[ome-users] NDPI files

Tue Aug 28 14:19:42 BST 2012

Hi Kim,

You and Anitha have both been CC'd now; you should see an automated
email confirming that shortly.

Regards,
-Melissa

On Tue, Aug 28, 2012 at 08:12:48PM +1000, Kim Linton wrote:
> 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