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ImageJ News

Version 1.52g 16 September 2018 (upgrade)

• 1.52g 16 September 2018
  • A text selection in an overlay can be deleted by alt-clicking on it and pressing backspace+delete (on Windows) or command+delete (on Macs).
  • Fixed a bug that caused polygon and polyline selections to lose properties like color, line width and name when a point is added by shift-clicking on an existing point.
  • Thanks to Dave Mason, fixed a bug that caused the File>Import>URL command to not correctly open Hyperstacks.
  • Thanks to Volko Straub, fixed a 1.52f regression that caused getDirectory("") on Windows to return a string ending in "/" instead of the expected "\".
• 1.52f 7 September 2018
  • Thanks to Norbert Vischer, added the Plot.addHistogram() macro function, which plots a histogram from an array (example).
  • Thanks to Norbert Vischer, any currently running macro is aborted when running an installed macro from the Plugins>Macros menu or the editor's Macros menu.
  • Thanks to Michael Schmid, added the "Error Function" [y=a+b*erf((x-c)/d)] curve fit option and the ij.util.IJ.Math.erf(x) method (example).
  • The Edit>Selection>Create Mask command works with line selections and overlays.
  • The "Black background" setting defaults to 'true'.
  • Thanks to Anna Povolna, the "Open all files in folder" and "Use virtual stack" options in the File>Import>raw dialog can be used at the same time.
  • Thanks to 'Sethur', ImageJ no longer sorts imported DICOM stacks by series number (tag 0020,0011) if "Sort images numerically" is not checked in the File>Import>ImageSequence dialog. Also added a recordable 'noMetaSort' option to the options string of the FolderOpener.open(dir,options) method.
  • Thanks to 'Alan', added the createThresholdMask() and createRoiMask() methods to the ImagePlus class. These methods are recorded when using the Edit>Selection>Create Mask command (JavaScript example).
  • Added the recordable Raw.open(), Raw.openAll() and Raw.openAllVirtual() methods (JavaScript example).
  • Thanks to Stein Rorvik, added the DicomTools.getTagName(tag) method.
  • Thanks to Christian Tischer, fixed bugs in the RoiManager.add(ImagePlus,Roi,int) method than caused it to not behave as expected if the ROI name was not null.
  • Thanks to Norbert Vischer, fixed bugs that caused the Edit>Cut and Analyze>Set Scale commands to not set the 'changes' flag.
  • Thanks to Stein Rorvik, fixed a bug that caused the Overlay.drawString macro function to ignore the justification set by the setJustification() function.
  • Thanks to Stein Rorvik, fixed a bug that caused output of the Overlay.drawString() function to be lost when text is added using Overlay.addSelection().
  • Thanks to Lorenzo Cangiono, fixed a bug that caused selections pasted into images to not be saved.
  • Thanks to Mahmoudi Sidi Ahmed, fixed a bug that caused the Analyze>Calibrate command to not work with signed 16-bit images.
  • Thanks to Menelaos Symeonides, fixed an ROI Manager bug that caused the stack position to be ignored when measuring renamed ROIs.
  • Thanks to Ron DeSpain, fixed a bug that caused attempts to add to (by holding shift key down) and subract from (by holding alt key down) elliptical selections to fail.
  • Thanks to Ron DeSpain, fixed a bug that caused the Window>Tile command to overlap the "ImageJ" window with image titles.
  • Thanks to Pete Bankhead, fixed a bug the caused the Process>Batch>Convert command to not work correctly on Macs.
  • Thanks to 'Hamish', fixed a bug that caused the roiManager("delete") macro function to throw an exception when used in a loop.
  • Thanks to Stein Rorvik, fixed a bug that caused one column results tables to not be displayed correctly.
  • Thanks to Stein Rorvik, fixed a bug that caused File>Import>Raw to silently fail when importing a stack and the file size was smaller than the size of a single image.
  • Thanks to Stein Rorvik, fixed a bug that caused the Overlay.drawString() macro function to not correctly display right-justified text.
  • Thanks to Stein Rorvik, fixed bugs that caused the run("Raw...",options) and run("Image Sequence...",options) macro functions to fail silently if the file or folder did not exist.
  • Thanks to Stein Rorvik, fixed a bug that caused the stack title to be incorrect after importing an image sequence on Windows using a file path with forward slashes.
  • Thanks to Stein Rorvik, fixed a bug that caused File>Open Next to not correctly open a non-composite image after having opened a composite image.
  • Thanks to Ved Sharma, fixed an ROI Manager bug that caused a "Rename ROI" dialog do be unexpectadly displayed when running macro using setKeyDown("alt") and makeOval() to create a composite selection.
  • Thanks to Ved Sharma, fixed an ROI Manager bug that caused an exception when saving an ROI set containing a point selection followed by a composite selection.
  • Thanks to Salim Kanoun, fixed a bug that caused RoiManager.addRoi(roi) calls to be ignored if the ROI was a duplicate.
  • Thanks to 'TMC', fixed a bug that caused the ROI Manager's "Interpolate ROIs" command to throw an exception.
  • Thanks to 'Agnieszka', fixed a bug that caused the ImagePlus.getFileInfo() method to throw a NullPointerException.
  • Thanks to Stein Rorvik, fixed a bug that caused the Macros>Evaluate commands in the text editor to not update the Window menu.
  • Thanks to Norbert Vischer, fixed a bug that caused the macro editor to not always abort any existing macro before running another one.
  • Thanks to Manel Bosch, fixed a 1.52e regression that caused image conversions to RGB to not preserve the color coding.
• 1.52e 11 July 2018
  • The "Threshold" tool no longer resets the display range of 16-bit and 32-bit images.
  • Restored the "Set" button (removed in 1.51r) to the "Threshold" dialog,
  • Thanks to Kai Schleicher, the options string of the FolderOpener.open(dir,options) method can now include a file name filter (example).
  • Added a no-argument constructor to the PointRoi class (example at Help>Examples>JavaScript>Points).
  • Added the Roi.size() method, equivalent to Roi.getPolygon().npoints.
  • Added the FFT.forward(), FFT.multiply(), FFT.inverse() and FFT.filter() methods (JavaScript example).
  • The open("/path/to/file.avi") macro function and the IJ.openImage("/path/to/file.avi") method now open AVI files by default as virtual stacks.
  • Thanks to Volko Straub and Michael Schmid, fixed bugs that caused the ImageProcessor.isInvertedLut() and ImageProcessor.isColorLut() methods to sometimes incorrectly return 'true' with thresholded images.
  • Thanks to Volko Straub, fixed a bug that could cause non-thresholded pixels in 16-bit and 32-bit images to be highlighted in red (example).
  • Thanks to Thomas Boudier and Jan Eglinger, fixed a bug that caused macro file name parameters containing a "]" character to not be read correctly.
  • Thanks to Michael Nonet, fixed a bug caused the median to always be set to zero when measuring line selections.
  • Thanks to Norbert Vischer, fixed a bug that caused errors after running the run("RGB Stack") or run("HSB Stack") macro functions on large images when running Java 8 on macOS.
  • Thanks to Chris Wood and Curtis Rueden, fixed a bug that caused the Image>Stacks>Delete Slice command to deadlock when deleting the last channel of a hyperstack.
  • Thanks to Stein Rorvik, fixed a bug that caused the Process>Math>NaN Background command to throw an exception when attempting to process a non-32-bit stack.
  • Thanks to Stein Rorvik, fixed a bug on Windows that caused text to be pasted into text editor windows at the wrong position.
  • Thanks to Stein Rorvik, fixed a bug that caused print("\n\n") to do nothing instead of outputting two blank lines as expected.
  • Thanks to 'mryellow', fixed a bug that caused polygonal ROIs with more than 65,535 points to not be saved correctly.
  • Thanks to Stein Rorvik, fixed a bug that caused right justified TextRois. to not be displayed correctly if the fill color was not set.
  • Thanks to Lorenzo Cangiano and Jan Eglinger, fixed a 1.52c regression that caused a "Save changes?" dialog to be unexpectedly displayed when closing an image with a multi-point selection.
  • Thanks to Stein Rorvik, fixed a 1.52d regression that caused density calibration to be lost when duplicating 8-bit and 16-bit images.
• 1.52d 11 June 2018
  • The Image>Show Info command no longer truncates one line slice labels to 60 charactera.
  • Thanks to Norbert Vischer, the changeValues() macro function can now be used to replace NaNs. (example).
  • Thanks to Mark Histed, when the shift key is down, the display range is no longer changed when stepping forward/back in a stack.
