Online Manual for the
MBF-ImageJ collection


Link to ImageJ homepage
 
 

 

Updates to MBF ImageJ

Updates listed in no particular order.

See: http://rsb.info.nih.gov/ij/notes.html, for information on core updates and the ImageJ Documentation Wiki for information and documentation about ImageJ.

See the guidelines for image manipulation at Journal of Cell Biology.

v1.42l Apr 2009
Updated to ImageJ 1.42l and Bioformats Build4951.

v1.41n Oct 2008

FLIM plugin menu

Several plugins to open Text-images exported from Becker and Hickl SPCImage. Plugins>FLIM

Texture analysis

 Several plugins to calculate Haralick's texture features (GLCM) from Julio E. Cabrera (jcabrera at mail.nih.gov). http://rsbweb.nih.gov/ij/plugins/texture.html

Fractal Count: http://www.pvv.org/~perchrh/imagej/fractal.html

High content screening (HCS)

 Several plugins to open and process Opera FLEX files and Nikon/Thermo Biostation image series.

 

v1.39o Jan 2008

 

Added "Plugins>Colour>Colour Composite Merge" to merge greyscale images to Colour composite. This format has the advantage over conventional RGB colour images in that there can be more than three channels and  the original channels can be adjusted after merging and also split back off.

If the active window is greyscale, the RGB button now activates the plugin "Composite Merge" to generate a colour composite image. If the active image  is 24 bit then it does an 'RGB split' (+Alt keeps original RGB).

Brightness and contrast button now opens "Color Adjust" dialog if the active window is 24-bit.

Added toolbar button to open "Set Threshold" dialog.
 

Added option to have channels as greyscale in RGB to Montage plugin.
 

Added support for Perkin Elmer FLEX file format through LOCI Bio-Formats and Lurawave libraries. Requires Registration for this particular function.

 

 

 

 

 

 

 v1.39d Oct 28 2007

  • "Plugins>ROI>BG subtract from ROI" no longer clears existing results table.

  • Added updated LOCI Bio-Formats (Oct 17 2007).

  • Added updated JRE to v6 update 3.

  • Replaced Colour Contour toolbar button with one to open Brightness and Contrast dialog.

  • Replaced ROI push tool with RGB merge/split tool.
    Tool opens the RGB merge dialog; shift+click performs an RGB split; shift+alt+click splits and keeps the original.
    If the active window is a 3-channle stack, then the tool performs a "Convert stack to RGB" function.

  • Added Z-projection tool for a one-click maximum intensity projection of the current stack. Removed shift-Z shortcut for Z-projection as this is now being used for channel assignment by the core ImageJ appication.

  • Replaced Sigma filter with "Sigma Filter Plus" filter from Michael Schmid. Updated Enhance Image to use the Sigma Filter Plus with default values.

  • Added Piotr Wendykier's "Spectral Deconvolution" plugins to "Plugins>Deconvolution"

  • Updated "Mander's Coefficients" so that if the ch1 image is RGB the analysis is done on this iamge alone; the ch2 selection is ignored.

  • Added "Plugins>Colocalisation Analysis>Mander's ROI Manager" that runs the "Mander's Coefficients" plugin on all the ROIs in the current ROI manager.

 

v1.39d Aug 28 2007

  • Added updated "Plugins>Particle Analysis>Object Counter3D" that returns calibrated volume measurements.

  • Added FRAP profiler.

  • Added updated LOCI Bio-Formats (Aug 1st 2007).

v1.38r May 18 2007

  • Updated LOCI Bio-Formats (May 3 2007) plugins.

  • Updated JRE to v6 update1

  • Added Plugins/Stacks - T Functions/Ratio ROI manager which performs ratio analysis of a dual-channel, interleaved, time-course stack, e.g. Fura 2, using the ROIs from the ROI manager. Returns mean ch1, mean Ch2 and ratio of mean ch1 ÷ mean ch2 as a multi column results window.

  • Updated the toolbar sets to include Gilles Carpentier's suite; Jerome Mutterer's RGB Profiles tool and James Norman's ROI Push Tool.

  • Based on Gilles' macro set, the StartUpMacros have been updated to allow rapid access to common LUTs from the toolbar ('palette' button); one click access to this manual site ('question mark' button and one click access to the "add scale bar" function ('µm' button). The Draw functions have been moved to a Toolset menu accessible as an alternate macro toolset (Click the ">>" button on the toolbar).

  • Added Plugins/FLIM menu and plugins to import Becker and Hickl exported text images and generate photon weighted lifetime images based on the Tau and photon number images.

  • Added ImageJ/lut folder and copied some LUT files there to list them in the Image/Lookup Table submenu.

  • The Enhance Image plugin now stores the options in the ImageJ preferences file.

  • The Z_Coded_Stack plugin allows user defined LUT for the depth coding or the option to use the current LUT. This option is stored.

 

v1.38m March 19 2007

  • Updated LOCI Bio-Formats (March 16 2007) plugins.

  • Changed "rename" Hotkey from "R" to "F2". "Range Indicator" LUT can be called using "F3" now.

