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ImageJ News

Version 1.47i 25 January 2013 (upgrade)

• Photos from the 2012 ImageJ conference in Luxembourg are available online.
• 1.47i 25 January 2013
  • Thanks to Curtis Rueden, the command finder (Plugins>Utilities>Find Commands) uses a table to display additional information about the commands it finds.
  • Improved the Plugins>Shortcuts>Create Shortcut command.
  • The Image>Stacks>Plot Z-axis Profile command works with hyperstacks.
  • Thanks to Adam Brin, added the IJ.getErrorMessage() method.
  • The "Startup Macros" command in the toolbar's ">>" menu looks for a file named StartupMacros.fiji.ijm if StartupMacros.txt is not found in the macros folder.
  • Added the Overlay.addSelection() and Overlay.activateSelection() macro functions.
  • Michael Schmid fixed a bug that sometimes caused Process>Noise>Remove Outliers and Process>Binary>Erode to not work correctly when processing stacks using multiple threads.
  • Thanks to Alistair MacDougall, fixed a v1.47f regression in the saveAs("tiff",path) macro function that caused it to not update the image title.
  • Fixed a 1.47f regression that caused the saveAs("tiff") macro function to throw an exception.
  • Fixed a bug that caused the String.copyResults() macro function to ignore selections, which is not consistent with the Results window's Edit>Copy command.
  • Thanks to Ved Sharma, fixed a bug that caused the macro language return statement to not correctly return string array values.
  • Thanks to Erik Belanger, fixed a bug the caused Image>Stacks>Delete Slice to not work correctly with hyperstacks.
  • Thanks to Julien Vaubourgeix, fixed a bug in Image>Stacks>Label that caused it to delete any existing overlay when the "Use overlay" option was enabled.
  • Fixed a bug that caused the saveAs(path) macro function to display a "Save As" dialog box.
• 1.47h 23 December 2012
  • Thanks to Denis Meuthen, you can now create a straight line selection by defining the start of the line with one click and the end with another click.
  • Thanks to Curtis Rueden, Image>Stacks>Tools>Make Substack now works with hyperstacks.
  • Thanks to Jerome Mutterer, the arrow, brush, pencil and pixel inspector tools remember the location of their options dialogs.
  • Thanks to Rainer Engel, the "Log" window remembers its dimensions.
  • File>Save As>Image Sequence displays a warning if the first file in the sequence will overwrite an existing file.
  • The File>New>Hyperstack command can be invoked by pressing alt-n.
  • Thanks to Gilles Carpentier, fixed a bug that caused the run("Make Composite") macro function to sometimes not work as expected.
  • Michael Schmid fixed a bug that prevented the AVI Reader from correctly opening as virtual stacks AVI files with blank frames.
  • Thanks to Alex Hughes, fixed a bug that caused the ROI Manager's Multi Plot command to disregard the "Vertical profile" option in the Edit>Options>Profile Plot Options dialog box.
  • Thanks to Kees Straatman, fixed a bug that caused Analyze>Tools>Analyze Line Graph to hang with non-thresholded images.
  • Thanks to John Oreopoulos, fixed a bug that caused File>Import>Image Sequence to sometimes not work as expected when all the images in the sequence were not the same type.
  • Thanks to Jerome Mutterer, fixed a bug that caused an exception when pasting, in a macro, a non-recangular ROI that was partially outside the target image.
  • Thanks to Vanessa Bell, fixed a bug that caused the getSelectionCoordinates() macro function and Roi.getPolygon() method to sometimes unexpectedly return the bounding rectangle of composite selections.
  • Thanks to Aivar Grislis, fixed a v1.47g regression that caused the setLocation() macro function to not work with some non-image windows.
  • Thanks to Michael Schmid, fixed a bug that caused "Cancel" to not work as expected for dialogs in "Preview" mode with commands called from macros.
  • Thanks to Jarek Sacha, fixed a bug that caused ImageListeners to sometimes not be notified when the image was updated.
  • Michael Schmid fixed two PlugInFilterRunner bugs related to Preview and PARALLELIZE_IMAGES.
• 1.47g 2 December 2012
  • Changed the "Brightness/Contrast", "Channels", "Threshold" and "Color Picker" windows to modeless dialogs that do not have the iconize and maximize buttons that are problematic on Windows.
  • Thanks to Bill Christens-Barry, added an "Auto contrast stacks" option to the Edit>Options>Appearance dialog box. Alternatively, hold down the shift key when scrolling stacks.
  • Thanks to Thomas Kuhne, Emil Kesler and Yili Zhao, Plugins>Compile and Run, on Java 1.6 or later, uses javax.tools.JavaCompiler instead of com.sun.tools.javac.Main.
  • Thanks to Norbert Vischer, added the close(pattern) macro function (example) and the ij.util.WildcardMatch class.
  • Thanks to Jerome Mutterer, added the getValue("rgb.foreground") and getValue("rgb.background") macro functions.
  • Thanks to Norbert Vischer, added the setForegroundColor(rgb) and setBackgroundColor(rgb) macro functions.
  • Thanks to Bill Christens-Barry, added the setOption("auto contrast",boolean) macro function.
  • Worked around a bug on Windows 8 that made scrollbar thumbs nearly invisible.
  • Fixed a bug that caused an exception when File>Revert was used on a duplicated image.
  • Thanks to Olivier Cardoso, fixed a bug that could cause an exception when calling an Ext macro function.
• Jerome Mutterer and Edda Zinck have released FigureJ, a plugin that makes it easy to create figures for scientific articles.
• Dimiter Prodanov contributed Mexican Hat Filter, a plugin that convolves a 2D image with a Laplacian of Gaussian filter.
• 1.47f 18 November 2012
  • Added the IJ.saveAsTiff() method.
  • Fixed a v1.46f regression that caused the applet version of ImageJ to not open images specified using HTML parameters.
  • Thanks to Erik Belanger, fixed a bug that caused the setMinAndMax() macro function to not work with batch mode composite color images.