  • Thanks to Hugo, the Process>FFT command displays an error message if the padded image is going to be 65536x65536 or larger.
  • Thanks to Roger Leigh, the IJ.javaVersion() method works with Java 11.
  • Added the IJ.Roi(x,y,w,h) and IJ.OvalRoi(x,y,w,h) methods.
  • Thanks to Gregor and Michael Schmid, added the ImageProcessor.createMask() method (example).
  • Thanks to David Kysela, added the PointRoi.promptBeforeDeleting(boolean) method (example).
  • Thanks to Laurent Thomas, added the ImagesToStack.run(images) method (example).
  • Added the Tools.getStatistics(double[]) method.
  • Thanks to Ximo Soriano and Michael Schmid, fixed a bug that could cause the newImage("Name","RGB noise",width,height,1) macro function to throw an exception.
  • Thanks to Ruben Gres, fixed a bug that caused the Overlay.duplicate() method to not keep the 'isCalibrationBar' and 'selectable' settings.
  • Thanks to David Schreiner, fixed bugs that caused the File>Import>Image Sequence command to not correctly handle image metadata longer then 60 characters.
  • Thanks to 'yahbai', fixed bugs that caused the saveAs("jpg",path), saveAs("gif",path) and Overlay.measure macro functions to not work in headless mode.
  • Thanks to 'yahbai', fixed a bug that caused the ImagePlus.deleteRoi() method to throw an exception in headless mode.
  • Thanks to Michael Kaul, fixed a 1.52a regression that caused an EOFException when opening Analyze format RGB images.
  • Thanks to Bill Christens-Barry, fixed a 1.52b regression that caused the label set with the setMetadata("Label", label) macro function to not be displayed in the image subtitle of single images.
  • Thanks to Michael Cammer, fixed a 1.52c regression that caused the Image>Crop command to not work as expected with 16-bit images.
  • Thanks to Peter Meijer, fixed a 1.52c regression that could cause ClassCastExceptions when converting RGB images to stacks.
• 1.52c 20 May 2018
  • Activating an ROI in an overlay created by Measure (with “Add to overlay" enabled), or by the particle analyzer, selects the corresponding row in the "Results" table.
  • ImageJ displays a "Delete Points?" dialog before deleting a multi-point selection with counters.
  • Thanks to "zzyzyman", fixed a bug that caused ImageJ to fail to open odd-width RGB AVI files.
  • Thanks to Merijn van Erp, fixed a bug that caused the CurveFitter.getSortedFitList() method to throw an exception.
  • Thanks to Kees Straatman and Bill Christens-Barry, fixed a bug in the macro interpreter that caused it to not detect a missing '[' after an array variable.
  • Thanks to Mike, fixed a 1.52b regression that caused the AVI Reader to fail with a "Required item ‘00ix’ not found" error.
  • Thanks to Curtis Rueden, fixed a 1.51t regression that caused errors in headless mode macros to throw a HeadlessException.
  • Thanks to 'cortig' and Curtis Rueden, fixed a 1.52b regression that caused the "Apply" option of the Image>Adjust>Threshold command to not behave as expected with 16 and 32 bit images.
• 1.52b 6 May 2018
  • Changed "Random" to "Noise" in the "Fill with:" choice of the File>New>Image dialog box.
  • Thanks to Christian Evenhuis, fixed a bug with the Edit>Selection>Line to Area command that caused the resulting area selection to translated if the source was a polyline or freeline selection less than 5 pixels wide.
  • Added the IJ.javaVersion() method.
  • Thanks to Fred Damen, fixed bugs that caused the Image>Stacks>Tools>Concatenate command to sometimes not work as expected.
  • Thanks to Aryeh Weiss and Michael Schmid, worked around a Linux problem with large images not showing at low magnification.
  • Thanks to Fred Damen, fixed bugs that sometimes caused slices labels of single slice stacks to be lost.
  • Thanks to BrainPatcher and Stefan Helfrich, fixed a bug that caused the ROI Manager's "Multi Measure" command to not work correctly with point selections.
  • Thanks to "zzyzyman", fixed a bug that caused ImageJ to fail to open AVI files that used the 'indx'/'ix00' indexing schema.
  • Thanks to Moses, fixed a 1.52a regression that caused row labels to be omitted from tables created by the ROI Manager's "Multi Measure" command.
  • Thanks to Jerome Mutterer, fixed a 1.52a regression that caused imported Results tables to be displayed without row numbers.
• 1.52a 23 April 2018
  • Thanks to Michael Schmid, added Apply Macro commands to the Edit and contextual (right click pop-up) menus of table windows. Also added the ResultsTable.applyMacro() method (JavaScript example).
  • Thanks to Ron DeSpain, tables created by the Image>Overlay>List Elements command can be renamed "Results" and the values accessed using the getResults() and getStringResult() macro functions.
  • Removed the obsolete Plugins>New>Table command. Macros that use this command will continue to work.
  • Thanks to Michael Kaul, added an optional 5th argument ('stepSize') to the Dialog.addSlider() macro function (example).
  • Thanks to Gabriel Landini, on Linux, added the “Cancel button on right” option to the Edit>Options>Appearance dialog box.
  • The "showRowNumbers" property of the ResultsTable class now defaults to 'false'.
  • Thanks to Adrian Daerr, when importing ".raw" files with dimensions encoded in the name (e.g. "myfile-640x480.raw"), the byte order is set to big-endian if the name ends in "be.raw" and to little-endian if the name ends in "le.raw".
  • Thanks to Arttu Miettinen, imported ".raw" files with dimensions encoded in the name can have a width and/or height less than 10.
  • Thanks to Stein Rorvik, added toScaled(x,y,z) and toUnscaled(x,y,z) macro functions.
  • Added 20 macro functions that work with tables. They operate on the current (frontmost) table or an optional title argument can be provided (e.g., Table.size("My Table")). Examples: Sine/Cosine Tables, Rearrange Table and Access Tables.
    • Table.create() - opens a new table
    • Table.reset() - resets (clears) the table
    • Table.size() - number of rows in the table
    • Table.title() - title of the current table
    • Table.headings() - column headings as a tab-delimited string
    • Table.get(columnName, rowIndex) - returns a numeric value
    • Table.getColumn(columnName) - returns a column as an array
    • Table.getString(columnName, rowIndex) - returns a string value
    • Table.set(columnName, rowIndex, value) - sets numeric or string value
    • Table.setColumn(columnName, array) - sets an array as a column
    • Table.update() - updates table window
    • Table.applyMacro(macro) - applies macro code to table
    • Table.rename(title1, title2) - renames a table
    • Table.save(filePath) - saves the table
    • Table.open(filePath) - opens a table
    • Table.deleteRows(index1, index2) - deletes specified rows
    • Table.renameColumn(oldName, newName) - renames a column
    • Table.deleteColumn(columnName) - deletes specified column
    • Table.showRowNumbers(boolean) - enable/disable row numbers
    • Table.showArrays(titleAndOptions, array1, array2, ...) - displays arrays in a table (like Array.show)
  • Thanks to Trevor Joyce and A Schain, added the macro-callable RoiManager.getIndexesAsString() method.
  • Thanks to Michael Schmid, added the Tools.copyFile(path1,path2) method.
  • Thanks to Salim Kanoun, added the RoiManager.setRoi(roi,index) and Overlay.set(roi,index) methods.
  • Thanks to Fred Damen, fixed a bug that caused the SubHyperstackMaker.makeSubhyperstack() method to not work when extracting a single frame.
  • Thanks to Fred Damen and Michael Schmid, fixed a curve fitter bug that could cause a NullPointerException.
  • Thanks to Norbert Vischer, fixed a bug that caused the File.copy() macro function to not preserve the modification date.
  • Thanks to Philippe Carl, fixed a bug that caused the Image>Hyperstacks>Reduce Dimensionality command to not preserve the "Info" image property.
  • Thanks to Jan Eglinger, fixed bugs that caused the roiManager("open",path) macro function to ignore the roi name and roiManager("save",path) not to be recorded when 'path' ended in ".roi".
  • Thanks to Norbert Vischer, fixed a bug that caused the Image Calculator to not correctly calculate the result when the operation is MULTIPLY or DIVIDE, the 1st image is 8 or 16 bit, the 2nd image is 32 bit and "32-bit result" is unchecked.
  • Thanks to Mark Rivers, fixed a bug that caused ImageJ to not correctly open some uncompressed planar RGB TIFFs.
  • Fixed a 1.51s regression that caused statistical calculations on small 16-bit images or selections to be much slower.
  • Thanks to Michael Schmid, fixed a 1.51o regression that caused the particle analyzer to hang when processong 32-bit images.

