nd.2 file not importing

[lstrotman]

Hi I have been having trouble importing an nd.2 file using your loci plugin on both image j and fiji. I was wondering if you could help me as to why I might be having trouble. Here is the output I get back from Image J. Also I checked the build of the plugin and it is the most recent one.

ImageJ 1.47v; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 11MB of 18430MB (<1%)
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:888)
at loci.formats.FormatReader.setId(FormatReader.java:1244)
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:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.IJ.runPlugIn(IJ.java:149)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:258)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
at ij.IJ.runUserPlugIn(IJ.java:195)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.IJ.runPlugIn(IJ.java:149)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:438)
at ij.io.Opener.openImage(Opener.java:310)
at ij.io.Opener.openImage(Opener.java:333)
at ij.io.Opener.open(Opener.java:143)
at ij.io.Opener.openAndAddToRecent(Opener.java:246)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:619)

Any help would be much appreciated!

Thank you,

Lindsay

[rleigh]

Dear Lindsay,

Do you know which version number of the plugin you are using? If it's a 4.4 version, you could try the 5.0 prerelease version (in FiJi, you can select this in the updater by clicking on "Manage Update Sites" and then choosing "Bio-Formats 5".

If you could possibly upload one of the images you're having a problem with using http://qa.openmicroscopy.org.uk/qa/upload/ then we can take a look in more detail for you, and if there are any issues with Bio-Formats not being able to read this image file correctly, we can use this to fix it.

Many thanks,
Roger Leigh

[lstrotman]

Sorry it took so long for me to get back to your response. I checked my version and updated yet I still can't open the file. I uploaded a file I have been having trouble with let me know if you have any other suggestions.

Thanks,

Lindsay

[rleigh]

Dear Lindsay,

Thanks for uploading the file. I can reporoduce your problem with our current development release as well, and so I've opened a ticket to track this issue (https://trac.openmicroscopy.org.uk/ome/ticket/11873). You should be notified on any changes to the ticket, so you should be informed when it is fixed.

Thanks,
Roger