  • Fixed several stack flattening bugs.
  • Fixed several hyperstack related bugs in the Image>Scale command.
  • Fixed a bug that caused the saveAs("tif",path) macro function to not work correctly on consecutive command line macro calls.
  • Thanks to Norbert Vischer, fixed a bug that caused Copy from the "Log" window to not work correctly for lines containing tabs when "Copy row numbers" was not enabled in Edit>Options>Input/Output.
  • Thanks to Jerome Mutterer, fixed a bug that prevented the FigureJ plugin from being able to restore tools.
• 1.47e 9 November 2012
  • Added the Macros>Evaluate BeanShell command to the macro editor. This command requires that a copy of BeanShell.jar be in the plugins folder.
  • Thanks to Michael Kaul, bilinear interpolation works better with float images containg NaNs.
  • Thanks to Michael Schmid, added a "Gaussian (no offset)" curve fitting option.
  • The recorder displays a warning when the options string in run(command,options) calls contain one or more non-ascii characters.
  • Added the Toolbar.restoreTools() method (example).
  • Added the ParticleAnalyzer.setFontColor(String) method and the call("ij.plugin.filter.ParticleAnalyzer.setFontColor","blue") macro function. .
  • Thanks to Thomas Boudier, added a public GaussianBlur3D.blur() method.
  • Thanks to Michael Schmid, fixed a v1.46 regression that could cause curve fitting errors.
  • Simon Bear fixed a bug that caused black pixel data to be ignored when loading CMYK TIFFs.
  • Fixed a bug that caused the source stack to become corrupted when scaling by x=1.0 and y=1.0 in Image>Scale.
  • Thanks to Thorsten Wagner and Michael Schmid, fixed a bug that caused the Analyze>Summarize command to fail if the Results table contained headings with spaces.
  • Thanks to David Gauntt, fixed a bug in the FHT class that caused it to fail when calculating the power spectrum of 1D arrays larger than 32K.
  • Thanks to Jarek Sacha, fixed a bug that cuased File>Import>Image Sequence to sometimes not set the correct slice labels when opening a series as a virtual stack.
• Gilles Carpentier contributed Angiogenesis Analyzer, a macro toolset for analysis of cellular networks, for example the pseudo vascular organization of endothelial cells cultured in a gel medium (documentation).
• 1.47d 5 October 2012
  • Thanks to Norbert Vischer, added the Image>Color>Arrange Channels command.
  • Thanks to Michael Cammer, when processing stacks, added "Method" and "Background" choices to the Process>Binary>Convert to Mask dialog.
  • Thanks to Ved Sharma, the arrow tool draws bolder outlined arrows.
  • Deleted the redundent Image>Hyperstacks>Channels Tool menu command.
  • Thanks to Norbert Vischer, added the getInfo("command.name") macro function (example).
  • Added the setOption("jfilechooser") macro function.
  • Fixed a bug that caused the roiManager("select",n) macro function, and RoiManager.select() method, to display an error message if no images were displayed.
  • Thanks to John Page, fixed a bug that caused CMYK TIFFs to open inverted.
  • Thanks to Birgit Möller, fixed a bug that sometimes caused the ImagePlus.show() method to not work as expected on closed images.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the Edit>Selection>Line to Area command to not work as expected.
  • Thanks to Gilles Carpentier, fixed bugs in Process>Binary>Skeletonize that caused it to sometimes not remove all skeleton pixels.
  • Thanks to Leon Espinosa, fixed a bug that caused "Apply" in the "Threshold" tool to always use the default thresholding method.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording, when the recoder was in "JavaScript" or "Plugin" mode, of plugins that used the run(imp,..) methods of the Duplicator class.
  • Norbert Vischer fixed a bug that caused line numbers in macro error messages to be incorrect with macros containing emptly lines inside SlashStar comments.
  • Thanks to Jiri Janacek, fixed a bug the caused the perimeter of composite ROIs in spatially calibrated images to be incorrect.
  • Thanks to Michael Schmid, fixed a bug that could cause file corruption if the Crop command was used while a stack was being saved.
  • Thanks to Eric Denarier, fixed a bug in Process>Batch>Macro that caused it to somestimes not output the correct images.
• Kota Miura has made available two textbooks ("Basics of Image Processing and Analysis" and "Macro Programming in ImageJ") he uses for the ImageJ classes he teaches.
• 1.47c 8 September 2012
  • Added a "Source" (display source code of selected command) button to Plugins>Utilities>Find Commands.
  • Dorai Iyer added a "Bar" option to the arrow tool.
  • Bill Mohler modified the ROI Manager to use a JList instead of a List, which makes loading and sorting the large (>10,000) ROI sets faster.
  • Added an "Append results" checkbox to the ROI Manager's "Multi Measure" command.
  • When opening images, the transfer rate in MB/sec is displayed in the status bar.
  • Thanks to Sébastien Tosi, opening TIFF files using File>Import>URL is faster and requires less memory.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording of commands implemented in JavaScript when the recorder was in "JavaScript" mode.
  • Thanks to Sébastien Tosi, fixed a bug that caused File>Import>URL to not correctly read TIFF files larger than 2GB.
  • Fixed a bug in the Analyze>Tools>Synchronize Windows command that caused it to not work as expected when changing the channel of composite color images.
  • Thanks to Christoph Deil, fixed a bug in Plugins>Utilities>Find Commands that caused esc and ctrl-w key presses to not close the window after "Show full information" was enabled.
  • Thanks to Christoph Deil, fixed bugs in the "Save changes?" dialog that caused it to not work as expected after the focus was changed (by tabbing) to the "Don't Save" or "Cancel" buttons.
• 1.47b 12 August 2012
  • Added the Image>Stacks>Statistics command.
  • Thanks to Michael Schmid, the built in brush, pencil and overlay brush tools draw using the background color when alt key is down, are constrained to draw horizontally when shift is down, are resized when shift&control are down (shift&cmd on Macs), and "pick up" the foreground color when control is down (cmd on Macs).
