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

[Ewan McGhee]

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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