Fiji Update August 2020

haesleinhuepf · August 5, 2020, 5:40am

Dear Fiji users,

there was recently a major update to Fiji with a lot of changes under the hood. Unfortunately, there have been reports of minor issues regarding ~~creating custom tables [1, 2], opening example images [3], using the Big Data Viewer [4], Big Warp [7] and Big Stitcher [9]~~, the MoBIE/PlatyBrowser update site [10], starting the 32-bit Windows version of Fiji [5] and starting Fiji on Ubuntu Linux [6, 8].

(Edit: Items marked with ~~strikethrough~~ have been fixed.)

While the developers are working on these issues, consider backing up Fiji before updating it. In the worst case, you find archived Fijis from the recent weeks here:
https://downloads.imagej.net/fiji/archive/

Furthermore, feel free to post any issues you experience here or as github issue if you have an account there.

Thanks for your support!

Cheers,
Robert

haesleinhuepf · August 3, 2020, 7:33am

JimageJ1 · August 3, 2020, 1:18pm

Hey folks,

I ran into problems getting the latest version to run on Ubuntu 20.04 after the update. I’ve got it working now but thought I’d post what my issue was.

Ran the update and Fiji won’t start. Redownloaded the latest and it won’t start. The 2017 build starts fine, until I update it.

Running from the command line gives this:

Could not load Java library '/home/jim/Downloads/Fiji.app/java/linux-amd64/jdk1.8.0_172/jre//lib/server/libjvm.so': /home/jim/Downloads/Fiji.app/java/linux-amd64/jdk1.8.0_172/jre//lib/server/libjvm.so: cannot open shared object file: No such file or directory Warning: falling back to System JVM Could not launch system-wide Java (No such file or directory)

This made me realise that there is an issue with the Java the Fiji installs, so I’ve updated my Ubuntu Java installation and it now runs.

sudo apt install default-jre

Cross-posted as a GitHub issue:

axtimwalde · August 3, 2020, 8:47pm

Same here, but I have s system wide Java installation, actually several of them. This is what Fiji reports after upgrade:

Could not load Java library '/home/saalfeld/packages/Fiji.app/java/linux-amd64/jdk1.8.0_172/jre//lib/server/libjvm.so': /home/saalfeld/packages/Fiji.app/java/linux-amd64/jdk1.8.0_172/jre//lib/server/libjvm.so: cannot open shared object file: No such file or directory
Warning: falling back to System JVM
[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@468dda3e
ClassLoader: java.net.URLClassLoader@1e95b653

-- 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.table.io.DefaultTableIOService [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 --
/home/saalfeld/packages/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)

axtimwalde · August 3, 2020, 8:48pm

java -version
openjdk version "1.8.0_252"
OpenJDK Runtime Environment (build 1.8.0_252-8u252-b09-1ubuntu1-b09)
OpenJDK 64-Bit Server VM (build 25.252-b09, mixed mode)

ctrueden · August 8, 2020, 3:36pm

@axtimwalde To me that appears like the fallback to system Java does work, but then something is wrong with the configuration of JAR files in the installation. Clearly, Java is starting. That error is super weird.

Does it work for you to launch Fiji using jgo?

jgo sc.fiji:fiji:2.1.0

?

axtimwalde · August 3, 2020, 11:09pm

@ctrueden solved the issue by downgrading the imagej-launcher so it finds the shipped Java. He also noticed that the N5 update site shadowed scijava-common at an outdated version which lead to my above error. He marked the shadowing artifacts in the N5 update site as obsolete. Thanks as always @ctrueden!

imagejan · August 4, 2020, 10:53am

5 posts were split to a new topic: java.lang.NoClassDefFoundError: org/apache/xml/serializer/TreeWalker

haesleinhuepf · August 4, 2020, 10:21am

A post was split to a new topic: Particle Analysis / Macro issue in recent Fiji

ctrueden · August 4, 2020, 12:58pm

A post was merged into an existing topic: java.lang.NoClassDefFoundError: org/apache/xml/serializer/TreeWalker

ctrueden · August 5, 2020, 5:34am

7 posts were split to a new topic: Fiji August 2020 update broke MoBIE

ctrueden · August 6, 2020, 8:40pm

3 posts were split to a new topic: Error with CellCounter in a macro

imagejan · August 7, 2020, 4:45pm

A post was split to a new topic: EzColocalization plugin freezes after recent Fiji update

oburri · August 7, 2020, 12:43pm

Hello,

There is currently an issue with Noise2Void and SCIFIO since the update, you can find it here

frauzufall · August 8, 2020, 8:15pm

Thanks @oburri, the N2V issue is fixed now. Gave me the chance to sneak in some LoopBuilder multithreading magic ^^ And the CSBDeep site was also shadowing artifacts which I now marked obsolete. Please let me know if this causes any issues.

But I get a new error when starting the “train and predict” command (before the input dialog pops up) which might be unrelated to N2V, a io.scif.FormatException: Invalid TIFF file during org.scijava.module.DefaultModuleService.loadInputs… It does not seem to have any impact, the command runs successfully. The “train” command, which has no image input parameter, does not throw this error… Anyone else noticing something similar? Will have a closer look ~Monday,

imagejan · August 14, 2020, 8:03am

13 posts were split to a new topic: LUMoS update site breaks Fiji after August 2020 update

LPUoO · August 21, 2020, 5:31pm

Hi, Is the updater currently working ?
I’m getting

[ERROR] Cannot connect to the Internet.
Do you have a network connection?
Are your proxy settings correct?
[ERROR] java.net.ConnectException: Connection timed out: connect
	at java.net.DualStackPlainSocketImpl.connect0(Native Method)
	at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:589)
	at java.net.Socket.connect(Socket.java:538)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
	at sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
	at sun.net.www.http.HttpClient.New(HttpClient.java:339)
	at sun.net.www.http.HttpClient.New(HttpClient.java:357)
	at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
	at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:984)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1564)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
	at net.imagej.ui.swing.updater.ImageJUpdater.testNetworkConnection(ImageJUpdater.java:370)
	at net.imagej.ui.swing.updater.ImageJUpdater.errorIfNetworkInaccessible(ImageJUpdater.java:323)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:100)
	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)

(I do have a working internet connexion)

Thanks

camlloyd · August 21, 2020, 5:43pm

imagej.net appears to be down.

See also https://github.com/fiji/fiji/issues/266.

ctrueden · August 21, 2020, 8:25pm

Sorry for the inconvenience. One of our web servers went down for unknown reasons. I am troubleshooting now—stay tuned.

ctrueden · August 22, 2020, 1:13am

Power cable was jostled loose during some maintenance work earlier today. I reseated the plug and everything is fine, and back online.