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Hi Kurt,
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<div class="">many thanks for the report and the uploaded sample files. We were able to reproduce the</div>
<div class="">exception below using Bio-Formats 5.2.2 and I have created a card to track the investigation [1].</div>
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<div class="">The issue comes from the underlying assumption of the MicroManagerReader that the TIFF</div>
<div class="">files will be named as img_00000000t_channel_00z.tif [2]. However this is not true in this</div>
<div class="">fileset which is why the dimensions are read incorrectly. We will be in contact with the Micro-Manager</div>
<div class="">team to clarify what should be expected when reading these filesets.</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://trello.com/c/n6aaUC9u/47-micromanager-separate-image-files-illegalargumentexception" class="">https://trello.com/c/n6aaUC9u/47-micromanager-separate-image-files-illegalargumentexception</a></div>
<div class="">[2] <a href="https://micro-manager.org/wiki/Micro-Manager_File_Formats#Separate_image_files" class="">https://micro-manager.org/wiki/Micro-Manager_File_Formats#Separate_image_files</a> </div>
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<div class="">On 16 Sep 2016, at 19:08, Thorn, Kurt <<a href="mailto:Kurt.Thorn@ucsf.edu" class="">Kurt.Thorn@ucsf.edu</a>> wrote:</div>
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<div style="direction: ltr; font-family: Tahoma; font-size: 10pt;" class="">Hi All -
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<div class="">We have some Micro-manager files saved as one tiff per channel taken with a recent version of Micro-manager 2.0 that will not open properly in the Bio-formats importer. I've put examples of the problematic files at
<a href="http://nic.ucsf.edu/MMexamples.zip" class="">http://nic.ucsf.edu/MMexamples.zip</a>. I get the following error:</div>
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<div class="">Thanks for your help.</div>
<div class="">Kurt</div>
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<div class="">java.lang.IllegalArgumentException: ZCT size vs image count mismatch (sizeZ=1, sizeC=1, sizeT=3, total=27)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatTools.getZCTCoords(FormatTools.java:578)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.MicromanagerReader$Position.getFile(MicromanagerReader.java:1125)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.MicromanagerReader$Position.getFile(MicromanagerReader.java:1119)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:444)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:298)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.formats.FormatReader.setId(FormatReader.java:1401)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.showDialogs(Importer.java:140)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.in.Importer.run(Importer.java:76)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at loci.plugins.LociImporter.run(LociImporter.java:78)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runUserPlugIn(IJ.java:217)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.IJ.runPlugIn(IJ.java:181)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.runCommand(Executer.java:137)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at ij.Executer.run(Executer.java:66)</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>at java.lang.Thread.run(Thread.java:745)</div>
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