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

[Biofysikos Biologos]

Thank you. Looking forward to it.

Biofysikos

On Thu, Feb 14, 2019 at 11:37 AM David Gault (Staff)
<d.gault at dundee.ac.uk> wrote:
>
> Hi Biofysikos,
>
> A PR is a Pull Request 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> 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> 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> 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> 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> 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
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel