LUMoS update site breaks Fiji after August 2020 update

Hi,
I also have run into an issue starting Fiji on a Mac, I am able to open it at first, but after updating plugins the Fiji application will not open (the starting logo comes up for one second and then disappears).
Error message in terminal:

[ERROR] Invalid service: net.imagej.legacy.LegacyService
java.lang.NoSuchMethodError: org.scijava.Context.getClassLoader()Ljava/lang/ClassLoader;
	at net.imagej.util.AppUtils.findResources(AppUtils.java:107)
	at net.imagej.lut.DefaultLUTService.findLUTs(DefaultLUTService.java:124)
	at net.imagej.lut.DefaultLUTService$1.get(DefaultLUTService.java:242)
	at org.scijava.object.ObjectIndex.resolvePending(ObjectIndex.java:388)
	at org.scijava.object.ObjectIndex.get(ObjectIndex.java:133)
	at org.scijava.object.ObjectIndex.getAll(ObjectIndex.java:122)
	at org.scijava.module.DefaultModuleService.getModules(DefaultModuleService.java:141)
	at net.imagej.legacy.LegacyService.initialize(LegacyService.java:498)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:354)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:195)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:167)
	at org.scijava.Context.<init>(Context.java:281)
	at org.scijava.Context.<init>(Context.java:237)
	at org.scijava.Context.<init>(Context.java:177)
	at org.scijava.Context.<init>(Context.java:163)
	at net.imagej.ImageJ.<init>(ImageJ.java:77)
	at net.imagej.Main.main(Main.java:54)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)
[ERROR] No match: net.imagej.legacy.LegacyService
[ERROR] null
java.lang.IllegalArgumentException: Required service is missing: net.imagej.legacy.LegacyService
Context: org.scijava.Context@14b11598
ClassLoader: java.net.URLClassLoader@653d504c

