Open Microscopy Environment

Hello,

I am trying to open jp2 files (sized between 1 and 5 MB) using the Bio-Formats importer on Image J and I keep receiving this error message:

java.lang.StringIndexOutOfBoundsException: String index out of range: -9532
at java.lang.AbstractStringBuilder.substring(AbstractStringBuilder.java:881)
at java.lang.StringBuffer.substring(StringBuffer.java:416)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1377)
at loci.formats.FormatReader.setId(FormatReader.java:1183)
at loci.formats.DelegateReader.setId(DelegateReader.java:259)
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:185)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.Executer.runCommand(Executer.java:127)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:680)

I tried selecting "crop on import" and was met with the same message. Any ideas on how to fix this??

Thanks,
Lauren

Hi Lauren,

Could you please confirm that you are using a recent version of Bio-Formats? If you select "Help > About Plugins > LOCI Plugins", the version number and date will be shown. 4.4.8 is the latest stable version, so if you see a version number prior to that then I would suggest upgrading.

If upgrading does not solve the problem, then could you please send one of the files that causes this error message so that we can better fix the problem? You can upload the file to:

http://qa.openmicroscopy.org.uk/qa/upload/

Regards,
-Melissa