  • Added a "16 bit range" choice to the Edit>Options>Appearance dialog box. This is the same as the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog.
  • Thanks to Olivio Donati, File>Import>Image Sequence opens any associated ROIs that are in a file named RoiSet.zip.
  • Thanks to David Knecht, added a "sum" option to Image>Transform>Bin.
  • The getHistogram() macro function no longer limits the number of bins to 256 with 8-bit and RGB images.
  • Added the IJ.createHyperStack(title,width,height,channels,slices,frames,bitdepth) method, where 'bitdepth' is 8, 16, 24 (rgb), or 32 (float).
  • Thanks to Qingzong Tseng, fixed a bug that caused overlays to be lost when converting composite stacks to RGB.
  • Thanks to Jan Eglinger, fixed a bug that caused images created by the particle analyzer's "Show:" option to not use the calibration of the original image.
  • Thanks to Guenter Giese, fixed bugs that caused the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog to not work as expected with multi-channel images.
  • Thanks to Barry DeZonia, fixed a bug that caused the command recorder to not work with Image>Stacks>3D Project when processing 16 and 32 bit images.
  • Thanks to William Edwards, fixed a bug that sometimes caused the median of 32-bit float images to be calculated incorrectly.
  • Thanks to Michael Cammer, worked around a bug that could cause commands in the Image>Type submenu to not work as expected in non-batch-mode macros.
• 1.47a 17 July 2012
  • Thanks to Thomas Boudier, added five new 3D filters (Median, Mean, Minimum, Maximum and Variance) to the Process>Filters submenu.
  • Added the "Restore Startup Tools" command to the toolbar's >> menu.
  • Thanks to Tiago Ferreira, built-in and plugin tools can be added to toolsets and the startup macros (example).
  • Michael Schmid modified the Overlay Brush tool for constrained motion (vertical or horizontal) with shift and resizing with ctrl-shift (cmd-shift on Macs).
  • Thomas Tongue added support for the CDELT and CTYPE headers to the FITS Reader.
  • Added the getinfo("selection.color") and getValue("selection.width") macro functions.
  • Thanks to Simon Roussel, fixed a bug that could cause overlays to not be displayed on virtual stacks.
  • Fixed a bug that caused the brush and pencil tools to activate overlay selections.
  • Michael Schmid fixed a bug that sometimes caused Preview to not work correctly with commands in the Process>Filters submenu.
  • Fixed a 1.46 regression that caused the ROI Manager to generate incorrect ROI labels when the Associate 'Show All" ROIs with Slices" option was not enabled.
  • Thanks to Stephan Semmler, fixed a regression that caused the ImagePlus.getNDimensions() method to sometimes return the wrong value.
  • Thanks to Glen MacDonald, fixed a 1.46 regression that caused the setOption("Show All",boolean) macro function to not work.
• Kevin Eliceiri and Caroline Schneider published the article "NIH Image to ImageJ: 25 years of image analysis" in Nature Methods.
• 1.46r 26 June 2012
  • Thanks to Bob Loushin, fixed a bug that caused dashed line ROIs to only display correctly at 100% zoom.
  • Thanks to Raymond Coory, fixed a v1.46o regression that caused the TurboReg plugin to throw an exception.
  • Fixed a v1.46n regression that caused the ROI Manager's "Associate 'Show All' ROIs with Slices" option to not work as expected.
  • Thanks to Olivier Bardot, fixed a v1.46p16 regression that caused the Image>Hyperstacks>Temporal-Color Code command in Fiji to fail.
• 1.46q 19 June 2012
  • Thanks to Michael Cammer, added the ROI Manager More>>List command.
  • Thanks to Jerome Mutterer, added the Macros>Macro Functions command to the macro editor.
  • On Windows, the preferences file (IJ_Prefs.txt) is now saved in the .imagej directory, in the user's home directory.
  • Thanks to Norbert Vischer, fixed a bug that caused the wrong image window to have focus after another window was closed.
  • Thanks to Kees Straatman, fixed bugs that caused Image>Color>Merge Channels to sometimes lose the scale and to sometimes not work as expected when used in a macro.
  • Thanks to Michael Schmid, worked around a race condition in the run("Make Composite") macro function that could cause non-batch mode macros using it to fail.
  • Thanks to Carlos Becker, fixed a bug that caused File>Open and File>Import>TIFF Virtual Stack to fail when importing TIFF stacks larger than 2GB.
  • Thanks to Michael Schmid, fixed a bug that could cause a 'for' loop, at the end of a macro, containing a single 'if' statement to terminate prematurely.
  • Thanks to Christophe Leterrier, fixed a bug that caused the ResultsTable.open() method to not correctly open results tables with row labels but without row numbers.
• Tiago Ferreira added a "Print list" button to the Built-in Macro Functions page.
• Tiago Ferreira updated and improved the ImageJ User Guide for v1.46p, adding sections on overlays, 3D volumes, sub-pixel selections, curve fitting and interface customization. The User Guide, which contains 200 pages and 270 illustrations, is available online, as a 10 MB PDF, and as US and A4 booklets.
• 1.46p 4 June 2012
  • Added the Edit>Options>Reset command.
  • The line of information at the top of image windows is displayed antialiased.
  • Added the rotate(), setAngle() and setZeroTransparent() methods to the ImageRoi class (example).
  • Fixed a bug that caused an exception when Image>Stacks>Add Slice was used to add a channel to a 7 channel composite color image.
  • Fixed a bug that caused Edit>Selection>Rotate to not work with ImageRois.
  • Thanks to Hiroki Hakoshima, fixed a bug that caused the saveAs() macro function to fail if the file path contained a "]" character.
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Stacks>Add Slice and Image>Stacks>Delete Slice to not set the 'changes' flag.
  • Thanks to Norbert Vischer, fixed a bug that caused the macro interpreter to not correctly parse hex constants larger than 0x7fffffff.