-- Services known to context --
org.scijava.event.DefaultEventService [priority = 100000.0]
net.imagej.legacy.display.LegacyImageDisplayService [priority = 100.0]
net.imagej.lut.DefaultLUTService [priority = 100.0]
fiji.plugin.trackmate.TrackMateService [priority = 0.0]
io.scif.DefaultMetadataService [priority = 0.0]
io.scif.codec.DefaultCodecService [priority = 0.0]
io.scif.formats.qt.DefaultQTJavaService [priority = 0.0]
io.scif.formats.tiff.DefaultTiffService [priority = 0.0]
io.scif.gui.DefaultGUIService [priority = 0.0]
io.scif.img.DefaultImgUtilityService [priority = 0.0]
io.scif.img.converters.DefaultPlaneConverterService [priority = 0.0]
io.scif.ome.services.DefaultOMEMetadataService [priority = 0.0]
io.scif.ome.services.DefaultOMEXMLService [priority = 0.0]
io.scif.refs.DefaultRefManagerService [priority = 0.0]
io.scif.services.DefaultDatasetIOService [priority = 0.0]
io.scif.services.DefaultFilePatternService [priority = 0.0]
io.scif.services.DefaultFormatService [priority = 0.0]
io.scif.services.DefaultTranslatorService [priority = 0.0]
io.scif.services.JAIIIOServiceImpl [priority = 0.0]
io.scif.xml.DefaultXMLService [priority = 0.0]
net.imagej.DefaultDatasetService [priority = 0.0]
net.imagej.DefaultImgPlusService [priority = 0.0]
net.imagej.animation.DefaultAnimationService [priority = 0.0]
net.imagej.autoscale.DefaultAutoscaleService [priority = 0.0]
net.imagej.display.DefaultImageDisplayService [priority = 0.0]
net.imagej.display.DefaultOverlayService [priority = 0.0]
net.imagej.display.DefaultWindowService [priority = 0.0]
net.imagej.display.DefaultZoomService [priority = 0.0]
net.imagej.legacy.plugin.MacroExtensionAutoCompletionService [priority = 0.0]
net.imagej.measure.DefaultMeasurementService [priority = 0.0]
net.imagej.measure.DefaultStatisticsService [priority = 0.0]
net.imagej.notebook.DefaultNotebookService [priority = 0.0]
net.imagej.operator.DefaultCalculatorService [priority = 0.0]
net.imagej.ops.DefaultNamespaceService [priority = 0.0]
net.imagej.ops.DefaultOpMatchingService [priority = 0.0]
net.imagej.ops.DefaultOpService [priority = 0.0]
net.imagej.roi.DefaultROIService [priority = 0.0]
net.imagej.sampler.DefaultSamplerService [priority = 0.0]
net.imagej.table.DefaultTableService [priority = 0.0]
net.imagej.threshold.DefaultThresholdService [priority = 0.0]
net.imagej.types.DefaultDataTypeService [priority = 0.0]
net.imagej.ui.DefaultImageJUIService [priority = 0.0]
net.imagej.ui.awt.AWTRenderingService [priority = 0.0]
net.imagej.ui.awt.AWTScreenCaptureService [priority = 0.0]
net.imagej.ui.swing.ops.DefaultOpFinderService [priority = 0.0]
net.imagej.ui.swing.overlay.JHotDrawService [priority = 0.0]
net.imagej.units.DefaultUnitService [priority = 0.0]
net.imagej.updater.DefaultUpdateService [priority = 0.0]
net.imagej.updater.DefaultUploaderService [priority = 0.0]
org.scijava.app.DefaultAppService [priority = 0.0]
org.scijava.app.DefaultStatusService [priority = 0.0]
org.scijava.command.DefaultCommandService [priority = 0.0]
org.scijava.console.DefaultConsoleService [priority = 0.0]
org.scijava.convert.DefaultConvertService [priority = 0.0]
org.scijava.display.DefaultDisplayService [priority = 0.0]
org.scijava.download.DefaultDownloadService [priority = 0.0]
org.scijava.event.DefaultEventHistory [priority = 0.0]
org.scijava.input.DefaultInputService [priority = 0.0]
org.scijava.io.DefaultIOService [priority = 0.0]
org.scijava.io.DefaultRecentFileService [priority = 0.0]
org.scijava.io.handle.DefaultDataHandleService [priority = 0.0]
org.scijava.io.location.DefaultLocationService [priority = 0.0]
org.scijava.io.nio.DefaultNIOService [priority = 0.0]
org.scijava.main.DefaultMainService [priority = 0.0]
org.scijava.menu.DefaultMenuService [priority = 0.0]
org.scijava.module.DefaultModuleService [priority = 0.0]
org.scijava.object.DefaultObjectService [priority = 0.0]
org.scijava.options.DefaultOptionsService [priority = 0.0]
org.scijava.parse.DefaultParseService [priority = 0.0]
org.scijava.platform.DefaultPlatformService [priority = 0.0]
org.scijava.plugin.DefaultPluginService [priority = 0.0]
org.scijava.prefs.DefaultPrefService [priority = 0.0]
org.scijava.run.DefaultRunService [priority = 0.0]
org.scijava.script.DefaultScriptHeaderService [priority = 0.0]
org.scijava.script.DefaultScriptService [priority = 0.0]
org.scijava.script.process.DefaultScriptProcessorService [priority = 0.0]
org.scijava.search.DefaultSearchService [priority = 0.0]
org.scijava.search.javadoc.DefaultJavadocService [priority = 0.0]
org.scijava.startup.DefaultStartupService [priority = 0.0]
org.scijava.task.DefaultTaskService [priority = 0.0]
org.scijava.text.DefaultTextService [priority = 0.0]
org.scijava.thread.DefaultThreadService [priority = 0.0]
org.scijava.tool.DefaultToolService [priority = 0.0]
org.scijava.ui.DefaultUIService [priority = 0.0]
org.scijava.ui.dnd.DefaultDragAndDropService [priority = 0.0]
org.scijava.ui.swing.SwingIconService [priority = 0.0]
org.scijava.ui.swing.script.DefaultLanguageSupportService [priority = 0.0]
org.scijava.welcome.DefaultWelcomeService [priority = 0.0]
org.scijava.widget.DefaultWidgetService [priority = 0.0]
sc.fiji.compat.DefaultFijiService [priority = 0.0]
io.scif.services.DefaultInitializeService [priority = -100.0]
net.imagej.display.DummyScreenCaptureService [priority = -100.0]
net.imagej.render.DummyRenderingService [priority = -100.0]
org.scijava.batch.FileBatchService [priority = -100.0]
org.scijava.log.StderrLogService [priority = -100.0]
org.scijava.platform.DefaultAppEventService [priority = -100.0]
org.scijava.cache.DefaultCacheService [priority = -10000.0]

