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ImageJ News

Version 1.43b, 23 June 2009 (upgrade)

• 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 (download)

• 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 Adjust>>Threshold tool to 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 (download)

• 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 rsb.info.nih.gov/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 rsb.info.nih.gov/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 (download)

• 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 (download)

• 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 (download)

• 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/FunctionLibrary.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., http://rsb.info.nih.gov/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., http://rsb.info.nih.gov/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 (download)

• 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.
  • IJ.getDirectory() calls are recorded.
  • Added support for plugins that have the main class in a package. Look at the Bio-Formats plugin (loci_tools.jar) for examples.
  • 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").

Complete Release Notes

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