Labkit import labeling/bitmap

I’m trying to import a bitmap tiff labelling into lab kit but every time I try to import I get the following error:

java.lang.NullPointerException
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:87)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:483)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:242)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:152)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:133)
	at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:138)
	at net.imglib2.labkit.actions.BitmapImportExportAction.importLabel(BitmapImportExportAction.java:75)
	at net.imglib2.labkit.actions.AbstractFileIoAction.lambda$runAction$1(AbstractFileIoAction.java:98)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

I have tried to update the site and it still doesn’t work. Can someone help me? Thank you

Good morning,

Same problem here with Labkit and Big Data viewer plugins. Uninstalling, re-installing and updating didn’t solve it. Installing Labkit on a fresh clean Fiji installation does sort the problem.

Console Labkit error

[INFO] Reading available sites from https://imagej.net/
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addGroup(BasicViewerState.java:1117)
	at bdv.viewer.SynchronizedViewerState.addGroup(SynchronizedViewerState.java:822)
	at bdv.viewer.state.ViewerState.lambda$new$1(ViewerState.java:85)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:83)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.util.BdvHandlePanel.<init>(BdvHandlePanel.java:77)
	at net.imglib2.labkit.BasicLabelingComponent.initBdv(BasicLabelingComponent.java:61)
	at net.imglib2.labkit.BasicLabelingComponent.<init>(BasicLabelingComponent.java:49)
	at net.imglib2.labkit.SegmentationComponent.<init>(SegmentationComponent.java:50)
	at net.imglib2.labkit.LabkitFrame.initSegmentationComponent(LabkitFrame.java:62)
	at net.imglib2.labkit.LabkitFrame.<init>(LabkitFrame.java:52)
	at net.imglib2.labkit.LabkitFrame.show(LabkitFrame.java:46)
	at net.imglib2.labkit.LabkitFrame.showForImage(LabkitFrame.java:40)
	at net.imglib2.labkit.plugin.LabkitPlugin.run(LabkitPlugin.java:27)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.BigDataViewer.open(BigDataViewer.java:518)
	at bdv.ij.OpenImagePlusPlugIn.run(OpenImagePlusPlugIn.java:133)
	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:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addGroup(BasicViewerState.java:1117)
	at bdv.viewer.SynchronizedViewerState.addGroup(SynchronizedViewerState.java:822)
	at bdv.viewer.state.ViewerState.lambda$new$1(ViewerState.java:85)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:83)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.util.BdvHandlePanel.<init>(BdvHandlePanel.java:77)
	at net.imglib2.labkit.BasicLabelingComponent.initBdv(BasicLabelingComponent.java:61)
	at net.imglib2.labkit.BasicLabelingComponent.<init>(BasicLabelingComponent.java:49)
	at net.imglib2.labkit.SegmentationComponent.<init>(SegmentationComponent.java:50)
	at net.imglib2.labkit.LabkitFrame.initSegmentationComponent(LabkitFrame.java:62)
	at net.imglib2.labkit.LabkitFrame.<init>(LabkitFrame.java:52)
	at net.imglib2.labkit.LabkitFrame.show(LabkitFrame.java:46)
	at net.imglib2.labkit.LabkitFrame.showForImage(LabkitFrame.java:40)
	at net.imglib2.labkit.plugin.LabkitPlugin.run(LabkitPlugin.java:27)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Console Big Data Viewer error

