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StarDist 2D bugging after latest updates of ImageJ #267

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mpalaibmb opened this issue Jan 27, 2025 · 1 comment
Closed

StarDist 2D bugging after latest updates of ImageJ #267

mpalaibmb opened this issue Jan 27, 2025 · 1 comment

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@mpalaibmb
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mpalaibmb commented Jan 27, 2025

Good morning everyone!
This morning, while initializing ImageJ, it proposed me numerous updates that I accepted as usual.
The problem is that after them, StarDist 2D plugin, which is the one I use mostly for my analysis, started to bug.
I attach following the type of error that it gives me, which before today I never had:

[INFO] No TF library found in C:\Users\mpabm\DOWNLO~1\FIJI-W~1\Fiji.app\lib\.
[INFO] Using default TensorFlow version from JAR: TF 1.15.0 CPU
[INFO] Loading TensorFlow model GenericNetwork_aea3be563cb56b8824f53a8c2382aaa5 from source file file:/C:/Users/mpabm/AppData/Local/Temp/stardist_model_8155415352555340585.zip
[INFO] Caching TensorFlow models to C:\Users\mpabm\DOWNLO~1\FIJI-W~1\Fiji.app\models
java.util.concurrent.ExecutionException: java.lang.NoSuchMethodError: org.tensorflow.framework.MetaGraphDef.makeExtensionsImmutable()V
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at de.csbdresden.csbdeep.commands.GenericCoreNetwork.run(GenericCoreNetwork.java:420)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.NoSuchMethodError: org.tensorflow.framework.MetaGraphDef.makeExtensionsImmutable()V
	at org.tensorflow.framework.MetaGraphDef.<init>(MetaGraphDef.java:168)
	at org.tensorflow.framework.MetaGraphDef.<init>(MetaGraphDef.java:25)
	at org.tensorflow.framework.MetaGraphDef$1.parsePartialFrom(MetaGraphDef.java:4257)
	at org.tensorflow.framework.MetaGraphDef$1.parsePartialFrom(MetaGraphDef.java:4252)
	at com.google.protobuf.AbstractParser.parsePartialFrom(AbstractParser.java:135)
	at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:168)
	at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:180)
	at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:185)
	at com.google.protobuf.AbstractParser.parseFrom(AbstractParser.java:25)
	at org.tensorflow.framework.MetaGraphDef.parseFrom(MetaGraphDef.java:2680)
	at de.csbdresden.csbdeep.network.model.tensorflow.TensorFlowNetwork.loadModel(TensorFlowNetwork.java:174)
	at de.csbdresden.csbdeep.network.model.DefaultNetwork.loadModel(DefaultNetwork.java:76)
	at de.csbdresden.csbdeep.network.DefaultModelLoader.loadNetwork(DefaultModelLoader.java:69)
	at de.csbdresden.csbdeep.network.DefaultModelLoader.run(DefaultModelLoader.java:48)
	at de.csbdresden.csbdeep.commands.GenericCoreNetwork.tryToPrepareInputAndNetwork(GenericCoreNetwork.java:524)
	at de.csbdresden.csbdeep.commands.GenericCoreNetwork.initiateModelIfNeeded(GenericCoreNetwork.java:303)
	at de.csbdresden.csbdeep.commands.GenericCoreNetwork.mainThread(GenericCoreNetwork.java:445)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	... 4 more
[INFO] CSBDeep plugin exit (took 861 milliseconds)
[ERROR] Command errored: StarDist 2D
java.lang.NullPointerException
	at de.csbdresden.stardist.StarDist2D.splitPrediction(StarDist2D.java:338)
	at de.csbdresden.stardist.StarDist2D.run(StarDist2D.java:307)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:125)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:64)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:247)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)

I tried to update TF models, used them through a GPU, and download new packages and versions of CUDA and cuDNN.
But nothing changed. Maybe I am missing the point.

Thank you in advance for whoever can provide me with insights!

@ctrueden
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@mpalaibmb Thanks for the report!

Since this is about the StarDist plugin for ImageJ, I migrated your issue there; see stardist/stardist-imagej#23. Hopefully someone there will have an idea what's going wrong for you.

@ctrueden ctrueden closed this as not planned Won't fix, can't repro, duplicate, stale Jan 28, 2025
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