
  • The text tool works, more or less, on Mac OS X. (o)
  • Plugin writers can use IJ.log(String) to display debugging information in a text window. (o)
  • "Debug Mode" information enabled in Edit/Options/Miscellaneous is displayed in a separate "Log" window. (o)
  • "Results" window column widths are calculated for each of the first 10 measurements. (n)
  • The "Set" option in Image/Adjust/Threshold Image/Adjust/Contrast/Brightness works with calibrated pixel values. (m)
  • Column widths are no longer reset after using Analyze/Clear Results. (l)
  • Holding down the shift key prevents the window from enlarging when zooming in. (k)
  • The Image Calculator Plus plugin adds, subtracts, multiplies or divides two images or stacks using scale and offset values.
  • Joachim Walter contributed the Sync Windows plugin, an enhanced version of Patrick Kelly's SyncWindows_ plugin.
  • Bill O'Connell contributed the Color Comparison plugin that uses color to compare grayscale images.
  • Ryan Raz contributed the Gif Stack Writer plugin for saving stacks as animated gifs.
  • The Thumbnail Maker plugin creates thumbnails and provides an example of how to use ImageJ on "headless" (no display) servers.
  • Non-rectangular ROIs that extend beyond the image boundary are now handled correctly. A test case is available. (h)
  • Fixed keyboard focus and text window size bugs associated with Mac OS X Java 1.3.1 Update 1. (h)
  • File/Import/Image Sequence now sets the stack width and height to the width and height of the first selected image. (f)
  • Process/Binary/Set Interations now works with stacks. (f)
  • Jarek Sacha has written plugins that use JAI to open images.
  • Bill O'Connell contributed the Oval Profile Plot plugin.
  • The wand tool is now recordable. (e)
  • Fixed several problems with Image/Properties and Image/Stacks/Reslice. (e)
  • The Windows and Linux distributions now include Sun's JRE 1.3.1 Java 2 runtime environment.
  • The "Process Stack?" dialog is no longer displayed when editing stacks using the keyboard shortcuts for Edit/Fill (F) and Edit/Clear (backspace). (d)
  • Added the 'Hide "Process Stack?" Dialog' checkbox to Edit/Options/Miscellaneous. (d)
  • Fixed a bug that caused BMP files with a gap between the header and pixel data to open incorrectly. (d)
  • Joachim Walter contributed the Stack Normalizer plugin.
  • The File/Import/Image Sequence dialog now allows the user to enter the number of images, the starting image, and a string used to filter by file name. (c)
  • Image/Properties now does automatic unit conversions. (c)
  • Added the getLine(int) method to the TextPanel class. (c)
  • Worked around a bug on Linux where the "Save Changes?" and "Process Stack?" dialog boxes were sometimes too small. (b)
  • On the Macintosh, dialog boxes are now fixed size without a "grow" region in the lower right hand corner. (a)

  Version 1.26, 17-January-2002

  • Clicking on "List" in Histogram and Plot windows opens a separate text window instead of overwriting the "Results" window. (r)
  • Fixed a bug that could cause problems when importing 16 bit signed stacks. (q)
  • File/Import/Raw now always adds 32,768 to imported 16 bit signed images. It also adds a calibration function to the image so that he original signed values are correctly displayed. (q)
  • Added the Image/Properties dialog, which allows stack slice spacing and frame rate to be set. (q)
  • Stack slice spacing and frame rate are now saved in the TIFF header. (q)
  • Image/Rotate/Flip Vertically is up to 10 times faster. (p)
  • The Voxel Counter plugin counts the number of thresholded voxels in a stack.
  • The Stack Inserter plugin inserts a stack (or image) into another stack.
  • Added an example that shows how to use Java packages for plugin utility classes.
  • The Twelve Bit Expander plugin unpacks 12-bit images.
  • Tony Parker has written a plugin that opens interfile format nuclear medicine image sets. He also makes available 92 lookup tables from the NucMed_Image program.
  • Worked around a Mac OS 8/9 memory leak/crashing bug that was uncovered in v1.26n. (o)
  • Image animation (e.g. Image/Run/Run Benchmark) is now faster when using JDK 1.3. (n)
  • Thanks to Greg Joss, Analyze/Histogram now has a log scaling option. (n)
  • Dialog boxes on the Macintosh no longer have extra space at the top. (n)
  • Fixed a bug that caused an exception with Analyze/Analyze Particles when no image was open. (n)
  • Submitted a bug report and test case to Apple regarding the poor performance of ImageJ on Mac OS X.
  • Updated the Plasma plugin/benchmark.
  • The RGB Stack Merge, RGB Stack Splitter and HSB Stack Splitter plugins are now faster.
  • Eugene Tkachenko contributed a plugin that merges up to four 8-bit stacks into one RGB stack.
  • Amrit Aneja contributed a plugin that copies/pastes images to the system clipboard (requires JDK 1.4).
  • Thanks to code contributed by Heinz Klar, the Median filter is much faster and the Median, Minimum, and Maximum filters work with images outside the range 0-255 and with non-integer radii. (k)
  • Added the Process/Filters/Show Circular Masks command that uses a stack to display one hundred of the masks used by the Median, Minimum, Maximum and Mean filters. (k)
  • Thanks to code contributed by Jason Orendorff, the number of zoom tool magnification levels increases from 11 to 21. (k)
  • Jim Ekstrom is using ImageJ with his "Ugly Bug" contest.
  • The Path Writer plugin saves ROIs as a list of evenly spaced points.
  • Added constructors to the FloatProcessor that accept int and double arrays. (j)
  • Image/Rotate/Arbitrarily now now does 180 degree rotations correcly. (j)
  • Nick Linnenbrugger contributed the FFTJ and DeconvolutionJ plugins.
  • Kas Thomas contributed the Color Picker plugin.
  • Added cyan, magenta and yellow LUTs to the Image/Lookup Tables submenu. (i)
  • Tool changes are now recordable. (i)
  • With single images, Analyze/Analyze Particles now displays the particle count and threshold levels when "Show Results" is not checked. With stacks, it always displays the particle count for each slice. (h)
  • Daniel Sage and Michael Unser of the Swiss Federal Institute of Technology Lausanne have written a paper that describes how they use ImageJ to help teach image processing.
  • Added Cut, Copy, Paste and Print commands to Plugins/Edit. (g)
  • Fixed an OS X image window closing bug. (f)
  • Line profile plots are now generated using bilinear interpolation. (f)
  • The RGB Stack Browser plugin by Kunito Yoshida allows the user to browse each channel of an RGB stack.
  • The ROI Importer plugin creates a freehand ROI from a text file list of coordinates.
  • Fixed a bug in v1.26d that caused null pointer exceptions when processing byte images. (e)
  • Added an "Vertical Profile" checkbox to Edit/Options/Profile Plot Options. (d)
  • Added support for DICOM MONOCHROME1 Photometric Interpretation. (d)
  • Most commands process stacks much faster. Edit/Invert, for example, inverts a 256x256x256x8-bit stack 13 times faster! (c)
  • Image/Stacks/Plot Z-axis Profile now works with the "Limit to Threshold" option in Analyze/Set Measurements. (b)
  • Newly opened image windows are less likely to extend off the bottom of the screen. (b)
  • The state of "Scale When Converting" in Edit/Options/Miscellaneous is no longer saved to the preferences file. (b)
  • The "Draw" and "Fill" options in Analyze/Tools/ROI Manager are now undoable. (b)
  • Plugins/Compile and Run now uses the -deprecation option. (a)
  • File/Save As/XY Coordinates now saves absolute coordinates instead of coordinates relative to the selection's bounding rectangle. (a)
  • Plugins/Utilities/Commands is now faster. (a)

  Version 1.25, 3-November-2001

  • On the Mac, files dropped on the ImageJ icon are opened, the Apple menu "About" command works, and the Apple menu "Quit" command saves preferences and prompts to save changes. Note: drag and drop may not work until you delete all older versions of ImageJ and rebuild the desktop. (t)
  • File/Revert revert now works correctly when pasting. (s)
  • Fixed a bug that could cause an exception after having used Image/Crop. (s)
  • Added the addTool() method to the Toolbar class. (r)
  • Added Window/Cascade and Window/Tile commands. (q)
  • Fixed a bug that caused images saved using File/Save As/ZIP to lose calibration. (q)
  • Added support for bitmap and ARGB image types to File/Import/Raw. (p)
  • Edit/Undo now works after using Image/Type to convert 16 and 32 bit images to another type. (p)
  • Numbers are now always displayed using a decimal point. (p)
  • Fixed a bug that could cause an exception after having used the text tool. (p)
  • Joachim Walter has written a plugin that does gaussian filtering in fourier space.
  • Werner Bailer has written a plugin for doing Discrete Cosine Transforms.
  • An updated version of the Werner Bailer's plugin writing tutorial (v. 1.5) is available at http://www.fhs-hagenberg.ac.at/staff/burger/ImageJ/tutorial/.
  • The Gaussian Blur and Unsharp Mask filters are now much faster. (o)
  • Fixed a bug in Image/Stacks/Reslice that cuased it to fail with 32-bit stacks. (o)
  • Analyze/Analyze Particles now correctly processes a single slice in a stack. (m)
  • The Brightness/Contrast and Threshold tools no longer leave threads running when the window is closed. (l)
  • The Image/Adjust/Brightness/Contrast tool has a new "Set" button and improved histogram support. (l)
  • Amrit Aneja has put together a collection of 72 plugins from the ImageJ Web site.
  • Added support for the Window Center and Window Width DICOM tags. (i)
  • Kurt De Vos has written a cell counting plugin.
  • Removed the TextPanel from the main ImageJ window and added a separate "Results" window. (h)
  • Added an option to Analyze/Analyze Particles to display fitted ellipse for each particle. (f)
  • Analyze/Analyze Particles now displays the labels for particle outlines in red. (f)
  • Mike Martin has written a plugin for opening uncompressed Planetary Data System (PDS) images.
  • Added the Analyze/Tools/ROI Manager command. (e)
  • Added a "Zip" and "Text" choices to File/Save As/Image Sequence. (c)
  • Added a "Fit Ellipse" option to Analyze/Set Measurements which adds "Major", "Minor" and "Angle" columns to the results table. (b)
  • Tony Parker has written a plugin that allows the user to align two stacks.
  • Erik Meijering has written a package of plugins (TransformJ) for geometrical transformation and manipulation (chunking, embedding, mirroring, rotation, shifting, scaling or resizing, affine transformation) of up to four-dimensional (4D) images.
  • Fixed a bug that caused ImagePlus.setCalibration() to reset the xOrigin and yOrigin fields. (a)
  • Fixed a rounding error in Process/Noise/Add Noise. (a)

