Feature "Spot intensity" calculation error

[drchrisch]

Spot intensity calculation error

I analyze a two-channel dataset (20 timepoints, 3D images 20x1024x1024) with Mastodon (Fiji v1.53o, everything updated). It works fine to extract spots and links. But when I run "compute features" I get a java error for feature "Spot intensity" and only for this feature.

Exception in thread "Feature computation thread" java.lang.ArrayIndexOutOfBoundsException: 76 at org.mastodon.mamut.feature.SpotIntensityFeatureComputer.run(SpotIntensityFeatureComputer.java:200) at org.mastodon.feature.DefaultFeatureComputerService.compute(DefaultFeatureComputerService.java:253) at org.mastodon.mamut.feature.MamutFeatureComputerService.compute(MamutFeatureComputerService.java:79) at org.mastodon.mamut.MamutFeatureComputation$MyFeatureComputerService.compute(MamutFeatureComputation.java:138) at org.mastodon.feature.ui.FeatureComputationController$2.run(FeatureComputationController.java:128)

I did analyze a few other dataset earlier whithout getting this error. Were there some changes in the feature calculation part recently?

[tinevez]

Hello @drchrisch

Not super recently this is suspect.

Can share the image and the files?

[drchrisch]

Sharing image is a bit difficult, I could send a link to the mastodon file. The procedure is a follows: I load the two-channel bdv image set, run tracking detection and linking on channel 1, start feature computation, then I (without reloading) repeat tracking and linking but now on channel 2, feature computation then gives the error just as shown above.

[tinevez]

Ok I will try to reproduce. Thanks for the procedure.

[tinevez]

Hello @drchrisch Well I could not reproduce with a 2-channel image I have at hand. I would need the image, or even a portion of it small enough to reproduce the error. If it is very big you can use our FEX instance to send it to me (see your PMs).

[drchrisch]

Well, 200 MB is not that small. Sorry, silly question, but how does this FEX works and how do I restrict access to the data?

[tinevez]

Email me please.

On Thu, Feb 10, 2022, 18:44 drchrisch @.***> wrote:

Well, 200 MB is not that small. Sorry, silly question, but how does this FEX works and how do I restrict access to the data?

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[tinevez]

@drchrisch Thank you for the data. I could open it and test Mastodon with it. But I could not reproduce the error. When I start from scratch and do detection with sensible parameters, I have no bug. When I try to compute features on your Mastodon file, again I have no error. So I have to ask, what is the version of mastodon you use?

[drchrisch]

That's really weird, but matches expectation. I had this problem on two computers (Windows) with Fiji.app/jars/mastodon-1.0.0-beta-20.jar.

[tinevez]

Ok we run the same. Can you give me the parameters with which you run the detection and linking steps?

[drchrisch]

DoG (diameter 4.0, threshold 100), simple LAP (15, 15, 2) (there should be a *.mastodon file as well?).

[tinevez]

Yes. And the mastodon file does not give an error :) this is interesting.

[tinevez]

Yes I got the bug! On the 2nd channel results.

[drchrisch]

Cool! It's all in the data, right?

[tinevez]

Could you try to replace the core mastodon .jar file in your Fiji.app/jars by this one? https://dl.pasteur.fr/fop/8R1jRnNN/mastodon-1.0.0-beta-22-SNAPSHOT.jar

[drchrisch]

Great, looks conving. Many thanks!

[tinevez]

So the bug is fixed? If yes I will do a release but not immediately.

[drchrisch]

Yes, solved. That's it for me and I will close the issue.