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

[Melissa Linkert]

Hi Ewan,

> 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:

Thank you for the feedback.  From the error message, it looks like the 5.0.0
version of Bio-Formats is not installed.  Could you please verify the
version number shown in "Help > About Plugins > Bio-Formats Plugins" (or
"Help > About Plugins > LOCI Plugins")?  If that does not show "5.0.0"
as the version number, then I would suggest upgrading first to see if
that fixes things.

> 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.

If you see the same problem with 5.0.0, then it would be very much
appreciated if you could upload one of the problematic files to:

http://qa.openmicroscopy.org.uk/qa/upload

Regards,
-Melissa

On Fri, Feb 28, 2014 at 10:26:15AM +0000, Ewan McGhee wrote:
> Hi,
> 
> 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:
> 
> java.lang.NegativeArraySizeException
> 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.
> 
> Cheers,
> 
> Ewan
> 
> —
> 
> --
> 
> Dr Ewan McGhee
> 
> Senior Scientific Officer
> Beatson Advanced Imaging Resource
> Beatson Institute for Cancer Research
> Glasgow
> 
> Tel: +44-(0)141-330-6872
> 
> 
> 

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