NeuronJ: Release Notes

1.4.1, November 8, 2008

• The plugin now requires Java 1.5 and ImageJ 1.41g or higher.
• Improved code for unexpected exception catching and messaging.
• Added option to specify the number of decimal places used in measurements.
• Added units to the column heads in all measurement result windows.
• Replaced "StDev" by "SD" in all measurement result windows.

1.4.0, February 20, 2008

• The plugin now requires Java 1.5 or higher.
• Added a choice in the parameters dialog to trace either bright or dark neurites.
• Added an option in the parameters dialog to use the image name in result window titles.
• Added exception catching and messaging in the event handling code.

1.3.1, November 14, 2007

• Added an option in the parameters dialog to toggle automatic image window activation.

1.3.0, November 9, 2007

• Improved neurite centerline tracing in gray-scale images showing clipped intensities.
• Added the possibility to export tracings as segmented line selections (polyline ROIs).
• Zooming in/out can now be done by pressing the +/- keys (if the image window is active).
• Improved key listening when the mouse pointer is outside the active image window.
• Solved checkbox interaction problem in the export dialog on Macintosh systems.
• The snap cursor is now shown only when adding tracings and the mouse is on canvas.

1.2.0, July 16, 2007

• The plugin now requires ImageJ 1.38x and Java 1.4 or higher.
• Replaced function calls that were deprecated in Java 1.5.
• Added menu item ImageJ > Help > About Plugins > NeuronJ...
• Slightly improved the magnification and quit toolbar buttons.
• Added a toolbar button for launching the default browser showing the online manual.
• Added version checking of the Java VM and the ImageJ and ImageScience libraries.
• Renamed debug messaging to log messaging in the parameters dialog.
• Log messaging for NeuronJ is now done in a separate text window.
• An error message is now shown when trying to run NeuronJ in batch mode.
• Double buffering is now enabled for drawing tracings to reduce flicker.
• The last ImageJ tool before running NeuronJ is now restored after quitting.
• The image window is now automatically moved to the front when the mouse enters.
• Removed text antialiasing in message dialogs and yes/no dialogs.
• Renamed several dialog classes to improve naming consistency.
• All dialogs are now closable by clicking the "x"-icon in the title bar.
• All dialogs (except messages) now open in the same location they were last closed.
• The attributes and measurements dialogs are now closed when switching toolbar modes.
• Reordered group and tracing measurements in the measurements dialog.
• Added vertex measurements (coordinates/values) to the measurements dialog.
• Added an option in the measurements dialog to show (non-)calibrated results.
• Added an option in the measurements dialog to interpolate value measurements.
• Improved NeuronJ data file version checking for possible future versions.
• Data files now contain real tracing numbers with segment numbers starting at 1.

1.1.0, March 22, 2006

• The program is now distributed as a single jar-file to facilitate installation. Before installing the new version, you should delete all of the following files and folders of older versions (note that not all of these may have been present in all older versions, so please check carefully whether these indeed belong to your version of NeuronJ or to some other package):

     ImageJ
       |- NJOptions.dat        (file)
       |- plugins
             |- Basics         (folder)
             |- BasicsJ        (folder)
             |- NeuronJ        (folder)
             |- imagescience   (folder)

• The program now provides the possibility to make a snapshot of the image and the tracings. A new button has been added to the NeuronJ toolbar for this purpose.
• It is now possible to export the tracing vertex coordinates as tab- or comma-delimited text files. This facilitates using the tracings in other programs or plugins, such as for example the Straighten plugin.
• Tracings can now be manually corrected afterwards by individually moving the vertices. A new button has been added to the NeuronJ toolbar for this purpose.
• NeuronJ now not only measures tracing lengths but also (calibrated) image value (intensity) statistics along the tracings.
• When moving the mouse over the image, the program now shows both calibrated and (between parentheses) non-calibrated positions and values. For those who are not familiar with it: the intensity calibration can be specified under ImageJ > Analyze > Calibrate. For 8-bit gray-scale images, the program uses the original image values. For 8-bit index-color images, the program converts indexed RGB-values in the lookup table to intensities using the formula I = 0.3R + 0.6G + 0.1B.
• It is no longer possible to specify the pixel sizes and units in the parameters dialog. These are image specific properties and can be specified under ImageJ > Image > Properties. The values of these properties stored in older NeuronJ data files are ignored.
• Apart from pixel sizes and units, the auto-save and debug settings are no longer saved to NeuronJ data files along with the other parameter settings and the tracings. These two options are considered global program settings, not tracing specific settings, and are ignored when loading older NeuronJ data files.
• The program parameters are no longer stored in a separate file (NJOptions.dat) but in ImageJ's preferences file (IJ_Prefs.txt).
• Empty tool buttons have been replaced by spaces in the toolbar.
• It is now possible to set the line width used by the program to draw the tracings.
• Made some minor modifications to solve the problem (with recent versions of ImageJ) of tracings not being shown when loading the next image.

1.0.1, March 4, 2004

• Thanks to Daniel Sage of the Swiss Federal Institute of Technology Lausanne, Switzerland, the software now also works properly on Mac OS X 10.3.2 (Java 1.4.2).

1.0.0, February 12, 2004

• First release. The software was tested and found to function properly with ImageJ 1.31v running on Windows XP (Java 1.3.1 and 1.4.0), Linux Redhat 7.3 (Java 1.3.1), and Sun Solaris 5.8 (Java 1.3.1). I haven't had the possibility yet to test the software on other systems or with other Java versions, so I don't guarantee anything there.