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

[David Gault (Staff)]

Hi Biofysikos,

A PR is a Pull Request<https://help.github.com/articles/about-pull-requests/> which allows us to submit proposed changes for review and testing before integrating them for a scheduled release. At the moment we don’t have a fixed date for when this will be included but we will schedule this fix to be tested for the first follow up release after Bio-Formats 6.0.0 (which we will be releasing next week).

With Thanks,
David Gault

On 12 Feb 2019, at 15:41, Biofysikos Biologos <biofysikos at gmail.com<mailto:biofysikos at gmail.com>> wrote:

Thank you! Btw, what is a PR and what is the estimate for
incorporating the corrections in the next release?

Thanks again,

Biofysikos

On Mon, Feb 11, 2019 at 1:29 PM David Gault (Staff)
<d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:

Thanks Biofysikos,

We received the file you submitted and have been able to test and reproduce the problem you described.
I have opened a PR to prevent this exception in the future: https://github.com/openmicroscopy/bioformats/pull/3319

With Thanks,
David Gault

On 8 Feb 2019, at 15:20, Biofysikos Biologos <biofysikos at gmail.com<mailto:biofysikos at gmail.com>> wrote:

Hi David,

Thank you for your message. I have uploaded 181109_e3_cut.msr at the
location you have requested. Please let me know if you can access the
file.

Thanks,
Biofysikos

On Fri, Feb 8, 2019 at 12:48 PM David Gault (Staff)
<d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>> wrote:


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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