  • Fixed bugs in the Image>Hyperstacks>Stack to Hyperstack and Hyperstack to Stack commands that caused them to not work as expected in batch mode macros.
  • Thanks to Dorai Iyer, fixed a 1.46o regression that caused the ROI Manager "Flatten" command to stop working.
• 1.46o 18 May 2012
  • Set the stroke width to 0 in the Edit>Selection>Properties, Image>Overlay>Overlay Options and ROI ManagerProperties dialogs to have selections drawn using a width of one pixel regardless of the image magnification.
  • Fixed a bug that could cause selections being moved to not be displayed correctly when the "Use ROI names as labels" option in the ROI Manager was enabled.
  • Fixed a bug that caused Analyze>Plot Profile to fail with line selections with widths less than 1.0.
  • Thanks to Franklin Shaffer, fixed a bug that sometimes a caused a stack overflow error when importing large image sequences.
  • Thanks to Tiago Ferreira, fixed a 1.46n regression that caused overlay items to be removed when toggling the ROI Manager "Show All" checkbox.
• 1.46n 11 May 2012
  • In "Show All" mode, the ROI Manager now uses an overlay to display the selections.
  • Added the More>>Labels... command to the ROI Manager, as a shortcut to Image>Overlay>Labels.
  • Add a "Show plot" checkbox to the Analyze>Calibrate dialog box.
  • File>Save As>XY Coordinates now correctly saves subpixel resolution selections, and it works with more kinds of selections.
  • Tiago Ferreira added a list of valid factors to the Image>Stacks>Tools>GroupedZProjector dialog.
  • Made the IJ.runPlugIn(String,String,String) method public.
  • Added the IJ.getFullVersion() method.
  • Thanks to Burri Olivier, fixed a bug that caused Image>Adjust>Threshold, when the "Stack histogram" option was enabled, to use the histogram of all channels instead of only the current channel.
  • Tiago Ferreira fixed a bug that caused stacks binned with Image>Stacks>Tools>GroupedZProjector to loose spatial calibration.
  • Thanks to Burri Olivier, fixed a bug that caused incorrect auto stack thresholds when "Limit to threshold was enabled in Analyze>Set Measurements.
  • Thanks to Thomas Boudier and Michael Schmid, fixed a bug that caused the Analyze>Summarize command to not work correctly on reopened results tables.
  • Thanks to Jim Passmore, fixed a bug that caused NonBlockingDialogs to not handle the yes/no/cancel option.
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Show Info to incorrectly display the selection location when the image origin was not (0,0).
• 1.46m 23 April 2012
  • ROIs in an overlay can be activated by alt-clicking, control-clicking or long-pressing (1/4 second or longer).
  • Thanks to Gabriel Landini, the Brush and Pencil tools installed from the toolbar's >> menu can be resized by shift-dragging.
  • The icons for drawing tools installed from the toolbar's >> menu reflect the foreground color and are updated when the foreground color changes.
  • Commands in the Edit>Selection submenu that modify the selection now support Undo/Redo and transfer color and line width properties.
  • Fiji saves and loads custom tool configurations.
  • Thanks to Ved Sharma, removed the restriction in Image>Stacks>Tools>Insert that the destination must be a stack.
  • Thanks to Richie Mort, fixed a bug that could cause the contents of multiple custom results tables created by plugins to be invalid.
• Dimiter Prodanov has published a chapter summarizing parts of his research with ImageJ.
• 1.46k 11 April 2012
  • Custom tool configurations created using the toolbar's ">>" menu are saved in the preferences file.
  • Process>Filters>Gaussian Blur 3D works with hyperstacks.
  • Thanks to Tiago Ferreira, fixed a bug that caused FIle>Import>Image Sequence to throw an exception of the first file in the folder was a stack and other files were not stacks.
  • Thanks to Norbert Vischer, fixed a bug that caused metadata to be lost when saving and reopening 3-channel composite 16-bit images.
  • Fixed a bug that caused Edit>Selection>Properties to change selection stroke widths less than 1.0 to 1.0.
  • Fixed a bug that caused Edit>Selection>Fit Spline and Edit>Selection>Interpolate to reset stroke colors and widths.
  • Fixed regressions that caused Analyze>Measure to not work with angle selections and to sometimes throw an exception.
• Tiago Ferreira contributed ROI Manager Tools, a macro toolset that renames selections stored in the ROI Manager.
• Gilles Carpentier contributed Multi-Channel Image and Stack Helper, a macro toolset for working with composite color images and stacks.
• The Transparent Image Overlay plugin demonstrates how to draw an image with a transparent background in an overlay.
• 1.46j 27 March 2012
  • Added the Process>Filters>Gaussian Blur 3D command.
  • When the ROI Manager window is closed, a dialog box is displayed that provides the option of moving displayed ROIs to an overlay.
  • File>Import>Image Sequence displays warnings if the folder contains tiff stacks and the "Use virtual stack" option is enabled.
  • Image>Calibrate now uses scientific notation to draw fit parameters, if needed.
  • Thanks to Wilhelm Burger, added a ByteProcessor(ip, scale) constructor.
  • Thanks to Gabriel Landini, fixed a bug that caused an invalid 0.0 to be entered into the Analyze>Calibrate dialog box if "Stack position" was enabled in Analyze>Set Measurements.
  • Thanks to Mark Krebs, fixed a 1.46e regression that could cause Image>Stacks>Tools>Concatenate to fail when called from a macro.
  • Thanks to Michael Cammer, fixed a v1.46g regression that caused the "Use stack histogram" option in Process>Ehance Contrast to not work as expected.
  • Thanks to Norbert Vischer, fixed a v1.46i regression that could cause an exception when using using Analyze>Measure to measure Feret's Diameter.
• Ved Sharma contributed Measure Hyperstack, a macro that runs "Measure" on a hyperstack in a user-selected (c,t,z) order.
