[ome-users] [locisoftware] Error opeing Zeiss ZVI Mosaic

[Melissa Linkert]

Hi Sam,

> I get an exception when attempting to open a ZVI containing a mosaic. This is using the latest Bio-format importer from within Fiji.
> It seems the issue is caused by the Stitch Tiles option. If stitch tiles is off then the images can be loaded individually.
> 
> Files were saved with Axiovision, and can be loaded fine back with it.
> 
> Any ideas would be appreciated because I'm like to look at this images on a Mac, and ImageJ/Fiji seems to be the only option.

Would you be willing to upload the file using "Help > Upload Sample
Image" in Fiji?  I wasn't able to reproduce this using the files
that I have here, but given that the file opens with the "Stitch tiles"
option turned off, I doubt that this will be difficult to fix once we
have a file that demonstrates the problem.

Regards,
-Melissa

P.S. Please note that the 'locisoftware' mailing list should no longer be
used for Bio-Formats questions.  The ome-users mailing list:

http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

is CC'd and is the correct place to send questions.

On Mon, Sep 10, 2012 at 06:09:11AM -0500, Samuel Inverso wrote:
> Hi,
> I get an exception when attempting to open a ZVI containing a mosaic. This is using the latest Bio-format importer from within Fiji.
> It seems the issue is caused by the Stitch Tiles option. If stitch tiles is off then the images can be loaded individually.
> 
> Files were saved with Axiovision, and can be loaded fine back with it.
> 
> Any ideas would be appreciated because I'm like to look at this images on a Mac, and ImageJ/Fiji seems to be the only option.
> 
> Sincerely,
> -Sam
>  
> 
> java.lang.IndexOutOfBoundsException: Index: 2, Size: 1
> 	at java.util.ArrayList.RangeCheck(ArrayList.java:547)
> 	at java.util.ArrayList.get(ArrayList.java:322)
> 	at ome.xml.model.Pixels.getPlane(Pixels.java:600)
> 	at loci.formats.ome.OMEXMLMetadataImpl.getPlanePositionZ(OMEXMLMetadataImpl.java:3626)
> 	at loci.formats.TileStitcher.setId(TileStitcher.java:235)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> 	at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682)
> 	at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)
> 	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:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 	at ij.IJ.runPlugIn(IJ.java:141)
> 	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:375)
> 	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:53)
> 	at ij.IJ.runUserPlugIn(IJ.java:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 	at ij.IJ.runPlugIn(IJ.java:141)
> 	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:413)
> 	at ij.io.Opener.openImage(Opener.java:288)
> 	at ij.io.Opener.openImage(Opener.java:309)
> 	at ij.io.Opener.open(Opener.java:138)
> 	at ij.io.Opener.openAndAddToRecent(Opener.java:224)
> 	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
> 	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
> 	at java.lang.Thread.run(Thread.java:662)
>