[ome-users] problem opening CZI files in FIJI

Bruckbauer, Andreas a.bruckbauer at imperial.ac.uk
Tue Jan 10 13:59:45 GMT 2017


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!


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>


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