BioFormats/Micromanager Clash

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 will also email the Bio-Formats and µManager teams as well.

Thanks,

Eric

Note that this was cross-posted on the ome-users list.

I second Sebastien’s suggestion to verify which update sites you have enabled, and in particular disable the Bio-Formats update site to see if that fixes the issue.

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I made the change that Seb suggested and it fixed the issue.

Thanks,

Eric

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Thanks for updating the post, @Eric. Note the Java 8 update site now ships Bio-Formats 5.3.0.

@ctrueden: the issue reported here is largely related to the architectural changes performed in Bio-Formats 5.3.0. Some of the assumptions made by the scripts populating the update site e.g. the fact the Bio-Formats JARs have all the same groupId and the same version are not longer valid. Let us know if we should initiate a technical discussion on how to resolve this in another forum thread.