-- Classpath of ClassLoader --
/Applications/Fiji.app/plugins/

	at org.scijava.Context.inject(Context.java:474)
	at org.scijava.Context.inject(Context.java:386)
	at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:238)
	at org.scijava.ui.DefaultUIService.discoverUIs(DefaultUIService.java:503)
	at org.scijava.ui.DefaultUIService.getDefaultUI(DefaultUIService.java:193)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:140)
	at org.scijava.AbstractGateway.launch(AbstractGateway.java:104)
	at net.imagej.Main.main(Main.java:55)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)
Error while executing the main() method of class 'net.imagej.Main':
java.lang.NullPointerException
	at net.imagej.legacy.ui.LegacyUI.ij1Helper(LegacyUI.java:119)
	at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:130)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:157)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:142)
	at org.scijava.AbstractGateway.launch(AbstractGateway.java:104)
	at net.imagej.Main.main(Main.java:55)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)

I had this problem today.
I am on Windows 10.
I removed the old version of FIJI, updated Java then re-register FIJI. It works now.

1 Like

Hi,

Thank you for your response
How did you re-register Fiji?

From there:

Thank you for the link!
I have tried downloading this link and the link from the Fiji.sc page (on separate occasions) and I am still having the same problem (I have downloaded and re-downloaded Fiji 7 times now). I am bit unsure what to do now. It seems that every time I close the application after downloading a program I receive this error.

Can you try downloading a Fiji from 3 weeks ago?

https://downloads.imagej.net/fiji/archive/20200721-1931/

Does the issue happen with this one as well?

Hi!

Thank you for the link to the older version, I tried downloading it and installing the plugins and I have run into the same issue again. Could it be caused by the plugins I am trying to install?

This is the error message that I receive

[ERROR] Invalid service: net.imagej.legacy.LegacyService
java.lang.NoSuchMethodError: org.scijava.Context.getClassLoader()Ljava/lang/ClassLoader;
	at net.imagej.util.AppUtils.findResources(AppUtils.java:107)
	at net.imagej.lut.DefaultLUTService.findLUTs(DefaultLUTService.java:124)
	at net.imagej.lut.DefaultLUTService$1.get(DefaultLUTService.java:242)
	at org.scijava.object.ObjectIndex.resolvePending(ObjectIndex.java:388)
	at org.scijava.object.ObjectIndex.get(ObjectIndex.java:133)
	at org.scijava.object.ObjectIndex.getAll(ObjectIndex.java:122)
	at org.scijava.module.DefaultModuleService.getModules(DefaultModuleService.java:141)
	at net.imagej.legacy.LegacyService.initialize(LegacyService.java:498)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:354)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:195)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:167)
	at org.scijava.Context.<init>(Context.java:281)
	at org.scijava.Context.<init>(Context.java:237)
	at org.scijava.Context.<init>(Context.java:177)
	at org.scijava.Context.<init>(Context.java:163)
	at net.imagej.ImageJ.<init>(ImageJ.java:77)
	at net.imagej.Main.main(Main.java:54)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)
[ERROR] No match: net.imagej.legacy.LegacyService
[ERROR] null
java.lang.IllegalArgumentException: Required service is missing: net.imagej.legacy.LegacyService
Context: org.scijava.Context@14b11598
ClassLoader: java.net.URLClassLoader@ee14322

