[ome-users] ND2 file from Nikon NIS element4

[Melissa Linkert]

Hi Chloë,

> I have a MAC running with Mac OS 10.6.8. I use ImageJ 1.46m to open all my
> files. Until last week, we had a Nikon microscope, with NIS element3. I
> could open the files with Bio-Formats, wich was really  really great. I
> used the stable version and the trunk build version. We updated our NIS
> element, and all the acquisition made with NIS element4 cannot be opened
> with Bio-formats. The export mode of NIS element viewer for mac, is
> horrible since it save each picture individually...and I have 4D
> acquisition with differents xy points...I cannot work with the viewer it
> will putt a mess in my computer!
> Here is the message I have while trying to open and ND2 file from NIS
> element4:

Thank you very much for reporting this problem.

As far as I can tell, there is no actual image data in the file that was
attached.  Are you able to open this specific file in Elements 4?  If
so, are the images all black?

Regards,
-Melissa

On Mon, May 07, 2012 at 09:44:11AM -0400, Chloe van Oostende wrote:
> Hi,
> I have a MAC running with Mac OS 10.6.8. I use ImageJ 1.46m to open all my
> files. Until last week, we had a Nikon microscope, with NIS element3. I
> could open the files with Bio-Formats, wich was really  really great. I
> used the stable version and the trunk build version. We updated our NIS
> element, and all the acquisition made with NIS element4 cannot be opened
> with Bio-formats. The export mode of NIS element viewer for mac, is
> horrible since it save each picture individually...and I have 4D
> acquisition with differents xy points...I cannot work with the viewer it
> will putt a mess in my computer!
> Here is the message I have while trying to open and ND2 file from NIS
> element4:
> 
> *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:587)*
> 
> *            at loci.formats.FormatReader.setId(FormatReader.java:1091)*
> 
> *            at loci.formats.DelegateReader.setId(DelegateReader.java:232)*
> 
> *            at
> loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)*
> 
> *            at
> loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)*
> 
> *            at loci.plugins.in.Importer.showDialogs(Importer.java:139)*
> 
> *            at loci.plugins.in.Importer.run(Importer.java:77)*
> 
> *            at loci.plugins.LociImporter.run(LociImporter.java:79)*
> 
> *            at ij.IJ.runUserPlugIn(IJ.java:184)*
> 
> *            at ij.IJ.runPlugIn(IJ.java:151)*
> 
> *            at ij.Executer.runCommand(Executer.java:127)*
> 
> *            at ij.Executer.run(Executer.java:64)*
> 
> *            at java.lang.Thread.run(Thread.java:680)*
> 
> Please find in attached file, an acquisition I have from NIS element4.
> Hope you will be able to update Bio-Formats, for the pleasure of all ImageJ
> users!
> Thanks!
> Best regards,
> 
> Chloë
> 
> -- 
> *Chloë van Oostende*
> *PhD molecular and plant cell biology*
> 
> Department of Biology
> Concordia University
> 7141 Sherbrooke Street West
> SP-553.05
> Montreal, Quebec
> *Canada H4B 1R6**
> *
> *Lab: (514) 848-2424 ext.5983*
> *
> *
> *http://www.chloevanoostende.net*


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