File Menu

New

Creates a new image or text window. Image windows are filled with the current background color. New image windows inherit the look-up table, as well as any spatial or density calibration, of the currently active window. The size of newly created images is limited by the amount of free RAM, which is displayed in the About NIH Image dialog box.

Text windows can be used to create macros accessed using the Load Macros command or convolution kernels to be used by the Convolve command. Text windows have a maximum size of 32K.

manual6

Open

Use the Open command to load and display images (in TIFF, PICT, PICS and MacPaint format), text files, color look-up tables (LUTs) or region of interest outlines. The following file types are supported:

  1. TIFF files created by Image and many other programs. Image will open (as a stack) a TIFF file containing multiple images, but the images must all have the same width and height. Image is unable to open bitmap (1-bit) or compressed TIFF files. TIFF files that were created on other systems, such as an IBM-PC, usually need to be opened using the Import command. 16-bit TIFF files can be opened using the Import command. 24-bit (RGB) TIFF files are opened into a 3-slice (red, green and blue) stack.

  2. PICT files created by Image and numerous other Macintosh programs. Check Keep LUT in the Open dialog box (shown below) if you want to display the image using the current look-up table, instead of the one contained in the PICT file.

  3. MacPaint documents. You will want to set Undo Buffer Size in Preferences to 405K if you regularly open large MacPaint drawings, since this is the memory required for a full size ( 576 x 720) MacPaint document.

  4. PICS files created by Image and by many Macintosh animation programs.

  5. QuickTime movies. The Open command will place images from a QuickTime movie into a new stack. Note, however, that the current LUT is always used. Therefore, before opening the movie, you must switch to the Grayscale LUT when opening a grayscale movie and to the System LUT when opening a color movie.

  6. Look-up tables created by Image and by several other Macintosh programs, including PixelPaint, Canvas and UltraPaint. These programs have palette editors that can be used to create color tables for use by Image . The public domain PalEdit program from NCSA can also be used to create color tables that can be opened by Image .

  7. Selection outlines created using the Save As command in Image .

  8. Text files, such as macros and convolution kernels, up to 32K in size.

manual7

If you check Open All , select an image, and then click on the Open button, Image will open all the images in that folder, not just the one selected.

Check Keep LUT if you want the image to be displayed using the current video look-up table, rather than the one saved with the image. This feature can be used to combine PICT files with different palettes into a montage. When the PICT file is opened, and the image and screen LUTs are different, the pixel values are remapped to make the colors consistent.

Import

Use this command to read image files created by non-Macintosh based systems, to display spreadsheet data (text) as an image, or to import raw color look-up tables. It presents the following dialog box that allows you to select the type of file to be imported.

manual8

Select TIFF to open 8 and 16-bit TIFF files imported from other systems, such as an IBM PC. Once a 16-bit TIFF file has been imported, you can use Rescale (a k a Revert to Saved) to find the optimum 16-bit to 8-bit mapping. 16-bit TIFF files that represent white as zero open inverted.

Select DICOM to import 16-bit files in the DICOM-3 (Digital Imaging and Communications in Medicine) and ACR-NEMA formats used in radiology. A DICOM dictionary is required to decode the DICOM or ACR-NEMA header. This dictionary is available from rsbweb.nih.gov, in the /pub/nih-image/documents directory. It must be located in the same folder as NIH Image or in the System folder. When opening a DICOM file, hold the option key down to get a full header dump. When using the "Open All" option, hold the shift key down to fix 16-bit to 8-bit scaling. NIH Image's DICOM reader was written by Jim Nash, www.SynergyResearch.com.

Select Text to import a two-dimensional array of numbers stored in tab-delimeted text format, for example, a spreadsheet saved as "Text Only". Values do not have to be in the range 0-255, and may be in decimal or scientific format. By reading in the text file twice, image is able to determine the number of rows and columns, and to scale to 8-bits (1-254). Blank cells are assumed to have a value of zero. If Fixed Scale is checked then automatic scaling is disabled, values are scaled to 8-bits from the range Min-Max, values less than Min are set to Min, and values greater than Max are set to Max .

Select Look-Up Table to import a 768 byte binary LUT consisting of 256 consecutive red values, 256 consecutive green values, and 256 consecutive blue values. The values should be in the range 0-255.

