[ome-users] Bug in Fiji

[Melissa Linkert]

Hi Tereza,

Thank you for reporting this problem, and for offering to upload the
dataset.  I will send FTP instructions in a private email.

In the meantime, could you please let us know which version of
Bio-Formats you are using?  "Help > About Plugins > Bio-Formats
Plugins..." will show the version installed in Fiji; the most recent
version is 5.7.1.  You might also try checking the "Open files
individually" option in the "Bio-Formats Import Options" window when
opening .stk files, as that may provide a temporary work-around for
opening single files.

Regards,
-Melissa

On Tue, Oct 10, 2017 at 4:19 AM, Faflikova, Tereza
<tereza.faflikova at fu-berlin.de> wrote:
> Dear OME users,
>
> recently I experienced an error within the Fiji. I tried to open a .nd file
> and this error message popped up:
>
>
>
> (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51q; Java 1.8.0_66 [64-bit]; Windows 7
> 6.1; 64MB of 12131MB (<1%)
>
> java.lang.IndexOutOfBoundsException: Index: 4, Size: 2
>  at java.util.ArrayList.rangeCheck(ArrayList.java:653)
>  at java.util.ArrayList.get(ArrayList.java:429)
>  at ome.xml.model.Instrument.getLightSource(Instrument.java:353)
>  at ome.xml.meta.OMEXMLMetadataImpl.setLaserID(OMEXMLMetadataImpl.java:9512)
>  at ome.xml.meta.FilterMetadata.setLaserID(FilterMetadata.java:1557)
>  at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:970)
>  at loci.formats.FormatReader.setId(FormatReader.java:1397)
>  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:219)
>  at ij.IJ.runPlugIn(IJ.java:183)
>  at ij.Executer.runCommand(Executer.java:137)
>  at ij.Executer.run(Executer.java:66)
>  at java.lang.Thread.run(Thread.java:745)
>
> The file was an over-night Experiment consisting of 4 stages, 151 time
> Points and 17 Z-stacks (and 3 channels).
>
> Can you please also send me the FTP Server address in order to upload the
> non-working file? The whole file has 41GB. I also cannot open single .stk
> files.
>
>
>
> Thank you for your help
>
> If you need more info about the Problem, please let me know.
>
>
>
> All the best,
>
> Tereza
>
>
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