  • Updated Volume Viewer plugin.

  • Improved ROI handling in "Colocalisation threshold" plugin.

 

v1.38i  Feb 8 2007

  • Updated LOCI Bio-Formats (Feb 2007) plugins.

  • Changed the Plugins/ROI/BG_Subtraction_from_ROI macro to a plugin to speed it up and facilitate the use of the hotkey (="B". Note. "b" activates rolling ball subtraction in MBF_ImageJ)

  • Added Plugins/Colour Functions/Whiten Background. The user defines a background cutoff value and a grey level. All values below this cutoff are changed to this grey level. Saves on printer toner!

  • Added Plugins/Stacks - building/Stack Building by Name which creates a stack from all open images with a user defined string in the window title. I found this useful to stack multiple plot windows during analysis.

  • Updated Plugins/Stacks - T-functions/Quick Ratio Profiler.

v1.38f Jan 4 2007 - MBF_ImageJ released

  • Added LOCI Bio-Formats (Dec 2006) import plugin to File/Import/LOCI Bio-Formats Importer and HandleExtraFileTypes plugin so the functionality of the LOCI Bio-Formats plugin can be accessed via the menu command File/Open.

  • Added LOCI Bio-Formats Export plugin to File/Save As/LOCI Bio-Formats Exporter.

  • Added new Plugin sub-menu: Plugins/Stacks - Multi-D to include the LOCI group's LOCI 4D Data browser, Joachim Walter's  Image5D and Michael Abramoff's  HyperVolume Browser (moved from Plugins/Stacks - Shuffling).

  • Added Plugins/Stacks - T-functions/Ratio Stack macro to perform a crude ratio of an interleaved stack allowing the user to subtract either a max-intensity projection mask of the stack or the auto-threshold mask of the entire stack. Allows users to override the default Ch1÷Ch2 (i.e. odd slices divided by even slices) and specify Rmin and Rmax. For visualisation only. Ratiometric measurements for an ROI should be calculated (meanCh1 ÷ meanCh2), not mean(Ch1÷Ch2).

  • Updated RGB Gray Merge to allow user defined subtraction of fluorescence from bright-field 'grey' image and be compatible with 16-bit images. The 8 and 16-bit images are scaled using the min and max displayed value when merged. Let me know if you have any trouble with it.

  • Updated to JRE 1.6.0.

  • Replaced RGB_Measure with Dimiter Prodanov's RGB_Measure_Plus in Plugins/Colour functions menu.

  • Added Guy Levy's Particle Tracker to Plugin/Particle Analysis menu.

  • Added Erik Meijering's MTrackJ as the menu item Plugins/Particle Analysis/Manual Tracking - MTrackJ.

  • Updated Plugins/Stacks- shuffling/Deinterleave to carry over spatial calibration from source stack.

  • Added Plugins/Movies/Emboss plugin.

  • Improved Plugins/Movie/TimeStamper to allow optional anti-aliased text and digital number format* (HH:MM:SS) (*this code was taken from a related plugin some time ago and I can't remember the source. Please let me know if you recognise it...).

  • Updated Plugins/Stacks - building/Concatenate with Johnathon Jackson's improved version.

  • Added Plugins/Update menu to contain ImageJ Update item which is Patrick Pirotte's IJUpdate plugin and also his IJ_Proxy plugin.

  • Added toolsets macros.

  • Added Curtis Ruedens' "Improvision TIFF importer" which imports calibrated TIFF images exported from Volocity. File/Import/*.TIF Improvision TIFF file.

 

v1.37b April 2006 - Last WCIF_ImageJ

  • Added Gabriel Landini's toolbar 'LUT-cycler' button to the right-hand end of the toolbar.
    Clicking the button cycles between "Red", Green", "Blue" and "Grey" lookup tables.
    Pressing the "alt-key" when you click the button cycles "Fire", "Ice" "Spectrum" and "Grey".
    Pressing the space-bar cycles "Red Hot", "Green Hot", "Cyan Hot" and "Grey".
    Pressing the "shift-key" reverses the cycling.
    If no image is open or the current image is 24-bit image, a new 'ramp' image is generated.

v1.37a March 21 2006

v1.35q Feb 24 2006

  • Updated Windows installer to include George Silva's upgraded ImageJ.exe add to ImageJ to the registry. This will allow users to assign ImageJ as the default viewer for file types. See here for details.

  • Added "File/Import/*.TXT Leica SP2 series" import plugin. See here for details.

  • Renames Plugin/Toolbars to Plugin/Tools

  • Added two 'Lab calculator' macros: "Plugins/Tools/Concentrations" and "Plugins/Tools/Dilutions". The former calculates concentrations; the latter dilutions. See links for details.

v1.35p 3 Feb 2006

  • Updated online manual to be more friendly to non-Microsoft browsers.

  • Updated Windows ImageJ.exe launcher to new version from George Silva.

  • Updated JRE to 5.0 Update6 (aka.1.5.0_06).

v1.35j, 9 Dec 2005

  • Added Jerome Mutterer and Ulf Dittmer's PDF writer to "File/Save As/PDF export".