• 1.46i 15 March 2012
  • Added the Image>Transform>Bin command, based on Nico Stuurman's Binner plugin.
  • Added the Edit>Selection>Interpolate command. To view the interpolated points, use this command on small selections created on images zoomed 1200% or greater.
  • Added the Image>Transform>Image to Results and Results to Image commands.
  • Added a "Remove Tool" command to the toolbar's >> menu;
  • The Image>Stacks>Add Slice command works with hyperstacks.
  • The Fly Brain and T1 Head sample stacks open displaying the middle slice instead of the first.
  • Added the getChannel(int, ByteProcessor) and setChannel(int, ByteProcessor) methods to the ColorProcessor class (example).
  • Added the getTableAsImage() (example), createTableFromImage() (example) and open2() methods to the the ResultsTable class.
  • Added the ImageProcessor.bin() and Roi.getInterpolatedPolygon() methods.
  • Thanks to Michael Schmid, added the ImageProcessor.isGrayscale() method and the is("grayscale") macro function.
  • Added JavaScript-compatible constructor and methods to the Plot class (examples).
  • Thanks to Jan Eglinger, fixed a bug that caused Image>Transform>Rotate Right and Image>Transform>Rotate Left to not work with square composite color images.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused Image>Stacks>Z Project to not work with 3D composite color images.
  • Fixed a bug that caused overlays to be lost when opening TIFF files using a URL.
  • Fixed a bug that caused an exception when the user canceled the File>Import>Results dialog box.
  • Fixed a bug in Process>Binary>Skeletonize that caused it to sometimes create skeletons that were more than one pixel wide.
  • Fixed a bug that caused the setf() functions to not round when storing values in ByteProcessors and ShortProcessors.
  • Fixed a bug that caused the Sync_Windows plugin to not work with hyperstacks.
  • Fixed bugs that caused an error message, or caused the command to be ignored, when saving results created by some MBF plugin using File>Save As>Results.
  • Thanks to Arttu Miettinen, fixed bugs that sometimes caused histogram bin counts of stacks larger than 2 gigapixels to be incorrect.
  • Thanks to Michael Cammer, fixed a bug in Image>Stacks>Reslice that caused it to not work as expected if there was global calibration and "Avoid interpolation" was not checked in the dialog box.
• 1.46h 28 February 2012
  • Added the Arrow, Overlay Brush, Pixel Inspector, Spray Can and LUT Menu tools to the toolbar's >> menu.
  • Image>Color>Merge Channels now works with up to 7 channels.
  • Added the String.getResultsHeadings() macro function (example).
  • Thanks to Xiao Chen, fixed a bug that caused ImageJ to not correctly open PNG images with alpha.
  • Fixed a bug that caused the Results window to flicker when the ResultsTable.show("Results") method was called repeatedly (example).
  • Thanks to Andrew French, fixed a bug that caused the ImageStack.getVoxel() method to fail with RGB stacks.
  • Fixed a bug that could cause File>Import>Text Image to fail with files containing empty lines.
  • Thanks to Gregory Reneff, fixed a bug that caused the call("ij.plugin.frame.RoiManager.getName", index) macro function to not work in batch mode.
• Vilppu Tuominen and Jorma Isola have released ImmunoMembrane, a plugin for analyzing HER-2 immunohistochemistry.
• 1.46g 16 February 2012
  • The ">>" toolbar menu lists installed plugin tools.
  • Added "Help" buttons to the Image>Stacks>3D Project and Process>Enhance Contrast dialog boxes.
  • Fixed a bug that caused hyperstacks to be converted to interleaved stacks in macros that opened a hyperstack and did a crop or type conversion operation.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused commands in the Image>Lookup Tables submenu to not work as expected with single channel composite images.
  • Thanks to Michael Cammer, fixed a bug that caused Process>Enhance Contrast to not work as expected when the "Equalize histogram", "Process all n slices" and "Stack histogram" options were enabled.
  • Thanks to Rainer Engel, fixed bug that caused Image>Stacks>Z Project to not correctly perform "Median" and "Standard Deviation" projections of RGB stacks.
  • Thanks to Eik Schumann, fixed a bug that caused the run("Merge Channels...","...") macro function to not close source images in batch mode macros.
  • Thanks to Zeljka Maglica, fixed a bug that caused position-dependent overlays to not be saved when using the Image>Overlay>Flatten, File>Save As>AVI and Image>Stacks>QuickTime Movie commands.
  • Thanks to Fabian Svara, fixed a bug that caused an incomplete ROI to be added to the ROI Manager if you pressed "t" (Edit>Selection>Add to Manager) before you finished drawing the ROI.
• 1.46f 5 February 2012
  • Michael Schmid contributed an improved Curve Fitter.
  • Built in Joachim Walter's Sync Windows plugin as the Analyze>Tools>Synchronize Windows command.
  • Thanks to Denny Hugg, ImageJ uses a custom crosshair cursor if there is a GIF image named "crosshair-cursor.gif" in the ImageJ/images folder. There is an example custom cursor at imagej.nih.gov/ij/images/crosshair-cursor.gif.
  • With hyperstacks, the Image>Stacks>Delete Slice command can delete the current channel, slice or frame.
  • Michael Schmid added support for I420, YV12 (a.k.a. IYUV), NV12 and NV21 formats to the AVI Reader.
  • The GifWriter now uses ImageIO to save single images.
  • Thanks to Norbert Vischer, fixed a bug that made it impossible to select an image with a duplicate name from the Window menu.
  • Thanks to Michael Schmid, added the IJ.d2s(n,significantDigits,maxDigits) method, which is used by the macro language to convert numbers to strings, by Analyze>Histogram to display values in histogram windows, and by ImageJ to display values in the status bar as the curser is moved over float images.
  • Replaced the SocketListener class with Johannes Schindelin's RMI-based OtherListener class from Fiji, which works on multi-user machines and is more secure.
  • Thanks to David M. Gauntt, added the FHT(ImageProcessor,boolean) constructor to the FHT class.
