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In timelapse mode, when a particle is analyzed that produces two skeletons in a few frames, the program crashes.
CiliaQ version: v0.0.7
Error message:
java.lang.NullPointerException at ciliaQ_jnh.CiliaQMain.analyzeCiliaIn4DAndSaveResults(CiliaQMain.java:2481) at ciliaQ_jnh.CiliaQMain.run(CiliaQMain.java:436) at net.imagej.legacy.IJ1Helper.run(IJ1Helper.java:753) at net.imagej.legacy.LegacyCodeRunner.run(LegacyCodeRunner.java:61) at org.scijava.run.RunService.run(RunService.java:59) at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:137) at org.scijava.script.ScriptModule.run(ScriptModule.java:160) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:228) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

Work progress is lost if the active image is processed by CiliaQ. This carries the risk of loosing unsaved progress, thus, it would advantageous if the image is saved automatically, a warning is shown, or an copy is used for processing, so the original images is not closed.

When a 2D image is analyzed and the setting

is selected, CiliaQ does not output the results for any cilium.

It would be convenient for the users to
A) notify them that no output will be available due to this setting or
B) automatically switch the setting to
.

When running CiliaQ on a Mac OS it stops working during generation of 3D visualizations - but just randomly for some images and not specific for any images (repeating analysis of the same image runs without errors).

The following error is output:
(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_202 [64-bit]; Mac OS X 10.15.5; 766MB of 3582MB (21%) java.lang.NullPointerException at javax.swing.RepaintManager.getVolatileOffscreenBuffer(RepaintManager.java:1030) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1489) at javax.swing.RepaintManager.paint(RepaintManager.java:1272) at javax.swing.JComponent.paint(JComponent.java:1042) at ciliaQ_jnh.volumeViewer3D.ImageRegion.getImage(ImageRegion.java:215) at ciliaQ_jnh.volumeViewer3D.Volume_Viewer.get3DVisualization(Volume_Viewer.java:218) at ciliaQ_jnh.Visualizer3D.get3DVisualization(Visualizer3D.java:151) at ciliaQ_jnh.CiliaQMain.saveSkeletonOverviewImageNonTimeLapse(CiliaQMain.java:3326) at ciliaQ_jnh.CiliaQMain.analyzeCiliaIn3DAndSaveResults(CiliaQMain.java:2375) at ciliaQ_jnh.CiliaQMain.run(CiliaQMain.java:437) at ij.IJ.runUserPlugIn(IJ.java:230) at ij.IJ.runPlugIn(IJ.java:193) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748)

When analyzing a 3D image of cilia, the following error occured for an unknown reason:
java.lang.NullPointerException at ciliaQ_jnh.CiliaQMain.analyzeCiliaIn3DAndSaveResults(CiliaQMain.java:2049) at ciliaQ_jnh.CiliaQMain.run(CiliaQMain.java:440) at ij.IJ.runUserPlugIn(IJ.java:221) at ij.IJ.runPlugIn(IJ.java:185) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748)

CiliaQ constantly produces empty output txt and no skeleton file for certain file (provided privately).

Hi!! I was just measuring some cilia in cells and I realized that length measurements make sense when cilia are straight but not when they are curved. Is this a common issue? I see that the skeleton of the cilia are correct.

Hello!! Thanks for your hard work!! It is very helpful!
Would it be possible to implement a new measurement parameter: cilia percentage or number of cilia vs number of cells? In order to do so, CiliaQ should be able to detect nuclei... maybe the user can let it know that one of the channels is nuclei (DAPI).
Best,

Laura

Originally posted by @lbozal in #7 (comment)