-- Services known to context --
org.scijava.event.DefaultEventService [priority = 100000.0]
net.imagej.legacy.display.LegacyImageDisplayService [priority = 100.0]
net.imagej.lut.DefaultLUTService [priority = 100.0]
fiji.plugin.trackmate.TrackMateService [priority = 0.0]
io.scif.DefaultMetadataService [priority = 0.0]
io.scif.codec.DefaultCodecService [priority = 0.0]
io.scif.formats.qt.DefaultQTJavaService [priority = 0.0]
io.scif.formats.tiff.DefaultTiffService [priority = 0.0]
io.scif.gui.DefaultGUIService [priority = 0.0]
io.scif.img.DefaultImgUtilityService [priority = 0.0]
io.scif.img.converters.DefaultPlaneConverterService [priority = 0.0]
io.scif.ome.services.DefaultOMEMetadataService [priority = 0.0]
io.scif.ome.services.DefaultOMEXMLService [priority = 0.0]
io.scif.refs.DefaultRefManagerService [priority = 0.0]
io.scif.services.DefaultDatasetIOService [priority = 0.0]
io.scif.services.DefaultFilePatternService [priority = 0.0]
io.scif.services.DefaultFormatService [priority = 0.0]
io.scif.services.DefaultTranslatorService [priority = 0.0]
io.scif.services.JAIIIOServiceImpl [priority = 0.0]
io.scif.xml.DefaultXMLService [priority = 0.0]
net.imagej.DefaultDatasetService [priority = 0.0]
net.imagej.DefaultImgPlusService [priority = 0.0]
net.imagej.animation.DefaultAnimationService [priority = 0.0]
net.imagej.autoscale.DefaultAutoscaleService [priority = 0.0]
net.imagej.display.DefaultImageDisplayService [priority = 0.0]
net.imagej.display.DefaultOverlayService [priority = 0.0]
net.imagej.display.DefaultWindowService [priority = 0.0]
net.imagej.display.DefaultZoomService [priority = 0.0]
net.imagej.legacy.plugin.MacroExtensionAutoCompletionService [priority = 0.0]
net.imagej.measure.DefaultMeasurementService [priority = 0.0]
net.imagej.measure.DefaultStatisticsService [priority = 0.0]
net.imagej.notebook.DefaultNotebookService [priority = 0.0]
net.imagej.operator.DefaultCalculatorService [priority = 0.0]
net.imagej.ops.DefaultNamespaceService [priority = 0.0]
net.imagej.ops.DefaultOpMatchingService [priority = 0.0]
net.imagej.ops.DefaultOpService [priority = 0.0]
net.imagej.roi.DefaultROIService [priority = 0.0]
net.imagej.sampler.DefaultSamplerService [priority = 0.0]
net.imagej.table.DefaultTableService [priority = 0.0]
net.imagej.threshold.DefaultThresholdService [priority = 0.0]
net.imagej.types.DefaultDataTypeService [priority = 0.0]
net.imagej.ui.DefaultImageJUIService [priority = 0.0]
net.imagej.ui.awt.AWTRenderingService [priority = 0.0]
net.imagej.ui.awt.AWTScreenCaptureService [priority = 0.0]
net.imagej.ui.swing.ops.DefaultOpFinderService [priority = 0.0]
net.imagej.ui.swing.overlay.JHotDrawService [priority = 0.0]
net.imagej.units.DefaultUnitService [priority = 0.0]
net.imagej.updater.DefaultUpdateService [priority = 0.0]
net.imagej.updater.DefaultUploaderService [priority = 0.0]
org.scijava.app.DefaultAppService [priority = 0.0]
org.scijava.app.DefaultStatusService [priority = 0.0]
org.scijava.command.DefaultCommandService [priority = 0.0]
org.scijava.console.DefaultConsoleService [priority = 0.0]
org.scijava.convert.DefaultConvertService [priority = 0.0]
org.scijava.display.DefaultDisplayService [priority = 0.0]
org.scijava.download.DefaultDownloadService [priority = 0.0]
org.scijava.event.DefaultEventHistory [priority = 0.0]
org.scijava.input.DefaultInputService [priority = 0.0]
org.scijava.io.DefaultIOService [priority = 0.0]
org.scijava.io.DefaultRecentFileService [priority = 0.0]
org.scijava.io.handle.DefaultDataHandleService [priority = 0.0]
org.scijava.io.location.DefaultLocationService [priority = 0.0]
org.scijava.io.nio.DefaultNIOService [priority = 0.0]
org.scijava.main.DefaultMainService [priority = 0.0]
org.scijava.menu.DefaultMenuService [priority = 0.0]
org.scijava.module.DefaultModuleService [priority = 0.0]
org.scijava.object.DefaultObjectService [priority = 0.0]
org.scijava.options.DefaultOptionsService [priority = 0.0]
org.scijava.parse.DefaultParseService [priority = 0.0]
org.scijava.platform.DefaultPlatformService [priority = 0.0]
org.scijava.plugin.DefaultPluginService [priority = 0.0]
org.scijava.prefs.DefaultPrefService [priority = 0.0]
org.scijava.run.DefaultRunService [priority = 0.0]
org.scijava.script.DefaultScriptHeaderService [priority = 0.0]
org.scijava.script.DefaultScriptService [priority = 0.0]
org.scijava.script.process.DefaultScriptProcessorService [priority = 0.0]
org.scijava.search.DefaultSearchService [priority = 0.0]
org.scijava.search.javadoc.DefaultJavadocService [priority = 0.0]
org.scijava.startup.DefaultStartupService [priority = 0.0]
org.scijava.task.DefaultTaskService [priority = 0.0]
org.scijava.text.DefaultTextService [priority = 0.0]
org.scijava.thread.DefaultThreadService [priority = 0.0]
org.scijava.tool.DefaultToolService [priority = 0.0]
org.scijava.ui.DefaultUIService [priority = 0.0]
org.scijava.ui.dnd.DefaultDragAndDropService [priority = 0.0]
org.scijava.ui.swing.SwingIconService [priority = 0.0]
org.scijava.ui.swing.script.DefaultLanguageSupportService [priority = 0.0]
org.scijava.welcome.DefaultWelcomeService [priority = 0.0]
org.scijava.widget.DefaultWidgetService [priority = 0.0]
sc.fiji.compat.DefaultFijiService [priority = 0.0]
io.scif.services.DefaultInitializeService [priority = -100.0]
net.imagej.display.DummyScreenCaptureService [priority = -100.0]
net.imagej.render.DummyRenderingService [priority = -100.0]
org.scijava.batch.FileBatchService [priority = -100.0]
org.scijava.log.StderrLogService [priority = -100.0]
org.scijava.platform.DefaultAppEventService [priority = -100.0]
org.scijava.cache.DefaultCacheService [priority = -10000.0]

