[ome-users] bioformats czi file reading

[Douglas Richardson]

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
>
>
>
>   _______________________________________________
> ome-users mailing list
> 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
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150121/28949e05/attachment.html>