TrackMate not working after Fiji update

Hi everyone,

After updating Fiji in December (and January, but the error occurred before the latest one), TrackMate gives me the following error:

Exception in thread “TrackMate spot detection thread 1/4” java.lang.ArrayIndexOutOfBoundsException: 2
at net.imglib2.algorithm.convolution.LineConvolution.requiredSourceInterval(LineConvolution.java:46)
at net.imglib2.algorithm.convolution.Concatenation.tmpIntervals(Concatenation.java:110)
at net.imglib2.algorithm.convolution.Concatenation.process(Concatenation.java:60)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:207)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:168)
at fiji.plugin.trackmate.detection.DogDetector.process(DogDetector.java:84)
at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
Exception in thread “TrackMate spot detection thread 4/4” Exception in thread “TrackMate spot detection thread 3/4” Exception in thread “TrackMate spot detection thread 2/4” java.lang.ArrayIndexOutOfBoundsException: 2
at net.imglib2.algorithm.convolution.LineConvolution.requiredSourceInterval(LineConvolution.java:46)
at net.imglib2.algorithm.convolution.Concatenation.tmpIntervals(Concatenation.java:110)
at net.imglib2.algorithm.convolution.Concatenation.process(Concatenation.java:60)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:207)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:168)
at fiji.plugin.trackmate.detection.DogDetector.process(DogDetector.java:84)
at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.ArrayIndexOutOfBoundsException: 2
at net.imglib2.algorithm.convolution.LineConvolution.requiredSourceInterval(LineConvolution.java:46)
at net.imglib2.algorithm.convolution.Concatenation.tmpIntervals(Concatenation.java:110)
at net.imglib2.algorithm.convolution.Concatenation.process(Concatenation.java:60)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:207)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:168)
at fiji.plugin.trackmate.detection.DogDetector.process(DogDetector.java:84)
at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.ArrayIndexOutOfBoundsException: 2
at net.imglib2.algorithm.convolution.LineConvolution.requiredSourceInterval(LineConvolution.java:46)
at net.imglib2.algorithm.convolution.Concatenation.tmpIntervals(Concatenation.java:110)
at net.imglib2.algorithm.convolution.Concatenation.process(Concatenation.java:60)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:207)
at net.imglib2.algorithm.gauss3.Gauss3.gauss(Gauss3.java:168)
at fiji.plugin.trackmate.detection.DogDetector.process(DogDetector.java:84)
at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)

Could anyone please help with this?

Thanks

Hi @AnneE

Yep, we know about the bug. Check this: https://github.com/fiji/TrackMate/issues/131

It’s just that I could not find the time to work on it (yet) and have a todo list crazy long. Please be patient with me a bit more. In the meantime, the LoG detector still works.

sorry again
jy

Okay, thanks for the quick reply anyway. I will use a non-updated version of Fiji in the meanwhile.