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

[Anthony, Neil]

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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