Version 1.51 23 April 2018 (download)

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

Version 1.50 26 March 2016 (download)

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

Version 1.49 23 June 2015

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

Version 1.48 19 April 2014

• 1.48v 19 April 2014
  • Plot and Histogram windows are no longer centered on the screen.
  • Added the Overlay.clear and setOption("Add to overlay",boolean) macro functions.
  • Thanks to David Knecht, commands listed in the Plugins>Shortcuts>List Shortcuts and Plugins>Shortcuts>Create Shortcut dialogs are sorted with case ignored.
  • Thanks to Denis Roussel, changed an incorrect Javadoc reference in PlugInFilter.java from SUPPORTS_STACKS to DOES_STACKS.
  • Thanks to Johannes Schindelin, added @link tags to the PlugInFilter.java Javadocs.
  • Fixed a bug that caused the progress bar to not terminate after dragging a jar file to the "ImageJ" window.
  • Fixed a bug that caused the roiManager("add") macro function to unexpectedly set the stack position of the source selection.
• 1.48u 9 April 2014
  • Selections added to overlays by the Measure command when "Add to Overlay" is enabled in Analyze>Set Measurements are labeled with the measurement number.
  • Thanks to Ted Toal, Image>Zoom>Set sets the zoom center based on a point selection and it no longer enlarges the window.
  • Thanks to Norbert Vischer, the macro debugger's Array Inspector now flags array value changes.
  • Added getStringProperty(key) and getNumericProperty(key) methods to the ImagePlus class.
  • Added a TextWindow constructor that accepts an ArrayList.
  • Thanks to Johannes Schindelin, added the GenericDialog#isPreviewActive() method.
  • Thanks to Herbie Gluender, fixed a bug that caused the output of the Plot Profile and Measure commands to be inconsistent with horizontal or vertical one pixel wide straight line selections.
  • Thanks to Gabriel Landini, fixed a bug that could cause the Results table to be displayed very slowly on Java 1.7 and 1.8.
  • Thanks to Burni, fixed a bug that prevented the ImageWindow.setNextLocation() method from working with windows normally centered on the screen, such as plot windows.
  • Fixed a v1.48 regression that caused the run("Add Selection...", options) macro function to not work as expected with text selections.
  • Thanks to Johannes Schindelin, fixed a v1.48r regression that caused the "Fonts" dialog to be displayed multiple times or incorrectly if you double-clicked the text tool icon multiple times.
  • Thanks to Johannes Schindelin, Gabriel Landini and Volker Baecker, fixed a v1.48r regression on Linux that caused ImageJ to freeze when opening a NonBlockingGenericDialog such as the text tool or arrow tool options dialogs.
• 1.48t 28 March 2014
  • Thanks to Ted Toal, holding down the alt key prevents the '+' command (Image>Zoom>In) from enlarging the window.
  • ImageJ remembers the location of the first small image opened.
  • Thanks to Norbert Vischer, Plugins>Utilities>Capture Image hides the zoom indicator.
  • Thanks to Dimiter Proanov, Image>Stacks>Plot Z-axis Profile displays the plot in calibrated units.
  • Thanks to Michael Schmid, added a File>Revert command to the text editor.
  • Fixed the Undo command in the text editor and added the Edit>Balance command, which locates the pair of curly braces or parentheses that surround the insertion point.
  • Thanks to Norbert Vischer, the text editor's Edit>Balance command handles '{' and '}' in comments and quotes, handles '[' and ']' brackets, handles escaped characters and detects errors if nested pairs are not balanced.
  • The Edit>Options>Compiler command now supports Java 1.8.
  • Thanks to Lorenz Maier, the run("Macro...", options) function now works when the options string starts with "v=" instead of "code=v=".
  • Thanks to Nico Stuurman, fixed a bug that caused the GaussianBlur.blurGaussian() method to throw an exception if the image had an ROI.
  • Thanks to Michael Schmid, fixed a bug that could cause the BackgroundSubtracter#rollingBallBackground() method to throw an exception when called with a FloatProcessor.
  • Thanks to Carnë Draug and Johannes Schindelin, fixed a bug that caused the File.directory macro function to not return the expected value after calling open(path).
  • Thanks to Carnë Draug, fixed a bug that precluded running macro files without extensions from the command line.
  • Thanks to Bill Heeschen, fixed a bug that caused Image>Duplicate to shift any non-rectangular selection in the source image to x=0, y=0.
  • Thanks to Jochen Cammin, fixed a bug in File>Import>Raw that caused it to only load the first slice from each file when "Open all files in folder" was checked.
  • Thanks to Julio Buonfigli, fixed a bug that caused the File>Compile and Run command in the text editor to throw an exception if the file name did not end in ".java".
  • Thanks to Philippe Carl, fixed bugs that caused the drawLine(), drawNormalizedLine() and drawDottedLine() methods of the Plot class to not work with log plots.
  • Thanks to Norbert Vischer, fixed a bug in Image>Zoom>Set that caused it to not correctly set the window size of stacks with selections.
  • Thanks to Eric Denarier, fixed a bug that caused Image>Overlay>From ROI Manager to not work in batch mode macros.
  • Thanks to Ted Toal, fixed a bug in the setResult() macro function that caused it to not work as expected when changing a string value in the Results table.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the getProfile() and run("Plot Profile") macro functions to not work as expected.
  • Thanks to Lorenz Maier, fixed a bug that could cause Process>Math>Macro to throw a null pointer exception.
  • Thanks to Michael Schmid, fixed a bug that caused Process>Math>Gamma to not check for invalid gamma values in preview mode.
  • Thanks to Ilan Tal, fixed a regression that caused the "B&C" and "Threshold" windows to not remember their positions when the "ImageJ" window was closed.
• 1.48s 7 March 2014
  • Thanks to Johannes Schindelin, added the Window>Main Window [return] menu command. On Windows, the command is Main Window [enter].
  • Thanks to Philippe Gendre, added a "Marker size:" menu to the Edit>Options>Point Tool dialog box. The choices are "Tiny", "Small" (the default), "Mediam" and "Large".
  • Thanks to Jeremy Sword, added a "Zero transparent" option to the Edit>Selection>Image to Selection and Image>Overlay>Add Image commands.
  • The recorder no longer records default options (e.g., 'size=0-Infinity') when recording Analyze>Analyze Particles, File>Import>Image Sequence and Image>Stacks>Z Project.
  • Image>Show Info displays the image's screen location and, in parentheses, the screen dimensions.
  • Plugins>Utilities>ImageJ Properties displays "Max window bounds" and the bounds of all monitors on systems with multiple monitors.
  • When creating a straight line selection, the angle displayed in the status bar is now calculated using sub-pixel resolution.
  • Added the GenericDialog.setSmartRecording() method, which allows plugins to suppress recording of default dialog box parameters.
  • Thanks to Matt Smith, fixed a bug that could cause a deadlock when using the stack window scrollbar to move through the slices.
  • Thanks to Jiri Janacek, fixed a bug that caused alt-click removal of a point selection to fail if the point was over an overlay element.
  • Thanks to Aaron Schain, fixed a bug that caused Image>Stacks>Tools>Concatenate to sometimes not work as expected with hyperstacks.
  • Thanks to Stoyan Pavlov, fixed a bug in the Roi Manager that caused ROIs to not be updated after changing the position in the More>>Properties dialog box.
  • Thanks to Josh Balsam, fixed a bug in Image>Stacks>Tools>Make Substack that caused it to not work in batch mode macros.
  • Thanks to Ryota Homma, fixed a bug that caused NonBlockingGenericDialogs to not be removed from the Window menu when the dialog was closed.
  • Thanks to Jan Brocher, fixed a bug that caused Edit>Selection>Make Band to fail if "EDM output" was not set to "Overwrite" in Process>Binary>Options.
  • Fixed a bug that could cause the "ImageJ" window to open behind the Windows taskbar.
  • Thanks to Gabriel Landini, fixed a 1.48r regression that caused the Image>Adjust>Threshold dialog to throw an exception if it was activated when already open.
  • Thanks to John Lim, fixed a 1.48q regression that caused the run("RGB Color") macro function to not work as expected with composite color images in batch mode macros.
• 1.48r 18 February 2014
  • Added "Angle", "Color" and "Bkdg" (background color) choices to the dialog displayed when you double click on the text tool or use the Edit>Options>Fonts command.
  • Thanks to Michael Schmid, the Image>Adjust>Threshold dialog displays the percentile of thresholded pixels, along with other improvements (details).
  • With text selections, the Edit>Selection>Properties dialog adds a "Angle:" field and a "Antialiased text" checkbox.
  • Improved text tool recording.
  • NonBlockingGenericDialogs are added to the Window menu.
  • Thanks to Michael Schmid, the Edit>Crop command is undoable.
  • Thanks to Aryeh Weiss, added the RoiEncoder.save() and RoiDecoder.open() methods (example).
  • Thanks to Aryeh Weiss, fixed bugs that caused the recorder to not work as expected when using the ROI Manager to save a single ROI.
  • Thanks to Norbert Vischer, Analyze>Set Scale no longer changes the voxel depth if it is set to a value other than 1.0 (the default value).
  • Thanks to Michael Kummer, fixed a bug that caused ROIs with widths or heights greater than 65535 to not be saved correcty.
  • Fixed a 1.48q reqression that caused CompositeImage unit test errors.
  • Thanks to Norbert Vischer, fixed a bug that caused voxel depths of zero to not be saved in the TIFF header.
  • Thanks to Michael Schmid, fixed bugs that caused the ImageJ menus to disappear on Macs when using the "Threshold", "B&C", "Channels", "CP" (Color Picker) and "Command Finder" dialogs.
  • Fixed a bug that caused the text tool to draw the text outline in the foreground color instead of the selection color.
• 1.48q 1 February 2014
  • Image>Overlay>Flatten now works with non-RGB stacks and hyperstacks.
  • Thanks to Michael Schmid, the Edit>Selection>Specify command adds a "Constrain square/circle" option, supports non-integer numbers and no longer moves the selection when 'Centered' or 'Scaled units' are checked.
  • Thanks to Jerome Mutterer, added a setAngle() method to the TextRoi class (example1, example2, example3).
  • Thanks to Dimiter Prodanov, Image>Stacks>Plot Z-axis Profile, in "Live" mode, draws a vertical line on the plot that corresponds to the current stack position.
  • Thanks to Jean-Olivier Irisson, added setNormalize(boolean), setProcessStack(boolean) and setUseStackHistogram(boolean) methods to the ContrastEnhancer class.
  • Added the Overlay.setFillColor() macro function (example).
  • Thanks to Mark Hiner, the CompositeImage constructor no longer converts stacks to channels when the number of slices is less than eight if the dimensions have been set or if the mode is IJ.GRAYSCALE.
  • Thanks to Marcel Boeglin, added the ImagePlus.flattenStack() method.
  • Fixed a bug that caused horizontal and vertical lines in overlays in to be deleted when duplicating or cropping images.
  • Thanks to Nicolas Brouilly, fixed a bug that caused scales greater than 2,147,483 pixels/unit to be saved incorrectly in the TIFF header.
  • Fixed a bug that caused File>Open Next to not work as expected with TIFF files with overlays.
  • Thanks to Norbert Vischer, fixed a bug that caused the close(wildcard) macro function to sometimes not keep current image active.
  • Fixed a bug that caused the ImagePlus.hide() method to remove overlays.
  • Fixed a bug that caused macro run() calls using the keyword 'stack' in the options string to fail after the "d" (Draw) or "f" (Fill) keyboard shortcuts had been used.
