Problem opening certain .nd2 files in ImageJ
Posted: Fri Feb 01, 2013 4:12 pmI'm had an annoying problem with ImageJ today, well, the problem is still there actually since I haven't been able to solve it. Maybe someone here can help me?
It's the following: I need to convert .nd2 files containing time measurements to a tiff stack for my image analysis program (= in house developed) to be able to process them. The easiest way is (supposed to be) using ImageJ. So far, it worked for half of my movies, but not for the other half. As far as I can tell, there is no difference in image acquisition or the way I save the images. The only difference is that for the movies that open fine in ImageJ, I used the 488nm laser and the part that gives an error and does not want to open in ImageJ was imaged using the 561 nm laser.
The error I get is:
java.lang.ArrayIndexOutOfBoundsException: 503
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:533)
at loci.formats.FormatReader.setId(FormatReader.java:1320)
at loci.formats.DelegateReader.setId(DelegateReader.java:267)
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:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.IJ.runPlugIn(IJ.java:140)
at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:192)
The .nd2 files were recorded with a very recent version of NISElements (confocal). Can someone help me out on this? I really really need the tiff stacks, otherwise I cannot analyse my data...
It's the following: I need to convert .nd2 files containing time measurements to a tiff stack for my image analysis program (= in house developed) to be able to process them. The easiest way is (supposed to be) using ImageJ. So far, it worked for half of my movies, but not for the other half. As far as I can tell, there is no difference in image acquisition or the way I save the images. The only difference is that for the movies that open fine in ImageJ, I used the 488nm laser and the part that gives an error and does not want to open in ImageJ was imaged using the 561 nm laser.
The error I get is:
java.lang.ArrayIndexOutOfBoundsException: 503
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:533)
at loci.formats.FormatReader.setId(FormatReader.java:1320)
at loci.formats.DelegateReader.setId(DelegateReader.java:267)
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:184)
at ij.IJ.runPlugIn(IJ.java:151)
at ij.IJ.runPlugIn(IJ.java:140)
at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:192)
The .nd2 files were recorded with a very recent version of NISElements (confocal). Can someone help me out on this? I really really need the tiff stacks, otherwise I cannot analyse my data...