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

[Melissa Linkert]

Hi HadiM,

> I just updated bioformats toggling the Bio-Formats daily builds update site
> and I can't reproduced the bug. But I have another one which prevent me to
> open OME Tif from Micro Manager. Maybe the last one has been fixed or the
> new one is raised before the last one, I can't tell.

...snipped error message...

> Error message seems logic. Reader because as I said one channels contains
> only one frame every ten so images count is not Z*C*T but Z*T+Z*T/10.
> 
> I attached an OME Tiff file to this mail.

For the acquisition that you describe, this OME-TIFF file is incorrect; this
would need to be corrected in Micromanager.

There are two ways to record acquisitions with holes in OME-TIFF:

1) Store a blank plane for each of the non-recorded planes.  This means
   that you would have Z * C * T planes in the file, but only Z * T + Z * T/10
   would be valid.

2) Store each of the channels in a separate stack (i.e. OME Image).  The
first OME Image (representing channel 0) would contain Z * T planes; the
second OME Image (representing channel 1) would contain Z * T / 10 planes.

Simply omitting planes as is the case here is not currently supported.  If you
are already in contact with the Micromanager developers, then you may wish to
pass this along; otherwise, let us know and we'll get in touch with them.

Regards,
-Melissa

On Sat, Oct 26, 2013 at 04:04:28PM +0200, HadiM wrote:
> I just updated bioformats toggling the Bio-Formats daily builds update site
> and I can't reproduced the bug. But I have another one which prevent me to
> open OME Tif from Micro Manager. Maybe the last one has been fixed or the
> new one is raised before the last one, I can't tell.
> 
> This is the new bug:
> 
> ```
> (Fiji Is Just) ImageJ 1.48e; Java 1.7.0_25 [64-bit]; Linux
> 3.11.0-12-generic; 31MB of 922MB (3%)
> 
> java.lang.IllegalArgumentException: ZCT size vs image count mismatch
> (sizeZ=6, sizeC=1, sizeT=100, total=660)
> at loci.formats.FormatTools.getIndex(FormatTools.java:355)
> at loci.formats.FormatTools.getIndex(FormatTools.java:289)
> at loci.formats.DimensionSwapper.getIndex(DimensionSwapper.java:277)
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)
> at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:403)
> at loci.plugins.in.ImagePlusReader.getPlanesToLoad(ImagePlusReader.java:541)
> 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: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)
> ```
> 
> Error message seems logic. Reader because as I said one channels contains
> only one frame every ten so images count is not Z*C*T but Z*T+Z*T/10.
> 
> I attached an OME Tiff file to this mail.
> 
> 
> 
> --
> HadiM
> 
> 
> On Sat, Oct 26, 2013 at 3:36 PM, HadiM <marelo64 at gmail.com> wrote:
> 
> >  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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