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Hi Biofysikos,
<div class=""><br class="">
</div>
<div class="">A PR is a <a href="https://help.github.com/articles/about-pull-requests/" class="">Pull Request</a> 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).</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 12 Feb 2019, at 15:41, Biofysikos Biologos <<a href="mailto:biofysikos@gmail.com" class="">biofysikos@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Thank you! Btw, what is a PR and what is the estimate for<br class="">
incorporating the corrections in the next release?<br class="">
<br class="">
Thanks again,<br class="">
<br class="">
Biofysikos<br class="">
<br class="">
On Mon, Feb 11, 2019 at 1:29 PM David Gault (Staff)<br class="">
<<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
<blockquote type="cite" class=""><br class="">
Thanks Biofysikos,<br class="">
<br class="">
We received the file you submitted and have been able to test and reproduce the problem you described.<br class="">
I have opened a PR to prevent this exception in the future: <a href="https://github.com/openmicroscopy/bioformats/pull/3319" class="">
https://github.com/openmicroscopy/bioformats/pull/3319</a><br class="">
<br class="">
With Thanks,<br class="">
David Gault<br class="">
<br class="">
On 8 Feb 2019, at 15:20, Biofysikos Biologos <<a href="mailto:biofysikos@gmail.com" class="">biofysikos@gmail.com</a>> wrote:<br class="">
<br class="">
Hi David,<br class="">
<br class="">
Thank you for your message. I have uploaded 181109_e3_cut.msr at the<br class="">
location you have requested. Please let me know if you can access the<br class="">
file.<br class="">
<br class="">
Thanks,<br class="">
Biofysikos<br class="">
<br class="">
On Fri, Feb 8, 2019 at 12:48 PM David Gault (Staff)<br class="">
<<a href="mailto:d.gault@dundee.ac.uk" class="">d.gault@dundee.ac.uk</a>> wrote:<br class="">
<br class="">
<br class="">
Hi,<br class="">
<br class="">
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?<br class="">
If you have a sample file you can upload to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">
https://www.openmicroscopy.org/qa2/qa/upload/</a> then we can test the issue further.<br class="">
<br class="">
With Thanks,<br class="">
David Gault<br class="">
<br class="">
On 7 Feb 2019, at 15:16, Biofysikos Biologos <<a href="mailto:biofysikos@gmail.com" class="">biofysikos@gmail.com</a>> wrote:<br class="">
<br class="">
Hello,<br class="">
<br class="">
I have downloaded the latest bioformats MATLAB package and I would<br class="">
like to use it to read the metadata from an .msr<br class="">
(<a href="https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/lavision-imspector.html" class="">https://docs.openmicroscopy.org/bio-formats/5.8.2/formats/lavision-imspector.html</a>)<br class="">
<br class="">
When I try it in MATLAB I get the following error:<br class="">
<br class="">
Error using bfGetReader (line 85)<br class="">
Java exception occurred:<br class="">
java.lang.NullPointerException<br class="">
<br class="">
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:417)<br class="">
<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br class="">
<br class="">
at loci.formats.ImageReader.setId(ImageReader.java:842)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)<br class="">
<br class="">
<br class="">
Error in bfopen (line 114)<br class="">
r = bfGetReader(id, stitchFiles);<br class="">
<br class="">
Would the developers be interested in having more .msr files in order<br class="">
to improve the bfread function?<br class="">
<br class="">
Thank you<br class="">
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