[ome-devel] In house written .ims file question

[Melissa Linkert]

Hi Neil,

> I have written some matlab code to write .ims files, but on opening with Bioformats I get the below pasted error list.  The files open fine with Imaris (the underlying file format is listed as v5.5, but it appears that different things in the HDF5 structure come and go with different versions of Imaris.  I'm currently using 8.4)
>
> Do you guys have a breakdown of the group and attribute structure that Bioformats uses?

Our reference page for Imaris HDF is:

http://www.openmicroscopy.org/site/support/bio-formats5.3/formats/bitplane-imaris.html

and the relevant section of Bio-Formats' Imaris HDF reader:

https://github.com/openmicroscopy/bioformats/blob/v5.3.2/components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java#L480

The error message you are seeing is a result of the channel count not
being found in the file.  Bio-Formats expects the channel count to be
set in a "NumberOfChannels" attribute; according to the current
specification from Bitplane, it looks like this has been replaced by
the "Noc" attribute in the "Image" group (section 3.2 of
http://open.bitplane.com/Default.aspx?tabid=268).  If your code sets
"Noc" and the resulting file has the correct dimensions in Imaris,
then this is likely something we need to fix in Bio-Formats.

If you are willing to upload one or more of the .ims files that
exhibit this problem, then we should have enough information to test a
fix, or better advise you as to what needs to change in the file.
Files can be uploaded to:

http://qa.openmicroscopy.org.uk/qa/upload/

Regards,
-Melissa


On Mon, Jan 30, 2017 at 8:46 AM, Anthony, Neil <nantho2 at emory.edu> wrote:
> Hi all, I hope the data treats you well.
>
> I have written some matlab code to write .ims files, but on opening with Bioformats I get the below pasted error list.  The files open fine with Imaris (the underlying file format is listed as v5.5, but it appears that different things in the HDF5 structure come and go with different versions of Imaris.  I'm currently using 8.4)
>
> Do you guys have a breakdown of the group and attribute structure that Bioformats uses?
>
> Thanks
> Neil
>
>
> java.lang.IllegalArgumentException: Invalid C size: 0
>     at loci.formats.FormatTools.getZCTCoords(FormatTools.java:620)
>     at loci.formats.FormatTools.getZCTCoords(FormatTools.java:560)
>     at loci.formats.FormatReader.getZCTCoords(FormatReader.java:1099)
>     at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)
>     at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:312)
>     at loci.formats.FormatReader.setId(FormatReader.java:1399)
>     at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
>     at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
>     at loci.plugins.in.Importer.showDialogs(Importer.java:140)
>     at loci.plugins.in.Importer.run(Importer.java:76)
>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>     at ij.IJ.runUserPlugIn(IJ.java:217)
>     at ij.IJ.runPlugIn(IJ.java:181)
>     at ij.Executer.runCommand(Executer.java:137)
>     at ij.Executer.run(Executer.java:66)
>     at java.lang.Thread.run(Thread.java:745)
>
>
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