  • Added Kevin (Gali) Baler's Multi-Thresholder to "Plugins/Segmentation". This allows different threshold algorithms to be more easily evaluated.

  • Added Vladimir Pilny and Jiri Janacek's Anisotropic Diffusion 2D edge-preserving filter to "Process/Filter/Anisotropic Filter".

  • Added MCID *.IM reader courtesy of Wayne Rasband.

  • Update to JRE 5.0 Update 6.

v1.35g, 4 Nov 2005

  • Added updated "Colour Deconvolution" plugin.

  • Added Jon and Jeff Hardin's updated QuickTime plugins and QuickTime Java.

  • Added Dimiter Prodanov's Granulometric Filtering plugin to "Plugins/Particle Analysis".

  • Updated Java version to 5.0 update 5 (a.k.a. 1.5.0_05).

  • Added updated "Extended Depth of field" plugin. This update can be run in Easy or Expert mode.

  • Added Daniel Sage's SpotTracker plugin to "Plugins/Particle Analysis".

  • Added example of using the core FFT Bandpass Filter to correct for uneven background and horizontal banding.

v1.35d, 29 Sept 2005 

  • Added the StackReg and TurboReg plugins  from Philippe Thévenaz (Biomedical Imaging Group), as Align Slices to the "Plugins/Stacks - Shuffling" menu.

  • Upgraded LSM reader plugin.

  • Added Pirrotte Mutterer and Jeff Brandenburg's  HyperVolume Browser to "Plugins/Stacks - Shuffling".

  • Added "Plugins/LUT/Add Ramp" plugin which will add a greyscale ramp to an 8-bit image in a user defined rectangular selection. This is similar to the native "Analyze/Tools/Calibration Bar" but without the text labels. See entry in the manual here.

v1.34q, 5 Jul 2005

  • Added the DeltaVision *.DV and MetaMorph *.ND import plugins to the "File/Import" menu. Plugins from Fabrice Cordelieres.

  • Added 3D Objects Counter to "Plugins/Particle Analysis", also from Fabrice Cordelieres.

  • Added RGB to Montage plugin to the menu "Plugins/Colour functions" which will convert a single slice RGB image to a montage of its seprated red, green and blue channels. This was inspired by Gilles Carpentier Three Channel Fluorescence Image Exploration Tools macro which has greater functionality.

  • Added Z Code Stack plugin to the menu "Plugins/Stacks - Z-functions". This plugin  colour codes the slices in a 8-bit z-series based on their z-position. This can enhance subsequent processing on the stack (z-projections; 3D rotations). The idea is based on M. Abràmoff's depth coded volume rendering.

v1.34p, 13 Jun 2005

v1.34o, 9th Jun 2005

  • Added a small routine to get the user to set memory allocation after installation (Windows only).

  • Added "Plugins/Movies/Zoomify" plugin to create a 'zoom' sequence from an ROI. e.g. See here for details.

  • Added Gabriel Landini's Colour Correct plugin to the "Plugins/Colour functions/" menu as well as a modified version of this plugin called 'Colour Balance' which performs a white correction from a single ROI, sets the black level from the minimum intensity in each colour channel from the whole image.

  • Added the updated Align RGB planes plugin from Gabriel Landini.

  • Added two tool-bars modified from the Align RGB planes plugin. The "Common toolbar" starts when ImageJ starts and the LUT toolbar can be accessed via the menu command "Plugins/Toolbars/LUT toolbar".

  • The IJ_Prefs.txt file is write-protected by default so new preferences are not written to it. It can be write enabled by right clicking on the IJ_Prefs.txt file and unchecking the "read-only" attribute. 

  • Added "Draw Arrow" toolbar tool from Gilles Carpentier.

  • Added details of the MacOSX ImageJ update script for Gilles Carpentier. See Upgrade section.

 

v1.34m, 10th May 2005

  • Updated Java version to 5.0 update 3 (a.k.a. 1.5.0_03).

  • Updated the Nucleus Counter plugin to have more options. See here.

  • Bundled Bob Dougherty's 3D Deconvolution plugins. See here.

 

v1.34l, 22nd April 2005

  • Reorganised the colocalisation related plugins to "Plugins/Colocalisation/".

  • "Image Correlator Plus" plugin renamed "Manders Coefficients" and upgraded.

  • Added two plugins for Coste's Colocalisation analysis
    "Plugins/Colocalisation/Colocalisation Test"
    "Plugins/Colocalisation/Colocalisation Threshold"
    See Colocalisation Collection manual for details.

 

v1.34i, 3rd  March 2005

  • Zeiss ZVI reader plugin from Curtis Rueden.

  • Segmentation and thresholding plugins reorganised and can now be found in Plugins/Segmentation.

  • Kai Uwe Barthel's Volume Viewer included (Plugins/Stacks - Z-Functions/).

  • Macro for rotating a stack around the X-axis, then around the y-axis (Plugins/Z-functions/X and Y rotation).