[ome-users] Saving as Quicktime fails after latest Fiji update

[Melissa Linkert]

Hi Matt,

> Thanks, Melissa!  I appreciate your prompt reply.

No problem at all.

> Also -- and you can treat this as a low priority bug report -- previous
> versions of Bio-Formats crashed when I tried to write a 32-bit image stack
> as a quicktime movie. Of course, the work-around is straightforward
> (convert to some other format) so this is not a pressing issue.

That's actually expected behavior.  The QuickTime movie format to my
knowledge does not support 32-bit image data, so Bio-Formats will
produce an error when attempting to save 32-bit images to QuickTime.
Using another format (e.g. OME-TIFF) is the best plan, otherwise you
will need to downsample to 8 bits before saving as QuickTime.

Regards,
-Melissa

On Mon, Feb 11, 2013 at 12:22:58PM -0600, Matt Wyczalkowski wrote:
> Thanks, Melissa!  I appreciate your prompt reply.
> 
> Also -- and you can treat this as a low priority bug report -- previous
> versions of Bio-Formats crashed when I tried to write a 32-bit image stack
> as a quicktime movie. Of course, the work-around is straightforward
> (convert to some other format) so this is not a pressing issue.
> 
> Regards,
> 
> Matt
> 
> ---
> Matthew A. Wyczalkowski, Ph.D.
> NIH NRSA Postdoctoral Fellow
> Taber Lab, Department of Biomedical Engineering
> Washington University in St. Louis
> http://taberlab.seas.wustl.edu
> wyczalkowskim at wustl.edu
> 
> 
> On Mon, Feb 11, 2013 at 12:08 PM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > Hi Matt,
> >
> > > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime
> > > functionality fails.  This has worked well in the past.
> > >
> > > I am running Mac OS X 10.6.8.
> > > ImageJ: 1.47i
> > > Java: 1.6.0_37 (64 bit)
> > > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013
> > > Release: 4.5-DEV
> > >
> > > "Update Fiji" indicates Fiji is up to date.
> > >
> > > Steps to reproduce error:
> > > 1) File -> New... -> Image.  400x400 pix, 3 stacks
> > > 2) Plugins -> LOCI -> BioFormats Exporter.
> > > 3) Save as: foo.mov, Quicktime Format.
> > > 4) None of the "Write each..." boxes checked.
> > >
> > > I get the following exception:
> >
> > Thank you for the detailed bug report.  We have just now fixed this
> > problem, and so the next version of Bio-Formats should work as before
> > (see: https://github.com/openmicroscopy/bioformats/pull/373).
> >
> > In the meantime, checking one of the "Write ... to a separate file" boxes
> > should
> > allow you to save QuickTime files.
> >
> > Regards,
> > -Melissa
> >
> > On Mon, Feb 11, 2013 at 08:20:17AM -0600, Matt Wyczalkowski wrote:
> > > Hi,
> > >
> > > After a recent update by Fiji, the Loci Bio-formats Exporter Quicktime
> > > functionality fails.  This has worked well in the past.
> > >
> > > I am running Mac OS X 10.6.8.
> > > ImageJ: 1.47i
> > > Java: 1.6.0_37 (64 bit)
> > > Loci Plugins for ImageJ, revision d58fa88, built 31 Jan 2013
> > > Release: 4.5-DEV
> > >
> > > "Update Fiji" indicates Fiji is up to date.
> > >
> > > Steps to reproduce error:
> > > 1) File -> New... -> Image.  400x400 pix, 3 stacks
> > > 2) Plugins -> LOCI -> BioFormats Exporter.
> > > 3) Save as: foo.mov, Quicktime Format.
> > > 4) None of the "Write each..." boxes checked.
> > >
> > > I get the following exception:
> > >
> > > 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:148)
> > >     at ij.Command.runCommand(Command.java:97)
> > >     at ij.Executer.run(Executer.java:64)
> > >     at java.lang.Thread.run(Thread.java:680)
> > > Caused by: java.lang.IllegalArgumentException: Invalid Z size: 0
> > >     at loci.formats.FormatTools.getZCTCoords(FormatTools.java:403)
> > >     at loci.plugins.out.Exporter.run(Exporter.java:545)
> > >     at loci.plugins.LociExporter.run(LociExporter.java:77)
> > >     at
> > >
> > ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
> > >     at
> > > ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
> > >     at ij.IJ.runUserPlugIn(IJ.java:187)
> > >     at ij.IJ.runPlugIn(IJ.java:152)
> > >     ... 8 more
> > >
> > > Any help would be appreciated.
> > >
> > > Regards,
> > >
> > > Matt
> > >
> > > ---
> > > Matthew A. Wyczalkowski, Ph.D.
> > > NIH NRSA Postdoctoral Fellow
> > > Taber Lab, Department of Biomedical Engineering
> > > Washington University in St. Louis
> > > http://taberlab.seas.wustl.edu
> > > wyczalkowskim at wustl.edu
> >
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> >
> >