  Version 1.24, 7-Sept-2001

  • Added the Hypervolume Shuffler plugin by Michael Abr�moff.
  • Fixed a bug in Process/Filters/Convolve that caused the dialog box not to show after the first time. (t)
  • Removed 20 item limit in GenericDialog class. (r)
  • Updated AVI Writer plugin.
  • Added the Stack Builder plugin by Nicolas Roggli.
  • Updated the Plugins Control Panel plugin.
  • Fixed a bug in the IJ.run() method used my the command recorder. (q)
  • Added Embyos and Leaf images, contributed by Larry Reinking, to the File/Open Samples submenu. (q)
  • Larry Reinking, Department of Biology, Millersville University, has written two great ImageJ handouts: ImageJ and Examples of Image Analysis Using ImageJ.
  • ImageJ now opens uncompressed TIFF bitmap images. (p)
  • ImageJ now opens the "hybrid" TIFF/DICOM files created by GE-Senographe 2000 D mammography systems. (p)
  • Added the Batch Statistics plugin.
  • The location of the plugins directory can now be specified from the command line. See the Linux x86 installation notes for an example. (n)
  • File/Open can open PNG images if ImageJ is running on a Java 2 JVM.
  • Improved Plugins/Utilities/Panel.
  • Added a link to a new plugin that uses cubic spline interpolation to resize images. This plugin was written by Daniel Sage of the Biomedical Imaging Group at the Swiss Federal Institute of Technology.
  • Updated the AVI Writer plugin to use the frame rate specified in Image/Stacks/Animation Options (requires ImageJ v1.24l).
  • Analyze/Analyze Particles has a new option to display selected particles in black on a white background. (k)
  • Modified the Mouse Listener example plugin to display the mouse pressed event modifiers and to keep a list of images it is listening to.
  • Image/Show Info displays the frame rate of imported NIH Image movies. (j)
  • Non-image windows are listed in the Window menu. (j)
  • Fixed bugs in the setImage(), setProcessor() and setStack() methods of the ImagePlus class. (j)
  • Analyze/Tools/Save XY Coordinates works with all image types. (h)
  • With non-rectangular selections, Image/Crop keeps the selection. (h)
  • Image/Colors displays more colors. (h)
  • Double-clicking on the straight line tool displays the Line Width dialog. (h)
  • Analyze/Analyze Particles now works with stacks. (g)
  • The location and size of the ImageJ window is now recorded in the preferences file (IJ_Prefs.txt). (g)
  • Most commands that generate an image now include the name of the original image in the title. (g)
  • Made the text tool easier to use. (g)
  • On systems other than the Macintosh, changed the order of the buttons in the "Save Changes" dialog box. (g)
  • Added the Help/ImageJ Web Site command that launches a browser and has it open the ImageJ home page. (g)
  • Maja Kizic and Muris Borovac at Chalmers Lindholmen University College, Gothenburg, Sweden have written a bachelor's thesis that evaluates the usability of ImageJ's user interface and offers suggestions on how it can be improved.
  • Added ability to cut, copy and paste non-rectangular selections. (e)
  • 32-bit stacks can now be converted to 16-bit stacks. (e)
  • 8-bit stacks can now be converted to 16-bit stacks. (d)
  • Fixed a bug in Process/Subtract Background that caused bluring of the background subtracted image. (d)
  • Process/Image Calculator now resets the display range. (b)
  • Process/Subtract Background now works with stacks and with images without inverted LUTs. (a)
  • Added the Process/Math/Square, Process/Math/Square Root and Image/Rename commands. (a)

  Version 1.23, 22-June-2001

  • ImageJ now opens uncompressed RGB DICOM images. (w)
  • Thanks to Java2HTML, the ImageJ source code is now online in a colorized and browsable format.
  • Improved the check done at startup for duplicate classes in the plugins folder. (v)
  • Add the Process/Filter/Unsharp Mask command. (t)
  • Added Gaussian Blur, Median, Mean, Minimum (grayscale erosion) and Maximum (grayscale dilation) filters to the Process/Filters submenu. (s)
  • Added the List Opener plugin for opening images using a text file list. (q)
  • Added the PlotWindow.addErrorBars() method and a plugin that demonstrates how to use it. (q)
  • Image/Adjust/Brightness/Contrast and Image/Adjust/Threshold now work with locked, non-RGB images. For example, you can be running Image/Bencharks/Waves and adjusting brightness/contrast at the same time. (p)
  • On Macintoshes, the ImageJ window is smaller and the menu bar no longer disappears when switching to none image windows. (p)
  • The "Apply" option in Image/Adjust/Brightness/Contrast now works correctly with color LUTs. (o)
  • Added a Mac OS X distribution.
  • Deleted Image/Stacks/Save Slices as Files and replaced it with File/Save As/Image Sequence. (m)
  • Changed the name of File/Import/All As Stack to File/Import/Image Sequence and added the ability to convert the images to 8-bits and/or open them half sized, resulting in stacks that use as little as 1/16th as much memory. (m)
  • Fixed a bug in Analyze/Calibrate that caused the "Global" option to not work correctly. (m)
  • Added the Edit/Options/Foreground Color and Edit/Options/Background Color commands. (m)
  • The ImagePlus(String) constructor now works with both paths and URLs. (m)
  • Added the Opener.OpenImage(String) method for opening images using a path. (m)
  • Fixed a bug in the QuickTime Movie Opener plugin that could result in duplicate or missing frames.
  • Added the AVI Writer plugin.
  • The Clear, Clear Outside and Fill commands can now process entire stacks. (k)
  • Commands that process entire stacks now work with selections. (k)
  • Fixed several problems with the DOES_STACKS and SUPPORTS_MASKING options of the PlugInFilter interface. (k)
  • Text fields in dialogs are now automatically selected when you click on the field or tab to it. (g)
  • Plugins/Utilities/List Properties now displays the directory where ImageJ saves the preferences file (IJ_Prefs.txt) and the directory where it looks for plugins. (f)
  • Fixed a binning problem with 16 and 32-bit histograms. (f)
  • The "Save As" command in the Plugins editor now changes the class name to match the file name. (e)
  • With 16 and 32-bit images, Process/Math/Min and Process/Math/Max now update the displayed image by doing the equavalent of clicking on "Reset" in Image/Adjust/Brightness/Contrast. (e)
  • Analyze/Set Scale now displays the scale, which is dynamically updated as the measured and known distances are changed. (d)
  • With stacks, Image/Duplicate can now gives you the option of duplicating the entire stack or just the current slice. (c)
  • Added the Plugins/Record command (under construction). (a)
  • Fixed several problems with histograms of calibrated 16-bit images (e.g. signed FITS images). (a)

  Version 1.22, 22-Mar-2001

  • Upgraded bundled Windows JRE to 1.1.8_006, which fixes JIT crashes on Pentium 4 CPUs and a scrolling problem in popup menus.
  • Added an icon for ImageJ.
  • An error message is now displayed when, under Windows, the user attempts to maximize the ImageJ window, causing other windows to be hidden. (c)
  • Analyze/Summarize now works with line and point measurements. (c)
  • The "Auto" feature in Image/Adjust/Threshold now works more reliably. (b)
  • Fixed a couple of problems with Analyze/Summarize. (b)
  • Image/Adjust/Contrast/Brightness, Image/Adjust/Threshold, Edit/Paste Control and Edit/Options/Fonts now open only one window. If the window is already open, it is brought to the front. (a)
  • On the Mac, the MRJ version is displayed by Plugins/Utilities/Show Java Properties. (a)

  Version 1.21, 27-Feb-2001

  • Added the Process/Math/Min and Process/Math/Max commands. (v)
  • The wand tool now works more reliable with Analyze/Gels. (v)
  • Added the Image/Stacks/Convert Stack to Images command. (u)
  • Hold down the alt key with Image/Stacks/Add Slice to add a slice in front of the current slice. (u)
  • Analyze/Histogram now uses the number of decimal places defined in the Analyze/Set Measurements dialog. (t)
  • Fixed several problems with histograms of floating-point images. (t)
  • XY coordinates generated by the crosshair tool are now saved in the ImageJ ResultsTable. (s)
  • Fixed several z-axis rotation bugs in Image/Stacks/3D Project. (s)
  • Simplex fitting parameters used by the Analysis/Tools/Do Curve Fitting tool can now be adjusted thanks to an improved CurveFitter class contributed by Kieran Holland. (r)
  • Image/Stacks/3D Project no longer requires thresholded stacks. Upper and lower transparency bounds are set in the dialog or are set automatically if the stack is thresholded. (r)
  • Updated Image/Stacks/Convert Stack to RGB to work with 2-slice stacks (red and green). (r)
  • Updated the RGB Stack Merge plugin to work with two stacks (red and green).
  • Image/Stacks/Reslice now works with rectangular selections. A rectangular selection is equivalent to a line selection corresponding to the top edge of the rectangle and a "Slice Width" equal to the height of the rectangle. (q)
  • Fixed a bug, introduced in v1.20, that caused reslicing of RGB stacks to fail. (q)
  • Stacks can now be converted to RGB. (q)
  • Added the Resize Canvas plugin contributed by Jeffrey Kuhn.
  • "Center of Mass" now reverts to "Centroid" when all pixels are zero. (o)
  • DICOM/ACR-NEMA reader improved. (o)
  • Fixed bugs, introduced in v1.18, with 16-bit add, subtract and multiple in Process/Image Calculator. (n)
  • Image/Adjust/Brightness/Contrast now correctly displays min/max of density calibrated images. (m)
  • Improved support for signed DICOM images by using a calibration function to restore the orginal negative values. (m)
  • For 16-bit and 32-bit images, File/Import/Raw (with "Open All" checked), File/Import/All As Stack and Image/Stacks/Convert Images to Stack now use the stack min/max to set the display range instead of the min/max of the first image. (l)
  • ROI movement via arrow keys no longer stops one pixel early at right and bottom of image. (k)
  • Analyze/Calibrate now works with images of type "8-bit Color". (j)
  • Added the Plugins/New command. (i)
  • File/Open now opens BMP, LUT and ZIP files with upper case file name extensions. (h)
  • File/Open now opens text files. (h)
  • Added a Paint Brush plugin contributed by Jeffrey Kuhn.
  • Added the Stack Histogram plugin.
  • For float and calibrated images, File/Save As/Text Image now uses the "Precision" setting in the Analyze/Set Measurements dialog. (f)
  • Added Process/Morphology/Euclidian Distance Map and ../Ultimate Eroded Points commands. (c)
  • Fixed a bug in Image/Stacks/Render that caused it to generate a blank image when "Total Rotation" was set to zero. (b)
  • Maximum values less than zero are now calculated correctly. (a)
  • Density calibration information in NIH Image TIFF files is now decoded. (a)

  Version 1.20, 20-Dec-2000

  • Fixed a bug, introduced in ~v1.20n, in the Image/Type/RGB Stack and Image/Type/HSB Stack commands. (p)
  • Added the "Bat Cochlea Volume" sample image, useful for testing the Image/Stacks/Render command and Michael Abramoff's VolumeJ plugin. This is a thresholded high resolution MRI dataset of the inner ear of a bat contributed by Art Keating of the University of North Carolina. (n)
  • Added the Image/Stacks/Render command, a port of the NIH Image "Project" command written by Michael Castle of the University of Michigan Mental Health Research Institute. (n)
  • Pressing the "=" key now starts/stops stack animation. (l)
  • Replaced static conversion methods in ImageConverter with the ImageProcessor methods convertToByte(boolean), convertToFloat(), convertToRGB() and convertToShort(boolean). (l)
  • Image/ColorTables/Invert LUT now works correctly with stacks. (l)
  • Image/Stacks/Next Slice (">") and Image/Stacks/Previous Slice ("<") now skip 9 slices if the alt key is held down. (k)
  • Fixed a bug in the ByteProcessor.getAutoThreshold method used by Image/Adjust/Threshold and by Process/Morphology/Threshold. (k)
  • A rare problem with endless rapid switching between windows is now (hopefully) fixed. Use the Focus Bouncer plugin to test for this problem. (i)
  • Class files in the plugins folder that have duplicates in subfolders are now automatically deleted. (h)
  • The Plugins/Shortcuts/Install Plugin command can now install plugins in the Filters, Tools and Utilities submenus. (g)
  • Moved the Do Curve Fitting, Fractal Box Count , Save XY Coordinates, Analyze Line Graph and Do Curve Fitting commands to the new Analyze/Tools submenu. (g)
  • The cross hair tool can now display results in calibrated units. (g)
  • Added the Process/Filters/Convolve command for performing convolutions using user-defined real kernels. (g)
  • Thumbnail images contained in some TIFF files are no longer displayed. (d)
  • The Image/Adjust/Threshold tool now works with 16-bit and 32-bit images. (b)
  • Added an "Apply" button to the Plugins/Utilities/Do Curve Fitting window that creates a new 32-bit image by using the curve fit function to transform the active image. (b)
  • Plugins in subfolders of the plugins folder are now installed in submenus of the Plugins menu. (a)
  • Fixed a bug in the plugin class loader that prevented newly compiled plugins from replacing previously loaded versions. (a)
  • Added a plugin, contributed by Cezar M. Tigaret, that uses a tabbed panel to provide access to plugins in subfolders of the main "plugins" folder.

