Open Microscopy Environment

Hello

We are trying to set up the Omero platform, but it appears to be unable to import files from our microscope, a Zeiss LSM 710. This is the Java error produced:

Code: Select all

2010-07-23 10:37:46,779 25347      [entQueue-0] INFO   me.formats.importer.gui.FileQueueHandler  - Handling import containers(1)=[/Users/MRC/Desktop/small-lsm.lsm]
2010-07-23 10:38:00,028 38596      [2-thread-1] INFO     ome.formats.importer.gui.ImportHandler  - Background: Importing images
2010-07-23 10:38:00,044 38612      [2-thread-1] INFO         ome.formats.importer.ImportLibrary  - Metadata only import? false
2010-07-23 10:38:00,046 38614      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - LOADING_IMAGE: small-lsm.lsm
2010-07-23 10:38:00,263 38831      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Creating root!
2010-07-23 10:38:02,413 40981      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Format exact match for: ZeissLSM
2010-07-23 10:38:02,561 41129      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Format exact match for: ZeissLSM
2010-07-23 10:38:02,565 41133      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Format exact match for: ZeissLSM
2010-07-23 10:38:02,635 41203      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Correction exact match for: Unknown
2010-07-23 10:38:02,651 41219      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Immersion exact match for: Unknown
2010-07-23 10:38:02,654 41222      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Correction exact match for: Fluar
2010-07-23 10:38:02,661 41229      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Immersion exact match for: Oil
2010-07-23 10:38:02,669 41237      [2-thread-1] WARN   el.enums.handlers.LaserMediumEnumHandler  - Unknown LaserMedium value '' will be stored as "Other"
2010-07-23 10:38:02,714 41282      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.LaserMedium exact match for: Unknown
2010-07-23 10:38:02,746 41314      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.LaserType exact match for: Unknown
2010-07-23 10:38:02,763 41331      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.LaserMedium exact match for: Other
2010-07-23 10:38:02,769 41337      [2-thread-1] WARN   odel.enums.handlers.LaserTypeEnumHandler  - Unknown LaserType value 'DPSS 561-10' will be stored as "Other"
2010-07-23 10:38:02,772 41340      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.LaserType exact match for: Other
2010-07-23 10:38:02,978 41546      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.PhotometricInterpretation exact match for: Monochrome
2010-07-23 10:38:03,018 41586      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: Unknown
2010-07-23 10:38:03,050 41618      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Binning exact match for: 1x1
2010-07-23 10:38:03,058 41626      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: PMT
2010-07-23 10:38:03,063 41631      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.PhotometricInterpretation exact match for: Monochrome
2010-07-23 10:38:03,069 41637      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: Unknown
2010-07-23 10:38:03,072 41640      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Binning exact match for: 1x1
2010-07-23 10:38:03,077 41645      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: PMT
2010-07-23 10:38:03,091 41659      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.PhotometricInterpretation exact match for: Monochrome
2010-07-23 10:38:03,093 41661      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: Unknown
2010-07-23 10:38:03,095 41663      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Binning exact match for: 1x1
2010-07-23 10:38:03,099 41667      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DetectorType exact match for: PMT
2010-07-23 10:38:03,124 41692      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Format exact match for: ZeissLSM
2010-07-23 10:38:03,153 41721      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.PixelsType exact match for: uint16
2010-07-23 10:38:03,171 41739      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DimensionOrder exact match for: XYCZT
2010-07-23 10:38:03,222 41790      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.Format exact match for: ZeissLSM
2010-07-23 10:38:03,479 42047      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.PixelsType exact match for: uint16
2010-07-23 10:38:03,481 42049      [2-thread-1] DEBUG      ome.formats.enums.IQueryEnumProvider  - Returning class omero.model.DimensionOrder exact match for: XYCZT
2010-07-23 10:38:03,486 42054      [2-thread-1] DEBUG        ome.formats.importer.ImportLibrary  - Image Count: 6
2010-07-23 10:38:03,487 42055      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - LOADED_IMAGE: small-lsm.lsm
2010-07-23 10:38:03,498 42066      [2-thread-1] INFO         ome.formats.importer.ImportLibrary  - Reader is not of HCS domain, use metafile: true
2010-07-23 10:38:03,635 42203      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - originalFile created
2010-07-23 10:38:03,636 42204      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - originalFile path created
2010-07-23 10:38:03,695 42263      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - BEGIN_POST_PROCESS
2010-07-23 10:38:03,698 42266      [2-thread-1] DEBUG        ome.formats.model.ChannelProcessor  - isGraphicsDomain: false
2010-07-23 10:38:03,756 42324      [2-thread-1] WARN       ome.formats.model.ReferenceProcessor  - Unknown target class for LSID: Image:0
2010-07-23 10:38:03,812 42380      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - END_POST_PROCESS
2010-07-23 10:38:03,815 42383      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - BEGIN_SAVE_TO_DB
2010-07-23 10:38:03,817 42385      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Starting containers....
2010-07-23 10:38:03,818 42386      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Image:0 == omero.model.ImageI@4e0add57,Image:0
2010-07-23 10:38:03,819 42387      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Instrument:0 == omero.model.InstrumentI@6f5e0eab,Instrument:0
2010-07-23 10:38:03,820 42388      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.ObjectiveSettings:0 == omero.model.ObjectiveSettingsI@2876b359,omero.model.ObjectiveSettings:0
2010-07-23 10:38:03,821 42389      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.OriginalFile:0 == omero.model.OriginalFileI@7e199049,omero.model.OriginalFile:0
2010-07-23 10:38:03,822 42390      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Pixels:0 == omero.model.PixelsI@3e5d9d90,Pixels:0
2010-07-23 10:38:03,824 42392      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:0 == omero.model.ChannelI@2a68097d,Channel:0:0
2010-07-23 10:38:03,831 42399      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:1 == omero.model.ChannelI@705789f3,Channel:0:1
2010-07-23 10:38:03,831 42399      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:2 == omero.model.ChannelI@1c7b0f4d,Channel:0:2
2010-07-23 10:38:03,832 42400      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Detector:0:0 == omero.model.DetectorI@3827de24,Detector:0:0
2010-07-23 10:38:03,832 42400      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Detector:0:1 == omero.model.DetectorI@5f57402b,Detector:0:1
