Trackmate Error

Hi,
Everytime i choose the intensity/diameter filter to select my spots in Trackmate. I get the following error and cannot change these paramemters. Any idea how i can fix this?

Thanks,
-Praveen

Exception in thread "pool-2257-thread-1" Exception in thread "pool-2257-thread-12" Exception in thread "pool-2257-thread-14" Exception in thread "pool-2257-thread-13" Exception in thread "pool-2257-thread-26" Exception in thread "pool-2257-thread-11" Exception in thread "pool-2257-thread-7" Exception in thread "pool-2257-thread-37" java.lang.NullPointerException
Exception in thread "pool-2257-thread-10" java.lang.NullPointerException
Exception in thread "pool-2257-thread-9" java.lang.NullPointerException
Exception in thread "pool-2257-thread-6" java.lang.NullPointerException
Exception in thread "pool-2257-thread-5" java.lang.NullPointerException
Exception in thread "pool-2257-thread-8" java.lang.NullPointerException
Exception in thread "pool-2257-thread-4" java.lang.NullPointerException
Exception in thread "pool-2257-thread-3" java.lang.NullPointerException
Exception in thread "pool-2257-thread-2" java.lang.NullPointerException
Exception in thread "pool-2257-thread-40" java.lang.NullPointerException
Exception in thread "pool-2257-thread-36" java.lang.NullPointerException
Exception in thread "pool-2257-thread-41" java.lang.NullPointerException
Exception in thread "pool-2257-thread-39" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "pool-2257-thread-35" java.lang.NullPointerException
Exception in thread "pool-2257-thread-34" java.lang.NullPointerException
Exception in thread "pool-2257-thread-32" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "pool-2257-thread-33" Exception in thread "pool-2257-thread-29" java.lang.NullPointerException
Exception in thread "pool-2257-thread-25" java.lang.NullPointerException
Exception in thread "pool-2257-thread-30" java.lang.NullPointerException
Exception in thread "pool-2257-thread-31" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "pool-2257-thread-23" java.lang.NullPointerException
Exception in thread "pool-2257-thread-28" java.lang.NullPointerException
Exception in thread "pool-2257-thread-27" java.lang.NullPointerException
Exception in thread "pool-2257-thread-24" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "pool-2257-thread-21" java.lang.NullPointerException
Exception in thread "pool-2257-thread-18" Exception in thread "pool-2257-thread-19" java.lang.NullPointerException
Exception in thread "pool-2257-thread-22" java.lang.NullPointerException
Exception in thread "pool-2257-thread-20" Exception in thread "pool-2257-thread-16" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "pool-2257-thread-17" Exception in thread "pool-2257-thread-15" java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException

Hum I cannot reproduce the problem.
Can you give me details on the TrackMate version and OS you use?

Sure. I have Trackmate 3.4 and i use Win 10. I also found some more info, I just get the error when i give the Estimated Blob diameter as 0.1 micron in the Log detector window. If i give a higher value it gives me no error.

Here is also a TIFF stack of one of my images.
Experiment-939.zip (9.2 MB)

Maybe i get the error as i give the blob diameter a value which is lesser than the size of a pixel. Do you think that could be the issue?

I have Java 1.8.0_66 (64 bit). I use the DOG detector and just set a blob diameter of 0.1 micron. Nothing more. Then i get the error when i try to add the mean intensity filter during spot detection.

Alright, I was able to kind of reproduce the issue with the Tracks for TrackMate sample image:

  • File > Open Samples > Tracks for TrackMate (807K)
  • Plugins > Tracking > TrackMate
  • Click Next using the LoG Detector with:
    • Estimated blob diamter: 0.5 pixel
    • Treshold: 100000
  • Continue clicking Next

Already in the Select a view tab, I get the following exceptions in the console:

[ECLIPSE HELPER] Indexing annotations...
Exception in thread "TrackMate spot feature calculating thread 12/16" Exception in thread "TrackMate spot feature calculating thread 6/16" Exception in thread "TrackMate spot feature calculating thread 5/16" Exception in thread "TrackMate spot feature calculating thread 14/16" Exception in thread "TrackMate spot feature calculating thread 11/16" Exception in thread "TrackMate spot feature calculating thread 15/16" Exception in thread "TrackMate spot feature calculating thread 10/16" Exception in thread "TrackMate spot feature calculating thread 16/16" Exception in thread "TrackMate spot feature calculating thread 3/16" Exception in thread "TrackMate spot feature calculating thread 1/16" Exception in thread "TrackMate spot feature calculating thread 7/16" Exception in thread "TrackMate spot feature calculating thread 9/16" Exception in thread "TrackMate spot feature calculating thread 2/16" Exception in thread "TrackMate spot feature calculating thread 8/16" Exception in thread "TrackMate spot feature calculating thread 4/16" Exception in thread "TrackMate spot feature calculating thread 13/16" java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)
java.lang.ArrayIndexOutOfBoundsException: 1
    at fiji.plugin.trackmate.features.spot.SpotIntensityAnalyzer.process(SpotIntensityAnalyzer.java:67)
    at fiji.plugin.trackmate.features.SpotFeatureCalculator$1.run(SpotFeatureCalculator.java:185)

When selecting the Mean intensity filter in the following tab, I get:

Exception in thread "pool-639-thread-1" Exception in thread "pool-639-thread-2" Exception in thread "pool-639-thread-3" Exception in thread "pool-639-thread-8" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-5" Exception in thread "pool-639-thread-4" Exception in thread "pool-639-thread-29" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-43" Exception in thread "pool-639-thread-32" Exception in thread "pool-639-thread-33" Exception in thread "pool-639-thread-26" Exception in thread "pool-639-thread-34" Exception in thread "pool-639-thread-41" Exception in thread "pool-639-thread-7" Exception in thread "pool-639-thread-38" Exception in thread "pool-639-thread-30" Exception in thread "pool-639-thread-10" Exception in thread "pool-639-thread-19" Exception in thread "pool-639-thread-31" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-9" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-6" Exception in thread "pool-639-thread-28" Exception in thread "pool-639-thread-25" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-21" Exception in thread "pool-639-thread-23" Exception in thread "pool-639-thread-20" Exception in thread "pool-639-thread-17" Exception in thread "pool-639-thread-15" Exception in thread "pool-639-thread-14" Exception in thread "pool-639-thread-12" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-47" Exception in thread "pool-639-thread-59" Exception in thread "pool-639-thread-50" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-27" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-49" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-54" Exception in thread "pool-639-thread-40" Exception in thread "pool-639-thread-48" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-46" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-18" Exception in thread "pool-639-thread-52" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-37" Exception in thread "pool-639-thread-36" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-42" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-44" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-24" Exception in thread "pool-639-thread-39" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-22" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Exception in thread "pool-639-thread-45" Exception in thread "pool-639-thread-35" java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
java.lang.NullPointerException
    at fiji.plugin.trackmate.SpotCollection$3.run(SpotCollection.java:325)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)

All right.
The error of course is caused by the iteration over a spot which is smaller than 1 pixel.
The cursor fails at computing proper bounds for such a small spot and generate an array out of bounds exception.

This should be fixed in TrackMate v3.4.1 that I just uploaded.
Can you confirm it works for you now?

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Yes, it works now. Thanks!
-Praveen

1 Like