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Task #12177 (closed)

Opened 6 years ago

Closed 6 years ago

BUG: IJ-plugin and Fiji

Reported by: pwalczysko Owned by: mlinkert
Priority: major Milestone: 5.0.2
Component: Bio-Formats Version: 5.0.0
Keywords: n.a. Cc: ux@…, jamoore, jmoore, mlinkert-x, mlinkert, graemeball@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


Graeme has found out during a drop-in session on 03 April 2014 that his insight-ii plugin in Fiji does not start at all and he cannot relieve this situation by updating Fiji either. Also, his updater/Manage Update Sites window shows Bio-formats 4 and Bio-formats 5 boxes as well as Bio-formats (with no number) box. His Bio-formats version shows 5.0.0-DEV and his OMERO.insigh-ij plugin is 5.0.0 (5.0.0 - release version). The error see below.
He pointed out that the situation is not urgent for him, because the same setup works with freshly downloaded Fiji. But I just wondered whether people trying to keep using their old Fiji will run into these problems as well ?

Graeme's setup

Bio-Formats for ImageJ rev c0951f7: 5.0.0-DEV

ls /Applications/Fiji?.app/jars/bio-formats/
formats-api.jar jai_imageio-4.4.10.jar ome-xml-5.0.0.jar
formats-bsd-5.0.0.jar mdbtools-java-5.0.0.jar specification-5.0.0.jar
formats-common-5.0.0.jar metakit-5.0.0.jar turbojpeg-5.0.0.jar
formats-gpl-5.0.0.jar ome-poi-5.0.0.jar

Stack trace:

(Fiji Is Just) ImageJ 1.48t; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2; 23MB of 12279MB (<1%)
java.lang.NoSuchFieldError: IS_OS_WINDOWS_7
	at org.openmicroscopy.shoola.util.ui.UIUtilities.isWindowsOS(
	at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildLogin(
	at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildGUI(
	at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(
	at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(
	at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(
	at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(
	at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(
	at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(
	at org.openmicroscopy.shoola.env.init.Initializer.doInit(
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(
	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(
	at ij.IJ.runUserPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(

Change History (2)

comment:1 Changed 6 years ago by pwalczysko

As indicated by Graeme, the bug is specific for the update for SPIM viewer in Fiji - when this is done, above bug appears with insight-ii plugin. Otherwise, no bug appears. The bug is not a version-specific one though.

comment:2 Changed 6 years ago by mlinkert

  • Resolution set to wontfix
  • Status changed from new to closed

If there are mixed 4.4.x and 5.0.x jars in Fiji, then it's pretty much a guarantee that very bad things will happen. Fully up to date versions of Fiji are expected to only have a single Bio-Formats update site (see; having a Bio-Formats 4 option indicates that Fiji is not up to date. The updater often needs to be run several times to make sure that all updates are applied, and in some cases the 4.4.x jars need to be manually selected for removal in the updater window.

There isn't much that we can do with this, so closing.

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