2010-07-23 10:38:03,833 42401      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Detector:0:2 == omero.model.DetectorI@6629a046,Detector:0:2
2010-07-23 10:38:03,833 42401      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Dichroic:0:0 == omero.model.DichroicI@373ee92,Dichroic:0:0
2010-07-23 10:38:03,834 42402      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Dichroic:0:1 == omero.model.DichroicI@12b0f0ae,Dichroic:0:1
2010-07-23 10:38:03,850 42418      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Dichroic:0:2 == omero.model.DichroicI@14327236,Dichroic:0:2
2010-07-23 10:38:03,882 42450      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Dichroic:0:3 == omero.model.DichroicI@105b3e5d,Dichroic:0:3
2010-07-23 10:38:03,885 42453      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.FileAnnotation:0:0 == omero.model.FileAnnotationI@5eb8f6d,omero.model.FileAnnotation:0:0
2010-07-23 10:38:03,887 42455      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Laser:0:0 == omero.model.LaserI@27261218,LightSource:0:0
2010-07-23 10:38:03,891 42459      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LogicalChannel:0:0 == omero.model.LogicalChannelI@2026c088,omero.model.LogicalChannel:0:0
2010-07-23 10:38:03,892 42460      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LogicalChannel:0:1 == omero.model.LogicalChannelI@204b7b1,omero.model.LogicalChannel:0:1
2010-07-23 10:38:03,893 42461      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LogicalChannel:0:2 == omero.model.LogicalChannelI@1648ff68,omero.model.LogicalChannel:0:2
2010-07-23 10:38:03,896 42464      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Objective:0:0 == omero.model.ObjectiveI@8746d23,Objective:0:0
2010-07-23 10:38:03,898 42466      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:0 == omero.model.PlaneInfoI@42b36022,omero.model.PlaneInfo:0:0
2010-07-23 10:38:03,908 42476      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:1 == omero.model.PlaneInfoI@73d742a1,omero.model.PlaneInfo:0:1
2010-07-23 10:38:03,910 42478      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:2 == omero.model.PlaneInfoI@2490fd20,omero.model.PlaneInfo:0:2
2010-07-23 10:38:03,912 42480      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:3 == omero.model.PlaneInfoI@6366de01,omero.model.PlaneInfo:0:3
2010-07-23 10:38:03,917 42485      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:4 == omero.model.PlaneInfoI@140c7272,omero.model.PlaneInfo:0:4
2010-07-23 10:38:03,946 42514      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.PlaneInfo:0:5 == omero.model.PlaneInfoI@27341e11,omero.model.PlaneInfo:0:5
2010-07-23 10:38:03,973 42541      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:0 == omero.model.DetectorSettingsI@6e3e48f2,omero.model.DetectorSettings:0:0
2010-07-23 10:38:03,981 42549      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:1 == omero.model.DetectorSettingsI@df5cbd6,omero.model.DetectorSettings:0:1
2010-07-23 10:38:03,986 42554      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:2 == omero.model.DetectorSettingsI@1b4d774f,omero.model.DetectorSettings:0:2
2010-07-23 10:38:03,987 42555      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:0 == omero.model.LightPathI@7096985e,omero.model.LightPath:0:0
2010-07-23 10:38:03,987 42555      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:1 == omero.model.LightPathI@69adff28,omero.model.LightPath:0:1
2010-07-23 10:38:03,987 42555      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Starting references....
2010-07-23 10:38:03,988 42556      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Image:0 == Instrument:0
2010-07-23 10:38:03,988 42556      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Image:0 == omero.model.FileAnnotation:0:0
2010-07-23 10:38:03,989 42557      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Image:0 == omero.model.DatasetI:1
2010-07-23 10:38:03,989 42557      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:0 == Detector:0:0
2010-07-23 10:38:03,990 42558      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:0 == Dichroic:0:0
2010-07-23 10:38:03,990 42558      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:1 == Detector:0:1
2010-07-23 10:38:03,990 42558      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:1 == Dichroic:0:1
2010-07-23 10:38:03,991 42559      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.DetectorSettings:0:2 == Detector:0:2
2010-07-23 10:38:03,993 42561      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.FileAnnotation:0:0 == omero.model.OriginalFile:0
2010-07-23 10:38:03,994 42562      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.ObjectiveSettings:0 == Objective:0:0
2010-07-23 10:38:03,995 42563      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - containerCache contains 32 entries.
2010-07-23 10:38:03,996 42564      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - referenceCache contains 10 entries.
2010-07-23 10:38:04,706 43274      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Saved Pixels with ID: 151
2010-07-23 10:38:04,708 43276      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - END_SAVE_TO_DB
2010-07-23 10:38:04,804 43372      [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - DATASET_STORED
2010-07-23 10:38:04,837 43405      [2-thread-1] ERROR      ome.formats.importer.gui.GuiImporter  - EXCEPTION_EVENT
2010-07-23 10:38:04,855 43423      [2-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-07-23 10:38:04,874 43442      [2-thread-1] ERROR  e.formats.importer.gui.GuiCommonElements  - Couldn't find icon: null
2010-07-23 10:38:04,876 43444      [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - Creating root!
2010-07-23 10:38:04,880 43448      [2-thread-1] ERROR    ome.formats.importer.gui.ImportHandler  - Generic error while importing image.
java.lang.ArrayIndexOutOfBoundsException
   at java.lang.System.arraycopy(Native Method)
   at loci.formats.ImageTools.splitChannels(ImageTools.java:211)
   at loci.formats.in.ZeissLSMReader.openBytes(ZeissLSMReader.java:310)
   at loci.formats.ImageReader.openBytes(ImageReader.java:384)
   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:183)
   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:209)
   at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
   at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
   at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:164)
   at ome.formats.importer.OMEROWrapper.openPlane2D(OMEROWrapper.java:130)
   at ome.formats.importer.ImportLibrary.writeDataPlanarBased(ImportLibrary.java:818)
   at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:700)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:527)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:384)
   at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
   at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
   at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
   at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
   at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
   at java.util.concurrent.FutureTask.run(FutureTask.java:138)
   at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
   at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
   at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
   at java.lang.Thread.run(Thread.java:637)


