[ome-users] nd2 files: IndexOutOfBoundsException

[David Gault (Staff)]

Hi,

Thank you for raising this bug. If you have any smaller files (< 2GB) that reproduce the same behaviour you can upload them to https://www.openmicroscopy.org/qa2/qa/upload/, otherwise we will arrange FTP details for you to transfer the larger original file for testing.
I have opened a Bio-Formats Trello card to track this issue: https://trello.com/c/dDcSZtur/296-indexoutofboundsexception

With Thanks,
David Gault

On 23 Nov 2018, at 18:05, Guilhem Chenon <guilhem.chenon at espci.fr<mailto:guilhem.chenon at espci.fr>> wrote:


Hello,

I am having trouble with several random .nd2 files which will  not open with Bio-Formats plugin either in ImageJ or Matlab. When I call bfGetReader on the file, I get this error message:

Error using bfGetReader (line 85)
Java exception occurred:
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0

    at java.util.ArrayList.rangeCheck(ArrayList.java:653)

    at java.util.ArrayList.get(ArrayList.java:429)

    at loci.formats.FormatReader.getSizeC(FormatReader.java:689)

    at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1348)

    at loci.formats.FormatReader.setId(FormatReader.java:1401)

    at loci.formats.DelegateReader.setId(DelegateReader.java:291)

    at loci.formats.ImageReader.setId(ImageReader.java:835)

    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)

    at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)

    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)

    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)

The original file is quite big (10Gb), so I can only upload it through FTP. When I crop the file in NIS, interestingly, it works, so for now my workaround is to crop the image itself because apparently NIS  re-encodes channels and timepoints during cropping so I can open it with Bio-Formats.

Moreover, these problematic files open fine with the ImageJ ND2 Reader plugin (https://imagej.nih.gov/ij/plugins/nd2-reader.html).

Thank you for your time.

Best regards,

--
Guilhem CHENON
LCMD - ESPCI Paris

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