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OMERO.insight with FIJI and Bio Formats

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

OMERO.insight with FIJI and Bio Formats

Postby slozosnitram » Thu Jun 16, 2016 11:18 am

Hi guys,

I'm trying to setup OMERO.insight with FIJI and BioFormats and getting error when launching it.

Error.PNG
Error.PNG (251.73 KiB) Viewed 1841 times


New update(s) found: 2.4.7 [http://www.terracotta.org/confluence/display/release/Release+Notes+Ehcache+Core+2.4].
Please check http://ehcache.org for the latest version.
no update needed
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: com.sun.java.swing.plaf.windows.WindowsTableHeaderUI$XPDefaultRenderer cannot be cast to org.jdesktop.swingx.table.ColumnHeaderRenderer
at org.openmicroscopy.shoola.util.ui.treetable.OMETreeTable.initialize(OMETreeTable.java:118)
at org.openmicroscopy.shoola.util.ui.treetable.OMETreeTable.<init>(OMETreeTable.java:126)
at org.openmicroscopy.shoola.agents.dataBrowser.view.ImageTable.<init>(ImageTable.java:403)
at org.openmicroscopy.shoola.agents.dataBrowser.view.ImageTableView.initComponents(ImageTableView.java:87)
at org.openmicroscopy.shoola.agents.dataBrowser.view.ImageTableView.<init>(ImageTableView.java:110)
at org.openmicroscopy.shoola.agents.dataBrowser.view.DataBrowserModel.createImageTableView(DataBrowserModel.java:334)
at org.openmicroscopy.shoola.agents.dataBrowser.view.DataBrowserUI.setSelectedView(DataBrowserUI.java:352)
at org.openmicroscopy.shoola.agents.dataBrowser.view.DataBrowserComponent.activate(DataBrowserComponent.java:229)
at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.setLeaves(TreeViewerComponent.java:2824)
at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserComponent.setLeaves(BrowserComponent.java:601)
at org.openmicroscopy.shoola.agents.treeviewer.ExperimenterDataLoader.handleResult(ExperimenterDataLoader.java:250)
at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

and data import screen looks weird

DataImport.PNG
DataImport.PNG (87.99 KiB) Viewed 1841 times
slozosnitram
 
Posts: 34
Joined: Tue Jan 26, 2016 4:39 pm

Re: OMERO.insight with FIJI and Bio Formats

Postby Dominik » Fri Jun 17, 2016 9:32 am

Which versions do you use? I was just trying to replicate the error, using the latest ImageJ1 (1) with the latest OMERO plugin (2) on Windows 8, couldn't see the error message.
But I agree, the import dialog looks a bit strange, but it works. You have to click on "Add to Queue". This will add the currently open Image in ImageJ to the import queue, which you then can import to OMERO.

Kind Regards,
Dominik

--
1) http://imagej.net/download/win32/
2) http://downloads.openmicroscopy.org/omero/5.2.4/
User avatar
Dominik
Team Member
 
Posts: 149
Joined: Mon Feb 10, 2014 11:26 am

Re: OMERO.insight with FIJI and Bio Formats

Postby slozosnitram » Fri Jun 17, 2016 10:56 am

I'm using OMERO.insight-ij-5.2.4-ice35-b23 with fiji-win32 and i tried with fiji-win64 same error.
As i understand fiji-win32 uses ImageJ 2.0.0-rc-49/1.51d/Java 1.8.0_66 (32bit)

UPDATE ... i removed FIJI version and installed only ImageJ 1.50i/ Java 1.8.0_77 (64bit) and no errors. Everything works fine for now. Thanks
slozosnitram
 
Posts: 34
Joined: Tue Jan 26, 2016 4:39 pm


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