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

Anthony, Neil nantho2 at emory.edu
Mon May 15 19:39:58 BST 2017 

Hi Melissa, I hope the weekend was fun.

I just wanted to follow up and let you know that I'm still not able to open my custom written .ims file.  I'm running Bio-Formats 5.4.0 and I see an error with "Invalid C size: 0" (see below), but when I inspect with HDFView I see that my Noc attribute is 1...  The location is /DataSetInfo/Image/Noc

In looking through the subtleties between different versions of Imaris files I see that not all attributes are needed for Imaris to open the files, and I wonder if we have a situation where the information is being pulled from a different attribute.

Do you have a .ims file you can share that I can compare to, and hopefully add the missing attributes?

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:1097)
    at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:434)
    at loci.formats.in.ImarisHDFReader.initFile(ImarisHDFReader.java:311)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    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)


________________________________
From: Anthony, Neil
Sent: Thursday, February 2, 2017 10:44:34 AM
To: Melissa Linkert
Subject: Re: [ome-devel] In house written .ims file question


Hi Melissa,

I found time to look at the attributes in my files, and it does have a Noc (number of channels) set in the Image group as you mention.  I looked at the error and it looks like it errors on line

435 in ImarisHDFReader.java:

int[] zct = getZCTCoords(no);
from the exception:

    at loci.formats.in.ImarisHDFReader.getImageData(ImarisHDFReader.java:435)

Maybe it is something your end, I don't know.

Looking back at my attributes vs the Bitplane document I see that I have unit=micron and they show unit=um, so maybe that is affecting things too.  I'll keep you updated if that unit text changes anything once I try it out.

Thanks for your time.

Neil



________________________________
From: Anthony, Neil
Sent: Tuesday, January 31, 2017 9:13:17 PM
To: Melissa Linkert
Subject: RE: [ome-devel] In house written .ims file question

Hi Melissa, thanks for the details.

I think the error might be my end.  I'll double check that all the attributes match up and post the result here asap.

Thanks for your time.

Neil


-----Original Message-----
From: Melissa Linkert [mailto:melissa at glencoesoftware.com]
Sent: Monday, January 30, 2017 11:55 AM
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk>
Cc: Anthony, Neil <nantho2 at emory.edu>
Subject: Re: [ome-devel] In house written .ims file question

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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