Open Microscopy Environment

Hi,

after updating our NIS-Elements software, the nd2 files cannot be opened with your library anymore. Trying to open it with Fiji (I used the trunk built of loci-tools), I got the following error:

Code: Select all

java.lang.ArithmeticException: / by zero

   at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:542)

   at loci.formats.FormatReader.setId(FormatReader.java:1072)

   at loci.formats.DelegateReader.setId(DelegateReader.java:232)

   at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)

   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)

   at loci.plugins.in.Importer.showDialogs(Importer.java:125)

   at loci.plugins.in.Importer.run(Importer.java:77)

   at loci.plugins.LociImporter.run(LociImporter.java:79)

   at ij.IJ.runUserPlugIn(IJ.java:193)

   at ij.IJ.runPlugIn(IJ.java:154)

   at ij.IJ.runPlugIn(IJ.java:143)

   at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:252)

   at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)

   at ij.IJ.runUserPlugIn(IJ.java:193)

   at ij.IJ.runPlugIn(IJ.java:154)

   at ij.IJ.runPlugIn(IJ.java:143)

   at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)

   at ij.io.Opener.openImage(Opener.java:290)

   at ij.io.Opener.openImage(Opener.java:309)

   at ij.io.Opener.open(Opener.java:141)

   at ij.io.Opener.openAndAddToRecent(Opener.java:229)

   at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:182)

   at ij.plugin.DragAndDrop.run(DragAndDrop.java:158)

   at java.lang.Thread.run(Thread.java:662)



I uploaded a test file via http://qa.openmicroscopy.org.uk/qa/upload/
The ID is: 4014
http://qa.openmicroscopy.org.uk/qa/feed ... 46e9ce6143

Hi,

after updating our NIS-Elements software, the nd2 files cannot be opened with your library anymore. Trying to open it with Fiji (I used the trunk built of loci-tools), I got the following error:

*snip*

I uploaded a test file via http://qa.openmicroscopy.org.uk/qa/upload/
The ID is: 4014
http://qa.openmicroscopy.org.uk/qa/feed ... 46e9ce6143

Are you able to open this file in NIS Elements? I do see an error when opening the file with Bio-Formats, but I also cannot open the file using NIS Elements. If you are also unable to open the file with Nikon's software, then it is likely that the file is corrupt.

If you can open the file in NIS-Elements, then could you please indicate what the expected image dimensions are?

Regards,
-Melissa

Hi,

I uploaded the file again in case something went wrong last time: ID: 4025
http://qa.openmicroscopy.org.uk/qa/feed ... 657f10288c

I am able to open it with NIS-Elements and also with the NIS-Elements Viewer (Version 3.20.02, Build 687). The dimensions are: 256x256 pixels, 14bit Mono, 194 frames in total (92 time x 2 in z)

Hi,

I uploaded the file again in case something went wrong last time: ID: 4025
http://qa.openmicroscopy.org.uk/qa/feed ... 657f10288c

I am able to open it with NIS-Elements and also with the NIS-Elements Viewer (Version 3.20.02, Build 687). The dimensions are: 256x256 pixels, 14bit Mono, 194 frames in total (92 time x 2 in z)

Thank you for re-uploading the file, and for clarifying the expected dimensions. I cannot open the file in the version of NIS Elements that I have; investigating further, it is clear that non-backwards-compatible changes were made to the file format.

I have filed a ticket on our issue tracking system to resolve this problem:

http://trac.openmicroscopy.org.uk/ome/ticket/7098

If you would like to be automatically notified of changes to that ticket, please let me know (along with a valid email address) and I will make sure that you are CC'd.

Regards,
-Melissa