[ome-users] Bio-Formats µManager Clash

[Sebastien Besson (Staff)]

Hi Eric,

glad to hear about it and thanks for updating forum post as well.

Happy holidays to you guys,
Seb

On 12 Dec 2016, at 15:08, Eric Griffis <ergriffis at gmail.com<mailto:ergriffis at gmail.com>> wrote:

Hi Seb,

I tried what you suggested, and it fixed the problem after a restart. Thanks so much for the rapid help.

Joyeux Noel.

Eric


On 11 Dec 2016, at 17:51, Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:

Hi Eric,

thanks for letting us know of this issue.

Can you let us know which version of Bio-Formats is used in Fiji
and which update sites are configured?

My suspicion is that you have this update site [1]. If this is the case,
could you try to disable this update site and see if it fixes the issue?
This should restore the release version of Bio-Formats which is pushed
to the Java-8 update site.

Best,
Sebastien

[1] http://sites.imagej.net/Bio-Formats/


On 11 Dec 2016, at 22:28, Eric Griffis <ergriffis at gmail.com<mailto:ergriffis at gmail.com>> wrote:


I am using Fiji File>Import>Bio-Formats to open µManager files. Everything was going well until Friday. Now, whenever I try to open a file using this method, I get the following message:

java.lang.NoClassDefFoundError: ome/xml/meta/MetadataConverter
at loci.formats.services.OMEXMLServiceImpl.convertMetadata(OMEXMLServiceImpl.java:876)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:554)
at loci.formats.FormatReader.setId(FormatReader.java:1399)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

My guess is that this is a problem due to a Bio-Formats update that was pushed out to Fiji. Does anyone have an idea of what the problem is and who could fix it? I have also posted this on the imageJ forum as well.

Thanks,

Eric

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