  • Thanks to Denny Hugg, fixed a bug that caused File>Save As>Gif to create GIF images that would not work as custom cursors.
  • Thanks to Gilles Carpentier, fixed a bug that cuased Image>Stacks>Z Project to throw an exceptions if no image window was open.
  • Thanks to Wilhelm Burger, fixed a bug that caused the Image>Adjust>Canvas Size command to not properly repositioned overlays.
  • Thanks to Christopher Harrison, fixed a bug that caused LUTs to be improperly applied to "Grayscale" mode composite images.
  • Fixed a bug that caused Analyze>Plot Profile to not work with rectangular selections containing NaN values.
• 1.46e 18 January 2012
  • Thorsten Wagner added a "Label" (display slice labels) option to the Image>Stacks>Label dialog box.
  • Changes made to options in the Edit>Options>Appearance dialog box cause the current image to be immediately updated.
  • Upgraded the Image>Stacks>Tools>Concatenate plugin to the Jon Jackson version from the MacBiophotonics distribution and Fiji.
  • Less memory is required to display float images.
  • Thanks to Michel Julier, images zoomed less than 100% are displayed with higher quality.
  • Edit>Selection>Rotate uses floating-point coordinates
  • Added the call("ij.gui.ImageWindow.setNextLocation",x,y) macro call.
  • Added the Roi.getFloatBounds() and FloatPolygon.getFloatBounds() methods.
  • Added the ParticleAnalyzer.setResultsTable() method.
  • Thanks to Jan Eglinger, ImageJ displays an error message when you attempt to apply a threshold or brightness/contrast change to a virtual stack.
  • Thanks to Martin Dressler, fixed bugs in Image>Duplicate and Image>Stacks>Tools>Make Substack that caused image "Info" metadata to be discarded.
  • Thanks to Johannes Schindelin, fixed a 1.46a regression that could cause plugins to fail if they extended the PolygonRoi class, did spline fitting and accessed the protected xp and yp arrays.
  • Thanks to Vytas Bindokas, fixed bugs that could cause Edit>Selection>Rotate to not work as expected with straight line selections.
  • Fixed a bug that caused the makeLine(x1,y1,x2,y2,width) macro function to round non-integer arguments.
  • Fixed a bug that caused thresholds to not be reset when converting from 16-bit to 8-bit.
  • Fixed a v1.45c regression that caused Process>Math>Macro to fail on multiprocessor machines with expressions containing "getPixel".
• Aleksandr Mironov contributed Merz grid, a macro that creates a Merz grid with semicircular lines and points as a non-destructive overlay.
• 1.46d 1 January 2012
  • Added the Plugins>New>Macro Tool and Plugins>New>Plugin Tool commands.
  • Single macro tools are now installed in the first available toolbar slot, or if no slots are free, in the last slot.
  • Added the ij.plugin.tool.PlugInTool class, which was inspired by Johannes Schindelin's AbstractTool class in Fiji (examples).
  • Added the getC(), getZ(), getT(), setC(), setZ() and setT() methods to the ImagePlus class.
  • Thanks to Norbert Vischer, fixed a bug the caused the setZCoordinate() macro function to not work as expected.
  • Thanks to Ian Lim, fixed a bug that prevented some AVI files from opening.
  • Thanks to Cheryl McCreary, fixed a bug that caused the run("Histogram","...") macro function to sometimes not work as expected.
  • Thanks to Jerome Mutterer, fixed bugs in Process>Batch>Macro and Process>Batch>Virtual Stack that caused them to fail with macro code that duplicated or opened images.
  • Thanks to Paul Jurczak, fixed a bug that caused some RGB BMP files to fail to open.
  • Fixed a bug that caused the makeText() macro function to not work if the text was too wide.
  • Fixed a regression, introduced in v1.46a, that caused measurements of spline fit freehand and traced selections to be inconsistent with earlier versions of ImageJ.
  • Wilhelm Burger fixed a bug that caused the Edit>Crop command to not correctly handle overlays.
• Dimiter Prodanov contributed Results Importer, a plugin that imports numeric values from text windows (e.g., histogram or profile plot lists) into the ResultsTable.
• 1.46c 12 December 2011
  • Thanks to Tiago Ferreira, the ColorChooser widget now displays hex values.
  • Thanks to Jesper Pedersen and Michael Schmid, ImageJ opens >2GB AVI 2.0 files, opens AVIs faster as virtual stacks and opens MJPEG encoded AVIs that are missing Huffman tables.
  • Thanks to Jerome Muttere, Process>Find Maxima, when the output type is "Count", respects the Analyze>Set Measurements "Display label" setting.
  • Added the "Sub-pixel resolution" option to the Edit>Options>Profile Plot Options dialog box (documentation).
  • Added the Array.concat(), Array.slice() and Array.print() macro functions (example1, example2).
  • Thanks to Norbert Vischer, fixed a bug that caused the Stack.setActiveChannels() macro function to not update the "Channels" window.
  • Thanks to Balazs Nyiri, fixed a bug that caused the image id of composite color images to change after using the Image>Stacks>Add Slice and Image>Stacks>Delete Slice commands.
  • Fixed a bug that caused the slice selector scrollbar to not be updated after using the Add Slice or Delete Slice commands.
  • Thanks to Jakob Preus, fixed a bug that caused use of "&" to pass directory path variables in macros using the File>Save As>Image Sequence command to fail.
• 1.46b 29 November 2011
  • Added the File>Import>XY Coordinates command.
  • Added a "List coordinates" checkbox to the Edit>Selection>Properties dialog box.
  • "Help" buttons in dialog boxes can display HTML formatted messages (macro, JavaScript).
  • The Edit>Selection>Line to Area command now works with one pixel wide straight lines.
  • The color of the rounded rectangle tool no longer defaults to the foreground color.
  • Thanks to Aryeh Weiss, the ROI Manager's "OR (Combine)" command now works with line selections.