  • Thanks to Marcel Boeglin, fixed bugs that caused Image>Overlay>Flatten to not work correctly with hyperstacks and to not be correctly recorded.
• 1.48p 12 January 2014
  • Added an "Overlay" option to the Analyze>Tools>Calibration Bar dialog box.
  • Image>Color>Split Channels and Image>Hyperstacks>Reduce Dimensionality are faster and preserve slice and frame positions.
  • The Image>Color>Make Composite command no longer displays the "Channels" window or resets the slice position.
  • The Help>Update ImageJ dialog now appends the daily build number, if it exists, to the "You are currently running" version.
  • When processing stacks, a "List thresholds" option is added to the Process>Binary>Make Binary dialog box.
  • The Image>Color>Merge Channels command no longer attempts to auto-fill its dialog unless there are open images created by Image>Color>Split Channels.
  • Added a DEBUG option to the ImageJ constructor. For example, a Java program can run ImageJ invisibly in debug mode using "new ImageJ(ImageJ.NO_SHOW+ImageJ.DEBUG)".
  • Thanks to Philippe Carl, added the GenericDialog.getRadioButtonGroups() method.
  • Added the TextRoi(String,double,double,Font) constructor that can be used as a drop-in replacement for the drawString() macro function and the ImagePlus.drawString() method.
  • Thanks to Jon Nathan, fixed a bug that caused radio buttons in GenericDialogs to not generate dialogItemChanged events (example).
  • Thanks to Ashley Peery, fixed bugs in Image>Color>Merge Channels that caused it to not correctly merge more than three RGB images and to ignore the "Make composite" option when merging RGB images.
  • Fixed a bug that caused Image>Stacks>Z Project to not correctly show progress when processing hyperstacks.
  • Fixed a bug that caused the getSelectionCoordinates() macro function to not work as expected with selections created using makeOval().
  • Thanks to Neil Fazel, fixed a bug that caused File>Import>Text Image to skip the first line of the text image if it consisted of all NaNs.
  • Thanks to Tiago Ferreira, fixed a bug that caused the particle analyzer to sometimes unexpectedly display the Results table if "Stack position" was enabled in Analyze>Set Measurements.
• 1.48o 31 December 2013
  • Fixed a 1.48n regression than caused the "-" (zoom out) command to sometimes display invalid zoom indicators.
• 1.48n 31 December 2013
  • Thanks to Norbert Vischer, Image>Zoom>Set now works with selections (example).
  • Added the Image>Zoom>Scale to Fit command.
  • Fixed a 1.48m regression than caused the "-" (zoom out) command to sometimes not work correctly with images magnified 100% or less.
• 1.48m 29 December 2013
  • Thanks to Dimiter Prodanov, Image>Stacks>Plot Z-axis Profile now supports "Live" profiling.
  • Thanks to "aschain", the channel-slice-frame priority used by the ">" (Next Slice) and "<" (Previous Slice) keyboard shortcuts can be reversed by enabling "Reverse CZT order of ">" and "<" in Edit>Options>Misc. Also, typing ">" or "<" no longer stops animation.
  • Image>Scale and Image>Adjust>Size no longer always use nearest neighbor interpolation when the image width or height is one (example).
  • Thanks to Norbert Vischer, fixed a bug that caused the close(wildcard) macro function to not work with batch mode images.
  • Fixed a bug that caused the active batch mode image to sometimes not remain the active image after setBatchMode("exit and display");
  • Thanks to Michael Schmid, fixed a bug that caused the value unit of 32-bit images to not be saved in the TIFF header.
  • Thanks to Christian Meggle, fixed a bug that caused the ImageProcessor.resize() method to throw an exception when the image width or height was one (test case).
  • Thanks to Norbert Vischer, fixed a bug that cause the close("*") macro function to throw an exception if no images were open.
  • Thanks to Marcel Boeglin, fixed bugs that sometimes caused hyperstacks with overlays to not be correctly duplicated or cropped (test case).
  • Fixed a bug that caused the ImageProcessor.setRoi(Roi) method to sometimes not work as expected with single point selections.
  • Fixed a bug that caused the "List" option in plot windows to sometlimes display duplicate arrays.
  • Thanks to Steffen Decker, fixed a bug that prevented images displayed at 100% from being scrolled after after the window was reduced in size.
  • Thanks to Kees Straatman, fixed a v1.47 regression that caused the getList("window.titles") macro function to not include the Threshold and B&C windows.
  • Thanks to Norbert Vischer, fixed a 1.48a regression that caused filters to not work on virtual stack slices.
• 1.48k 15 December 2013
  • Added a "previous" choice to the Help>Update ImageJ command.
  • Thanks to Marcel Boeglin, the Image>Stacks>Z Project, Image>Type>RGB Color and Image>Color>Stack to RGB commands now support overlays.
  • Added a TextRoi(x,y,width,height,string,font) constructor that is useful for creating centered and right-justified text selections (example).
  • Thanks to Marcel Boeglin, fixed a bug that caused right-justified text selections to not be correctly saved and/or retrieved.
  • Fixed a v1.48h regression that caused TrakEM2 tools to not work as expected.
• The Convert Overlay To Icon macro converts an overlay or selection in a 16x16 image into a tool icon.
• 1.48j 11 December 2013
  • The toolbar is now expandable, with support for up to 15 custom tools.
  • Added the String.show(string) and String.show(title,string) macro functions.
  • Added a 'G' (draw polygon) command to the macro tool icon generation language (example).
  • Thanks to Thomas Suchyna, the Image>Adjust>Threshold window is resizable on Linux and Windows.
  • Thanks to Norbert Vischer, fixed a bug that caused Edit>Selection>Straighten to throw an exception with composite color images with straight line selections.
  • Thanks to Marcel Boeglin, fixed a bug in the Overlay.crop() method that sometimes caused the cropped overlay to be shifted.
  • Thanks to Marcel Boeglin, fixed bugs in Image>Hyperstacks>Reduce Dimensionality that caused it to not work correctly with overlays and with one channel hyperstacks.
  • Thanks to Mats Nilsson, and Johannes Schindelin, fixed a 1.48h regression that caused the getInfo(DICOM-tag) macro function to return empty strings or unexpected values.
  • Thanks to Dietmar Kunz, fixed a v1.48f regression that caused the ImageProcessor.duplicate() method to sometimes not work as expected.
• 1.48i 2 December 2013
  • The "Abort Macro or Plugin" action tool (used by Fiji) is not installed if its installation would result in no free tool slots.
  • Thanks to Michael Cammer, fixed a bug that caused the Overlay.setPosition() macro function to not work as expected with Overlay.drawSting().
  • Thanks to Davide Heller, fixed a bug in Process>Binary>Skeletonize that could result in disconnected segments (test image).
  • Thanks to Pierre, fixed a bug that sometimes caused spline fit segmented lines to shift 0.5 pixels up and to the left after using Edit>Selection>Interpolate.
  • Thanks to Aryeh Weiss and Jay Unruh, fixed a 1.48h regression that could cause Fiji to fail to start if there were AutoRun macros.
• 1.48h 30 November 2013
  • Replaced the blank "Unused Tool" slot in the toolbar with a 9 pixel gap. The toolsets on the ImageJ website without an "Unused Tool" have been updated to use no more than seven tools.
  • Thanks to Jerome Mutterer, added a "List properties" option to the Edit>Selection>Properties dialog box.
  • Thanks to Sebastien Octeau, added a "Skip dialog when opening .raw file" option to the Edit>Options>Input/Output dialog box.
  • Thanks to Norbert Vischer, the information shown in the Help>About ImageJ window is displayed in a text window when you press "i" (Image>Show Info) and is therefore easily copied to the clipboard.
  • Changed the default file extension for tables from ".txt" to ".csv" (comma-separated values).
  • Added "Insert", "Info" and "Close" buttons to the dialog opened by the macro editor's Macros>Function Finder command.
  • Plots created by Analyze>Calibrate always use an x range of 0-255 with 8-bit images.
  • The makeRectangle() and makeOval() macro functions support subpixel resolution.
  • Thanks to Jerome Mutterer, added getProperty(), setProperty() and getProperties() methods to the Roi class and Roi.getProperty(), Roi.setProperty() and Roi.getProperties() macro functions (example).
  • Thanks to Norbert Vischer, added setBatchMode("show") and setBatchMode("hide") macro functions.
  • Added Roi.getBounds(), Roi.getColor, Roi.getFillColor, Roi.getCoordinates(), Roi.getName, Roi.setFillColor(), Roi.setLocation(), Roi.setName(), Roi.setStrokeColor() and setStrokeWidth() macro functions (example).
  • Fixed a bug that caused toolbar icons to sometimes be drawn incorrectly.
  • Thanks to Michael Schmid, fixed a bug in Process>Noise>Salt and Pepper that caused it to omit the last column and row of the image.
  • Thanks to Michael Schmid, fixed bugs in the macro interpreter that caused expressions in the form s+"abc", where 's' is a string variable, to cause macros to abort when used as a function argument or used in a 'return' statement.
  • Thanks to Patrick Page-McCaw, fixed a bug that sometimes caused the particle analyser, when run from a plugin, to display a "No particles were detected..." dialog.
  • Thanks to Norbert Vischer, fixed a bug that caused an exception if the Size or Circularity fields in the particle analyzer dialog box were blank.
  • Fixed a bug that caused the wand tool to not be correctly recorded if the Recorder was not in "Macro" mode.
  • Thanks to Rainer Engel, fixed a bug that caused the particle analyzer to sometimes unexpectedly add selections to overlays.
  • Thanks to Norbert Vischer, fixed a bug that caused the LUT to be incorrect after switching channels in a batch mode macro.
  • Fixed a bug that caused the ROI Manager to sometimes unexpectedly display a "Save n ROIs as an overlay" message.
• Holger Lorenz contributed the Sphere Builder and Ellipsoid Builder, macros that create spheres/ellipsoids as 3D stacks.
• Ved Sharma has released Invadopodia tracker, a plugin for analyzing invadopodia dynamics parameters from fluorescence time-lapse movies.
• 1.48g 14 November 2013
  • Increased the size of toolbar icons from 26x26 to 28x28 pixels, which increased the width of the "ImageJ" window by 42 pixels.
  • Reduced the height of the status bar and increased the font size.
  • Increased the default menu font size on Windows from 14 to 15 points.
  • Added a "Fill with" option of "Random" to the File>New>Image dialog box.
  • Thanks to Michael Schmid, File>Save As>Tiff and File>Save As>ZIP now save the FFT data of FFT windows, except for FFTs of RGB images.
  • The File>New>Hyperstack command now labels using an overlay.
  • The Image>Show Info command displays overlay information.
  • Thanks to Michael Schmid, added the getInfo("window.type") macro function.
  • Thanks to Nico Stuurman, added setPaintPending() and getPaintPending() methods to the ImageCanvas class.
  • Thanks to Marcel Boeglin, added translate(x,y) (JavaScript example) crop(Rectangle), crop(firstSlice,lastSlice) and crop(firstC,lastC,firstZ,lastZ,firstT,lastT) methods to the Overlay class.
  • Thanks to Marcel Boeglin, fixed bugs that caused Image>Crop and Image>Duplicate to sometimes not work correctly with images containing overlays.
  • Fixed a 1.48f regression that caused unexpected Feret's diameter angles to be returned.
  • Fixed a bug that sometimes caused selections to not be correctly restored to the last slice or frame of a hyperstack.
  • Thanks to Barry DeZonia, fixed bugs that could cause the Image>Transform>Bin command to not work correctly on float images with negative pixel values.
  • Fixed a bug that sometimes caused custom tool preferences to not be correctly saved.
• Packt Publishing has released Image Processing with ImageJ, a 140 page introduction to ImageJ available in either e-book or paperback format, written by Javier Pascau and José María Mateos Pérez.