  Version 1.19, 26-Oct-2000

  • Added direct 16-bit to RGB and 32-bit to RGB conversions. (x)
  • Fixed a bug that sometimes caused the color LUT not be saved when saving an 8-bit image in TIFF format. (x)
  • Fixed a bug that sometimes caused color LUTs to be reset to grayscale when converting to or from 16-bits or 32-bits. (x)
  • Image/Show Info now displays density calibration information. (w)
  • Fixed a bug in the cross hair tool that caused it to ignore foreground color changes. (v)
  • Changed the name of the Hot Keys submenu to Shortcuts. (v)
  • Added red, green and blue LUTs to the Image/Color Tables submenu. (u)
  • Added a plugin that saves stacks as QuickTime movies.
  • Fixed a bug in the TiffEncoder class that prevented other applications from being able to read 8-bit color tiff stacks created by ImageJ. (t)
  • Added a "Scale When Converting" checkbox to Edit/Options/Miscelleaneous that allows auto-scaling of data type conversions to be disabled. (r)
  • Added "Copy All", "Clear Results", "Summarize" and "Set Measurements" commands to the worksheet popup menu. (r)
  • Added three example plugins (FOV Calculator, Gear Math, and Circle Test) contributed by Joshua Gulick.
  • The calibration function, if there is one, is applied to the pixel data when converting 8-bit and 16-bit images to 32-bit floating-point. (q)
  • Improved support for signed 16-bit FITS images by using a calibration function to restore the orginal negative values. (q)
  • Added a "Precision" field to the Analyse/Set Measurements dialog for specifying the number of digits (0-8) displayed after the decimal point. (n)
  • Added the addLabel(heading, label) method to the ResultsTable class. (n)
  • Added an option to Analyze/Set Measurments to label rows in the results table with the file name and slice number. (l)
  • Settings in Edit/Options/Profile Plot Options are now saved. (k)
  • ImageJ now opens 8-bit color palette DICOM images. (j)
  • Fixed a NullPointerException bug in File/Import/All As Stack that was triggered when the first file in the folder was not an ImageJ compatible image. (i)
  • Added the Background Task plugin as an example of how to do time-consumming background processing.
  • Added a plugin that generates 3D surface plots.
  • The "Apply" button in the Image/Adjust/Brightness/Contrast tool will now apply the current brightness and contrast settings to the entire stack. (g)
  • Fixed a bug, introduced in v1.18, in the Image/Adjust/Brightness/Contrast tool that limited "min" and "max" of 8-bit and RGB images to the range 0-255. (f)
  • Fixed a NullPointerException bug in Analyze/Analyze Line Graph. (f)
  • The "MRI Stack", "M51 Galaxy" and "Scala Media Stack" sample images now download as ZIP compressed TIFFs. (d)
  • The Image/Adjust/Brightness/Contrast tool now works with animated stacks. (d)
  • Upgraded File/Import/URL to work with TIFF files. (b)
  • The ImagePlus.setSlice() method now updates the slice selection scrollbar. The new ClearOutside plugin takes advantage this feature. (b)
  • Same-size images now open at the same magnification (1:1, 2:1, etc.), regardless of their screen position. (a)

  Version 1.18, 5-Sept-2000

  • Worked around a bug that sometimes caused ImageJ to hang when quiting.
  • Added the Plugins/Hot Keys/Remove command for uninstalling hot keys and plugins. (u)
  • Fixed a bug that sometimes caused the "Y Max" and "Y Min" values in Edit/Options/Profile Plot Options to be reset. (t)
  • Fixed a bug that sometimes caused another ImageJ applet window to open when the user switched to another Web page and then returned to the ImageJ applet page. (s)
  • Added the Plugins/Hot Keys/Create Hot Key command for assigning keyboard shortcuts to menu commands. (r)
  • The title of the plot window produced by Image/Stacks/Plot Z-axis Profile now includes the name of the orginal stack and location of the selection. (r)
  • All 16-bit images are now unsigned. Imported signed images with negative pixel values are converted to unsigned by adding 32768. Use masking to access values in pixel arrays (e.g. int i=pixels[i]&0xFFFF). (p)
  • Added the Plugins/Hot Keys/Install Plugin command that enables plugins to be installed in the File/Import and File/Save As submenus. Assign a function key by entering "f1"-"f12" in the dialog's "Shortcut" field. (o)
  • Fixed a Analyze/Analyze Particles bug that was introduced in 1.18b. (k)
  • Fixed a bug that caused Analyze/Measure to set the image's "changed" flag. (k)
  • Fixed a bug in GenericDialog that caused it to work incorrectly if the dialog displayed a checkbox or message followed by a numeric field or text field. (j)
  • The "Global" option in Analyze/Set Scale and Analyze/Calibrate now works more reliably. (j)
  • Images created with File/New no longer inherit the spatial and density calibration of the current image. (j)
  • Fixed a bug in ParticleAnalyzer when it's called by a plugin and asked to calculate perimeters. (i)
  • Fixed a bug that sometimes caused multiple items in the Window menu to be checked. (i)
  • With straight line selections, Image/Show Info now displays the starting and ending coordinates. (e)
  • Analyze/Plot Profile now produces the expected reversed results when the same line is drawn in different directions. (e)
  • File/Import/Raw settings are now saved in IJ_Prefs.txt. (e)
  • Edit/Fill, Edit/Draw and Edit/Clear now work with 16-bit and float images that have min=max=0. (b)
  • The ImageProcessor.drawString() method now works with 16-bit and float images. (b)
  • Newly created unsigned 16-bit images are now initialized to 0 instead of 32768. (b)
  • To prevent annoying pauses, images loaded from a URL, such as those in the File/Sample Images submenu, are now converted to an ImageProcessor before being displayed. (a)

  Version 1.17, 22-June-2000

  • The Object Tracker plugin now allows the min/max object size to be specified.
  • Clicking "Apply" in the Image/Adjust/Threshold when the image is in the "B&W" mode no longer displays a dialog. (y)
  • Replaced Plugins/IP Demo with Plugins/Panel, a window with buttons for executing plugins in the plugins folder. (y)
  • Analyze/Analyze Line Graph now works with thresholded images. (y)
  • Added the Batch Converter plugin for converting a folder of images to another format.
  • Added the Display Updater plugin that sets an image's min and max displayed value. (w)
  • Added a constructor to GenericDialog that doesn't require a parent frame. (w)
  • Fixed a spatial calibration bug in Image/Adjust/Size . (w)
  • Added the "Fluorescent Cells" sample image and removed "Peppers"
  • Added the FFT plugin.
  • Edit/Invert now works with 16-bit unsigned images. (t)
  • Added the IJ.run() method so plugins and macro interpreters (e.g. BeanShell) can more easily run ImageJ menu commands. This method runs in the current thread and does not return until the command has finished. (s)
  • Added the Text Demo plugin that demonstrates how plugins can add text to images. (s)
  • Fixed a bug in ImageProcessor.drawString() that caused text larger than 12-points to not be displayed correctly. (s)
  • The fitted line in Analyze/Fractals/Box Count is now displayed correctly. (r)
  • Worked around a problem opening Spot Camera TIFF files. (r)
  • Added the Plugins/Edit command for editing, compiling and running plugins. Requires a Java Virtual Machine(JVM) that includes the javac compiler, such as one of the JDKs from Sun or Apple's MRJ plus the Java Software Development Kit. Note that the JRE 1.1.8 distributed with the Windows version of ImageJ does not include javac. When using JDK 1.2 or JDK 1.3, the tools.jar file must be in the classpath. To include it, run ImageJ using a command something like
       java -cp ij.jar;C:\jdk1.3\lib\tools.jar ij.ImageJ (o)
  • All measurements are now stored in a ResultsTable that is available to plugins using Analyzer.getResultsTable().
  • Added a plugin that draws arrows and removed the Plugs/Draw Arrow command. (o)
  • Added a plugin that does convolutions on real images using user-defined kernels. (j)
  • Added the Plugins/Compile and Run command. Like Plugins/Edit, it requires a JVM that inludes the javac compiler. (j)
  • The plugins folder no longer needs to be in the classpath since plugins are now loaded using a custom class loader. (j)
  • Spatial (e.g. pixels/mm) and density calibration data are now saved with TIFF images. (j)
  • Analyze/Analyze Particles is now up to 27 times faster! (i)
  • Updated the Image/Benchmarks/Particles benchmark results. (i)
  • Added a plugin that illustrates how to extend ImageJ's Particle Analyzer. (g)
  • The Analyze/Line Analyzer command now creates plots whose size is based on the size of the selection, not on the size of the curve being digitized. (f)
  • Added the Analyze/Calibrate command for calibrating 8-bit images to density standards. (e)
  • Added a "Standard Deviation" option to Image/Stacks/ZProject. (e)

  Version 1.16, 8-May-2000

  • Fixed a 1.15 bug that caused incorrect measurements of non-rectangular areas. (f)
  • Added a method that displays an error message and returns true if the ImageJ version is less than the one specified in the argument. For example, if (IJ.versionLessThan("1.16c")) return. (c)
  • Analyze/Fractals/Save XY Coordinates now saves the XY coordinates and pixel value of all non-background pixels . (b)
  • With 8-bit stacks, Image/Stacks/Convert Stack to RGB now displays the RGB image in a new window. (a)
  • Fixed a bug that caused status bar cursor y-coordinates to be incorrect when the Pixel Aspect Ratio in Analyze/Set Scale was not equal to 1.0. (a)
  • Fixed a bug in Image/Stacks/Delete Slice that caused the slice selector to be positioned incorrectly. (a)

  Version 1.15, 27-April-2000

  • Fixed a bug in Image/Stacks/Delete Slice that resulted in a blank window title.
  • On systems with JDK 1.2 or JDK 1.3 installed, you can now run ImageJ by double clicking on the ij.jar file. On Windows NT/2000, this method avoids the annoying DOS window.
  • The ij.jar file is now compressed, reducing its size from 778K to 432K.
  • The Primes plugin provides an example of how to process mouse moved interrupts. (z)
  • All Analyze/Measure results now use spatial calibration defined using Analyze/Set Scale. (v)
  • Analyze/Analyze Particles summary results are now reported in calibrated units such as mm^2. (v)
  • Analyze/Analyze Line Graph now plots and saves coordinate data using calibrated units. (v)
  • Fixed a bug that caused Analyze/Analyze Line Graph to corrupt the source image. (v)
  • Fixed a bug that caused File/Open to not "see" some DICOM files. (v)
  • Image/Stacks/Plot Z-axis Profile now displays all measurements specified in Analyze/Set Measurements.
  • Added a plugin that reverses the order of the slices in a stack.
  • Added a "Global" option to Analyze/Set Scale that causes all images to use the same spatial calibration.
  • Double-clicking on the line tool displays the Analyze/Set Scale dialog.
  • Double-clicking on the freehand outlining tool displays the Analyze/Set Measurements dialog.
  • Analyze/Gels/Label Peaks now labels each peak with its area as a percent of the total area.
  • Fixed a bug in Analyze/Gels that generated extra measurements when using the shift key shortcut to scroll.
  • When it can't recognize the header format, File/Open now displays a dialog listing the supported image types (TIFF, JPEG, GIF, BMP, DICOM, FITS, PGM, ZIP or LUT). (m)
  • When processing stacks, Image/Adjust/Size, Image/Crop and Image/Rotate/* are now better at showing progress. (l)
  • Double-clicking on dropper tool displays the "Colors" window but doesn't switch tools. (k)
  • The Image/Adjust/Threshold "Apply" option is now undoable. (h)
  • The dropper in the toolbar is now outlined with a box drawn in the background color. (g)
  • Alt-click in the Image/Colors window to set the background color. (g)
  • "Apply" in Image/Adjust/Threshold now displays a dialog with options for setting thresholded pixels to the foreground color and non-thresholded pixels to the background color. (g)
  • "Min & Max", "Centroid" and "Center of Mass" calculations now ignore non-thresholded pixels if "Limit to Threshold" is checked in Analyze/set Measurements. (g)
  • Added File/Save As/ZIP for saving an image in TIFF format within a compressed ZIP archive and extended File/Open to read files created by this command. (f)
  • Changed the labels in Process/Image Calculator to "Image1" and "Image2". For all operators, clicking "OK" now calculates image1=image1<op>image2. If "Create New Window" is checked, a new window is opened to store the result and "image1" is left unchanged. (f)
  • Fixed a bug in Process/Image Calculator that sometimes caused the first stack slice to not be processed. (d)
  • Multi-image tiff files with images that are not all the same size and type now open in separate windows. (c)
  • Fixed a bug that caused pasting of images with Edit/Paste Control modes other than "Copy" to fail. (b)
  • Changed the definition of "difference" in Process/Image Calculator from dst=(src-dst)/2+128 to dst=abs(src-dst). (b)
  • Added a "Create New Window" option to Process/Image Calculator. (b)
  • The "Apply" button in Image/Adjust/Threshold now works with stacks. (a)

  Version 1.14, 23-Feb-00

  • Fixed a v1.13 bug that caused Analyze/Analyze Particles to fail when "Perimeter" was checked in Analyze/Set Measurements . (c)
  • Edit/Cut now fills with the same background color as Edit/Clear. The only way currently to change the background color is by editing the value of "bcolor" in IJ_Prefs.txt. (a)
  • Added a "Bounding Rectangle" option to Analyze/Set Measurements. When this option is checked, the bounding rectangle of the selection is displayed using the headings "BX", "BY", "Width" and "Height". (a)

  Version 1.13, 18-Feb-00

  • With 16-bit and real images, Edit/Fill and Edit/Clear now fill with zero if the foreground or background color respectively is black, the images minimum pixel value is not less than zero and the LUT is not inverted. The background color can be set to black by changing the value of "bcolor" in IJ_Prefs.txt to #000000. (w)
  • Added keyboard shortcut support for plugins. For examples, look at the entries for File/Open Samples/Blobs, Plugins/IP Demo and Plugins/Draw Arrow in IJ_Props.txt. Note: you don't have to hold down the control key to use menu shortcuts. (u)
  • Moved Image/Adjust Contrast and Image/Adjust Threshold to the new Image/Adjust submenu. (u)
  • Fixed a bug that caused the middle point in lines generated by Analyze/Plot Profile and Image/Stacks/Reslice to be doubled. (t)
  • Added to the Analyze/Analyze Particles dialog box, a field for setting the number of bins used in size distribution histograms, and "Display Summary", "Exclude Edge Particles" and "Clear Worksheet" check boxes. (t)
  • Added to Edit/Options/Miscellaneous, a field for setting the number of bins used in histograms of 32-bit real images. (s)
  • Edit/Draw and the crosshair tool now work with 16-bit and real images as long as the image's maximum pixel value is not equal to its minimum. (r)
  • Double-click on the eyedropper tool to display the "Colors" window. (q)
  • Added the crosshair tool for counting, measuring and marking points. Marks are drawn in the foreground color. Double-click on the crosshair tool to change the mark size. To not leave a mark, set the size to zero. (p)
  • Analyze/Fractals/Box Count now plots log count vs. log box size and calculates the fractal dimension. (p)
  • Added the Plugins/Do Curve Fitting command for fitting functions to data. (j)
  • The Image/Stacks/Save Slices as Files dialog now allows the user to specify the file name prefix and number of digits. (h)
  • Added a plugin for tracking one or two objects through a stack. (c)
  • File/Import/All as Stack now uses a progress bar and no longer displays the file names in the status bar. (b)
  • Fixed a v1.12 bug that caused the ImageJ applet to fail to load when using the Netscape browser. (a)

  Version 1.12, 18-Jan-00

  • Changed the name of the File/Open submenu to File/Open Samples. (z2)
  • Changed the name of the File/Acquire submenu to File/Import. (z1)
  • Removed DICOM, BMP and FITS from the File/Acquire submenu. These file types can be opened using the File/Open command. (z1)
  • Keyboard focus in the File/Acquire/Raw dialog is now set to the first numeric field. (z1)
  • Changed the name of the ij.properties file to IJ_Props.txt. (y)
  • User preferences are now saved in a text file named "IJ_Prefs.txt". This file is saved in the Preferences folder on the Mac, in the user's home directory on Unix, and in the ImageJ folder on Windows. The drawing color, roi color, default directory, jpeg quality and measurement options are currently saved. Two preferences that cannot be set in ImageJ, background color and size distribution bins, can be changed by editing IJ_Prefs.txt. (v)
  • Removed the double quotes from the Image/Show Info text window's title bar. These quotes sometimes caused the Save As command in the text window popup menu to fail. (t)
  • Added the "Limit to Threshold" checkbox to Analyze/Set Measurements. When this option is checked, only thresholded pixels are included in measurement calculations. (s)
  • Added a link to Michael Abr�moff's volume rendering plugin.
  • Fixed several text window scrolling and selection problems. (r)
  • Process/Math/Gamma and Process/Math/Log now work correctly with 16 and 32-bit images. (n)
  • The wand tool now works with thresholded images. (m)
  • Image/Show Info now displays the threshold levels. (k)
  • Fixed a bug in Process/Math that occured when canceling an operation on a stack. (k)
  • Fixed a bug that caused problems when changing the data type of an image being manipulated by the Image/Adjust Contrast tool. (k)
  • Lowered the default position of the ImageJ window by 32 pixels to avoid the MS Office task bar. (i)
  • Updated Analyze/Analyze Particles to use the upper and lower threshold levels defined by the Image/Adjust Threshold and Image/Adjust Contrast tools. (h)
  • Added the Image/Adjust Threshold tool for interactively separating features of interest from background. This is similar to "density slicing" in NIH Image. As a shortcut, type shift-T to activate this tool. This tool currently only works with 8-bit images. (h)
  • In addition to TIFF, JPEG, GIF, DICOM, and FITS, File/Open and File/Acquire/All as Stack also now work with ACR/NEMA files. (g)
  • File/Acquire/All as Stack and Image/Stacks/Save Slices as Files work more reliably when free memory is low. (f)
  • Out of Memory messages should be less likely when processing stacks with Smooth, Sharpen or Find Edges. (f)
  • The progress bar is now displayed correctly after the ImageJ window is resized or uncovered. (d)
  • The x-axis labeling in profile plots. (d)
  • Worked around a v1.10 and v1.11 flickering problem with someJVM's when Analyze/Analyze Particles was displaying a large number of measurements in the ImageJ window. (c)
  • Worked around a scroll bar problem in v1.10 and v1.11 that showed up when running on the Mac and on some versions of the Microsoft JVM. (b)
  • High filter processing rates are now reported in the status bar in millions of pixels per second. (b)

  Version 1.11, 9-Dec-99

  • Added y-axis labels to profile plots. (z)
  • Fixed several bugs in Image/Stacks/ZProject. (w)
  • Type converted images are marked as changed. (v)
  • The window title bar is updated when an image is saved under a new name. (v)
  • Pressing Enter (or Return) is now equivalent to clicking "OK" in most ImageJ dialog boxes. (u)
  • Replaced the "Save..." button in the Analyze/Histogram window with "List", which lists the histogram values in the ImageJ window. (u)
  • Image/Duplicate now displays a dialog allowing the title of the new window to be specified. Hold the alt key down to skip the dialog. (t)
  • Added the Edit/Options/Divide by Zero command for specifying the value used by the Image Calculator when it detects divide by zero with 32-bit real images. (t)
  • Updated the Keyboard Shortcuts Table.
  • Added the Window/ImageJ command (shortcut=enter) for bringing the ImageJ window to the front. (s)
  • Added the Analyze/Analyze Line Graph command for extracting coordinate data from scanned line graphs. It is similar to NIH Image's Line Plot -> Data macro. (r)
  • Added a constructor to the PlotWindow class for generating XY line graphs. See ij/plugin/filter/LineGraphAnalyzer for an example. (r)
  • With 32-bit float images, Analyze/Image Calculator now detects divide by zero and sets the result to Float.MAX_VALUE (3.4e38). (q)
  • Process/Image Calculator will now optionally process entire stacks if the source and destination are stacks with the same number of slices or the source is a single image and the destination is a stack. (p)
  • Conversion of 8-bit and 16-bit stacks to 32-bits is now supported. (p)
  • For RGB images, Analyze/Histogram displays a luminance histogram instead of a histogram all red, green and blue values. This is the way it worked prior to v1.07. (n)
  • Added a "List" button to profile plot windows that displays the XY coordinates in the ImageJ window. (n)
  • Added the Image/Stacks/Plot Z-axis Profile command for plotting the ROI means of the slices in a stack. (m)
  • Fixed a bug that, when quiting ImageJ, caused "cancel" in the save changes dialog for stacks to be ignored. (m)
  • Fixed a bug in v1.10 that sometimes caused histogram min and max to be set to zero. (m)
  • Fixed a bug, introduced in v1.07, that caused area measurements of RGB images to be three times too large. (m)
  • Fixed a problem with text not being displayed in Histogram windows on Windows NT. (j)
  • In Analyze/Set Scale, in addition to setting "Unit of Measurement" to "pixel" or "Distance in Pixels" to 0, you can now also disable spatial calibration by clearing the "Unit of Measurement" field.
  • Added Edit/Clear Outside command for erasing everything outside the ROI. (f)
  • Analyze/Gels/Label Peaks now displays in the ImageJ window the band sizes as a percentage of the size of the largest band. (e)
  • Added an image autocorrelation plugin by Markus Hasselblatt.
  • DICOM images, without a .dcm extension, and FITs images can now be opened using File/Open and File/Acquire/All As Stack. (c)
  • Image/Show Info now displays the DICOM tags. (c)
  • The "Apply" option in Image/Adjust Contrast, when working with a stack, now allows the user to choose between applying the LUT to the current slice or to the entire stack. (c)
  • Fixed a v1.10 text selection problem. (c)
  • Added YesNoCancelDialog class. (c)

  Version 1.10, 8-Nov-99

  • The histogram display in the Image/Adjust Contrast tool is now double buffered to prevent flicker. (u)
  • Added a "Thresh" (threshold) button to the Image/Adjust Contrast tool. Use the brightness slider to adjust the threshold. Use the slider's arrows to make fine adjustments. (t)
  • Extended the DicomViewer sample program to display the header information. Chris Rorden's DICOM page is a good place to get more information about the DICOM standard.
  • The DICOM reader now reads files with "??" VRs. (s)
  • Fixed a bug that caused RGB stacks to be read incorrectly. (q)
  • Replaced (again!) the text panel in the ImageJ window with one based on the hGRID class. The new text panel features unlimited size, resizable columns and a popup menu for saving to a file or copying to the system clipboard. Right-click (command-click on the Mac) in the text panel to access this menu. Measurement results can also be copied to the clipboard using Edit/Copy or control-C (command-C on the Mac). Rows to be copied must first be selected using the mouse or the popup menu. Shift-click to extend a selection. The number of lines copied to the clipboard is displayed in the status bar. (p)
  • Added the File/Save As/Measurements command for saving measurement results to a tab-delimited text file. (p)
  • The arrow keys, with the alt key held down, now move the end of line selections. (p)
  • Added center of mass measurement option that works with 8-bit and 16-bit images. The center of mass is the pixel value weighted average of all the x and y coordinates in the selection. (i)
  • Added centroid measurement option. The centroid is calculated by averaging the x and y coordinates of all of the pixels in the selection. (h)
  • Added perimeter measurement option. Perimeter is calculated using the same algorithm as NIH Image, where edge pixels are counted as one and corner pixels as square root of two. (h)
  • Changed the name of Image/Get Info to Show Info. (h)
  • Show Info now displays DICOM and FITS header information. (h)
  • Multi-image DICOM files now open as a stack. (h)
  • Analyze Particles can now be canceled using the esc key. (h)
  • Fixed a bug in Analyze Particles that caused it to fail with images containing thousands of particles. (h)
  • Added the Particles sample image, contributed by Katriona Lightbody. This 2000x1000 binary image containing 5097 particles is useful for stress testing and benchmarking Analyze Particles. (h)

  Version 1.09, 19-Oct-99

  • Replaced the text panel in the ImageJ window with an improved version based on the Viewer class by Rene Grothmann. This version has no arbitrary size limit, supports color, and features a popup menu for saving the contents of the panel to a file or to the system clipboard. Right-click (command-click on the Mac) to access this menu.
  • Moving small (less than 25x25) rectangular ROIs causes the pixel value to be displayed in the status bar. Can be used, in conjunction with the arrow keys, to inspect individual pixels.
  • Added Analyze/Set Measurements to specify the values to be calculated and recorded by Analyze/Measure.
  • Added a progress bar to File/Save As Jpeg.
  • Default Jpeg compression quality increased from 50 to 75.
  • Newly opened grayscale Jpegs are automatically converted to 8-bits.
  • Added nine new sample images to the File/Open submenu.
  • Added File/Aquire/As Text File for opening text files in read-only mode.
  • Image/Rotate now use bilinear interpolation and rotates entire stacks.
  • The Process/Math command was converted to a submenu.
  • Image/Type now supports 16-bit to 32-bit and 32-bit to 16-bit conversions.
  • Added a plugin that does MRI t2 calculations (s2 = k/ln(s1/s2)) on two images or stacks.
  • Added plugins that load and save images in Analyze, PNG, Pict, SPE, AHF and other formats.
  • Process/Math/Log now works correctly for float images.
  • ImagePlus.getProperties() now automatically constructs a property object instead of returning null.
  • Added the TextWindow class that plugins (e.g. ij/plugin/System_Properties.java) can use to display text in a window.
  • Added ImagePlus.startTiming() method so filter plugins (e.g. ij/plugin/filter/Rotator.java) can avoid having dialog open times including in the displayed processing time.
  • Added OpenFile and SaveFile classes that plugins can use for opening and saving images. See the I/O plugins on the plugins page for examples.
  • Added the ImagePlus.setProperty(String,Object) method.

  Version 1.08, 21-Sept-99

  • Added the Image/Stacks/Reslice and Image/Stacks/ZProject commands. Descriptions of these commands are in the online manual. They were contributed by Patrick Kelly and Harvey Karten of the University of California, San Diego.
  • Added a bilinear interpolation option to the Image/Scale and Image/Transformations/Resize commands.
  • Added the Process/Repeat Command command for repeating the previous command. Note that the Undo and Close are ignored.
  • Added a batch file to the Windows distribution for running ImageJ using Microsoft'sJava. It contains the single command "jview /cp ij.jar;plugins ij.ImageJ".
  • Added the ImageProcessor.setInterpolate(boolean) method.
  • Added the ImagePlus.show(String) method for displaying an image in a window with a message in the status bar. The ZProject and Reslice commands use this method to display the processing time.
  • Fixed a rounding bug that caused Image/Scale and Image/Transformations/Resize to work incorrectly along the edge of images with an odd width or odd height.

  Version 1.07, 3-Aug-99

  • File/Save As/Tiff and File/Save As/Raw Data now support RGB and float stacks.
  • Added a plugin (RGB_Stack_Merge.java) for merging three 8-bit stacks into one RGB stack.
  • Added support for 8-bit indexed color to grayscale stack conversions.
  • Added the Image/Stacks/Make Montage command for creating a composite image from the slices in a stack.
  • Released a Mac 1.07 version that adds the File/Acquire/Video command for capturing images from QuickTime compatible video sources. Requires QuickTime for Java, a QuickTime 4.0 custom install. QT 4.0 is not required, but you have to use the QT 4.0 installer to install QT for Java (do a custom install).
  • Process/Equalize now works much better thanks to an improved histogram equalization algorithm contributed by Richard Kirk that uses the square root of the histogram values. Process/Equalize also now works with 16-bit images. Hold down the alt key use the standard histogram equalization algorithm.
  • Removed the Process/Enhance Contrast command. As a substitute, use Process/Equalize or the "Auto" button in the Image/Adjust Contrast window. The "Auto" button has the advantage of not altering the pixel values except for RGB images.
  • Added Process/Repeat, which repeats the previous command.
  • File/New can now create unsigned 16-bit images.
  • For RGB images, Analyze/Histogram now displays the histogram of all red, green and blue values. Previously it displayed a luminance histogram.
  • Clicking on an image's close box now invokes the File/Close command, which runs as a separate thread, instead of closing the image in the event queue thread. This should make exceptions and thread deadlocks less likely.
  • Changed the title of the IJ.error() dialog from "Error" to "ImageJ".
  • Changed the argument of the ImageProcessor.applyTable method from byte[] to int[] so it can be used with 16-bit images.
  • The ImageWriter class now writes short and float images using little-endian byte order if FileInfo.intelByteOrder is set true.
  • For stacks, ImagePlus.getFileInfo() now sets FileInfo.pixels to an array of images.
  • The ImageProcessor.getHistogram method now works with 16-bit images.
  • Added IJ.altKeyDown method for determining if the alt key is down.
  • Added the ImageProcessor.drawString method for drawing text on images. Use moveTo(x,y) to specify the position and getStringWidth() to determine how many pixels will be required to draw the text.
  • Fixed a recently introduced bug that caused File/Acquire/Raw to not work with RGB images.
  • Fixed a bug that sometimes caused the the slice selector to become invalid when converting a stack to a different data type.

  Version 1.06, 2-July-99

  • Plugins in the plugins folder are no longer loaded using a custom class loader. Consequently, the plugins folder must be in the classpath. This change fixes a bug that caused static variables in plugins to be reset.

  Version 1.05, 1-July-99

  • The Image/Stacks/Convert Stack to RGB command now works with 16-bit stacks.
  • Conversion of 16-bit stacks, real stacks and RGB stacks to 8-bit grayscale is now supported.
  • Added "Add Slice", "Delete Slice" and "Convert Images to Stack" commands to the Image/Stacks submenu.
  • Added the File/Acquire/Text command for opening tab-delimited text files as real images.
  • Values displayed in histograms of real images are now better formatted.
  • Analyze/Gels/Plot Lanes now displays large plots in an enlarged window zoomed 1:1.
  • Added the Analyze/Gels/Label Peaks command.
  • The Gel Analyzer now converts pixel values to uncalibrated OD before plotting the lanes. It also adds half the perimeter to the peak area to compensate for the area under the boundary line.
  • A 3-point running average is now used to measure freehand line lengths.
  • ImageJ now looks for the plugins folder in the folder containing ij.properties. Previous versions expected it to be in "user.dir".
  • Added the Image/Color Tables/Invert LUT command for inverting the lookup table. Inverted LUTs display zero pixels as white instead of black. Unlike Edit/Invert, Invert Lut does not alter the pixel data.
  • Roi outlines are no longer limited to 5000 points.
  • Edit/Draw now works with oval selections.
  • The display is now updated correctly after using Edit/Draw with a line width greater than one.
  • Added the createImagePlus method to ImagePlus for creating new ImagePlus objects that have the attributes, such as spatial scale, of the parent.
  • Added the hide method to ImagePlus. Use hide() to close an ImagePlus' window and show() to open it.
  • Added constructors to ShortProcessor and FloatProcessor for creating blank images. The ShortProcessor constructor has a boolean argument used to specify signed or unsigned.
  • Added the invertLut method to ImageProcessor. Inverted Luts display zero pixels as white.
  • Image/Stacks/Convert Stack to RGB is working again (It broke in v1.03).
  • The File/Acquire/LUT command is working again.
  • Fixed a bug that caused brightness and contrast modifications to be lost after using Image/Crop, Image/Duplicate or Image/Transformations/Resize on a 16-bit or 32-bit image or stack.
  • Fixed a bug that caused spatial calibration to be lost after using Image/Crop or Image/Transformations/Resize.
  • Fixed a bug that caused the lineTo() method of ImageProcessor to not draw the end pixel.

  Version 1.04, 13-May-99

  • Added a "Difference" operator (dst = (dst-src)/2+128) to the Process/Image Calculator and Edit/Paste Control.
  • Fixed a bug, introduces in v1.02, that caused profile plots of straight line selections to be incorrect.
  • Fixed a bug that caused the "Subtract" operator in Process/Image Calculator and Edit/Paste Control to produce incorrect results.

  Version 1.03, 6-May-99

  • Added a flush() method to the ImagePlus class that sets the pixel arrays to null, making it more likely that the garbage collector will reclaim memory when images are closed.
  • The "Apply" button in the contrast/brightness control now processes every slice in a stack, with the exception of RGB and HSB stacks.
  • The standalone Windows version now comes as a self-extracting zip archive and includes JRE 1.1.8.
  • Worked around a null cursor bug with JDK 1.1.8.
  • Fixed a bug, introduced in V1.02, that caused conversions to RGB and HSB stacks to fail.
  • Fixed a Windows NT specific bug that caused values typed in the File/Acquire/Raw dialog to be read incorrectly.

  Version 1.02, 4-May-99

  • Added the Acquire/Twain command for acquiring images from TWAIN sources (scanners, digital cameras, frame grabbers). Requires that the "twain.jar" and "JavaTwain32.dll" files from the Java Twain Package at http://internet.sk/gnome/ be moved to the ImageJ folder.
  • Added the Process/Morphology submenu with Erode, Dilate, Open, Close, Outline and Skeletonize commands.
  • Added the Process/Shadows submenu with commands for producing shadow effects. Includes a nifty demo that shows off the speed of the 3x3 convolution routine contributed by Glynne Casteel.
  • Added the Process/Noise submenu, moved to it the "Add Noise" and Despeckle commands, and added "More Noise" and "Salt and Pepper" commands.
  • Added the Save As/Text command for saving images as tab-delimited text files.
  • 8-bit images can now be pasted into RGB images.
  • Profile plots of irregular line selections are now supported.
  • The Smooth and Sharpen commands now work with 32-bit floating-point images.
  • Fixed several bugs relating to 16-bit unsigned images.
  • Fixed a Windows NT specific bug that caused values typed in the Image/Scale dialog to be read incorrectly.

  Version 1.01, 25-March-99

  • Plug-ins placed in a folder named "plugins" are now automatically installed in the PlugIns menu. The folder distributed with ImageJ contains source code for two example plug-ins.
  • The applet version of ImageJ now downloads as a JAR (Java ARchive) file. It is now slower to start up but the annoying class file downloading delays are gone.
  • Added the Image>Crop command, which works with all data types and with stacks. Note that there is no Undo available for operations on stacks.
  • Dialog boxes are now centered on the screen.
  • The Rotate Right, Rotate Left and Resize commands now work with 16-bit and 32-bit grayscale images, and with stacks.
  • The Cut, Copy, Paste and Enhance Contrast commands now work with 16-bit and 32-bit grayscale images.
  • Added the "3-3-2 RGB" LUT to the Image>Color Tables sub-menu. This palette uses 3-bits for red, 3-bits for green, and 2-bits for blue.
  • Moved the benchmark commands from the PlugIns menu to the Image>Benchmarks sub-menu.
  • Added methods to the FileSaver class for saving as tiff, gif, jpeg or raw using a file path.
  • Removed the RGBA and HSB public constants from the ImagePlus class.
  • Added isRGBA() and isHSB() methods to the ImageStack class.
  • Fixed a bug with the "Pixel Aspect Ratio" option in the Analyze>Set Scale dialog.
  • Fixed a masking bug that caused operations on non-rectangular ROIs to fail on some UNIX systems.

  Version 0.99, 2-March-99

  • Added the Image>Stack>Save Slices as Files command for saving a stack as separate tiff, gif, jpeg or raw files.
  • On the Macintosh, the menu bar no longer disappears when image windows are active.
  • Added the "Spectrum" LUT to the Image>Color Tables sub-menu.
  • Added the Image>Stacks:Convert Stack to RGB command for converting a 3 or 4-slice stack to a color image.
  • The File>Acquire>All as Stack command now sorts the file list to guarantee that images are loaded into the stack in alphabetical order.
  • The Image>Scale and Image>Transformations>Resize commands now work with 16-bit images.
  • Fixed a problem with the 16-bit version Process>Sharpen.

  Version 0.98, 2-February-99

  • The Image>Colors window no longer requires a network connection and colors can be "picked up" without switching to the eyedropper tool.
  • The spatial scale in TIFF and DICOM headers is now used.
  • Added the "Analyze>Set Scale" command for setting the spatial scale.
  • Added the "Image>Stacks>Set Speed" command for changing the stack animation speed. The default is 10 fps.
  • When opening a TIFF file, and ImageJ is in debug mode, the TIFF tags are dumped to the ImageJ window.
  • Added the "File>Page Setup" dialog for specifying the printer scaling (5-500%) and whether or not the image is centered on the page, has a border and/or a title.
  • Images are now printed centered, with a border, and are scaled to fit the page.
  • Added the Image>Color Tables sub-menu for applying color lookup tables to grayscale images to produce false-color images. If no image is open, a 256x32 ramp image is created to display the color table.
  • Added an "Open All" option to the Import dialog.
  • Added the "File>Acquire>Open All As Stack" command for opening all the image files in a folder as a stack. The images must all be the same size and type (8-bit, 16-bit or RGB). The images can be in tiff, gif, jpeg or bmp format.
  • When closing a stack, the references to the raster data are set to null so the memory used by the stack is more likely to be reclaimed.
  • The Adjust Contrast plug-in no longer prevents closed images from being garbage collected.
  • The IP Demo plug-in now runs commands in a separate thread and no longer prevents closed images from being garbage collected.
  • Changed the name of the getTitle method in ImageStack to getSliceLabel.
  • Added the setColorModel methed to the ImageProcessor class.
  • Changed the name of the Info class to IJ.
  • Added the static IJ.runPlugIn method that runs a plug-in and returns a reference to it.
  • Changed the name of the getImageJ method in IJ to getInstance.
  • Changed the name of the getLUT method in ImagePlus to createLUT.
  • Edit>Draw now works with rectangular ROIs created by a paste operation.
  • Fixed a thread synchronization bug that could sometimes cause ImageJ to hang.
  • Fixed a bug that caused the File>Quit command to sometimes fail when running ImageJ under JDK 1.2.

  Version 0.97, 11-December-98

  • Updated the "Waves" benchmark results for the released version of JDK 1.2. Vote for bug 4185726 if you want to see image display speeded up in JDK 1.2.
  • Added a "16-bit Unsigned" option to the File/Acquire/Raw dialog. Selecting this option causes ImageJ to subtract 32768 from each pixel value before creating a ShortProcessor to contain the image. Methods in ShortProcessor that return pixel values (getPixelValue, getMin, getMax, etc.) then add back the 32768.
  • The new MemoryMonitor plug-in continuously plots ImageJ's memory utilization. Hold down the alt/option key to use a 640x480 window and display the frame rate, simulating video acquisition. Click on the status bar in the ImageJ window to force the JVM to do garbage collection.
  • The class files for the stand alone Windows version are now packaged as a JAR file.
  • The stand alone Windows version no longer uses a minimized console window.
  • Upgraded the Java runtime bundled with the stand alone Windows version to JRE 1.1.7B, which seems to have fixed a problem with exporting text to the system clipboard.
  • The "fps" display in the "Waves" plug-in now works with zoomed images.
  • The List System Properties plug-in now displays the name of the JIT compiler (java.compiler).
  • The "Test Display Speed" plug-in can now be aborted by pressing the esc key.
  • Plug-in can now have "about boxes". See the source for the Invert, MemoryMonitor or Waves plug-ins for examples.
  • The Plot Profile command, for rectangular selections, now averages horizontally if the alt/option key is down.
  • Added the Edit/Options/Profile Plot Options command for fixing the y-axis scale in profile plots.
  • The "Memory: xxxxK" message shown when clicking in the status bar no longer displays the free heap space.
  • File/Acquire/Raw handles out of memory situations better.
  • Fixed a bug that caused some tiff files to be displayed with inverted pixels.
  • Fixed a bug that caused a null pointer exception when using Plot Profile with no current selection.
  • Fixed a bug that could cause a null pointer exception when using the Rotate 90 Degrees Right/Left commands.

  Version 0.96, 23-November-98

  • Made the ImageJ window slightly wider so lines displayed by the Measurement command are less likely to be split.
  • Added a constructor to the ImagePlus class for creating an ImagePlus given an ImageProcessor.
  • Changed the order of the arguments in the ShortProcessor and FloatProcessor constructors to be consistent with the ByteProcessor and ColorProcessor constructors.
  • Fixed a thread synchronization bug that could sometimes cause ImageJ to hang when closing a window.
  • Fixed a bug that caused the drawing color of 8-bit images to be set to 254 instead of 255.
  • Fixed a bug that caused a null pointer exception when clicking on a 16-bit or 32-bit image with the dropper tool.

  Version 0.95, 19-November-98

  • The Plug-Ins/"Show Display Speeds" command was updated to include results for JDK 1.2. The results show that the crucial drawImage method is up to 22 times slower compared to JDK 1.1.7. To encourage Sun to fix this problem, vote for bug 4185726 ("JDK 1.2rc1 drawImage very slow (50% slower) compared to JDK 1.1.7") on the Bug Parade. ImageJ is not going to run well under JDK 1.2 until this problem is fixed.
  • Added the "Waves" plug-in that continuously applies a sine wave to the x-coordinates of an image. Click on the image or press the escape key to stop. This plug-in is useful as a benchmark (it displays the frame rate), as a way to demonstrate ImageJ's multi-tasking ability, and as an example of a plug-in that processes both 8-bit and RGB images.
  • Added a "Transformations" sub-menu to the Image menu and moved the "Flip Vertical" and "Flip Horizontal" commands into it.
  • Added the "Rescale" command to the Transformations sub-menu for scaling an image to a specified width and height.
  • Added commands to rotate an image 90 degrees left or right to the Transformations sub-menu.
  • The "Show Benchmark Times" and "Show Display Speeds" commands no longer require that an image be open.
  • Stack animation is now much faster.
  • The slice selection scroll bar in stack windows now works more reliably.
  • The Invert, Smooth, Find Edges, Add Noise, Despeckle and Threshold commands now operate on all the slices of a stack.
  • The Reduce Noise command, a median filter, was renamed Despeckle.
  • Added a public "running" flag to the ImageWindow class. Plug-ins can use this flag to terminate themselves when the user clicks on the image or presses the escape key. See /ij/plugin/filter/Waves.java for an example.
  • Improved the interface used by plug-in filters. Filters must now implement the PlugInFilter interface and be in the the ij.plugin.filter package. They must also provide a setup method that ImageJ will call to determine the filters capabilities. See ij/plugin/filter/PlugInFilter.java for more information and ij/plugin/filter/Invert.java for an example.
  • Added the GenericDialog class that plug-in can use to acquire multipler numeric parameters. See /ij/plugin/filter/Resizer.java for an example of how to use this new class.
  • The lock method in ImagePlus beeps and displays a status bar message if the image is already locked.
  • The reserve and unreserve methods in the ImagePlus class were renamed lock and unlock.

  Version 0.94, 21-October-98

  • The File/Acquire/Raw command no longer generates extra blank slices at the end of the stack when more than the actual number of images is specified.
  • Added a "Gap Between Images" field to the File/Acquire/Raw dialog box. This allows import of multi-image files with gaps between the images (e.g. uncompressed 8-bit AVI movies with a 4104 byte header and a gap of 8). Set the gap to (n-1)*width*height*2*real-gap to read every nth frame in a movie.
  • Changes to RGB images made using the Image/Adjust Contrast command are now be limited to the interior of non-rectangular selections.
  • The Process/Math command now works correctly with non-rectangular selections.
  • The Open... command now opens BMP files with names ending in ".bmp".
  • Added a command to the Save As sub-menu for saving images in JPEG format. It uses the JPEG encoder from http://www.obrador.com. Use the Edit/JPEG Quality command to specify the compression level.
  • The wand tool now more reliably traces areas defined by a one pixel wide boundary line.