  • Added the ParticleAnalyzer.setRoiManager() method (example).
  • To support sub-pixel positioning, added constructors that accept double arguments to the Roi, OvalRoi and TextRoi classes (example).
  • Thanks to Norbert Vischer, added the ij.util.StringSorter.sortNumerically() method.
  • Thanks to Jose Wojnacki, fixed a bug that could cause a macro to fail if a drawing tool was used during a waitForUser() break.
  • Thanks to Norbert Vischer, fixed a bug that caused the "Sort names numerically" option in the File>Import>Image Sequence dialog to sometimes not work as expected.
  • Fixed a bug that caused the default stroke width and color to change when an arrow was added to an overlay.
  • Fixed a bug that caused lines to be displayed incorrectly in the ROI Manager "Show All" mode after adding a rounded rectangle.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the Plot.show() macro function to return before the plot window was fully displayed.
  • Thanks to Norbert Vischer, fixed a bug that caused macros displaying showMessage() dialogs to not be aborted when the user pressed the esc key.
  • Thanks to Jerome Mutterer, fixed a bug that sometimes caused selections in ROI Manager "Show All" mode and in overlays to be displayed with the wrong stroke width.
  • Thanks to Winfried Wurm, fixed a bug that could cause the run("Restore Selection") and run("Enlarge...") macro functions to fail in batch mode macros.
• 1.46a 12 November 2011
  • The segmented line, freehand line, point and multi-point tools now support sub-pixel resolution.
  • The Plot class constructors generate an X value sequence if the X array argument is null or empty (JavaScript examples).
  • An informative message is displayed when a batch mode macro attempts to open an ROI set using open(path) (which does not work) instead of roiManager("open",path).
  • Thanks to Tiago Ferreira, the ROI Manager "Multi Plot" command no longer ignores "Fixed y-axis scale" in Edit>Options>Profile Plot Options.
  • Thanks to Bob Hamilton, "Area Fraction" (renamed "%Area") in the Analyze Particles Summary window now uses the Set Measurements decimal places.
  • Added the MaximumFinder.getMaxima() method (example).
  • Fixed a bug that caused the length of non-straight line profile plots to be greater that the measured line length.
  • Michael Schmid fixed a bug that could cause the RankFilters (Mean, Minimum, Median, etc.) to hang.
  • Thanks to Jan Eglinger, fixed bugs that could cause the recorder to throw bogus error messages or to record "null" or "nullnull" when opening or saving files.
  • Fixed a bug that caused the elliptical selection tool to always have integer starting coordinates.
  • Thanks to Oliver Bannach, fixed a bug that caused Histograms in batch mode macros to not be properly closed.
  • Thanks to Norbert Vischer, fixed a bug that caused File>Import>TIFF as Virtual Stack to not correctly open c=3, z=1, t=1 16-bit hyperstacks.

Version 1.45, 29 October 2011 (download)

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

Version 1.44, 31 January 2011 (download)

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

Version 1.43, 22 April 2010

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

Version 1.42, 8 June 2009

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

Version 1.41, 24 October 2008

• 1.41o, 24 October 2008
  • Added the Process>Math>Set command.
  • Help>Update ImageJ, except when updating to the "daily build", deletes "functions.html" in the macros folder, which forces the macro editor's Macros>Function Finder command to download a fresh copy.
  • The call() macro function can now call static methods with integer arguments.
  • Added the getOutputImage() and setHideOutputImage(boolean) methods to the ParticleAnalyzer class.
  • Added the Toolbar.setBrushSize() method.
  • Fixed a bug, introduced in v1.41k, that caused macro functions not in an installed macro set to not be able to write to global (var) variables.
  • Fixed a bug that caused plugins using the ImagePlus.getImage() method to not work as expected when called from a stack-processing batch mode macro.
• Michael Schmid contributed a new Accurate Gaussian Blur plugin.
• 1.41n, 17 October 2008
  • Added the Edit>Options>Compiler command.
  • Added support for opening PackBits compressed TIFFs and ARGB TIFFs.
  • Added a "Scientific Notation" option to the Analyze>Set Options dialog box.
  • Files in the plugins folder with ".ijm" and ".js" extensions no longer require an "_" in the name to be installed in the Plugins menu.
  • JPEGs are saved using ImageIO if the JpegWriter class is removed, allowing ImageJ to be compiled with the OpenJDK.
  • Added "Exponential Recovery" [y=a*(1-exp(-b*x))+c] fitting to the CurveFitter class. This function is used by the FRAP_Profiler plugin included with the MBF package.
  • The d2s() macro function uses scientific notation if the second argument is negative.
  • Help>Update Menus resets the plugin class loader.
  • Added the ImageProcessor.getPixelInterpolated(double,double) method, which was contributed by Stephan Saalfeld.
  • Fixed bugs that caused the setThreshold(), getThreshold() and setMinAndMax() macro functions to not work correctly with intensity calibrated 8-bit images.
  • Fixed a bug, introduced in v1.41l, that caused File>Save As>FITS to create FITS files that could not be opened by some other FITS readers.
  • Fixed a bug that caused the calibration plot to be displayed when running the Analyze>Calibrate command in a macro.
  • Fixed a bug that caused run("Command", "stack") macro statements to not process the entire stack if "Hide 'Process Stack?' Dialog" was enabled in Edit>Options>Misc.
• Tiago Ferreira contributed Toolset Creator, a macro that creates toolbar menus for running plugins, macros and scripts.
• Janos Roszik, Janos Szollosi and Gyorgy Vereb have released AccPbFRET, a plugin for analysis of acceptor photobleaching FRET images.
• Jenoptik has released an ImageJ driver for their ProgRes microscope cameras.
• 1.41m, 19 September 2008
  • File>Save no longer displays a "Save As" dialog when resaving a TIFF stack.
  • A more informative error message is displayed when attempting to process a virtual stack.
  • Analyze>Plot Profile now uses the full file name, minus the extension, in plot window titles.