 [INFO] Reading available sites from https://imagej.net/
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addGroup(BasicViewerState.java:1117)
	at bdv.viewer.SynchronizedViewerState.addGroup(SynchronizedViewerState.java:822)
	at bdv.viewer.state.ViewerState.lambda$new$1(ViewerState.java:85)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:83)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.util.BdvHandlePanel.<init>(BdvHandlePanel.java:77)
	at net.imglib2.labkit.BasicLabelingComponent.initBdv(BasicLabelingComponent.java:61)
	at net.imglib2.labkit.BasicLabelingComponent.<init>(BasicLabelingComponent.java:49)
	at net.imglib2.labkit.SegmentationComponent.<init>(SegmentationComponent.java:50)
	at net.imglib2.labkit.LabkitFrame.initSegmentationComponent(LabkitFrame.java:62)
	at net.imglib2.labkit.LabkitFrame.<init>(LabkitFrame.java:52)
	at net.imglib2.labkit.LabkitFrame.show(LabkitFrame.java:46)
	at net.imglib2.labkit.LabkitFrame.showForImage(LabkitFrame.java:40)
	at net.imglib2.labkit.plugin.LabkitPlugin.run(LabkitPlugin.java:27)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.BigDataViewer.open(BigDataViewer.java:518)
	at bdv.ij.OpenImagePlusPlugIn.run(OpenImagePlusPlugIn.java:133)
	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:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addGroup(BasicViewerState.java:1117)
	at bdv.viewer.SynchronizedViewerState.addGroup(SynchronizedViewerState.java:822)
	at bdv.viewer.state.ViewerState.lambda$new$1(ViewerState.java:85)
	at java.util.ArrayList.forEach(ArrayList.java:1257)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:83)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.util.BdvHandlePanel.<init>(BdvHandlePanel.java:77)
	at net.imglib2.labkit.BasicLabelingComponent.initBdv(BasicLabelingComponent.java:61)
	at net.imglib2.labkit.BasicLabelingComponent.<init>(BasicLabelingComponent.java:49)
	at net.imglib2.labkit.SegmentationComponent.<init>(SegmentationComponent.java:50)
	at net.imglib2.labkit.LabkitFrame.initSegmentationComponent(LabkitFrame.java:62)
	at net.imglib2.labkit.LabkitFrame.<init>(LabkitFrame.java:52)
	at net.imglib2.labkit.LabkitFrame.show(LabkitFrame.java:46)
	at net.imglib2.labkit.LabkitFrame.showForImage(LabkitFrame.java:40)
	at net.imglib2.labkit.plugin.LabkitPlugin.run(LabkitPlugin.java:27)
	at org.scijava.command.CommandModule.run(CommandModule.java:196)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:165)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.BigDataViewer.open(BigDataViewer.java:518)
	at bdv.ij.OpenImagePlusPlugIn.run(OpenImagePlusPlugIn.java:133)
	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:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
[ERROR] Module threw error
java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.BigDataViewer.open(BigDataViewer.java:518)
	at bdv.ij.OpenImagePlusPlugIn.run(OpenImagePlusPlugIn.java:133)
	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:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

Exception Big Data Viewer

(Fiji Is Just) ImageJ 2.0.0-rc-72/1.53c; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 128MB of 12053MB (1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoSuchFieldError: list
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.NoSuchFieldError: list
	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:303)
	... 5 more
Caused by: java.lang.NoSuchFieldError: list
	at bdv.viewer.BasicViewerState.notifyListeners(BasicViewerState.java:1622)
	at bdv.viewer.BasicViewerState.addSources(BasicViewerState.java:724)
	at bdv.viewer.SynchronizedViewerState.addSources(SynchronizedViewerState.java:496)
	at bdv.viewer.state.ViewerState.<init>(ViewerState.java:81)
	at bdv.viewer.ViewerPanel.<init>(ViewerPanel.java:248)
	at bdv.viewer.ViewerFrame.<init>(ViewerFrame.java:103)
	at bdv.BigDataViewer.<init>(BigDataViewer.java:335)
	at bdv.BigDataViewer.open(BigDataViewer.java:518)
	at bdv.ij.OpenImagePlusPlugIn.run(OpenImagePlusPlugIn.java:133)
	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:124)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more

@tpietzsch @maarzt do you have any idea of what could be causing this issue? Thank you.

Hello @afonso,

I tried to reproduce the problem. But it doesn’t happen for me. I downloaded a fresh copy of FIJI, and activated the Labkit update site. “Import Bitmap” works, and there’s no exception.

Does the problem still occur for you? Could you please describe more in detail what you did!

Bests, Matthais

Hello @maarzt,

The problem still persists I use import Bitmap as I’ve always been doing. The curious thing is that I only encounter this issue in Mac computers. If I try to use that lab windows computer there’s no issue. I can share the data with you if you wish.

Regards,
Diana

This is almost certainly caused by some version skew with BigDataViewer. Possibly because LabKit was compiled against a different version of BigDataViewer?!

See also:


And this one is likely the same as reported here:

… and mentioned here:

@afonso

I get this exception when I try to open a file that doesn’t contain an image. So somehow ImageJ seems to have trouble opening the images that you are trying to open.

Please check if the image can be opened the regular way in imagej. Maybe save it as .tif an try agian.