  Version 0.93, 7-October-98

  • Added a constructor to the GifEncoder class for saving 8-bit AWT images.
  • Added the Edit/Fonts command for specifying the font, font size and font style. For a shortcut, double-click on the Text tool in the tool bar.
  • Double-clicking in the tool bar on any of the three line selection tools now brings up the set line width dialog.
  • Added a "Colors..." command to the Image menu. It downloads and displays an image that can be used, in conjunction with the dropper tool, to set the drawing color. Note that holding down the alt (option) key temporarily switches to the dropper tool.
  • Moved the Draw Arrow command from the PlugIns menu to the Edit menu.
  • Moved the Draw Arrow command from the PlugIns menu to the Edit menu.
  • Moved the Adjust Contrast command from the PlugIns menu to the Image menu.
  • The Fill and Clear commands now require a selection.
  • The Save As, Acquire/BMP and Acquire/Raw commands now "remember" the previously used directory.
  • Worked around a JDK 1.1.7 related bug that caused a null pointer exception when using ImageJ's GetNumberDialog or GetStringDialog classes.
  • Worked around a JDK 1.1.7 related bug that caused ImageJ to lock up when opening an 8-bit image.

  Version 0.92, 28-September-98

  • Fixed several bugs in "Adjust Contrast".
  • Added an "Hist." button to "Ajust Contrast" that generates a histogram and combines it with the LUT plot.
  • Added an "Apply" button to "Ajust Contrast" that, for 8-bit images, makes brightness and contrast changes permanent.
  • When running as an applet, the first time a command is executed, a progress bar is displayed as class files downloaded.
  • The 16-bit sample image "M51 Galaxy" now displays correctly.
  • Fixed a bug the that caused 16 and 32-bit images loaded over the network to become corrupted.
  • It's now possible to move text selections using the arrow keys.
  • Fixed a bug that could cause null pointer exceptions when generating line profiles.

  Version 0.91, 21-September-98

  • New downloadable versions for Mac OS, Windows and UNIX are available.
  • Increased the maximum heap size of the stand alone Windows version from 16MB to 64MB.
  • Updated the API documention.

  Version 0.90, 17-September-98

  • Worked around a bug in Sun's JDK/JRE 1.1.6 that caused the main ImageJ window to be too large.
  • Saved gif files now reflect changes made in the Adjust Contrast window.
  • Look-up table plots generated by Analyze/Show LUT now reflect changes made in the Adjust Contrast window.
  • Measurement results displayed in the ImageJ window are now formatted better.
  • Stacks are no longer limited to 100 slices.
  • Added "Next Slice" and "Previous Slice" commands to the Stacks sub-menu. Use the ">" and "<" keys as shortcuts.
  • Added a line of text to the top of each image window that displays current slice/total slices (stacks only), width, height, type and memory size.

  Version 0.89, 16-September-98

  • Added a text (annotation) tool. Use it to create a text rectangle, type some text, then use Edit/Draw to add the text to the Image. To draw the text on a white background, use Edit/Clear prior to Edit/Draw. To change the font size, use Edit/Font Size or double-click on the text tool. There is currently no way to select a different font or style. Text rectangles are currently limited to one line.
  • Added a Draw command to the pop-up menu. To use this menu, right-click on an image (option-click on the Mac).
  • Fixed a bug that sometimes caused operations on non-rectangular regions in stacks to fail.
  • Fixed a bug that could result in multiple checked items in the Type sub-menu after an attempt to do an unsupported conversion.
  • Fixed a bug that caused images larger than the screen (e.g. a 1024x1024 image on a 640x480 screen) to be displayed incorrectly after conversion to RGBA or HSB.
  • Fixed a bug that could cause null pointer exceptions when generating histograms.
  • Fixed a bug that caused the line width to be set to one if "Cancel" was clicked in the Edit/Line Width dialog box.

  Version 0.88, 8-September-98

  • Worked around a bug in SUN's JVM for Windows that could cause ImageJ to lock up when closing a window with changes.
  • Updated "Plug-Ins/Show Benchmark Times" to include results for Apple's MRJ 2.1ea2.
  • Fixed a bug that could cause images to become permanently locked when memory was low.
  • Fixed a minor bug in the Image/Scale command. To see the bug in action, use Acquire/URL to load the image http://imagej.net/~wayne/ij/images/dots.gif, and then use Image/Scale to scale it by 2.
  • When switching slices (channels) in RGBA or HSB stacks, the slice name ("red", "green", "blue", "hue", "saturation" or "brightness") is now displayed in the status bar.
  • Removed the Image/Channel sub-menu.

  Version 0.87, 20-August-98

  • Fixed several problems that caused Edit/Draw and Edit/Fill to use incorrect colors with in 8-bit images.
  • Hold down the alt (option) key to temporarily switch to the hand (panning) tool.
  • Alt-click (option-click) on an image with any tool except the magnifying glass to "pick up" a new drawing color. This is a shortcut for switching to the dropper tool, clicking on the image to select a drawing color, and then switching back to the original tool.
  • The Plug-Ins menu has a new command that tests to see how fast the JVM can draw images to the screen.

  Version 0.86, 2-July-98

  • The Benchmark plug-in has a new option that displays more times.
  • Images now display much faster when running under MRJ (MacOS Runtime for Java).
  • Lines rendered using the Draw command are now aligned better with the yellow ROI selection.
  • Worked around a problem with some versions of MRJ and Internet Explorer that caused ImageJ windows to be displayed under the the Mac menu bar.
  • Fixed another problem with the Draw command.

  Version 0.85, 22-June-98

  • Released new standalone versions for Mac OS8 and Windows. Reverted back to using JRE 1.1.5 with the Windows version because JRE 1.1.6 has a bug that causes ImageJ to hang when quiting with unsaved windows.
  • The Draw command works again.
  • Fixed a null pointer exception error (introduced in 0.83) that followed the "There are no Images open." dialog.

  Version 0.84, 19-June-98

  • New stand alone versions for Mac OS8 and Windows are available. The Mac version include source code and a Metrowerks CodeWarrior project file. The Windows version includes the source and Java Runtime Environment (JRE) 1.1.6. There is also a much smaller ZIP file containing the class files and source but not the JRE.
  • Updated the API documentation.

  Version 0.83, 18-June-98

  • Stacks can now be saved as tiff files.
  • 8-bit multi-image tiff files open as stacks if the images are all the same size.
  • The File/New command will now create 8-bit stacks.
  • Added an Image/Stacks submenu with commands to start/stop stack animation.
  • The Image/GetInfo command now displays "(inverted LUT)" for images with inverted look-up tables and, for stacks, displays the current slice number.
  • Fixed a bug that caused Edit/Clear to erase to black instead of white for images with inverted LUTs.
  • Added buttons to histogram windows that allow histogram values to be saved to a text file or copied to the system clipboard.
  • Fixed a bug that sometimes caused an array bounds exceptions when generating histograms of 32-bit real images.

  Version 0.82, 5-June-98

  • "Adjust Contrast" now changes the brightness and contrast of 8-bit images by updating the image's look-up table rather than its pixel values. This is particularly nice when working with stacks since brightness and contrast changes apply to all the slices in the stack.
  • Added two sample stacks to the Open menu. "MRI Stack" is a 3D MRI head scan consisting of 27 186x226 axial slices and "Scala Media Stack" is a 36 frame 3D movie of the scala media volume within the cochlea of the moustached bat.
  • Three of the larger sample images (Boats, Bridge and Gel) now download more reliably as a result of being converted from gifs to tiffs.
  • The FileOpener class now supports URLs and can open 8-bit stacks.
  • Acquire/Raw can now import multi-image 8-bit files.
  • Windows with multiple images (stacks) now have a scrollbar for selecting the image to be displayed. To see how this works, convert a color image to ARGB (alpha, red, green, blue) or to HSB (hue, saturation, brightness).

  Version 0.81, 14-May-98

  • Improved the DICOM plug-in so it now opens some aberrant GE MRI scans.
  • Copying text from the ImageJ window to the Clipboard now works more reliably.
  • Measurement results displayed in the ImageJ window are now tab-delimited so they can be easily pasted into a spreadsheet.
  • Moved the buttons in the profile plot window from the right side of the window to the bottom.
  • Fixed a problem with the "Copy" (to Clipboard) option in the profile plot window.
  • Moved the "Save XY Coordinates" and "Fractal Box Counter" plug-ins from the Plug-ins menu to the new Process/Fractals submenu.
  • The "Fractal Box Counter" now allows you to specify the box sizes and the results are now tab-delimited.

  Version 0.80, 11-May-98

  • The run() method plug-ins are required to implement is now passed a String instead of an ImagePlus. Plug-ins that need an ImagePlus object can call WindowManager.getCurrentImage(). One plug-in that used this new feature is URLOpener, which ImageJ uses to open the sample images in the Open submenu.
  • Changed the name of the URL plug-in to URLOpener.
  • The Acquire/Raw and Math commands now "remember" the popup menu selection.
  • Added a 16-bit image of the M51 galaxy to the Open submenu. As an exercise, try using Adjust Contrast to bring out detail in the galaxy. One useful trick is to select a region of interest and click on the "Auto" button.
  • Zoomed images now expand to fill the window as the window is enlarged.

  Version 0.79, 1-May-98

  • Resize rectangular selections by clicking and dragging the little box in the lower right corner.
  • Resize rectangular and oval selections by holding down the the option (alt) key and using the arrow keys.
  • Added a "Save Changes" dialog that is displayed when closing windows or quitting.
  • The Save command is now an alias for "Save as Tiff..." instead of "Save as Gif...".

  Version 0.78, 21-Apr-98

  • The "Adjust Contrast" plug-in is now multi-threaded to provide a more responsive user interface.
  • Added the wand tool. This tool automatically selects image areas with identical pixel values.
  • Fixed a problem with the interactive display of pixel values of zoomed RGB images.
  • Double-clicking in the toolbar now works more reliably. Currently you can double-click on the line tool to set the line width and on the zoom tool to unzoom.

  Version 0.77, 3-Apr-98

  • Added a plug-in (Acquire/URL) for opening GIF and JPEG images using a URL.
  • Added a class (GetStringDialog) that prompts the user for a string.
  • Converted the MessageDialog, MessageWithCancelDialog and GetNumberDialog classes to the Java 1.1 event model.
  • Added Select All and Select None commands.
  • Moved the Restore Selection command to the Edit menu and renamed it Restore Selection.
  • Profile plots are now larger for larger selections.
  • Added buttons to profile plots windows that allow the plot data to be saved to a text file or copied to the system clipboard.
  • Updated the API documentation.

  Version 0.76, 31-Mar-98

  • Added a plug-in for displaying 8, 16 and 32-bit FITS (Flexible Image Transport System) images.
  • Fixed a problem with ROI histograms of 16 and 32-bit grayscale images.
  • Fixed several image zooming and scrolling problems.
  • Added a plug-in for drawing arrows.
  • White (255,255,255) backgrounds are no longer changed to (248,248,248) when converting from RGB to 8-bit color.
  • File extensions are automatically changed when saving images in a different format.
  • Added a plug-in for adjusting the brightness and contrast and of all supported image types.

