[ome-users] bioformats czi file reading

[Curtis Rueden]

Hi Doug,

> Is this fix included in the daily build through the Fiji updater?

It will be uploaded to the Bio-Formats update site within 24 hours after
the following PR is merged:
    https://github.com/openmicroscopy/bioformats/pull/1535

Regards,
Curtis

On Wed, Jan 21, 2015 at 11:56 AM, Douglas Richardson <
ds.richardson at gmail.com> wrote:

> Hi Sebastien,
>
> Is this fix included in the daily build through the Fiji updater? Or do we
> need to wait for 5.0.7 or 5.1.0?
>
> Thanks,
>
> Doug
>
> On Mon, Jan 19, 2015 at 3:37 AM, Sebastien Besson (Staff) <
> s.besson at dundee.ac.uk> wrote:
>
>>  Hi Glyn,
>>
>>  Thank you for reporting and identifying this bug.  We are reviewing a
>> fix here:
>>
>> https://github.com/openmicroscopy/bioformats/pull/1531
>>
>>
>> I would expect this fix to be included in the 5.1.0 and 5.0.7 releases of
>> Bio-Formats.
>>
>> Best,
>>
>> Sebastien
>>
>>  On 16 Jan 2015, at 12:42, glyn nelson <glyn.nelson at ncl.ac.uk> wrote:
>>
>>  Hi,
>>
>>  The Bioformats website says to post bio-format bug reports here.
>>
>>  I can't get bioformats to open some czi files captured on a new Zeiss
>> LSM880.  I've tried to do so using Fiji and ImageJ with either
>> loci_tools.jar and bio-formats_plugins.jar, both stable and daily builds,
>> on a 64bit linux system.  Example error message below:
>>
>>  (Fiji Is Just) ImageJ 2.0.0-rc-19/1.49m; Java 1.6.0_24 [64-bit]; Linux
>> 3.11.10-21-desktop; 13MB of 10513MB (<1%)
>>
>> java.lang.NumberFormatException: null
>> at java.lang.Integer.parseInt(Integer.java:417)
>> at java.lang.Integer.parseInt(Integer.java:499)
>> at
>> loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2144)
>> at
>> loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1207)
>> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:689)
>> at loci.formats.FormatReader.setId(FormatReader.java:1317)
>> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
>> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>> at loci.plugins.in.Importer.run(Importer.java:79)
>> at loci.plugins.LociImporter.run(LociImporter.java:81)
>> at ij.IJ.runUserPlugIn(IJ.java:202)
>> at ij.IJ.runPlugIn(IJ.java:166)
>> at ij.Executer.runCommand(Executer.java:131)
>> at ij.Executer.run(Executer.java:64)
>> at java.lang.Thread.run(Thread.java:662)
>>
>>
>>  and in ImageJ using bioformats_package.jar (stable):
>>
>>  java.lang.NumberFormatException: null
>> at java.lang.Integer.parseInt(Integer.java:415)
>> at java.lang.Integer.parseInt(Integer.java:497)
>> at
>> loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2144)
>> at
>> loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1207)
>> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:689)
>> at loci.formats.FormatReader.setId(FormatReader.java:1317)
>> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
>> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
>> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
>> at loci.plugins.in.Importer.run(Importer.java:79)
>> at loci.plugins.LociImporter.run(LociImporter.java:81)
>> at ij.IJ.runUserPlugIn(IJ.java:183)
>> at ij.IJ.runPlugIn(IJ.java:150)
>> at ij.Executer.runCommand(Executer.java:127)
>> at ij.Executer.run(Executer.java:64)
>> at java.lang.Thread.run(Thread.java:619)
>>
>>  This was with a 3 channel (16bit depth each) z stack, but I have also
>> failed to open single channel z stacks taken with the same system too.
>>
>>  I'll upload an example image on the qa/upload site too.
>>
>>  Cheers,
>>
>>  Glyn
>>
>>
>>
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>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>>
>>   Dr Sébastien Besson
>> Open Microscopy Environment / Harvard Medical School
>> Wellcome Trust Centre for Gene Regulation and Expression,
>> College of Life Sciences, University of Dundee, Dow Street,
>> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
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>>
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