[ome-users] problem opening CZI files in FIJI

[Bruckbauer, Andreas]

Hello,

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:

(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%)
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)

Screenshots are attached.

Omero version is 5.3.2 from yesterday but I had the problem before.
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).

Many thanks!

Andreas

----------------------------------------------------
Dr Andreas Bruckbauer
FILM facility manager

Sir Alexander Fleming Building
South Kensington Campus
Imperial College London
Exhibition Road
London, SW7 2AZ

SAF 4th floor, open space desk 401
+44 (0)20 7594 2023
a.bruckbauer at imperial.ac.uk<mailto:a.bruckbauer at imperial.ac.uk>

http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/
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