[ome-users] Problem with msr file

[Melissa Linkert]

Hi Benjamin,

> I'm glad to hear that you found a workaround.  It would still be helpful to
> have the original file, so that we can update Bio-Formats to detect the
> second channel.

Thank you for uploading a sample file.  There is now a ticket for this
on our issue tracking system:

https://trac.openmicroscopy.org.uk/ome/ticket/11722

If you would like to be automatically notified of updates to that
ticket, please let us know.

Regards,
-Melissa

On Tue, Aug 26, 2014 at 10:32:20PM -0500, Melissa Linkert wrote:
> Hi Benjamin,
> 
> > thank you for your support. I opened the msr file again in Imspector and it seems it included another recording to the one I wanted to save. So I deleted the „other channel“ saved again and voila it could be opened. Sorry to bother you all. Nevertheless the other channel was for some reason not detected by the bioformats plugin. Do you still want my file as an example?
> 
> I'm glad to hear that you found a workaround.  It would still be helpful to
> have the original file, so that we can update Bio-Formats to detect the
> second channel.
> 
> Regards,
> -Melissa
> 
> On Tue, Aug 26, 2014 at 09:28:52PM +0200, Benjamin Sauer wrote:
> > Hi Melissa,
> > 
> > thank you for your support. I opened the msr file again in Imspector and it seems it included another recording to the one I wanted to save. So I deleted the „other channel“ saved again and voila it could be opened. Sorry to bother you all. Nevertheless the other channel was for some reason not detected by the bioformats plugin. Do you still want my file as an example?
> > 
> > Best regards
> > 
> > Benjamin 
> > ------------------------------------------------
> > Hr. Benjamin Sauer
> > Institut für biomedizinische Optik
> > Universität zu Lübeck
> > Peter-Monnik-Weg 4
> > 23562 Lübeck
> > 
> > Am 26.08.2014 um 05:49 schrieb Melissa Linkert <melissa at glencoesoftware.com>:
> > 
> > > Hi Benjamin,
> > > 
> > >> I tried to import a la vision importer msr file, with two channels via bioformats and I get the following error message;
> > > 
> > > Thank you for reporting this problem.  Are you using version 5.0.3 of
> > > Bio-Formats?  If not, I would suggest upgrading, as that may solve the
> > > problem.
> > > 
> > > If the same error occurs with 5.0.3, then it would be very helpful if
> > > you could send the problematic file.  The file can be uploaded to
> > > http://qa.openmicroscopy.org.uk/qa/upload (though you will need to Zip
> > > compress it first).
> > > 
> > > Regards,
> > > -Melissa
> > > 
> > > On Tue, Aug 26, 2014 at 10:12:54AM +0200, Benjamin Sauer wrote:
> > >> Hi everybody,
> > >> I tried to import a la vision importer msr file, with two channels via bioformats and I get the following error message;
> > >> 
> > >> ImageJ 1.47v; Java 1.6.0_65 [32-bit]; Mac OS X 10.9.4; 61MB of 400MB (15%)
> > >> 
> > >> java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=57, sizeC=3, sizeT=1, total=173)
> > >> 	at loci.formats.FormatTools.getIndex(FormatTools.java:383)
> > >> 	at loci.formats.FormatTools.getIndex(FormatTools.java:317)
> > >> 	at loci.formats.DimensionSwapper.getIndex(DimensionSwapper.java:272)
> > >> 	at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:411)
> > >> 	at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:411)
> > >> 	at loci.plugins.in.ImagePlusReader.getPlanesToLoad(ImagePlusReader.java:535)
> > >> 	at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:364)
> > >> 	at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
> > >> 	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
> > >> 	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
> > >> 	at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
> > >> 	at loci.plugins.in.Importer.readPixels(Importer.java:150)
> > >> 	at loci.plugins.in.Importer.run(Importer.java:89)
> > >> 	at loci.plugins.LociImporter.run(LociImporter.java:81)
> > >> 	at ij.IJ.runUserPlugIn(IJ.java:195)
> > >> 	at ij.IJ.runPlugIn(IJ.java:160)
> > >> 	at ij.Executer.runCommand(Executer.java:128)
> > >> 	at ij.Executer.run(Executer.java:64)
> > >> 	at java.lang.Thread.run(Thread.java:695)
> > >> 
> > >> I guess this wants to tell me 57 times 3 times 1 is not 173 but 171. I just recorded two channels although 6 would be possible. Other files with just one channel do not pose a problem.
> > >> 
> > >> Best regards
> > >> 
> > >> Benjamin
> > >> ------------------------------------------------
> > >> Hr. Benjamin Sauer
> > >> Institut für biomedizinische Optik
> > >> Universität zu Lübeck
> > >> Peter-Monnik-Weg 4
> > >> 23562 Lübeck
> > >> 
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> >