  Version 0.75, 17-Mar-98

  • Fixed an array bounds exception bug when using Enhance Contrast or Threshold with non-rectangular selections.
  • Fixed a bug that allowed freehand ROIs to extend beyond the left or top edge of the image.
  • Added a plug-in for displaying DICOM images. DICOM (Digital Imaging and Communications in Medicine) is an image file format widely used in the medical imaging community.
  • The DICOM plug-in dumps the DICOM tags (group, element, length, explicit VR) if debugging is enabled.
  • Added a plug-in for displaying uncompressed BMP images.
  • Added Acquire submenu for acquisition plug-ins such as the new DICOM and BMP plug-ins.
  • Changed Import command to a plug-in and moved it to the Acquire submenu.

  Version 0.74, 9-Mar-98

  • Three tools were added for creating straight, segmented and freehand line selections. Use the Draw command to draw the line. Use Measure to measure its length. Use Plot Profile to plot the pixel values along a straight line selection. To measure an angle, create a two-segment line selection and use the Measure command. Use the arrow keys to move line selections one pixel at a time.
  • A server bug was fixed that sometimes caused larger demo images such as "Boats" and "Bridge" to be downloaded incorrectly.
  • The status bar was moved to the top of the "ImageJ" window.
  • The new eyedropper tool "picks up" colors from image windows for use by the Draw and Fill commands.
  • A working JIT compiler is included with the standalone Win32 version.

  Version 0.73, 2-Mar-98

  • The Open command dumps TIFF tags to the Java console if debugging is enabled.
  • The "Lena" benchmark example times were updated.
  • The new "Draw" command outlines the ROI using the current color and line width. Note that this doesn't work yet with oval ROIs and there is currently no way to set the color.
  • Use the new "Line Width..." command, or double-click on the line tool, to set the line width.

  Version 0.72, 24-Feb-98

  • Keyboard shortcuts (without command or control) now work when the ImageJ window is active.
  • The "click on status bar to display memory used" feature works more reliably.
  • The ImageJ and IP_Demo classes were converted to the Java 1.1 event model.
  • Potential thread deadlock problem with the "IP Demo" plug-in fixed.
  • The "IP Demo" plug-in works with multiple images.
  • You can now quit the "IP Demo" plug-in by clicking on its close box.

  Version 0.71, 19-Feb-98

  • The "Save as Gif..." command now uses the GifEncoder class by Jef Poskanzer(http://www.acme.com). This GifEncoder is more reliable than the one previously used and it adds support for interlaced and transparent GIFs, although these features are currently not supported by ImageJ.
  • Added a simple example plug-in (Prototype PlugIn) that inverts grayscale images.
  • The ImageJ source code was divided into five packages: imagej, imagej.gui, imagej.process, imagej.io, and imagej.plugin.
  • The API documentation was updated.

  Version 0.70, 10-Feb-98

  • The New command now has a dialog box for specifing the name, size and content of newly created images.
  • The ImageWindow, ImageCanvas and ImportDialog classes were converted to the Java 1.1 event model.

  Version 0.63, 4-Feb-98

  • Support was added for cut, copy and paste of rectangular image selections. Support is limited to ImageJ's internal clipboard. Images cannot be copied to or from other programs.
  • Image windows now have a popup menu accessed using control-click on the Mac and right-click on PCs. This menu can be customized by editing the ij.properties file.
  • Keyboard shortcuts work without holding down the control key when an image window is active.
  • Use the keys "1" through "4" to switch image channels.
  • When switching channels, the channel name ("Red", "Hue", etc.) is displayed in the status bar.

  Version 0.62, 30-Jan-98

  • "Clear" now erases to white and "Fill" fills with black on images with inverted look-up tables.
  • ROI outlines are now more precisely drawn on magnified images whose width or height is not evenly dividable by the magnification factor.
  • A bug, introduced in v0.56, was fixed that prevented memory from being reclaimed when closing the last remaining image window.
  • A bug was fixed that prevented ROI outlines from being moved all the way to the right or bottom edge of an image.
  • A bug was fixed that caused operations to fail on images that had been duplicated using the Duplicate command.

  Version 0.61, 28-Jan-98

  • A plug-in was added that uses the "box counting" method to make measurements that allows one to calculate the fractal dimension of an object.
  • Text displayed in the ImageJ window can be selected and copied to the system clipboard. Note that this may not work when ImageJ is running as an applet due to security restrictions.
  • Stack traces due to run-time exceptions are now displayed in the ImageJ window.
  • Run-time exceptions such as array bounds errors no longer leave the active image in a locked state.

  Version 0.60, 21-Jan-98

  • The file open dialog box is now more likely to "remembers" the directory.
  • The window title is used as the default file name in the "Save as" dialog box.
  • Scrolling tool (looks like a hand) added.
  • Use function keys to select tools.
  • Values displayed by the Measure command are rounded and better formatted.

  Version 0.59, 13-Jan-98

  • ImageJ now requires a Java 1.1 virtual machine such as Sun's JDK 1.1.x, Netscape Navigator 4 with the JDK 1.1 patch (PC only), Internet Explorer 4 (Mac and PC), or MacOS Runtime for Java 2.0.
  • Horizontal scrollbar in ImageJ window is never used.
  • Keyboard shortcuts are shown in menus.
  • "Print" command added.
  • Zoom magnifications less than one are now supported.
  • "About..." command moved to standard help menu on Macs.
  • Integer pixel values now displayed in status bar without decimal points.
  • A number formating problem in the Rotate dialog box was fixed.
  • Status bar messages are now displayed using 12-point "SansSerif" font.
  • New image windows are positioned slightly offset from the previous window.
  • Images larger than the screen are scaled to fit.
  • Image windows increase/decrease in size as needed when zooming.

  Version 0.58, 22-Dec-97

  • Six more sample images were added.
  • The location and names of the sample images are now read from a file named ij.properties.
  • A plug-in was added that saves to a text file the x,y coordinates of black pixels in binary images.
  • A plug-in was added that displays the Java system properties.
  • The progress bar has a new 3D look.
  • Attempts to filter 8-bit indexed color images cause an error message to be displayed.

  Version 0.57, 4-Dec-97

  • "Window" menu added.
  • Keyboard shortcuts work more reliably.
  • The RGB to 8-bit color conversion dialog is now dismissed more quickly..
  • Keyboard shorcuts added for Enhance Contrast (Shift^E) and Threshold (Shift^T)
  • The revert command now works with images opened using Open... and with imported raw images.

  Version 0.56, 20-Nov-97

  • The new Measure command (control-1 or just 1) calculates and displays the pixel count, mean, standard deviation, and min and max pixel value. Note that results are truncated, rather than rounded. This will be fixed in a future version.
  • The new Restore Outline command restores the previous ROI outline or, when switching windows, transfers an outline from one window to another.
  • The arrow keys now move ROI outlines.
  • The Measure and Histogram commands now work with non-rectangular selections on 16 and 32-bit grayscale images.

  Version 0.55, 14-Nov-97

  • Filters no longer automatically convert 8-bit indexed color images to 32-bit RGB images.
  • All menu commands now run in a separate thread.
  • The Find Edges, Reduce Noise, Enhance Contrast and Threshold commands now work with RGB images.
  • The Enhance Contrast and Threshold commands now work correctly with non-rectangular selections.
  • ImageJ now compiles without error using the JDK 1.1.4 Java compiler. The command "javac ImageJ.java" compiles all the classes except for plug-ins.
  • Enhance Contrast now continues to increase contrast when used repeatedly.

  Version 0.54, 5-Nov-97

  • Get Info now displays the amount of memory used by ImageJ in kilobytes. You can also view this value by clicking on the status bar at the bottom of the ImageJ window.
  • Window and memory management are improved.
  • More information is displayed in the debug mode.
  • The Memory_Test plug-in displays a warning dialog box.
  • The applet version of ImageJ was moved to a faster server so images and class files should now load faster.

  Version 0.53, 29-Oct-97

  • A magnifying glass tool was added to the toolbar. Click on an image to zoom in. Option-click or right-click to zoom out. Double-click on the magnifying glass icon to reset the image. Eight magnification levels are available: 1:1, 2:1, 4:1, 8:1, 16:1, 32:1 and 64:1.
  • The outlining tools work on zoomed images. As an exercise, try outlining a single pixel with each of the four outlining tools.

  Version 0.52, 21-Oct-97

  • The memory requirements of the 3x3 neighborhood filters (Smooth, Sharpen, etc.) were reduced. They now require free memory equal to 2 times the image size instead of 3 times.
  • An error message is now displayed when OutOfMemoryError exceptions occur.
  • Use the "Memory_Test" plug-in to see how will your JVM handles low memory situations. It will open as many 1024x1024x8-bit images as possible and then attempt to calculate how much memory was used for each image. This is a demanding test that may require ImageJ to be restarted, may crash your browser, or may even crash your machine.

  Version 0.51, 17-Oct-97

  • A toolbar with four outlining tools was added.
  • The status bar and progress bar were moved to the bottom of the ImageJ window.
  • The cursor changes to a crosshair if it's inside an image window and not inside an ROI.
  • Holding the shift key down constrains selections to be square.
  • The Smooth and Sharpen filters no longer ignore ROIs on color images.

  Version 0.50, 23-Sep-97

  • ImageJ's functionality can now be expanded via plug-in class files that are automatically installed in the Plug-Ins (formerly Special) menu. This version is supplied with five example plug-ins: Benchmark, IPDemo_PlugIn, PlugIn_Macro, Thread_Lister and Timer. Future versions will allow plug-ins to be installed in any menu.

  Version 0.49

  • Filters and the built-in benchmark now run as separate threads. You can now run two or more benchmarks at the same time!
  • The entire image is no longer redrawn when ROIs are created or moved.
  • "Plot Profile" command added.

  Version 0.48

  • Histograms of 16 and 32-bit images now correctly labeled

  Version 0.47

  • Save grayscale (8, 16 and 32-bit) and color (8 and 24-bit) images as TIFF

  Version 0.46 and Earlier

  • Save byte, short, float and RGB images as raw data
  • Open uncompressed TIFF files
  • Now works with JDK 1.1.x and Hot Java 1.0
  • Progress bar when downloading images and class files
  • Support for 32-bit real images
  • Progress bar for filters
  • Import raw 8 and 16 bit images
  • Support for 16-bit (signed) images
  • Cursor location and value of pixel at that location are dynamically displayed
  • Pixel values and counts dynamically displayed in the Histogram window
  • Histogram command works correctly with indexed color images
  • Convert RGB color to 8-bit indexed color
  • Keyboard shortcuts using the Control key. ^N=New, ^O=Open, ^K=Open Color Lena, ^L=Open Lena, ^W=Close, ^S=Save As, ^R=Revert, ^D=Duplicate, ^I=Get Info, ^Z=Undo, ^F=Fill, E^=Scale, ^H=Histogram. You may need to click on a window to get keyboard focus.
  • Close, Save As (GIF) and Revert commands
  • New prototype macro in Special menu
  • Convert color images to RGB (red, green and blue) or HSB (hue, saturation and brightness)
  • Convert color to grayscale

  ---