Opening Olympus VSI Files from virtual Slide Scanner

[mlinkert]

Hi Oli,

My apologies for not replying sooner.

The good news is that the latest error is the same as what you originally reported. We've since fixed that problem (as noted here: http://trac.openmicroscopy.org.uk/ome/ticket/9618), and the latest trunk build does include the fix. If you're feeling adventurous you could try out the trunk build in Fiji, otherwise it might be best to wait for the upcoming 4.4.6 release.

-Melissa

[Oli]

Dear Melissa,

No worries! I'm so glad to have such great people and software available for all my petty problems; you make our lives and our users' so much easier as we can benefit form a truly open-source solution for all these commercial formats!

I've re-downloaded all of the LOCI jar files and it works great! I'll wait until the 4.4.6 release before making the new version of our little actionbar available.

Thanks again for your great help.

Oli

[Oli]

Dear Melissa,

Unfortunately, updating the Loci plugins manually has yielded old problems anew.

The Loci IDS/ICS exporter no longer works and is stuck after clicking the "save" button.

Best

Oli



** EDIT

Actually the error is also in the distribution from Fiji Update

The stack is 4ch 16z and 1t, and is a normal imageJ hyperstack (Also tried with the Mitosis3d sample dataset).

Code: Select all

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:662)
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


[mlinkert]

Hi Oli,

Thanks for the update, and my apologies for not getting back to you sooner.

We have now fixed the .ics/.ids export problem (see: https://github.com/openmicroscopy/bioformats/pull/373), so the next version of Bio-Formats should work. In the meantime, checking one of the "Write ... to a separate file" boxes or using the 'bfconvert' command line tool should allow you to convert files.

Regards,
-Melissa