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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I am trying to view .czi files generated from processing of SIM images from a Zeiss Elyra scope. These images should be 20 slice Z-stacks with three channels, but I think they must be exotic in some way,
because the standard ImageJ open only shows the first slice.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">When I open them with the Bio-Formats plugin (January 4 2017 version) I get the following exception:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.6; 2990MB of 6110MB (48%)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at java.util.ArrayList.rangeCheck(ArrayList.java:653)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at java.util.ArrayList.get(ArrayList.java:429)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:633)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.formats.FormatReader.setId(FormatReader.java:1399)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.plugins.in.Importer.run(Importer.java:76)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at ij.IJ.runUserPlugIn(IJ.java:217)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at ij.IJ.runPlugIn(IJ.java:181)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at ij.Executer.runCommand(Executer.java:137)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at ij.Executer.run(Executer.java:66)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> at java.lang.Thread.run(Thread.java:745)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The pre-processed SIM files (which are much larger files) open fine with Bio-Formats or standard open.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks for your help,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Sarah<o:p></o:p></span></p>
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