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

[Melissa Linkert]

Hi Ewan,

> I have this morning installed the BioFormats 5.0 package (just to make
> sure that I have the correct loci-tools.jar) and the files I tested on
> Friday are behaving the same as then.
> 
> I have uploaded as a zip file (Beatson Institute LaVision Imspector files):

Thank you for the additional details, and for uploading sample files.
There is now a ticket for this on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/12035

You have been CC'd, and so will be automatically notified of our
progress.  If you prefer not to receive updates, please let me know.

Regards,
-Melissa

On Mon, Mar 03, 2014 at 11:14:13AM +0000, Ewan McGhee wrote:
> Hi Melissa,
> 
> I have this morning installed the BioFormats 5.0 package (just to make
> sure that I have the correct loci-tools.jar) and the files I tested on
> Friday are behaving the same as then.
> 
> I have uploaded as a zip file (Beatson Institute LaVision Imspector files):
> 
> 	one troublesome file: 02 - not working.msr - 2 channel z-stack
> 
> 	One working file: 01 - working.msr - 2 channel z-stack
> 
> 	These were taken on the same day with the same version of Imspector
> controlling the trim-scope and so should be read the same by the file
> importer.
> 
> 	One test file: z-TC - for LOCI.msr - this was a test file of three
> channels a few few z-slices and a few time points.
> 
> Hope these help and if I can provide any other files or information please
> let me know.
> 
> Cheers,
> 
> Ewan
> 
> 
> 
> On 28/02/2014 17:14, "Melissa Linkert" <melissa at glencoesoftware.com> wrote:
> 
> >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.ja
> >>va: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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> >
>