• 1.48f 30 October 2013
  • The Recorder now records File>Import>Import URL as open(url) (macro mode) or imp=IJ.openImage(url) (script or Java mode).
  • Thanks to Michael Schmid and Audrey O'Neill, ImageJ can now open MJPG-encoded files where the size of the JPEG frames differs from the size of the movie frames.
  • Thanks to Jan Eglinger, fixed a bug that caused the Recorder to record duplicate parameters when recording IJ.getFilePath().
  • Thanks to Ivan Micetic, fixed a bug that caused File>Revert to not restore image properties and LUTs.
  • Thanks to Christophe Leterrier, fixed a v1.48a regression that caused selections names longer than 20 characters displayed in the results table to be truncated.
  • Thanks to Bill Heeschen, fixed a v1.48e regression that caused the Process>Filters>Convolve command to fail.
• Jerome Mutterer contributed the LineAndProfileTool macro tool, which creates a line selection while displaying the corresponding profile plot as an overlay.
• 1.48e 19 October 2013
  • Thanks to Michael Schmid, plots now use scientific notation for large numbers and the curve fitter no longer runs on the event queue and can be aborted.
  • Changed the ROI Manager's "Remove Slice Info" command to "Remove Positions...".
  • Line selections are always drawn offset 0.5 pixels down and to the right regardless of the "Sub-pixel resolution" option in Edit>Options>Profile Plot Options.
  • Thanks to Miettinen Arttu, File>Import>Raw now decodes image dimensions embedded in file names (e.g., "name1_512x512.raw", "name2_256x256x256.raw").
  • The default "Fill with:" option in the File>New>Image dialog is now "Black" and the default foreground color is white and the default background color is black.
  • Added a "Help" button to the Analyze>Gels>Gel Analyzer Options dialog box.
  • Fixed a 1.48d regression the caused the "Simplex Fitting Options" dialog in Analyze>Tools>Curve Fitting to throw and exception when performing user-defined fits.
  • Thanks to Michael Schmid, fixed a curve fitting bug which could cause unintended values for the initial parameters (resulting in more iterations than necessary).
  • Thanks to Peter Haub, fixed a bug that caused the CommandListener interface to not work as expected when ImageJ was exited by clicking on the "ImageJ" window's the close box.
  • Thanks to Pavol Bauer, fixed a bug that caused Process>Batch>Macro to not open .lsm files using Bio-Formats when the LSM_Reader plugin was not installed.
  • Fixed a bug in the new File>Open Samples>Cache Sample Images command that caused it to throw an exception.
  • Thanks to Michael Schmid, fixed a bug that caused the spline fitter to sometimes not work as expected (example).
  • Thanks to David Bragason, fixed a bug that made it impossible to subtract from a selection or create a centered oval selection if there was an underlying overlay.
  • Fixed a bug that caused the bounding box of spline fit selections to be incorrect.
• 1.48d 28 September 2013
  • Thanks to Johannes Schindelin, added the File>Open Samples>Cache Sample Images command.
  • Thanks to Stephan Saalfeld, Image>Type>32-bit now supports conversion of RGB stacks to 32-bit float and RGB to float conversions are done directly.
  • Thanks to Michael Schmid, added "Exponential Recovery (no offset)" and "Chapman-Richards" curve fitting options.
  • The File menu and popup menu of non-active results windows now contain "Rename..." and "Duplicate..." commands.
  • The title of a non-active results window changes if it is saved using a different name.
  • Thanks to Norbert Vischer, added the Array Inspector to the macro debugger (test macro).
  • In the macro language, 'break' and 'continue' statements are now supported in 'for' and 'while' loops.
  • Thanks to Norbert Vischer, added the Array.show() macro function (examples).
  • Thanks to Dimiter Prodanov, fixed a bug that caused the Recorder to not generate a plugin that would compile and run after recording Process>Image Calculator.
  • Thanks to Jonas Ogaard, fixed a bug that sometimes caused an exception when drawing ROIs created with the brush selection tool.
  • Thanks to Dimiter Prodanov, fixed bugs that caused Analyze>Plot Profile to not work correctly when the intensity was uniform.
  • Fixed a bug that caused the Recorder to not correctly record the polygon, segmented line and point tools in "JavaScript" mode.
  • Fixed a bug that caused the Recorder, when not in "Macro" mode, to sometimes not correctly record commands in the Edit>Selection menu.
  • Thanks to Eric Denarier, fixed a bug that could cause the Results window to become inconsistent when using the Measure command after running the particle analyzer.
  • Thanks to Guy Lyons, fixed a bug that caused the roiManager("Show All with labels") macro function to not work in batch mode.
  • Thanks to Dimiter Prodanov, fixed a bug that could cause ImageJ to throw an exception on startup.
  • Thanks to Barry DeZonia, fixed a bug that caused the ImageProperties.getUnitIndex() method to not work correctly when passed the string "mile".
  • Thanks to Barry DeZonia, fixed a bug that caused the Image>Properties dialog to not reset the Y and Z units when the "Unit of length" was changed.
  • Thanks to Michael Schmid, fixed a 1.46f regression that caused some user-defined curve fits to fail.
  • Fixed a 1.48 regression that caused the ROI Manager to not correctly associate hyperstack ROIs to CZT positions.
• 1.48c 12 September 2013
  • Thanks to Marcel Boeglin, plugins launched using Plugins>Compile and Run now display a full stack trace if they throw an exception.
  • Thanks to Chris Coulon, the "<" and ">" keyboard shortcuts no longer display "There are no images open" and "Stack required" error messages.
  • Thanks to Norbert Vischer, the output of the Array.print() macro function is better formatted.
  • Thanks to Norbert Vischer, added the Array.findMaxima() and Array.findMinima() macro functions and corresponding MaximumFinder.findMaxima() and MaximumFinder.findMinima() methods (examples).
  • Thanks to Volko Straub, added the Overlay.moveSelection(index,x,y) macro function (example).
  • Thanks to Wilhelm Burger, added convertToByteProcessor(), convertToShortProcessor(), convertToFloatProcessor() and convertToColorProcessor() methods to the ImageProcessor class.
  • Thanks to Arthur Edelstein, added the Prefs.paintDoubleBuffered flag.
  • Thanks to Jose Maria Mateo, fixed a bug that caused run() macro calls using "&" notation to incorrectly pass numeric variables to the GenericDialog's getNextChoice() method.
  • Thanks to Bjoern Thiel, fixed a bug that caused the Analyze>Plot Profile command to not work as expected with spatially calibrated image with non-square pixels.
  • Thanks to Norbert Vischer, fixed a bug that caused the Plot.create() macro function to throw an exception if the y array was shorter than the x array.
  • Thanks to Norbert Vischer, fixed a bug that caused plots created by batch mode macros to not be scaled.
  • Thanks to Ved Sharma, fixed a bug that caused Analyze>Tools>Synchronize Windows to not work as expected with c=1, z=1, t>1 stacks.
  • Thanks to Rainer Engel, fixed bugs that sometimes caused the IJ.redirectErrorMessages() macro function to not prevent file read errors from aborting macros (example).
  • Thanks to Norbert Vischer, fixed a bug that caused Image>Duplicate to throw an exception if there was a selection outside the image.
• 1.48b 25 August 2013
  • Thanks to Michael Doube and Johannes Schindelin, added the "Interpolate ROIs" command to the ROI Manager.
  • Thanks to Norbert Vischer, submenus are now supported in the Plugins>Macros menu (example).
  • Updated the templates generated by the Plugins>New>Plugin and Plugins>New>Plugin Filter commands.
  • Rather than display an error message, the Copy and Cut commands now copy or cut the entire image when there is a line or point selection.
  • Added the ImageProcessor.set(double) method, now used by the Process>Macro>Set command.
  • Thanks to Eric Barnhill, added the HyperStackConverter.toHyperStack() method. A call to this method is generated if the recorder is running in script mode and the Image>Hyperstacks>Stack to Hyperstack command is used.
  • The Plugins>Macros>StartupMacros command works when the startup macros file is names StartupMacros.ijm.
  • The ImageConverter class works with stacks.
  • Thanks to Johannes Schindelin and Hans Wurscht, fixed a bug that sometimes caused memory used by images opened in batch mode macros to not be reclaimed (test macro).
  • Fixed a bug that caused run("Command") macro calls to run in a separate thread if "Command" was a macro installed in the Plugins>Macros submenu.
  • Thanks to Jan Brocher, fixed a bug that caused Image>Overlay>Flatten to sometimes not work as expected with RGB stacks.
  • Thanks to Gilles Carpentier, fixed a bug in the macro interpreter that caused it to incorrectly assign expanded arrays.
  • Thanks to Michael Schmid, fixed a bug that caused the FFT command to incorrectly display power spectra of RGB images.
  • Thanks to Alberto Duina, fixed a 1.48a regression that sometimes caused the ImageJ.updateAndDraw() method to throw an exception.
  • Fixed a bug that caused the IJ.getImage() method to display a "...Macro cancelled" error when using the "Compile and Run" command and no image was open.
  • Thanks to Gilles Carpentier, fixed a bug that sometimes caused the particle analyzer to display a blank Results table.
  • Thanks to Michael Schmid, fixed a bug that caused ImageJ to not correctly save 16-bit grayscale images in PNG format.
  • Thanks to Alberto Duina, fixed bugs that caused Edit>Selection>Interpolate to create straight line selections shorter than the original and to not work correctly with straight lines selections wider than one.
• 1.48a 22 July 2013
  • Added the Image>Overlay>List Elements command.
  • Thanks to Peter Haub, color LUTs are saved with 16-bit and 32-bit TIFFs.
  • Thanks to Simon Roussel, added Edit>Find and Edit>Find Next commands to text windows, such as those created by Image>Show Info.
  • The Image>Show Info command displays the display range of each channel, up to 7.
  • The "Set stack positions" option in the Image>Overlay>Options dialog is enabled by default.
  • Added a "Position:" field to the Edit>Selection>Properties dialog box.
  • Thanks to Dimiter Prodanov, added duplicate(), crop() and convertToFloat() methods to the ImageStack class.
  • Thanks to Franz Graf, added the ColorProcessor.setRGBWeights() method, a thread-safe (non-static) version of ColorProcessor.setWeightingFactors().
  • Thanks to Michael Doube, fixed a bug that caused plugins in jar files with a plugins.config entry starting or ending in one or more spaces to not be installed correctly.
  • Thanks to Jason Rogers, fixed a bug that caused the Edit>Copy command in "Results" windows to not work with one line tables.
  • Thanks to Vytas Bindokas, fixed bugs that caused 3D filters in Process>Filters to not work correctly with hyperstacks and to sometimes throw exceptions.
  • Thanks to Fabrice Cordelieres, fixed a 1.47v regression that sometimes caused unexpected results from setting the "plugins.dir" Java property.
  • Thanks to Norbert Vischer, fixed a bug that caused some commands in Process>Filters to throw an exception if the selection was outside the image.
  • Thanks to Gilles Carpentier, fixed a bug that caused a corrupted file to be created when using the setMetadata("Info","") macro function on a composite color image with an overlay and saving in TIFF format.
  • Thanks to Dimiter Prodanov, fixed a bug that sometimes caused a displayed stack to become inconsistent after the ImageStack was updated.
  • Thanks to Julien Berro, fixed a bug the caused the ROI Manager "Update" function to sometimes not work as expected with hyperstacks.
  • Thanks to Karsten, fixed a bug that caused Analyze>Measure to add very long selection names (longer than 20 characters), or selection names duplicating the image name, to labels in the Results table "Label" column.

