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

[Melissa Linkert]

Hi Sam,

> I tried Upload Sample Image, however, Fiji doesn't give me any
> feedback that it's actually doing anything. I've placed the file here
> (103MB):
> http://www.saminverso.com/uploadMe/ADDLs3-48hrsMouse-Vib50-Biotyn-IHC-s1c2r2-5x-001-07.zvi

Fantastic, thank you.  This problem will be fixed in the upcoming 4.4.4
version of Bio-Formats, which will be available via the Fiji updater
shortly after being released.

Regards,
-Melissa

On Tue, Sep 11, 2012 at 11:38:49AM +0200, Samuel Inverso wrote:
> Hi Melissa,
> Thank you for the fast response.
> I'll use the ome-users list from now on (I read the mailing lists page
> a bit to quickly and didn't notice the "excluding Bio-Formats" part).
> 
> I tried Upload Sample Image, however, Fiji doesn't give me any
> feedback that it's actually doing anything. I've placed the file here
> (103MB):
> http://www.saminverso.com/uploadMe/ADDLs3-48hrsMouse-Vib50-Biotyn-IHC-s1c2r2-5x-001-07.zvi
> 
> Thank you for your help,
> Best,
> -Sam
> 
> 
> 2012/9/10 Melissa Linkert <melissa at glencoesoftware.com>:
> > 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)
> >>
> 
> 
> 
> -- 
> -