[ome-users] Micro-manager import

[Brian Loranger]

HI Scott,

Definitely a  metadata issue which we'll need to look into. A test set  
would be great if you can supply one to us. We've got a only a small  
set of that data here and its all importing fine.

On 13 Jul 2009, at 22:09, Scott Grieshaber wrote:

> Hi
>
> We are running OMERO 4.0.3 on OSX and are not able to import our  
> micromanager data sets.  If i generate a test data set using the  
> demo camera the importer works just fine.  However, when we take  
> images using our camera (Cascade II EMCCD) import fails with the  
> following exception.  I am guessing this is a metadata issue  
> differing between the different cameras?
>
>
> java.lang.NullPointerException
> 	at ome.util.LSID.<init>(LSID.java:62)
> 	at  
> ome 
> .formats 
> .OMEROMetadataStoreClient 
> .setDetectorSettingsDetector(OMEROMetadataStoreClient.java:992)
> 	at  
> loci 
> .formats 
> .meta.FilterMetadata.setDetectorSettingsDetector(FilterMetadata.java: 
> 264)
> 	at  
> loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java: 
> 439)
> 	at loci.formats.FormatReader.setId(FormatReader.java:327)
> 	at loci.formats.ImageReader.setId(ImageReader.java:581)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:76)
> 	at loci.formats.ChannelFiller.setId(ChannelFiller.java:187)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:76)
> 	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:83)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:76)
> 	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:189)
> 	at  
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:313)
> 	at  
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java: 
> 192)
> 	at ome.formats.importer.ImportHandler.access$0(ImportHandler.java: 
> 110)
> 	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:91)
>
> If you need a test data set let me know.
>
> All the Best
>
> Scott
>
>
> Scott Grieshaber Ph.D.
> Assistant Professor
> University of Florida
> Department of Oral Biology
> School of Dentistry
> PO BOX 100424 Room D5-33D
> 1600 SW Archer Road
> Gainesville FL 32610
> (352) 273-8856
> sgriesha at ufl.edu
>
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Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No:  
SC015096)

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