Version 1.47 8 July 2013

• 1.47v 8 July 2013
  • Thanks to Wilhelm Burger, Plugins>Compile and Run works with plugins in packages that correspond to subfolders of the plugins folder and the PluginClassLoader searches ImageJ/jars for library jar files and classes.
  • Thanks to Gilles Carpentier, the ROI Manager's More>>List command now displays ROI stack and hyperstack positions and Overlay ROIs are always displayed on composite color images regardless of the stack positions of the ROIs.
  • Thanks to Laurent Holtzer, fixed a bug that caused Image>Adjust>Brightness/Contrast to not work correctly with 16-bit virtual stacks opened using the Bio-Formats plugin.
  • Fixed a bug the caused the getBitDepth() method of ImageProcessor subclasses to sometimes return 0
• 1.47u 25 June 2013
  • Thanks to Tiago Ferreira, the Plugins>Utilities>Search command now displays "Double-click on a file name to open it" in the Log window header bar.
  • Added a "Keep after adding to overlay" option to the arrow tool options dialog box.
  • Thanks to Elyse Aurbach, Analyze>Calibrate supports four more calibration functions and displays better calibration plots.
  • Thanks to Norbert Vischer, added the debug("conditional") macro function.
  • Thanks to Ved Sharma, fixed a bug that caused the particle analyzer to always create a new "Summary of ..." table when processing stack slices.
  • Thanks to Tiago Ferreira, fixed a bug in the Overlay.activateSelection() macro function that caused it to ignore stack positions.
  • Thanks to Barry DeZonia, fixed a bug that caused Image>Stacks>Tools>Reverse to not work with virtual stacks defined in Imglib.
  • Thanks to C Heeney, fixed a bug in the PolygonRoi class that caused it to modify the contains of float arrays passed to it in the constructor.
  • Thanks to Sebastien Simard, fixed a bug that caused multi-line arguments passed to user plugins to be displayed in the Log window when ImageJ was in debug mode.
  • Thanks to Jerome Mutterer, fixed a v1.47 regression that caused command line options similar to "-Dplugins.dir=..\ImageJ" to not work as expected.
  • Fixed a bug that caused the paths returned by getDirectory("image") and getDirectory("macros") to be incorrect if the path specified in the "-Dplugins.dir=path" command line option ended in "plugins".
  • Thanks to Andrew York, fixed a bug that caused macros run from the command line to sometimes unexpectedly display dialog boxes.
  • Thanks to Alberto Duina and Gabriel Landini, fixed a v1.47t regression that caused an exception to be thrown if a string with a length less than 3 was entered into a dialog box and the recorder was running.
• 1.47t 7 June 2013
  • The macro intepreter provides a better error message when a macro tries to index an empty array, such as the ones returned by the split() function when no tokens are found.
  • Thanks to Gilles Carpentier, fixed a bug that caused Image>Stacks>Tools>Reverse to not work as expected with composite color images.
  • Fixed a bug that sometimes caused Edit>Options>Memory & Threads to fail when ImageJ was started using the Linux launcher.
  • Thanks to Josef Borkovec, fixed a bug that caused GenericDialogs to not correctly record strings containing Windows file paths with backslashes.
  • Thanks to Barry DeZonia, fixed a bug in Image>Color>Arrange Channels that caused it to throw an exception with stacks with more than 10 channels.
  • Thanks to Gilles Courtand, fixed a v1.47s regression that caused the Process>Batch>Macro and Process>Batch>Virtual Stack commands to throw exceptions.
• Peter Bankhead has made available Analyzing fluorescence microscopy images with ImageJ, a 184 page introduction to image analysis in PDF format.
• 1.47s 3 June 2013
  • Fixed a 1.47r regression that sometimes caused color composite images to not work as expected.
• 1.47r 2 June 2013
  • Added the Image>Color>Display LUTs command.
  • Improved the Plugins>Utilities>Search command, which now uses radio buttons in its dialog box.
  • Philippe Carl extended the Plot class to support log and arrow plots (example1, example2).
  • Thanks to Federico Luzzati, added a "Prepend" option to the Image>Stacks>Add Slice dialog box.
  • Added a "BeanShell" mode to the command recorder (Plugins>Macros>Record).
  • Thanks to Samuel Inverso, the File>Import>Raw dialog is displayed when a .raw file is dragged and dropped on the "ImageJ" window or opened using File>Open.
  • ImageJ now replaces underscores with spaces when adding .lut files in the ImageJ/luts directory to the Image>Lookup Tables menu.
  • Thanks to Ingo Bartholomaeus, several ImageProcessor methods (e.g. copyBits()) no longer display progress bars.
  • Thanks to Norbert Vischer, the setColor() and Plot.setColor() macro functions now accept hex strings such "#ff0000".
  • Added the getList("LUTs") macro function (example) and the IJ.getLuts() method.
  • Added the newImage(title,type,width,height,channels,slices,frames) macro function, which is recorded when using the File>New>Hyperstack command.
  • Added the addRadioButtonGroup() and getRadioButton() macro functions (example).
  • Added the addRadioButtonGroup() and getNextRadioButton() methods to the GenericDialog class (example).
  • Thanks to David Nauen, fixed a bug that caused Analyze>Measure to not calculate and display "Centroid" values of straight line selections.
  • Thanks to Matt Smith, fixed a bug that caused RGBA tiff stacks to not be opened correctly.
  • Thanks to Gilles Carpentier, fixed a bug that caused the Edit>Selection>Restore Selection command to sometimes fail.
  • Thanks to Gilles Carpentier, fixed a bug that caused Edit>Paste to not work as expected with selections that extend beyond the image boundary.
  • Thanks to Johannes Schindelin, fixed ROI Manager bugs that caused key presses to be recorded twice, caused multiple selections to be recorded incorrectly as single selections, and caused macro calls like roiManager("Select",newArray(1,2)) to not update the GUI.
  • Worked aroung a bug in Java 1.7 for OS X that caused the DirectoryChooser, used by File>Import>Image Sequence, to fail.
  • Thanks to Christophe Leterrier, fixed a bug in File>Import>Image Sequence that caused it to not set the slice label when the folder being opened contained a single image.
  • Thanks to Sebastian Rhode, fixed a bug that sometimes caused Analyze>Tools>Synchronize Windows to not work as expected when synchronizing hyperstack positions.
  • Thanks to Gilles Carpentier, fix a bug that sometimes caused ROIs with names containing dashes to not be displayed in a stack overlay.
• 1.47q 6 May 2013
  • Added the Image>Stacks>Tools>Set Label command.
  • Thanks to Stephan Saalfeld, fixed a bug that caused the width and height of selections to be capped at 99999.
  • Thanks to Burri Olivier and Michael Schmid, fixed a bug that caused Analyze>Distribution to not work with ranges containing negative numbers.
  • Thanks to Abed Alnaif, fixed a bug that caused Analyze>Plot Profile to sometimes not work correctly with wide segmented line selections.
  • Thanks to Brian Barford, fixed a v1.47j regression that caused the Chart White Balance plugin to not work correctly.
  • Fixed a v1.47o regression that caused Bio-Formats to throw an exception when opening virtual stacks.
• 1.47p 29 April 2013
  • Added the Edit>Selection>Scale command.
  • The roiManager("Rename",name) macro function adds "-1" to names that duplicate existing names.
  • Fixed a bug that caused the Edit>Selection>Rotate command to not work with composite selections.
  • Fixed a 1.47o regression that caused incorrect display of measurement results if "Stack position" was enabled in Analyze>Set Measurements and also caused the List.setMeasurements() macro function to fail.
• Jan Brocher contributed BioVoxxel Toolbox, which includes these macros: Advanced Particle Analyzer, Feature Extractor, Speckle Inspector, Watershed Irregular Structures, EDM Erosion and Dilation, Auto Binary Masking, Threshold Checker, Contrast Detection, Difference of Gaussian, Difference from Median and Hyperstack Color Coding. Documentation is at www.biovoxxel.de/macros.html.
• 1.47o 26 April 2013
  • Results tables can now contain columns of strings (example).
  • Added the File>Import>Table command.
  • Added an "Open images using Bio-Formats" option to Process>Batch>Convert.
  • Thanks to Norbert Vischer, File>Save As>PNG saves 4-image 8-bit stacks or hyperstacks as PNG with alpha if the label of the fourth image is "Alpha".
  • Thanks to Wilhelm Burger, added the ImagePlus.setAntialiasRendering(boolean) method, which enables/disables use of antialiasing by the ImagePlus.flatten() method and the Image>Overlay>Flatten command.
  • Updated the ColorProcessor.getChannel() and ColorProcessor.setChannel() methods to support the alpha channel (example).
  • Updated the setResult() macro function to work with string values and added the getResultString() function.
  • Updated the ResultsTable addValue() and setStringValue() methods to work with string values and added the getStringValue() method (example).
  • Added the IJ.getFilePath(dialogTitle) method.
  • Added the Opener.openUsingBioFormats(path) and Opener.openTable(path) methods.
  • Johannes Schindelin added missing close() calls that caused Eclipse's resource leak warnings.
  • Johannes Schindelin made the ImageJ source compatible with Java 1.5 again by removing an illegal @override annotation from SubHyperstackMaker.java.
  • Thanks to Tom Kazimiers, fixed a v1.47f regression that caused the saveAs("tif",path) macro function to convert ".tiff" extensions to ".tif".
  • Thanks to Curtis Rueden, fixed a bug the caused Image>Stacks>Make Montage to not work as expected with composite color images.
  • Fixed a bug the caused Edit>Selection>Fit Spline to not work correctly with polygon selections.
  • Thanks to Philippe Carl, fixed a bug that sometimes caused the ImagePlus.setProcessor() method to not work as expected with stacks.
  • Thanks to Fabrice Cordelieres, fixed a bug that caused the Image>Stacks>3D Project command to throw an exception when working with 16 or 32 bit stacks and the "Interpolate" option was enabled.
  • Thanks to Jan Eglinger, fixed a bug that caused the precision of imported results to always be set to 3 decimal places.
• Norbert Vischer released Perspective Stack View, a macro set that creates perspective views of stacks and hyperstacks for use in presentations or publications.
