[ome-users] Fwd: bug in ImageJ LOCI plugin?

[Melissa Linkert]

Hi Christian,

Thank you for the bug report.  For future reference, the best place to
report problems with Bio-Formats is on the ome-users mailing list:

http://www.openmicroscopy.org/site/community/mailing-lists

or the OME forums:

http://www.openmicroscopy.org/community/

> I hope you're the right person to contact. I'm trying to export an .lsm
> file which contains 28 z-planes of 256x256 pixels, 3 channels and 10
> timepoints using the Bioformats exporter. I check the options for
> separatingn the channels and time points but not the z-planes. I save in
> uncompressed format. After some files get created I always get the attached
> exception and the export stops.
> I'm working on a 32-bit Windows 7 machine. The problem occurs with Fiji and
> MBF ImageJ, both euipped with the latest stable release of the LOCI plugins.
> 
> Please let me know if you need the .lsm file in question, it is about 68MB.

There is no need to send the file, I can duplicate this problem already.
There is now a ticket on our issue tracking system to fix this:

http://trac.openmicroscopy.org.uk/ome/ticket/9829

...and I am optimistic that it will be fixed in the forthcoming 4.4.5
version of Bio-Formats.

Regards,
-Melissa

On Tue, Oct 30, 2012 at 03:12:44PM -0500, Curtis Rueden wrote:
> ---------- Forwarded message ----------
> From: Christian Liebig <christian.liebig at medizin.uni-tuebingen.de>
> Date: Tue, Oct 30, 2012 at 5:07 AM
> Subject: bug in ImageJ LOCI plugin?
> To: Curtis Rueden <ctrueden at wisc.edu>
> 
> 
> Dear Curtis,
> 
> I hope you're the right person to contact. I'm trying to export an .lsm
> file which contains 28 z-planes of 256x256 pixels, 3 channels and 10
> timepoints using the Bioformats exporter. I check the options for
> separatingn the channels and time points but not the z-planes. I save in
> uncompressed format. After some files get created I always get the attached
> exception and the export stops.
> I'm working on a 32-bit Windows 7 machine. The problem occurs with Fiji and
> MBF ImageJ, both euipped with the latest stable release of the LOCI plugins.
> 
> Please let me know if you need the .lsm file in question, it is about 68MB.
> 
> Thanks in advance for your help, kind regards,
> 
> Christian

> java.lang.reflect.InvocationTargetException
> 
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> 
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> 
> 	at java.lang.reflect.Method.invoke(Method.java:597)
> 
> 	at ij.Command.runPlugIn(Command.java:146)
> 
> 	at ij.Command.runCommand(Command.java:95)
> 
> 	at ij.Executer.run(Executer.java:64)
> 
> 	at java.lang.Thread.run(Thread.java:662)
> 
> Caused by: java.lang.ArrayIndexOutOfBoundsException: 30
> 
> 	at loci.plugins.out.Exporter.run(Exporter.java:547)
> 
> 	at loci.plugins.LociExporter.run(LociExporter.java:77)
> 
> 	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:256)
> 
> 	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:105)
> 
> 	at ij.IJ.runUserPlugIn(IJ.java:187)
> 
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 
> 	... 8 more
> 

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