[ome-devel] Issue importing ome.tiff from created by Micro Manager

[HadiM]

Hi,

I have issues importing OME Tiff files created by Micro Manager (with
oimave stack file option).

This is the error message I have:

(Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux
3.11.0-12-generic; 37MB of 1422MB (2%)

java.lang.ArithmeticException: / by zero
at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:277)
at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:235)
at loci.formats.MetadataTools.populatePixels(MetadataTools.java:136)
at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:817)
at loci.formats.FormatReader.setId(FormatReader.java:1244)
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:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:724)

Last thing, Tiff files contains ome “holes”. In fact during acquisition I
am imaging two channels and one of them is imaged every 6 frames. So for
this channel there is an image only every 6 frames.

I have the feeling that the issue is coming from there.

MM can open the OME Tiff file correctly. I think this is because they have
their own OME Tiff writer/reader.

Any idea on how to fix this and when ?

—
HadiM
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