Open Microscopy Environment

I've been able to open ND2 files with ImageJ/Bio-Formats previously, but with a new crop of files, I keep getting the error:

ImageJ 1.48v; Java 1.6.0_65 [32-bit]; Mac OS X 10.9.4; 25MB of 400MB (6%)

java.lang.NumberFormatException: empty String
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:992)
at java.lang.Double.parseDouble(Double.java:510)
at loci.formats.in.NativeND2Reader.parseText(NativeND2Reader.java:2048)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:718)
at loci.formats.FormatReader.setId(FormatReader.java:1317)
at loci.formats.DelegateReader.setId(DelegateReader.java:253)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
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:695)

Any help on this would be greatly appreciated!

Hi,

Thanks for being in touch.

Can you please submit an example of the failing file to or QA system?

https://www.openmicroscopy.org/qa2/qa/upload/

Many thanks,

Kenny

Thanks for your help -- I've uploaded a sample.

Thanks for uploading the example image which shows the problem. I can reproduce the problem with this image, and I have opened a ticket for it here:

https://trac.openmicroscopy.org.uk/ome/ ... #comment:1

I've added you as a CC on the ticket.


Thanks,
Roger Leigh

Thanks! It looks like the ticket is listed as fixed. Do I need to download a new version of Bio-Formats to access the fix? If so, which one?

Hi,

This fix will be in Bio-Formats 5.0.4, which is planned for release later in the week, or early next week.

Best,

Kenny