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

[HadiM]

If I am not posting to the right mailing list, feel free to tell me where I
can get help.

Thank you !


--
HadiM


On Sat, Oct 26, 2013 at 4:04 PM, HadiM <marelo64 at gmail.com> 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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