[ome-users] Cannot open Zeiss .czi files from SIM processing

[David Gault (Staff)]

Hi Sarah,

Thank you for bringing this to our attention. We have also received other reports for this same issue.
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.

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.
https://trac.openmicroscopy.org/ome/ticket/13317#ticket

With Thanks,
David Gault

On 10 Jan 2017, at 20:04, Clatterbuck Soper, Sarah (NIH/NCI) [F] <sarah.clatterbucksoper at nih.gov<mailto:sarah.clatterbucksoper at nih.gov>> wrote:


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.

When I open them with the Bio-Formats plugin (January 4 2017 version) I get the following exception:

(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%)
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
                at java.util.ArrayList.rangeCheck(ArrayList.java:653)
                at java.util.ArrayList.get(ArrayList.java:429)
                at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:633)
                at loci.formats.FormatReader.setId(FormatReader.java:1399)
                at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
                at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
                at loci.plugins.in.Importer.showDialogs(Importer.java:140)
                at loci.plugins.in.Importer.run(Importer.java:76)
                at loci.plugins.LociImporter.run(LociImporter.java:78)
                at ij.IJ.runUserPlugIn(IJ.java:217)
                at ij.IJ.runPlugIn(IJ.java:181)
                at ij.Executer.runCommand(Executer.java:137)
                at ij.Executer.run(Executer.java:66)
                at java.lang.Thread.run(Thread.java:745)

The pre-processed SIM files (which are much larger files) open fine with Bio-Formats or standard open.

Thanks for your help,

Sarah
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