[ome-users] [Software Feedback] LOCI not functioning at all

[Curtis Rueden]

Hi Andrew,

I am CCing the ome-users mailing list, which is the best place to go for
Bio-Formats issues.

> However, recently after an update, the LOCI tools do not seem to work
> at all for any function.  Specifically I want to export .tif stacks to
> .mov, but receive the following error:

Unfortunately, it seems the current release version of Bio-Formats has some
bugs when saving as QT.

1) If you attempt to export an RGB Color image, you get the exception you
mention.

2) Exporting an 8-bit grayscale image succeeds, but QuickTime Player is
unable to read the output movie (at least on OS X 10.8.3). You can,
however, read it back into ImageJ using Bio-Formats.

3) Running "Make Composite" on an RGB Color image, and then exporting it,
succeeds but produces a file with three times as many timepoints, and only
a single channel. And it also cannot be read by QuickTime Player.

We will keep you posted on any progress in fixing these issues.

Regards,
Curtis



On Tue, May 28, 2013 at 12:42 AM, <ajauregui at lrri.org> wrote:

> Andrew Jauregui sent a message using the contact form at
> http://loci.wisc.edu/contact.
>
> Dear LOCI:
> As a microscopist, I am an avid user of FIJI.  However, recently after an
> update, the LOCI tools do not seem to work at all for any function.
>  Specifically I want to export .tif stacks to .mov, but receive the
> following error:
>
> (Fiji Is Just) ImageJ 1.47q; Java 1.6.0_45 [64-bit]; Mac OS X 10.6.8; 34MB
> of 7995MB (<1%)
>
> 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: ZCT size vs image count
> mismatch (sizeZ=61, sizeC=3, sizeT=1, total=61)
>         at loci.formats.FormatTools.**getZCTCoords(FormatTools.java:**424)
>         at loci.plugins.out.Exporter.run(**Exporter.java:556)
>         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:**196)
>         at ij.IJ.runPlugIn(IJ.java:160)
>         ... 8 more
>
> What might I need to do to restore functionality to this plugin?
>
> Sincerely,
> Andrew
>
>
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