  • Added the eval("script", javascipt) macro function.
  • Fixed a bug, introduced in v1.41l, that caused infinite numbers to be displayed as "∞" instead of as "Infinity".
• 1.41l, 16 September 2008
  • Added the Help>Update Menus command, which allows plugins to be installed and/or removed without restarting ImageJ.
  • Area, line, angle and point measurements can be recorded in the same Results window.
  • The Roi Manager "Measure" function no longer requires that all selections be areas or all selections be lines.
  • Making a change in the Analyze>Set Measurements dialog box no longer caused the Results window to be reset.
  • The Particle Analyzer's "Summarize" option displays the average mean, mode, perimeter, major axis, minor axis, angle, circularity, Feret diameter, integrated density, median, skewness and kurtosis if the corresponding option is enabled in Analyze>Set Measurements.
  • Frederic Hessman contributed an improved version of File>Save As>FITS that preserves any existing FITS header.
  • Image>Stacks>Stack to Images no longer discards slice labels (e.g., DICOM headers).
  • Numbers displayed using scientific notation in plots, histograms, and in the Results window, now use a maximum of 3 decimal places.
  • The angle tool is now correctly recorded.
  • File>Save As>AVI now accepts frame rates as low as 0.5 (2 seconds per frame).
  • Fixed a bug that caused the Process>Binary>Erode and Dilate commands to throw an exception with one pixel wide images.
• Sebastian Rhode contributed Calc_Objective, a plugin that calculates parameters of interest for an objective lens.
• Gilles Carpentier contributed the Dot Blot Analyzer toolset (online documentation).
• 1.41k, 2 September 2008
  • The "Line Width", "Fonts", "Log" and "ROI Manager" windows remember their locations.
  • The Edit>Adjust>Adjust Line tool updates all images with lines selections and has increased slider range of 1-300.
  • The Measure command and getStatistics() macro function calculate area statistics of line selections wider than one.
  • Process>FFT>Inverse FFT improvements (courtesy of Michael Schmid):
    • Areas marked as "pass" or "filter" in the power spectrum are made symmetric.
    • The smoothing algorithm uses periodic boundary conditions.
    • Inverse FFT on a cropped power spectrum does not cause an exception.
    • The filter created after symmetrizing and smoothing is shown in debug mode or if the alt key is down.
  • The particle analyzer assumes the size is in pixels if it is followed by a "p", for example run("Analyze Particles...", "size=100p display clear").
  • Added a "Close when running" checkbox to the Plugins>Utilities>Find Command window and changed the "Cancel" button to "Close".
  • Added curve fitting functions (Fit.*) to the macro language (example).
  • Added the Plot.getValues() macro function.
  • The open() macro function now works with image URLs.
  • Gzip compressed FITS images on network drives open up to 10 times faster.
  • Fixed a bug, introduced in v1.41b, that caused the ImageJ applet to fail to load DICOM images on startup (example).
  • Fixed a bug in File>Import>AVI, introduced in 1.41h, that caused some color video formats to open as 16-bit grayscale.
  • Fixed a bug that caused the slider in the Image>Adjust>Line Width window to blink on Windows.
  • Fixed a bug that caused the setForegroundColor() macro function to reset the line width.
  • Reduced the likelyhood of a bug that caused the Image>Adjust>Threshold "Set" option to sometimes enter incorrect values on Linux.
  • Fixed a bug that caused upper case shortcuts created using Plugins>Shortcuts>Create Shotcut to open macros instead of running them.
• Jerome Mutterer contributed TiltedRectangleTool, a macro tool that creates tilted rectangular selections.
• Joel Sheffield has made available an ImageJ tutorial in PowerPoint format he gave at a recent Microscopy & Microanalysis meeting and the images and stacks used in the tutorial.
• David Webb contributed Toe_Indexer, a macro set for measuring footprints and calculating the toe index.
• 1.41j, 8 August 2008
  • Profile plots of segmented and freehand lines wider than 1 are averaged across the line.
  • File>Save As>Image Sequence exports hyperstacks as C/Z/T labeled files (e.g., "name_t01_z01_c01").
  • Added the Image>Adjust>Line Width command (or double click on the line tool).
  • Added a "Spline Fit" checkbox to the Image>Adjust>Line Width tool.
  • Added a "Background Value" field, and "Invert Y Coordinates" and "Suppress Log Output" options, to the Analyze>Tools>Save XY Coordinates dialog box.
  • The ROI Manager "Deselect" option is recorded.
  • Added the File.saveString(string,path) and File.append(string,path) macro functions, and corresponding IJ.saveString() and IJ.append() methods.
  • Fixed a bug, introduced in v1.41f, that could cause batch mode macros to fail.
  • Fixed a bug that could cause LZW-compressed TIFFs to be incorrectly decoded.
  • Fixed a bug in Image>Stacks>Reslice the caused the spatial calibration to not be correctly transformed if the voxel width and height were not the same.
  • Fixed a bug that sometimes caused the wrong selection to be copied when duplicating stacks with non-rectangular selections.
  • Fixed a bug that caused a "Data chunk size too short" error when opening uncompressed RGB AVI files.
  • Fixed a bug that caused .flex files to fail to open if the Bio-Formats plugin was not installed.
  • Fixed a bug that caused an exception when opening PGM images less than 20 pixels in size.
  • Fixed a bug that caused the LUT to not be correctly copied when duplicating a single image in hyperstack in a batch mode macro.
• 1.41i, 25 July 2008
  • Added the Edit>Selection>Straighten command.
  • An extension is added to file names in File>Save As dialogs that do not have one.
  • Added the substring(string,index) macro function.
  • Fixed a bug that caused the Analyze>Summarize command to not work with "IntDen" results.
• 1.41h, 18 July 2008
  • Added the Plugins>Macros>Edit command, which replaces the Plugins>Edit command removed in v1.41g. There is also a plugin version of this command at 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

Complete Release Notes

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