[ome-users] bioformats czi file reading

[Sebastien Besson (Staff)]

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<mailto: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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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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