[ome-users] Import of Nikon Elements .jp2 to Fiji through LOCI fails

Roger Leigh rleigh at dundee.ac.uk
Mon Feb 17 14:13:19 GMT 2014

On 13/02/14 14:07, Jonas Øgaard wrote:
> Dear all,
> I'm experiencing the following error upon attempting to load a jp2-image
> from Fiji through LOCI importer:
> (Fiji Is Just) ImageJ 1.48q; Java 1.6.0_24 [32-bit]; Windows XP 5.1;
> 15MB of 1529MB (<1%)
> java.lang.StringIndexOutOfBoundsException: String index out of range: -11198
> at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:881)
> at java.lang.StringBuffer.substring(StringBuffer.java:416)
> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1375)
> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> at loci.formats.DelegateReader.setId(DelegateReader.java:252)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> at loci.plugins.in.Importer.run(Importer.java:79)
> at loci.plugins.LociImporter.run(LociImporter.java:81)
> at ij.IJ.runUserPlugIn(IJ.java:199)
> at ij.IJ.runPlugIn(IJ.java:163)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
> Any ideas?
> Images have been uploaded at
> http://qa.openmicroscopy.org.uk/qa/feedback/7906/?token=ec71294c4313b9e97c090f48afeeaaf4

Dear Jonas,

Thank you for uploading the sample images.  I can reproduce the above
problem with the latest bioformats versions of 4.4 and 5.0.  This looks
like a problem with the ND2Reader and/or the JPEG2000 reader; the files
themselves appear to be fine, so this is likely to be a bug in one of
these readers.  I have opened a ticket for this issue, and added you as
a CC on it:

Many thanks,
Roger Leigh

Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096

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