[ome-devel] Zeiss ZEN

[Melissa Linkert]

Hi Rubén,

Thank you for uploading sample files.

> The latest build of loci_tools.jar can import successfully a file with 1 serie: z3time5.lsm

That's great!

> What didn't work was a file containing 2 series of 3 slices, 1 channel, 5 timepoints: 3z2positions5timesteps.lsm

Unfortunately, that's not surprising, as Bio-Formats' Zeiss LSM reader
currently assumes that each file contains only one series.  I have filed a
ticket to add support for this and CC'd you; for anyone else who is interested,
the ticket can be viewed here:

http://loci.wisc.edu/trac/java/ticket/527

Regards,
-Melissa

On Wed, Aug 04, 2010 at 01:45:18PM +0200, Rubén Muñoz wrote:
> Hi Melissa, 
> 
> Permit me to contact you again regarding the Zeiss LSM importer.
> I uploaded two different files generated with an offline version of the ZEN software. There seems to be something new in this software: multiple series in one LSM files.
> 
> The latest build of loci_tools.jar can import successfully a file with 1 serie: z3time5.lsm
> 
> What didn't work was a file containing 2 series of 3 slices, 1 channel, 5 timepoints: 3z2positions5timesteps.lsm
> 
> Please let me know if I can help more with testing or data.
> 
> java.lang.IllegalArgumentException: 0 must not be null and positive.
> 	at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:41)
> 	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:150)
> 	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:95)
> 	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:414)
> 	at loci.formats.FormatReader.setId(FormatReader.java:1067)
> 	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:433)
> 	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:137)
> 	at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> 	at loci.plugins.in.Importer.run(Importer.java:77)
> 	at loci.plugins.LociImporter.run(LociImporter.java:77)
> 	at ij.IJ.runUserPlugIn(IJ.java:189)
> 	at ij.IJ.runPlugIn(IJ.java:155)
> 	at ij.Executer.runCommand(Executer.java:147)
> 	at ij.Executer.run(Executer.java:78)
> 	at java.lang.Thread.run(Thread.java:637)
> 
> 
> Thanks,
> Rubén