[ome-users] NDPI files

Tue Aug 28 11:12:48 BST 2012

Hi Melissa,

Thanks for your response. It would be great to get automated emails on the
ticket. Could you please add myself and Anitha (cc'd)?

I hope all is going well with you,

Cheers,

Kim

On 28 August 2012 08:28, Melissa Linkert <melissa at glencoesoftware.com>wrote:

> Hi Kim,
>
> > I am trying to load an ndpi file for one of my researchers and get the
> > following error. If the file is too large are there any way for me to
> > convert it so it can be loaded and viewed in OMERO?
>
> At the moment, not really.  We are very aware of this problem, and have
> a solution in the works as documented here:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/5092
>
> We hope to have this working in time for the 4.5 release of OMERO.  If
> you would like to receive automated emails as we update the status of
> the above ticket, please let me know and I would be happy to CC you.
>
> Regards,
> -Melissa
>
> On Fri, Aug 24, 2012 at 09:30:49AM +1000, Kim Linton wrote:
> > Hi There,
> >
> > I am trying to load an ndpi file for one of my researchers and get the
> > following error. If the file is too large are there any way for me to
> > convert it so it can be loaded and viewed in OMERO?
> > Cheers,
> > Kim
> >
> >
> > ava.lang.RuntimeException: Width or height > 65500 is not supported.
> > at
> loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:117)
> >  at loci.formats.in.NDPIReader.setupService(NDPIReader.java:360)
> > at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:113)
> >  at loci.formats.ImageReader.openBytes(ImageReader.java:414)
> > at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
> >  at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189)
> > at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197)
> >  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
> > at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273)
> >  at
> >
> ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:872)
> > at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:797)
> >  at
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:573)
> > at
> >
> org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
> >  at
> >
> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
> > at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
> > at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> >  at
> >
> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> >  at java.lang.Thread.run(Thread.java:680)
> >
> > at
> >
> org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6384)
> >  at
> >
> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1248)
> > at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
> > at
> >
> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> >  at
> >
> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> >  at
> >
> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
> > at
> >
> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> >  at java.lang.Thread.run(Thread.java:680)
> > Caused by: java.lang.RuntimeException: Width or height > 65500 is not
> > supported.
> > at
> loci.formats.codec.JPEGTileDecoder.initialize(JPEGTileDecoder.java:117)
> >  at loci.formats.in.NDPIReader.setupService(NDPIReader.java:360)
> > at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:113)
> >  at loci.formats.ImageReader.openBytes(ImageReader.java:414)
> > at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
> >  at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189)
> > at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197)
> >  at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
> > at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:273)
> >  at
> >
> ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:872)
> > at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:797)
> >  at
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:573)
> > at
> >
> org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6335)
> >  ... 11 more
> >
> >
> > --
> >   Kim Linton
> > Senior Research Systems Facilitator/Lead for the e-Research Portfolio
> > Monash e-Research Centre
> > Building 75
> > Monash University
> > Clayton Victoria 3800, Australia
> > Ph:      +61 3 99020712
> > Mob:    0408 972 629
> > Fax:    +61 3 9902-0193
> > Email:  kim.linton at monash.edu
> > Web:    http://www.monash.edu.au/eresearch
> > Part time: Mon, Tues, Thurs & Fri
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>

-- 
Kim Linton
Senior Research Systems Facilitator/Lead for the e-Research Portfolio
Monash e-Research Centre
Building 75
Monash University
Clayton Victoria 3800, Australia
Ph:      +61 3 99020712
Mob:    0408 972 629
Fax:    +61 3 9902-0193
Email:  kim.linton at monash.edu
Web:    http://www.monash.edu.au/eresearch
Part time: Mon, Tues, Thurs & Fri
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