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Hi Glyn,
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<pre><font face="Helvetica">Thank you for reporting and identifying this bug. We are reviewing a
fix here:</font></pre>
<pre><pre><font face="Helvetica"><a href="https://github.com/openmicroscopy/bioformats/pull/1531">https://github.com/openmicroscopy/bioformats/pull/1531</a></font></pre></pre>
<pre><font face="Helvetica">
I would expect this fix to be included in the 5.1.0 and 5.0.7 releases of
Bio-Formats.
<br></font></pre>
<pre><font face="Helvetica">Best,</font></pre>
<pre><span style="font-family: Helvetica;">Sebastien</span></pre>
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<div>On 16 Jan 2015, at 12:42, glyn nelson <<a href="mailto:glyn.nelson@ncl.ac.uk">glyn.nelson@ncl.ac.uk</a>> wrote:</div>
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<div dir="ltr">Hi,
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<div>The Bioformats website says to post bio-format bug reports here.</div>
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<div>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:</div>
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<div>(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%)</div>
<div> </div>
<div>java.lang.NumberFormatException: null</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:417)</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:499)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2144)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1207)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:689)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1317)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:141)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:79)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:81)</div>
<div><span class="" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:202)</div>
<div><span class="" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:166)</div>
<div><span class="" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:131)</div>
<div><span class="" style="white-space:pre"></span>at ij.Executer.run(Executer.java:64)</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:662)</div>
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<div><br>
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<div>and in ImageJ using bioformats_package.jar (stable):</div>
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<div>java.lang.NumberFormatException: null</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:415)</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Integer.parseInt(Integer.java:497)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateExperiment(ZeissCZIReader.java:2144)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.translateMetadata(ZeissCZIReader.java:1207)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:689)</div>
<div><span class="" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1317)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:141)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:79)</div>
<div><span class="" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:81)</div>
<div><span class="" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:183)</div>
<div><span class="" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:150)</div>
<div><span class="" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:127)</div>
<div><span class="" style="white-space:pre"></span>at ij.Executer.run(Executer.java:64)</div>
<div><span class="" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:619)</div>
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<div><br>
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<div>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.</div>
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<div>I'll upload an example image on the qa/upload site too.</div>
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<div>Cheers,</div>
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<div>Glyn</div>
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</blockquote>
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<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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