Replacing TextPanel with FileWriter for ouput of txt files

New

With the previous version there were still problems to run the plugin in headless mode, since MotiQ used the ij.text.TextPanel to create output text files and save them. However the TextPanel needs a graphical interface, even when it is not displayed. In the new version, a new method has been implemented to save output files that uses java.io.FileWriter, which reduces memory and time for writing and outputing text files and avoids the need of a graphical interface. This should improve the issue mentioned in #3.

Improving Headless running mode - Issue #3

New

• With the previous version there were still problems to run the plugin in headless mode. In this version, the "ProgressDialog" is entirely avoided which should avoid the issue mentioned in #3 with MotiQ 3D Analyzer version v0.3.2.
• The new plugins now provide a help button in the Settings dialog, directing to the MotiQ wiki.

Running without GUI / Multi-Task-Manager

New in this version

From this version on, MotiQ Thresholder, MotiQ 2D Analyzer, and MotiQ 3D Analyzer can be run from a macro in a window-less mode, e.g., on a server, further fixing #3.

Add noGUI to the macro option string to suppress any GUIs/Windows like the Multi-Task-Manager window.

Example command:
run("MotiQ 3D Analyzer (v0.3.2)","minimum-particle-volume=50 calculate=[all detected particles merged into one object] skeleton=[derive skeleton from a copy of the input image] gauss-xy=1.000000 gauss-z=0.000000 number-format=[US (0.00...)] noGUI");

Fix macro recording - Issue #3

New:

From this version on, the macro recorder can record functional commands from runs of MotiQ Thresholder, MotiQ 2D Analyzer, and MotiQ 3D Analyzer, further fixing #3.

Make plugins callable from Macro - #3

New features

Fixing request/issue #3, from now on the plugins MotiQ Thresholder, MotiQ 3D Analyzer, MotiQ 2D Analyzer can be launched from a macro to process an active image. Recording the commands with the Macro recorder does not work yet and will be implemented in the future. However, all commands that can be used are included in the example macro calls below. To deselect the boolean commands such as local-threshold or include-date simply remove them from the command string. You can modify the values after the = signs to the settings you wish to use.

run("MotiQ Thresholder (v0.2.0)", "use-alternate automatically-find begin-of-suffix=[_CUT] additional-suffix=[.tif] restrict scale=0.5 convert threshold=MinError stack-handling=[apply threshold determined in a maximum-intensity-projection] threshold-every-time-step threshold-only-distinct-times start-time=1 end-time=10 local-threshold local-threshold-radius=5 fill-holes keep-intensities automatically-save include-date");

run("MotiQ 2D Analyzer (v0.2.0)", "re-calibrate length=0.5 calibration-unit=micron time-interval=0.10 time-unit=min minimum-particle-area=50 remove-all-but-largest time-steps-grouped=12 calculate=[every particle seperately (track particles by overlap)] skeleton=[derive skeleton data from a BINARIZED copy of the input image] gauss=1.0 number-format=[US (0.00...)] include-date");

run("MotiQ 3D Analyzer (v0.3.0)", "re-calibrate length=0.4170 depth=1.0000 calibration-unit=um time-interval=0.50 time-unit=min minimum-particle-volume=50 time-steps-grouped=10 calculate=[all detected particles merged into one object] skeleton=[derive skeleton from a copy of the input image] gauss-xy=1.0 gauss-z=0.0 number-format=[US (0.00...)] include-date");

Bug fixes

In the previous version of MotiQ Thresholder there was a bug in the Fill holes function when processing stacks. The plugin prompted the user when inverting images and asked whether the whole stack should be processed. Also the fill holes function depending on a setting of ImageJ (Process - Binary - Options... -> Black Background) did not work and did rather remove cells than filling holes in cells. These bugs are now fixed.

Warn when processing unsaved images / when reference image cannot be found

New in this release:

• All plugins: Plugins from previous releases crashed when processing images that were not saved (since the software could not detect where the image was stored it could not output files to the place where the input image would be stored). This led to cryptic error messages (see issue #2 ). From this release on, the plugins check at start-up whether an image is saved and refuse processing / report a warning message when an image that was not saved is submitted as an input image. Example warning message:

• MotiQ Thresholder: Previous versions of MotiQ Thresholder crashed when they could not find the "reference image". From this version on, a warning message is printed when this is the case so that the user knows why MotiQ Thresholder does not succeed in processing the image (see issue #2). Example error message:

IntegrateSkeletonizeMethodsAndBugfixes

Changes in MotiQ_2D and MotiQ_3D (all other plugins not changed):

• Solves compatibility issues of MotiQ with other versions of the plugins
  Skeletonize3D and AnalyzeSkeleton than those required for MotiQ, when
  these other versions were installed in parallel into the FIJI or ImageJ
  working distribution. Solution: The plugins Skeletonize3D and AnalyzeSkeleton required for
  MotiQ are now integrated into MotiQ and used locally in MotiQ.
• The source code integrated into MotiQ for the plugin Skeletonize3D by I. Arganda-Carreras was copied on 12th of Dec 2016 from: https://github.com/fiji/Skeletonize3D/blob/master/src/main/java/sc/fiji/skeletonize3D/Skeletonize3D_.java
• The source code integrated into MotiQ for the plugin AnalyzeSkeleton by Arganda Carreras et al. was copied from: https://github.com/fiji/AnalyzeSkeleton/releases/tag/v3.1.1 (Original publication: Ignacio Arganda-Carreras, Rodrigo Fernandez-Gonzalez, Arrate Munoz-Barrutia, Carlos Ortiz-De-Solorzano, '3D reconstruction of histological sections: Application to mammary gland tissue', Microscopy Research and Technique, Volume 73, Issue 11, pages 1019-1029, October 2010).
• Smaller bugfixes: e.g. adapt particle IDs in output file names (MotiQ2D) to those numbers in the output text files (before: difference of 1 between the IDs in the text files and the IDs in the images)
• Update e-mail adress in plugins

ImprovedOutputFiles

To decrease the length of output directory paths, the automatically generated filenames of output files in the created results folder was reduced to a minimum prefix ("M2D..." or "M3D...", respectively).
Additionally, the thickness of scale bars in 3D output images was unified for all three dimensions.

BugFixedInThresholder

Along with this release, a bug was fixed in the plugin MotiQ Thresholder.

1st release

This is the first release of the MotiQ toolbox.