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Hi Sarah,
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<div class="">Thank you for bringing this to our attention. We have also received other reports for this same issue.</div>
<div class="">I was able to test and reproduce the exception as you were seeing it and this does appear to be a bug in the Bio-Formats reader for some Zeiss CZI files.</div>
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<div class="">I have opened a trac bug ticket to manage this issue and added it to our Bio-Formats inbox for further investigation into a potential bug fix.</div>
<div class=""><a href="https://trac.openmicroscopy.org/ome/ticket/13317#ticket" class="">https://trac.openmicroscopy.org/ome/ticket/13317#ticket</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 10 Jan 2017, at 20:04, Clatterbuck Soper, Sarah (NIH/NCI) [F] <<a href="mailto:sarah.clatterbucksoper@nih.gov" class="">sarah.clatterbucksoper@nih.gov</a>> wrote:</div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">When I open them with the Bio-Formats plugin (January 4 2017 version) I get the following exception:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">(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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at java.util.ArrayList.rangeCheck(ArrayList.java:653)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at java.util.ArrayList.get(ArrayList.java:429)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:633)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.formats.FormatReader.setId(FormatReader.java:1399)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.plugins.in.Importer.showDialogs(Importer.java:140)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.plugins.in.Importer.run(Importer.java:76)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at loci.plugins.LociImporter.run(LociImporter.java:78)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at ij.IJ.runUserPlugIn(IJ.java:217)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at ij.IJ.runPlugIn(IJ.java:181)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at ij.Executer.runCommand(Executer.java:137)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at ij.Executer.run(Executer.java:66)<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class=""> at java.lang.Thread.run(Thread.java:745)<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">The pre-processed SIM files (which are much larger files) open fine with Bio-Formats or standard open.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
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<span style="font-size: 11pt;" class="">Thanks for your help,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""> </span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">Sarah<o:p class=""></o:p></span></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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