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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have problems opening CZI files in FIJI. They are z-stacks, but when I open in Fiji with drag and drop I get only one slice. When I open through the bioformats importer, I get the following error message:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 80MB of 12191MB (<1%)<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<o:p></o:p></p>
<p class="MsoNormal"> at java.util.ArrayList.rangeCheck(ArrayList.java:653)<o:p></o:p></p>
<p class="MsoNormal"> at java.util.ArrayList.get(ArrayList.java:429)<o:p></o:p></p>
<p class="MsoNormal"> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:633)<o:p></o:p></p>
<p class="MsoNormal"> at loci.formats.FormatReader.setId(FormatReader.java:1399)<o:p></o:p></p>
<p class="MsoNormal"> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<o:p></o:p></p>
<p class="MsoNormal"> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<o:p></o:p></p>
<p class="MsoNormal"> at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p></o:p></p>
<p class="MsoNormal"> at loci.plugins.in.Importer.run(Importer.java:76)<o:p></o:p></p>
<p class="MsoNormal"> at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p></o:p></p>
<p class="MsoNormal"> at ij.IJ.runUserPlugIn(IJ.java:217)<o:p></o:p></p>
<p class="MsoNormal"> at ij.IJ.runPlugIn(IJ.java:181)<o:p></o:p></p>
<p class="MsoNormal"> at ij.Executer.runCommand(Executer.java:137)<o:p></o:p></p>
<p class="MsoNormal"> at ij.Executer.run(Executer.java:66)<o:p></o:p></p>
<p class="MsoNormal"> at java.lang.Thread.run(Thread.java:745)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Screenshots are attached.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Omero version is 5.3.2 from yesterday but I had the problem before.
<o:p></o:p></p>
<p class="MsoNormal">The files were generated with a Zeiss Elyra PS.1 microscope, processed in Zen to reconstruct SIM images and saved as CZI files. This usually works fine, but doing this in a batch process somehow generates files which are not properly read
in Fiji. I am able to load them in Zen, please tell me where I can upload the offending file (120 MB).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Many thanks!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Andreas<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black;mso-fareast-language:EN-GB">----------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">Dr Andreas Bruckbauer<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">FILM facility manager<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">Sir Alexander Fleming Building<br>
South Kensington Campus<br>
Imperial College London<br>
Exhibition Road<br>
London, SW7 2AZ<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">SAF 4th floor, open space desk 401<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">+44 (0)20 7594 2023<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB"><a href="mailto:a.bruckbauer@imperial.ac.uk"><span style="color:#0563C1">a.bruckbauer@imperial.ac.uk</span></a><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB"><a href="http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/"><span style="color:#0563C1">http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/</span></a><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="color:black;mso-fareast-language:EN-GB">----------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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