Open Microscopy Environment

Hi,


I've noticed that since a recent Fiji update (which upgrade bio-formats to "4.5"), the ImageJ plugin can't open images from OMERO (stuck at "populating metadata"). Before the upgrade, I used an empty "loci_tools.jar" to bypass the error message, but it now seems this prevents the plugin from running properly.

And if I put the real "loci_tools.jar" along with the "loci_plugins-4.5-SNAPSHOT.jar", I have a warning due to the duplicate functions, but the OMERO plugin works...

Is there a way around it ?

Are you using the OMERO ImageJ plugin? If so, I cannot reproduce on my system. That is, with a fully up to date Fiji, and a 0-byte dummy loci_tools.jar, I am still able to connect to an OMERO server, browse it, etc.

However, you mention being stuck at "Populating metadata", which is a Bio-Formats status that could come up if you are using the ome_tools.jar plugins. Are you using those?

I am able to connect to the server and browse the images. I am unable to open the images through ImageJ though (double-click): it gets stuck at "populating metadata".

What do you mean by "using the ome_tools.jar" ? All I have is a default Fiji setup that was upgraded regularly and the OMERO plugin. And a dummy "loci_tools.jar" of course.

Thanks for the additional information. I was able to reproduce the problem on my system as well (I hadn't tried actually viewing one of the OMERO images in ImageJ).

To fix, please download the following file:

http://curtis.imagej.net/ome-io.jar

And overwrite the old one in your OMERO.imagej installation (e.g., plugins/OMERO.insight-ij-4.4.5-ice33-b20/libs/ome-io.jar).

Restart Fiji, and viewing OMERO images should work again.

In case you are curious: the issue is a mismatch between the version of Bio-Formats installed in Fiji, and the one expected by the OMERO.imagej plugin. If you go to Edit > Options > Misc and turn on Debug mode, the ImageJ log shows more information. Specifically in this case:

Code: Select all

LOCI: parse core options
LOCI: display option dialogs
LOCI: loci.plugins.in.UpgradeDialog: prompt
LOCI: loci.plugins.in.LocationDialog: skip
LOCI: loci.plugins.in.IdDialog: skip
LOCI: loci.plugins.in.MainDialog: prompt
Exception in thread "AWT-EventQueue-0"
java.lang.NoSuchFieldError: core
   at loci.ome.io.OmeroReader.initFile(OmeroReader.java:337)
   at loci.formats.FormatReader.setId(FormatReader.java:1320)
   at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
   at loci.plugins.in.Importer.showDialogs(Importer.java:141)
   at loci.plugins.in.Importer.run(Importer.java:79)
   at loci.plugins.LociImporter.run(LociImporter.java:81)
   at ij.IJ.runUserPlugIn(IJ.java:185)
   at ij.IJ.runPlugIn(IJ.java:152)
   at ij.IJ.runPlugIn(IJ.java:141)
   at org.openmicroscopy.shoola.env.ui.TaskBarManager.runAsImageJ(TaskBarManager.java:349)
   at org.openmicroscopy.shoola.env.ui.TaskBarManager.handleViewInPluginEvent(TaskBarManager.java:369)
   at org.openmicroscopy.shoola.env.ui.TaskBarManager.eventFired(TaskBarManager.java:1005)
   at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:91)
   at org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:222)
   at org.openmicroscopy.shoola.agents.dataBrowser.actions.ViewInPluginAction.actionPerformed(ViewInPluginAction.java:131)


The problem is that the version of ome-io.jar shipped with the OMERO.imagej plugin is out of sync with the version of Bio-Formats provided by Fiji. We will discuss the best way of addressing this situation, to avoid these sorts of problems in the future.

Thank you very much !

Hi,

Apparently, this solution does not work anymore...
I updated the ome-io.jar, but Fiji does not open the images (it's stuck on "populating metadata").

(We use OMERO 4.4.7 server and client. )


Edit:
Nevermind: I downloaded the latest ome-io.jar from
http://hudson.openmicroscopy.org.uk/vie ... ble-ice34/