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

[Ewan McGhee]

Hi,

Have tested the files I had which did not work with 5.0 and can confirm
that they work fine with the stable 5.0.2 release of Bio-Format importer.

Cheers,

Ewan

On 03/03/2014 05:43, "Melissa Linkert" <melissa at glencoesoftware.com> wrote:

>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(RandomAccessInputStrea
>>>>m.
>> >>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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>> >
>>