-- Classpath of ClassLoader --
/Applications/Fiji.app/plugins/

	at org.scijava.Context.inject(Context.java:474)
	at org.scijava.Context.inject(Context.java:386)
	at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:238)
	at org.scijava.ui.DefaultUIService.discoverUIs(DefaultUIService.java:503)
	at org.scijava.ui.DefaultUIService.getDefaultUI(DefaultUIService.java:193)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:140)
	at org.scijava.AbstractGateway.launch(AbstractGateway.java:104)
	at net.imagej.Main.main(Main.java:55)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)
Error while executing the main() method of class 'net.imagej.Main':
java.lang.NullPointerException
	at net.imagej.legacy.ui.LegacyUI.ij1Helper(LegacyUI.java:119)
	at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:130)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:157)
	at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:142)
	at org.scijava.AbstractGateway.launch(AbstractGateway.java:104)
	at net.imagej.Main.main(Main.java:55)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:291)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:198)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:89)

Ok, but after downloading it worked?

Which plugins did you install? :upside_down_face:

After I download the app with no updates it works.
The plugins are ilastik, BaSiC, and LuMos.
I tried downloading the plugins on separate occasions to check to see if a plugin is causing the issue, but any plugin I add, the application stops launching after I try to restart it.

1 Like

Maybe stupid question: Did you try updating Fiji without installing any plugins? Did it still work then?

1 Like

I did try updating Fiji without installing plugins, and it worked okay.
As soon as I try to include one of the plugins, it stops launching.
Is there a plugin I should test to download with?
Thanks!

Indeed, the LUMoS update site (https://sites.imagej.net/Tmcrae) ships some now-outdated jar files (e.g. scijava-common, imagej, and several others) that are shading the versions shipped from the Java-8 update site, and therefore causing issues with incompatible versions.

@tristan_mcrae could you please have a look and mark those files as obsolete, so that your update site stops shipping them?

1 Like

Hi, thank you for this information.
Is it possible now to still use the LuMoS plugin?

It still breaks Fiji.

But if you need LUMos, you can download Fiji with LUMos here as well as an Imaris XTension.

3 Likes

THANK YOU! Like OP this issue was driving me crazy. I kept re-installing Fiji a bunch of times and LUMoS (but not other plugins) kept breaking it. I’m glad there’s a workaround for now.

It looks like the version you linked is running ImageJ v1.52e and the latest Fiji version is v1.53c. Maybe the newer ImageJ version broke the plugin? Also looks like I need to avoid doing Help > Update because that seems to break it again.

1 Like

This problem has been fixed. You should be able to install the plugin with the newest version of Fiji. Please let us know if there are still issues using the plugin.

Hi, I’ve installed LUMoS using ‘update’ in Fiji (v1.53c) on Mac.

I can open the image and LUMoS but Fiji keeps turned off right after starting the unmixing.