[ome-users] NDPI files

[Melissa Linkert]

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

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