• 1.47n 30 March 2013
  • The Image>Show Info command uses the Exif Reader plugin (version 2013/03/29 or later) to display Exif data of JPEG images.
  • Added a Macros>Show Log Window command to the macro editor.
  • Thanks to Johannes Schindelin, the eval("script",JavaScriptCode) macro function now returns, as a string, the value of the last expression evaluated.
  • The ImageListener interface triggers an image updated event when an image is renamed.
  • The Compile and Run command downloads the Java compiler to the plugins/jars folder as needed.
  • Added the blurGaussian() and applyMacro() methods to the ImageProcessor class (example1, example2).
  • Added the Overlay.setPosition(c,z,t) and Overlay.drawLabels() macro functions.
  • Fixed a bug that caused the Python print statement to not work as expected.
  • Thanks to Julian Cooper, fixed a bug that caused bounding box values displayed in the Results window, when measuring lines selections, to always be in pixel units.
  • Thanks to Curtis Rueden, fixed a bug that caused the ROI Manager to not restore hyperstack ROIs to the current CZT position.
  • Thanks to Julian Cooper, fixed a bug that caused vertical lines selections at the left image edge or horizontal line selections at the top image edge to not be restored correctly.
  • Thanks to Dimiter Prodanov, fixed a bug that could cause the ROI Manager to throw an exception if it contained a zero-point PolygonRoi.
  • Thanks to Michael Epping, fixed bugs that caused the Flip Horizontally, Flip Vertically, Rotate Left and Rotate Right commands to not correctly transform the image origin.
  • Thanks to Rich VanMetter, fixed a bug that caused some DICOM images to open slowly.
  • Thanks to Stephen Cody, fixed a bug that caused the "Select" option in Image>Adjust>Color Threshold to sometimes not work as expected.
• 1.47m 6 March 2013
  • Added the Plugins>Install command.
  • Thanks to John Hayes, added a Macros>Evaluate Python command to the macro editor. The 8MB Jython interpreter is downloaded as needed from the ImageJ website to ImageJ/plugins/jars.
  • Scripts in the plugins folder with ".bsh" and ".py" extensions are added to the Plugins menu.
  • "Exception" windows now display the ImageJ version, Java version, OS version and memory usage.
  • Plugins>Utilities>ImageJ Properties now displays values returned by IJ.getDirectory() and all Java properties.
  • Improved recording of foreground/background color settings and the "Black background" option.
  • Thanks to Wilhelm Burger and Johannes Schindelin, output to System.out and System.err is redirected to the Log window when ImageJ is in the debug mode.
  • Wilhelm Burger's IjLogStream class is built into ImageJ as ij.io.LogStream.
  • Thanks to Christophe Deroulers, added the roiManager("save selected", path) macro function.
  • Added the eval("bsh",script) and eval("python",script) macro functions.
  • Fixed a v1.47d regression that sometimes caused the Process>Binary>Convert to Mask command to change the "Black Background" option.
  • Thanks to Leon Espinosa, fixed a v1.47j regression that caused ROIs added to the ROI Manager by the particle analyzer to have null names.
  • Thanks to Norbert Vischer, fixed a bug that caused the Edit>Selection>Rotate command to not work as expected with rounded rectangle selections.
  • Thanks to Antti Niemisto and Gabriel Landini, fixed a bug that caused the "Minimum" thresholding method to set the wrong threshold for some unusual histograms.
• Gilles Carpentier contributed Sort Selections in Overlays, a macro that sorts selected overlay elements by color (requires v1.47k).
• 1.47k 17 February 2013
  • Thanks to Norbert Vischer, fixed a 1.47j regression that caused the Analyze>Plot Profile command to not work with line selections wider than 1.
• 1.47j 15 February 2013
  • The Edit>Selection>Enlarge command is much faster.
  • Thanks to Norbert Vischer, the macro debugger now flags changed variables.
  • Thanks to Norbert Vischer, Edit>Selection>Line to Area, with straight line selections, now creates 4-corner polygons instead of traced selections.
  • Added the "Enhanced line tool" option to Edit>Options>Misc, which allows straight line selections to be created by clicking at the start and at again the end.
  • The File.openAsString() macro function no longer has a file size limit.
  • Thanks to Rainer Engel, added the File.copy(path1,path2) macro function.
  • Thanks to Norbert Vischer, added the Array.resample(arr,len) macro function.
  • Added the Overlay.addSelection(color), Overlay.addSelection(color, strokeWidth) and Overlay.addSelection("", 0, fillColor) macro functions.
  • Thanks to Miso Mitkovski, fixed a 1.47i regression that caused the command finder to sometimes not work as expected when using the down arrow and enter keys.
  • Thanks to Gilles Carpentier, fixed a bug that could cause the ROI Manager to not work correctly if ROIs with duplicate names were programatically added.
  • Thanks to Norbert Vischer, fixed a bug that caused the split() macro function to not return a zero length array when no tokens were found.
  • Thanks to Ignacio Arganda-Carreras, fixed a bug that caused the SaveDialog class to add the extension twice if it was longer than four characters.
  • Thanks to Sebastien Tosi, fixed a bug that sometimes caused the getHistogram() macro function to not work as expected with 16-bit images.
• Photos from the 2012 ImageJ conference in Luxembourg are available online.
• 1.47i 25 January 2013
  • Thanks to Curtis Rueden, the command finder (Plugins>Utilities>Find Commands) uses a table to display additional information about the commands it finds.
  • Improved the Plugins>Shortcuts>Create Shortcut command.
  • The Image>Stacks>Plot Z-axis Profile command works with hyperstacks.
  • Thanks to Adam Brin, added the IJ.getErrorMessage() method.
  • The "Startup Macros" command in the toolbar's ">>" menu looks for a file named StartupMacros.fiji.ijm if StartupMacros.txt is not found in the macros folder.
  • Added the Overlay.addSelection() and Overlay.activateSelection() macro functions.
  • Michael Schmid fixed a bug that sometimes caused Process>Noise>Remove Outliers and Process>Binary>Erode to not work correctly when processing stacks using multiple threads.
  • Thanks to Alistair MacDougall, fixed a v1.47f regression in the saveAs("tiff",path) macro function that caused it to not update the image title.
  • Fixed a 1.47f regression that caused the saveAs("tiff") macro function to throw an exception.
  • Fixed a bug that caused the String.copyResults() macro function to ignore selections, which is not consistent with the Results window's Edit>Copy command.
  • Thanks to Ved Sharma, fixed a bug that caused the macro language return statement to not correctly return string array values.
  • Thanks to Erik Belanger, fixed a bug the caused Image>Stacks>Delete Slice to not work correctly with hyperstacks.
  • Thanks to Julien Vaubourgeix, fixed a bug in Image>Stacks>Label that caused it to delete any existing overlay when the "Use overlay" option was enabled.
  • Fixed a bug that caused the saveAs(path) macro function to display a "Save As" dialog box.
• 1.47h 23 December 2012
  • Thanks to Denis Meuthen, you can now create a straight line selection by defining the start of the line with one click and the end with another click.
  • Thanks to Curtis Rueden, Image>Stacks>Tools>Make Substack now works with hyperstacks.
  • Thanks to Jerome Mutterer, the arrow, brush, pencil and pixel inspector tools remember the location of their options dialogs.
  • Thanks to Rainer Engel, the "Log" window remembers its dimensions.
  • File>Save As>Image Sequence displays a warning if the first file in the sequence will overwrite an existing file.
  • The File>New>Hyperstack command can be invoked by pressing alt-n.
  • Thanks to Gilles Carpentier, fixed a bug that caused the run("Make Composite") macro function to sometimes not work as expected.
  • Michael Schmid fixed a bug that prevented the AVI Reader from correctly opening as virtual stacks AVI files with blank frames.
  • Thanks to Alex Hughes, fixed a bug that caused the ROI Manager's Multi Plot command to disregard the "Vertical profile" option in the Edit>Options>Profile Plot Options dialog box.
  • Thanks to Kees Straatman, fixed a bug that caused Analyze>Tools>Analyze Line Graph to hang with non-thresholded images.
  • Thanks to John Oreopoulos, fixed a bug that caused File>Import>Image Sequence to sometimes not work as expected when all the images in the sequence were not the same type.
  • Thanks to Jerome Mutterer, fixed a bug that caused an exception when pasting, in a macro, a non-recangular ROI that was partially outside the target image.
  • Thanks to Vanessa Bell, fixed a bug that caused the getSelectionCoordinates() macro function and Roi.getPolygon() method to sometimes unexpectedly return the bounding rectangle of composite selections.
  • Thanks to Aivar Grislis, fixed a v1.47g regression that caused the setLocation() macro function to not work with some non-image windows.
  • Thanks to Michael Schmid, fixed a bug that caused "Cancel" to not work as expected for dialogs in "Preview" mode with commands called from macros.
  • Thanks to Jarek Sacha, fixed a bug that caused ImageListeners to sometimes not be notified when the image was updated.
  • Michael Schmid fixed two PlugInFilterRunner bugs related to Preview and PARALLELIZE_IMAGES.
• 1.47g 2 December 2012
  • Changed the "Brightness/Contrast", "Channels", "Threshold" and "Color Picker" windows to modeless dialogs that do not have the iconize and maximize buttons that are problematic on Windows.
  • Thanks to Bill Christens-Barry, added an "Auto contrast stacks" option to the Edit>Options>Appearance dialog box. Alternatively, hold down the shift key when scrolling stacks.
  • Thanks to Thomas Kuhne, Emil Kesler and Yili Zhao, Plugins>Compile and Run, on Java 1.6 or later, uses javax.tools.JavaCompiler instead of com.sun.tools.javac.Main.
  • Thanks to Norbert Vischer, added the close(pattern) macro function (example) and the ij.util.WildcardMatch class.
  • Thanks to Jerome Mutterer, added the getValue("rgb.foreground") and getValue("rgb.background") macro functions.
  • Thanks to Norbert Vischer, added the setForegroundColor(rgb) and setBackgroundColor(rgb) macro functions.
  • Thanks to Bill Christens-Barry, added the setOption("auto contrast",boolean) macro function.