Select Custom to open other types of 8-bit and 16-bit binary images. Width is the width of the image in pixels and Height is the number of lines in the image. For 16-bit images, the maximum value that can be entered for Width is 4096. Offset specifies the number of bytes Image will skip before it starts reading the pixel data. For example, use an offset of 512 to skip over a 512 byte file header. Set Slices to more than one to import 3D data sets such as multi-slice volumes from medical scanners

Image computes the minimum and maximum pixel values of 16-bit images and uses this information to linearly scale to 8-bits (1-254). Check Swap Bytes when importing 16-bit images from "little-endian" systems, such as an IBM-PC or VAX. If Calibrate is checked Image automatically sets up a linear density calibration function to provide an approximation of the original 16-bit pixel values. The approximated values should not vary from the original 16-bit values by more than (Max-Min)/254, where Min and Max are the minimum and maximum 16-bit values. If Fixed Scale is checked then automatic scaling is disabled and the 16-bit data is linearly scaled from Min -Max to 1-254. You can redo the 16-bit to 8-bit scaling at any time using the Rescale command. Note that the Calibrate feature is disabled when importing a 16-bit stack and Fixed Scale is not checked.

Use the Import command to scale 16-bit images from medical scanners to the 8 bit format required by Image . For example, to import raw MRI scans from a GE SIGNA scanner, set width and height to 256, select 16-bit Signed , and set Offset to 14336. The macro "Import GE Signa Files" (in the file Stacks) will automatically import a series of raw GE SIGNA files.

Check Open All to import all of the images in a folder. The images must all have the same width, height, etc. Open All does not work with imported text files and look-up tables.

Check Invert to invert imported 8-bit images.

Close

Closes the currently active image, text, Plot, or Histogram window, i.e., the one with the highlighted title bar. Hold down the option key to close all currently open image windows. Typing option-command-w or option-clicking in the close box of an image window will also close all the image windows.

Save

Resaves the currently active image or text window to disk. You will be prompted for a name in the case of an image newly created using New, Duplicate or Start Capturing. Files are resaved in their original format. In other words, TIFF files are resaved in TIFF format, and PICT files are resaved in PICT format.

Hold down the option key (notice how Save changes to Save All) to save all currently open image windows.

Save As

Allows you to saves the currently active image (or rectangular selection) in TIFF, PICT or MacPaint) format, to save a stack in TIFF or PICS format, or to save the current look-up table, selection outline, or text window.

manual9

TIFF
 Saves the currently active image or stack to a file in uncompressed 8-bit TIFF format. You will be asked to enter a name for the new file. The menu command changes to Save Selection As if a rectangular selection is active, allowing you to save a subsection of the image. Note that the ability to save selections does not work for stacks, but there are macros available to get around this limitation. TIFF is the default file format in Image, and is usually the best format for saving digitized or scanned images.

PICT
 Saves the currently active image to a PICT file. PICT files can be exported to many other Mac programs, including Canvas, Photoshop, SuperPaint and MacDraw. Because they are compressed, PICT files also have the advantage of being more compact if the image contains large homogeneous regions, which is typical of computer generated images. Unfortunately, the run length compression scheme used with PICT files is ineffective with most scanned images.

You should avoid PICT files if you are doing quantitative image analysis. The Mac imaging model is most concerned with the color of each pixel, and does not care so much about the actual pixel value. Thus PICT files cannot guarantee that the pixel values remain fixed. TIFF is a machine and system independent image standard that avoids this problem.

QuickTime
 Saves the currently active stack to disk as a QuickTime movie. A dialog box allows you to select the compression scheme and image quality level.

PICS
 Saves the currently active stack to disk in PICS format, a file format supported by many Mac animation programs. PICS files are compressed using the same run length encoding scheme used for PICT files. Stacks containing areas of uniform color or gray value saved in PICS format will be smaller than stacks saved in TIFF format. Use the "Movie Player" utility that comes with QuickTime to convert PICS files into QuickTime movies.

Note that the stack's spatial and density calibration data are not saved as part of the PICS file.

Color Table
 Saves the current look-up table (LUT) as a separate file.

Outline
 Saves the X-Y coordinates of the current selection outline. X-Y coordinates of curved line selections, and selections that have been edited, cannot be saved.

Export

Exports images, look-up tables, measurement results, density profile plot values, or histogram values to disk for use with programs other than Image.

manual10

Raw Pixel Data
 Exports the current image (or selection) as binary pixel data, in row order, one byte per pixel, without a header.

MCID
 Exports the current image (or selection) as an MCID file. MCID files have the same format as raw pixel data files, but are preceded by a four byte header which contains the width (minus one) and height (minus one), stored as two 16-bit numbers in Intel byte order.

Text
 Exports the current image (or rectangular selection) as a tab-delimited, spreadsheet compatible text file consisting of uncalibrated pixel values.

Look-Up Table
 Saves the current video Look-Up Table (LUT) as a 768 byte binary file consisting of 256 red values, 256 green values, and 256 blue values.

