[ome-users] LaVision Biotec Imspector .msr file import with version 5 bio-importer

Ewan McGhee e.mcghee at beatson.gla.ac.uk
Fri Feb 28 10:26:15 GMT 2014


I have been trying out the version 5 bio-importer plugin for ImageJ with my .msr files from ImSpectorPro (LaVision Biotec) and have been having mixed success.

It is quite strange as of two files saved ~10 minutes apart, one will load and one will not, even though they are both two channel, z-stacks.

The exceptions window for the file which does not load is as follows:

at ome.scifio.io.RandomAccessInputStream.readString(RandomAccessInputStream.java:403)
at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:275)
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:166)
at loci.formats.FormatReader.setId(FormatReader.java:1360)
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:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.Executer.runCommand(Executer.java:124)
at ij.Executer.run(Executer.java:61)
at java.lang.Thread.run(Thread.java:695)

I can upload them somewhere if that is possible or use my public folder on Dropbox. Also I can export the metadata for both files from ImspectorPro if that is of use as well.

Please let me know if I can help in any other way.





Dr Ewan McGhee

Senior Scientific Officer
Beatson Advanced Imaging Resource
Beatson Institute for Cancer Research

Tel: +44-(0)141-330-6872

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