[ome-users] Fiji BioFormats TillVision import problems

[Melissa Linkert]

Hi Ian,

Thank you for sending example datasets privately, and my apologies for
the delay.

We fixed the problem yesterday evening as noted here:

https://github.com/melissalinkert/bioformats/commit/8bb3bee31898b428ef2f1257f6274ece4c43bf7e

A new trunk build of Bio-Formats that contains the fix will be available
in 1-2 weeks.  The upcoming 4.4 release of Bio-Formats will also contain
the fix.

Regards,
-Melissa

On Wed, Apr 11, 2012 at 11:22:29AM -0400, Melissa Linkert wrote:
> Hi Ian,
> 
> > I am having a little trouble reading in some TillPhotonics TillVision 4 .vws workspace files into Fuji using BioFormats import. Its very strange in that some workspace files work beautifully but others always produce this error:
> > 
> > Log for the misbehaving vws files is as follows:
> *snip*
> > 
> > There are of course images in the misbehaving workspaces that open fine in TillVision so its a little odd!
> > 
> > I am using Fuji w/ImageJ 1.46 on Java 1.6.0_31 64bit on OS X 10.7.3 and the trunk build of the LOCI plugins (though I have tried the stable and the dailies too). I have also the same error trying this on using ImageJ 2.00 Beta 1.
> > 
> > This problem looks similar to this OMERO issue which is marked as closed:
> > http://trac.openmicroscopy.org.uk/ome/ticket/5919  
> > 
> > 
> > 
> > I can happily ftp some working and non working .vws files as needed.  
> 
> Thank you for reporting this problem.
> 
> The best thing to do is to send us at least one of the datasets that
> doesn't open (the .vws file and a similarly named folder that ends in
> ".pst", if present).  I will send you information on how to upload
> datasets in a private email.
> 
> Regards,
> -Melissa
> 
> 
> On Wed, Apr 11, 2012 at 04:15:12PM +0200, Ian Dublon wrote:
> > Hello OME people,
> > 
> > I am having a little trouble reading in some TillPhotonics TillVision 4 .vws workspace files into Fuji using BioFormats import. Its very strange in that some workspace files work beautifully but others always produce this error:
> > 
> > Log for the misbehaving vws files is as follows:
> > loci.formats.FormatException: No images found.
> > at loci.formats.in.TillVisionReader.initFile(TillVisionReader.java:393)
> > at loci.formats.FormatReader.setId(FormatReader.java:1087)
> > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:480)
> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
> > at loci.plugins.in.Importer.showDialogs(Importer.java:139)
> > at loci.plugins.in.Importer.run(Importer.java:77)
> > at loci.plugins.LociImporter.run(LociImporter.java:79)
> > at ij.IJ.runUserPlugIn(IJ.java:183)
> > at ij.IJ.runPlugIn(IJ.java:150)
> > 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:680)
> > 
> > 
> > 
> > There are of course images in the misbehaving workspaces that open fine in TillVision so its a little odd!
> > 
> > I am using Fuji w/ImageJ 1.46 on Java 1.6.0_31 64bit on OS X 10.7.3 and the trunk build of the LOCI plugins (though I have tried the stable and the dailies too). I have also the same error trying this on using ImageJ 2.00 Beta 1.
> > 
> > This problem looks similar to this OMERO issue which is marked as closed:
> > http://trac.openmicroscopy.org.uk/ome/ticket/5919  
> > 
> > 
> > 
> > I can happily ftp some working and non working .vws files as needed.  
> > 
> > Any ideas shall be gratefully received,
> > 
> > Kind regards,
> > 
> > Ian Dublon
> > 
> > --
> > Ian Dublon Ph.D.
> > Postdoctoral Research Fellow
> > ian.dublon at slu.se (mailto:ian.dublon at slu.se) | ian.dublon at gmail.com (mailto:ian.dublon at gmail.com)
> > 
> > sv: +46(0)4041 5105 | m: +46(0)7035 81562  
> > uk: +44(0)7792 775262
> > 
> > http://www.slu.se/ian-dublon
> > Plant Protection Biology (Chemical Ecology Division)
> > Swedish University of Agricultural Sciences (SLU), P.O. Box 102, SE-230 53 Alnarp, Skåne, Sweden
> > 
> > 
> > Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
> > 
> > 
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