[ome-users] NDPI files

[Kim Linton]

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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