 Measurements
 Exports the current measurements to a tab-delimited text file compatible with spreadsheet and statistical analysis programs. Use the Analyze/Options dialog box to specify which measurements are recorded and/or exported. This option is also used to export angle measurements made with the angle tool, and X-Y coordinate measurements made with the cross hair tool. Measurements can also be exported by copying them to the Clipboard.

Plot Values
 Exports the data values representing the most recent density profile to a text file. If you have just used the Calibrate command to do density calibration, and are viewing the density calibration plot, then this option exports the 256 Y-values of the current calibration plot.

Histogram Values
 Exports the 256 gray level counts from the most recent histogram to a text file.

X-Y Coordinates
 Exports the X-Y coordinates of the current selection outline as a two column, tab-delimited text file. X-Y coordinates of rectangular and oval selections, and selections that have been edited, can not be exported.

Record Preferences

Saves the current state of the following Image program parameters:

Settings are saved in a file named 'Image Prefs' in the Preferences folder inside the System folder. You can revert to the default settings be deleting copies of this file in either the System or Preferences folders and restarting Image.

You can startup Image with customized settings by double-clicking on a copy of 'Image Prefs'. In this case, Image will use the settings in the copy. Note, however, that Record Preferences always saves the settings in the Preferences folder.

Revert to Saved

Reverts to the most recently saved version of the current image, effectively undoing all changes made since the last Save command. Reverting does not currently work with stacks or imported text files. For imported 16-bit images, this command changes to Rescale, described below.

Rescale

Replaces Revert to Saved whenever an imported 16-bit image or imported 16-bit TIFF file is active. This command linearly scales the 16-bit data (on disk) from the range Min -Max to 1-254, where Min and Max are determined by using the controls in the Map window or by using the LUT tool. 16-bit pixels with values less than Min are set to 1 and 16-bit pixels with values greater than Max are set to 254. The image's absolute minimum and maximum pixel values are used if the LUT has not been altered.

The Highlight Saturated Pixels option in the Preferences dialog box can be used determine locations within the image where density measurements may be invalid do to clipping at Min or Max . It causes pixels that were less than or equal to Min to be displayed in yellow and pixels that were greater than or equal to Max to be displayed in red.

Duplicate

Creates a new window displaying a copy of the current image, or of the current selection if only part of the image is selected. The newly created image inherits the look-up table, plus any spatial or density calibration, of the image being duplicated.

Get Info

Displays an image window, such as the one below, giving information about the currently active image and about the status of the system.

manual11

Acquire

Use this sub-menu to access Photoshop compatible acquisition plug-ins. The plug-ins must be stored in a folder named "Plug-ins" located either in the same folder as Image or in the System Folder. Using plug-ins, Image can acquire 8-bit grayscale, 8-bit indexed color, and 24-bit color images. 24-bit color images are stored in three slice stacks and displayed using 8-bit indexed color, similar to the way the Capture Color command works. Several of the plug-in listed below, including "Plug-in Digitizer" for use with the AV Macs, are available by anonymous FTP from rsbweb.nih.gov, in the /pub/nih-image/plug-ins directory.

The following plug-ins have been reported to work with Image :

Export

Use this sub-menu to access Photoshop compatible export plug-ins. Export plug-ins must be stored in a folder named "Plug-ins" located either in the same folder as Image or in the System Folder. Two export plug-ins have been successfully tested with Image : a plug-in that supports the Scion TV-3 video output card (used to drive a video printer) and the PhaserPrint plug-in for the Tektronix Phaser IIsd dye sublimation printer.

Page Setup

Lets you specify printing orientation (portrait or landscape) and scale (25% to 400%). The quality of density profile and calibration plots will be better if you leave the scale set at 100% and enlarge the plot window before printing the plot. Hold down the option key while selecting Page Setup to display a dialog box offering several custom grayscale halftoning options.

Print

Print images, text, plots, histograms, and measurement results. What gets printed is determined by which window is currently active. The print command changes (e.g., Print Image , Print Plot , etc.) depending on what kind of window is currently active.

Print Image - Prints the currently active image. Images larger than the printer page (normally 552 x 730 pixels) are automatically scaled to fit the page.

Print Plot - Prints the current density profile or calibration plot. The size of the printed plot is proportional to the size of the plot window, which can be made larger using the "grow box" in the lower right corner.

Print Histogram - Prints the contents of the histogram window.

Print Measurements - Prints the results of measurements made with the Measure command, or with the angle or the cross hair tools. This option is enabled whenever you have recorded one or more measurements and either the Info or Results window is active.

Print Text - Prints the contents of the current text window. Text is always printed using 9-point Monaco.

Quit

Closes all image windows after asking, in each case, whether changes made during the session should be saved, then quits to the Finder. If measurements have been made, but not saved, a dialog box will be displayed notifying you of that fact.

[Next] [Contents] [Home]