[ome-users] Problem with msr file

[Melissa Linkert]

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
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users