Hi. I recently updated Fiji/ImageJ-win64 on Windows 10 and 11 (different PCs) and starting receiving the following error messages when trying to run StarDist 2D on my tiff files, which had run fine prior to this update. Any help would be greatly appreciated. Thank you.
Events that occurred:
1) Started Fiji.
Was notified updates were ready and receive this first error message when prompted to check for updates. Was then prompted to restart Fiji and go to Help-Update to finishing installing updates, which I did (there were A LOT).
[INFO] Reading available sites from
https://imagej.net/
[INFO] Trying to install and execute the new updater
[ERROR] java.lang.ClassNotFoundException: net.imagej.ui.swing.updater.ImageJUpdater
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:206)
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)
2) Restarted Fiji
after installing many new updates. Opened my tiff file (94 MB, 8-bit) and went to run StarDist 2D. Received the following error message. I had previously been able to run StarDist on this file. I have tried running various files (all of which worked previously), restarting my computer, and deleting and re-downloading Fiji. This error was duplicated on a colleagues PC.
From Console:
[INFO] No TF library found in C:\Users\ae473\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/ae473/AppData/Local/Temp/stardist_model_4820228754128718314.zip
[INFO] Caching TensorFlow models to C:\Users\ae473\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.(MetaGraphDef.java:168)
at org.tensorflow.framework.MetaGraphDef.(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 781 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:279)
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)
From Exception:
(Fiji Is Just) ImageJ 2.16.0/1.54g; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 182MB of 5852MB (3%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:308)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:160)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
at java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.util.concurrent.FutureTask.get(FutureTask.java:192)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:304)
… 5 more
Caused by: java.lang.RuntimeException: Module threw exception
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:128)
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)
… 1 more
Caused by: java.lang.NullPointerException
at de.csbdresden.stardist.StarDist2D.splitPrediction(StarDist2D.java:338)
at de.csbdresden.stardist.StarDist2D.run(StarDist2D.java:279)
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)
… 6 more
