[ome-devel] Error when trying to open .msr file with bfopen

[David Gault (Staff)]

Hi,

The exception you are seeing seems to be caused by the parsing of the metadata key  'xyz-Table Z Resolution’. Are there any any unusual values, characters or empty fields for this value?
If you have a sample file you can upload to https://www.openmicroscopy.org/qa2/qa/upload/ then we can test the issue further.

With Thanks,
David Gault

On 7 Feb 2019, at 15:16, Biofysikos Biologos <biofysikos at gmail.com<mailto:biofysikos at gmail.com>> wrote:

Hello,

I have downloaded the latest bioformats MATLAB package and I would
like to use it to read the metadata from an .msr
(https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/lavision-imspector.html)

When I try it in MATLAB I get the following error:

Error using bfGetReader (line 85)
Java exception occurred:
java.lang.NullPointerException

   at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:417)

   at loci.formats.FormatReader.setId(FormatReader.java:1397)

   at loci.formats.ImageReader.setId(ImageReader.java:842)

   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

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

   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

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


Error in bfopen (line 114)
r = bfGetReader(id, stitchFiles);

Would the developers be interested in having more .msr files in order
to improve the bfread function?

Thank you
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