Posted by
Olivier Burri on
Apr 27, 2015; 8:15am
URL: http://imagej.273.s1.nabble.com/BioFormats-Issues-tp5012620.html
Dear All,
As of last week as far as we can tell, we are now having this error with bioformats while opening VSI files
(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 19MB of 18367MB (<1%)
java.lang.IllegalArgumentException: Invalid C index: 1/1
at loci.formats.FormatTools.getIndex(FormatTools.java:410)
at loci.formats.FormatTools.getIndex(FormatTools.java:337)
at loci.formats.FormatReader.getIndex(FormatReader.java:1083)
at loci.formats.in.CellSensReader.initFile(CellSensReader.java:805)
at loci.formats.FormatReader.setId(FormatReader.java:1395)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:493)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:140)
at loci.plugins.in.Importer.showDialogs(Importer.java:137)
at loci.plugins.in.Importer.run(Importer.java:75)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
So we contacted Bioformats through their forums and meanwhile tried to revert back to a version that was working. We tried removing all the files relevant to bioformats first by deselecting the update sites LOCI and BioFormats, then by removing anything related to LOCI or bioformats left in the jars and plugins folders, if any.
We then downloaded the previous release of bioformats as a single Jar and tried running it again. The same error. This feels a bit odd, what else should we downgrade to ensure that it is running the same way as before?
Best
Oli
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