  • Worked around a bug on Windows 8 that made scrollbar thumbs nearly invisible.
  • Fixed a bug that caused an exception when File>Revert was used on a duplicated image.
  • Thanks to Olivier Cardoso, fixed a bug that could cause an exception when calling an Ext macro function.
• Jerome Mutterer and Edda Zinck have released FigureJ, a plugin that makes it easy to create figures for scientific articles.
• Dimiter Prodanov contributed Mexican Hat Filter, a plugin that convolves a 2D image with a Laplacian of Gaussian filter.
• 1.47f 18 November 2012
  • Added the IJ.saveAsTiff() method.
  • Fixed a v1.46f regression that caused the applet version of ImageJ to not open images specified using HTML parameters.
  • Thanks to Erik Belanger, fixed a bug that caused the setMinAndMax() macro function to not work with batch mode composite color images.
  • Fixed several stack flattening bugs.
  • Fixed several hyperstack related bugs in the Image>Scale command.
  • Fixed a bug that caused the saveAs("tif",path) macro function to not work correctly on consecutive command line macro calls.
  • Thanks to Norbert Vischer, fixed a bug that caused Copy from the "Log" window to not work correctly for lines containing tabs when "Copy row numbers" was not enabled in Edit>Options>Input/Output.
  • Thanks to Jerome Mutterer, fixed a bug that prevented the FigureJ plugin from being able to restore tools.
• 1.47e 9 November 2012
  • Added the Macros>Evaluate BeanShell command to the macro editor. This command requires that a copy of BeanShell.jar be in the plugins folder.
  • Thanks to Michael Kaul, bilinear interpolation works better with float images containg NaNs.
  • Thanks to Michael Schmid, added a "Gaussian (no offset)" curve fitting option.
  • The recorder displays a warning when the options string in run(command,options) calls contain one or more non-ascii characters.
  • Added the Toolbar.restoreTools() method (example).
  • Added the ParticleAnalyzer.setFontColor(String) method and the call("ij.plugin.filter.ParticleAnalyzer.setFontColor","blue") macro function. .
  • Thanks to Thomas Boudier, added a public GaussianBlur3D.blur() method.
  • Thanks to Michael Schmid, fixed a v1.46 regression that could cause curve fitting errors.
  • Simon Bear fixed a bug that caused black pixel data to be ignored when loading CMYK TIFFs.
  • Fixed a bug that caused the source stack to become corrupted when scaling by x=1.0 and y=1.0 in Image>Scale.
  • Thanks to Thorsten Wagner and Michael Schmid, fixed a bug that caused the Analyze>Summarize command to fail if the Results table contained headings with spaces.
  • Thanks to David Gauntt, fixed a bug in the FHT class that caused it to fail when calculating the power spectrum of 1D arrays larger than 32K.
  • Thanks to Jarek Sacha, fixed a bug that cuased File>Import>Image Sequence to sometimes not set the correct slice labels when opening a series as a virtual stack.
• Gilles Carpentier contributed Angiogenesis Analyzer, a macro toolset for analysis of cellular networks, for example the pseudo vascular organization of endothelial cells cultured in a gel medium (documentation).
• 1.47d 5 October 2012
  • Thanks to Norbert Vischer, added the Image>Color>Arrange Channels command.
  • Thanks to Michael Cammer, when processing stacks, added "Method" and "Background" choices to the Process>Binary>Convert to Mask dialog.
  • Thanks to Ved Sharma, the arrow tool draws bolder outlined arrows.
  • Deleted the redundent Image>Hyperstacks>Channels Tool menu command.
  • Thanks to Norbert Vischer, added the getInfo("command.name") macro function (example).
  • Added the setOption("jfilechooser") macro function.
  • Fixed a bug that caused the roiManager("select",n) macro function, and RoiManager.select() method, to display an error message if no images were displayed.
  • Thanks to John Page, fixed a bug that caused CMYK TIFFs to open inverted.
  • Thanks to Birgit Möller, fixed a bug that sometimes caused the ImagePlus.show() method to not work as expected on closed images.
  • Thanks to Norbert Vischer, fixed a bug that sometimes caused the Edit>Selection>Line to Area command to not work as expected.
  • Thanks to Gilles Carpentier, fixed bugs in Process>Binary>Skeletonize that caused it to sometimes not remove all skeleton pixels.
  • Thanks to Leon Espinosa, fixed a bug that caused "Apply" in the "Threshold" tool to always use the default thresholding method.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording, when the recoder was in "JavaScript" or "Plugin" mode, of plugins that used the run(imp,..) methods of the Duplicator class.
  • Norbert Vischer fixed a bug that caused line numbers in macro error messages to be incorrect with macros containing emptly lines inside SlashStar comments.
  • Thanks to Jiri Janacek, fixed a bug the caused the perimeter of composite ROIs in spatially calibrated images to be incorrect.
  • Thanks to Michael Schmid, fixed a bug that could cause file corruption if the Crop command was used while a stack was being saved.
  • Thanks to Eric Denarier, fixed a bug in Process>Batch>Macro that caused it to somestimes not output the correct images.
• Kota Miura has made available two textbooks ("Basics of Image Processing and Analysis" and "Macro Programming in ImageJ") he uses for the ImageJ classes he teaches.
• 1.47c 8 September 2012
  • Added a "Source" (display source code of selected command) button to Plugins>Utilities>Find Commands.
  • Dorai Iyer added a "Bar" option to the arrow tool.
  • Bill Mohler modified the ROI Manager to use a JList instead of a List, which makes loading and sorting the large (>10,000) ROI sets faster.
  • Added an "Append results" checkbox to the ROI Manager's "Multi Measure" command.
  • When opening images, the transfer rate in MB/sec is displayed in the status bar.
  • Thanks to Sébastien Tosi, opening TIFF files using File>Import>URL is faster and requires less memory.
  • Thanks to Jan Eglinger, fixed a bug that caused incorrect recording of commands implemented in JavaScript when the recorder was in "JavaScript" mode.
  • Thanks to Sébastien Tosi, fixed a bug that caused File>Import>URL to not correctly read TIFF files larger than 2GB.
  • Fixed a bug in the Analyze>Tools>Synchronize Windows command that caused it to not work as expected when changing the channel of composite color images.
  • Thanks to Christoph Deil, fixed a bug in Plugins>Utilities>Find Commands that caused esc and ctrl-w key presses to not close the window after "Show full information" was enabled.
  • Thanks to Christoph Deil, fixed bugs in the "Save changes?" dialog that caused it to not work as expected after the focus was changed (by tabbing) to the "Don't Save" or "Cancel" buttons.
• 1.47b 12 August 2012
  • Added the Image>Stacks>Statistics command.
  • Thanks to Michael Schmid, the built in brush, pencil and overlay brush tools draw using the background color when alt key is down, are constrained to draw horizontally when shift is down, are resized when shift&control are down (shift&cmd on Macs), and "pick up" the foreground color when control is down (cmd on Macs).
  • Added a "16 bit range" choice to the Edit>Options>Appearance dialog box. This is the same as the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog.
  • Thanks to Olivio Donati, File>Import>Image Sequence opens any associated ROIs that are in a file named RoiSet.zip.
  • Thanks to David Knecht, added a "sum" option to Image>Transform>Bin.
  • The getHistogram() macro function no longer limits the number of bins to 256 with 8-bit and RGB images.
  • Added the IJ.createHyperStack(title,width,height,channels,slices,frames,bitdepth) method, where 'bitdepth' is 8, 16, 24 (rgb), or 32 (float).
  • Thanks to Qingzong Tseng, fixed a bug that caused overlays to be lost when converting composite stacks to RGB.
  • Thanks to Jan Eglinger, fixed a bug that caused images created by the particle analyzer's "Show:" option to not use the calibration of the original image.
  • Thanks to Guenter Giese, fixed bugs that caused the "Unsigned 16 bit range" choice in the Brightness/Contast Adjuster's "Set" dialog to not work as expected with multi-channel images.
  • Thanks to Barry DeZonia, fixed a bug that caused the command recorder to not work with Image>Stacks>3D Project when processing 16 and 32 bit images.
  • Thanks to William Edwards, fixed a bug that sometimes caused the median of 32-bit float images to be calculated incorrectly.
  • Thanks to Michael Cammer, worked around a bug that could cause commands in the Image>Type submenu to not work as expected in non-batch-mode macros.
• 1.47a 17 July 2012
  • Thanks to Thomas Boudier, added five new 3D filters (Median, Mean, Minimum, Maximum and Variance) to the Process>Filters submenu.
  • Added the "Restore Startup Tools" command to the toolbar's >> menu.
  • Thanks to Tiago Ferreira, built-in and plugin tools can be added to toolsets and the startup macros (example).
  • Michael Schmid modified the Overlay Brush tool for constrained motion (vertical or horizontal) with shift and resizing with ctrl-shift (cmd-shift on Macs).
  • Thomas Tongue added support for the CDELT and CTYPE headers to the FITS Reader.
  • Added the getinfo("selection.color") and getValue("selection.width") macro functions.
  • Thanks to Simon Roussel, fixed a bug that could cause overlays to not be displayed on virtual stacks.
  • Fixed a bug that caused the brush and pencil tools to activate overlay selections.
  • Michael Schmid fixed a bug that sometimes caused Preview to not work correctly with commands in the Process>Filters submenu.
  • Fixed a 1.46 regression that caused the ROI Manager to generate incorrect ROI labels when the Associate 'Show All" ROIs with Slices" option was not enabled.
  • Thanks to Stephan Semmler, fixed a regression that caused the ImagePlus.getNDimensions() method to sometimes return the wrong value.
  • Thanks to Glen MacDonald, fixed a 1.46 regression that caused the setOption("Show All",boolean) macro function to not work.
• Kevin Eliceiri and Caroline Schneider published the article "NIH Image to ImageJ: 25 years of image analysis" in Nature Methods.

Version 1.46, 26 June 2012

• 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

• 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.

Complete Release Notes

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