Could anyone advise us? Is this just a case of waiting for a bug fix or is something wrong at our end?

Upon failure have you already submitted the data file that's causing the problem via the built-in QA system? If we have the file we should be able to help you out. If you want to do this without triggering the error you can do so here:

http://qa.openmicroscopy.org.uk/qa/upload/

Well, upon further examination, there seems to be more to this: we can in fact upload the files if there are 3 lsm files in the same directory. If not, they will not import. If there are 3 files then they will usually be sent to the server, but in triplicate: each upload attempt sends all three files!

I have sent two of these files to you via the link. I didn't see the opportunity elsewhere in the Omero.importer client to do so. One is a small test file (2 slices) whereas the other is a full file typical of what we use.

Thanks, we've got the files. I've tested them using Beta 4.2.0 and they seem to import fine. Which version of OMERO are you trying to import these files with?

You can see a movie detailing the feedback system in OMERO.importer here:

http://cvs.openmicroscopy.org.uk/snapsh ... edback.mov

(It appears that the message didnt submit, so sorry if this appears as a double post)

Thanks for checking. We are running beta 4.2.0 on a Mac Pro, and the clients are similarly the Mac versions. It's a new install, have we configured something incorrectly?

I don't believe so, no. The basic way LSM imports work is that when the LSM files themselves are isolated (in existence without an accompanying MDB file) they are imported as a single LSM dataset. When the MDB file is present, all LSM files referenced in that MDB are imported.

So, in order to reproduce your problem we'll need the MDB file and the LSM files from the folder you're having problems with.

I believe that the newer LSM format doesn't have MDB files associated with it. The older microscope (Zeiss 510) did, and the import does seem to work fine with those, but the newer microscope (Zeiss 710) doesn't generate those files, and is what appears to be causing problems.

Does it seem likely that the importer used is assuming that the .lsm's are of the older type then? I did notice when I uploaded the test files that there were very few Zeiss images amongst the test set, so perhaps this has been overlooked.

It doesn't help that the different versions use the same extension!

The stranger thing again is that I've been able to import all those files you sent with 4.2.0 without trouble. MDB files certainly aren't required and we're not explicitly looking for them other than to recognize their existence and use them if they exist. We have 100's of LSM datasets in the test suite, including many 710 datasets, so I wouldn't say we have bad coverage there.

You said the problem only happens when all three files are in the directory, correct?

If the three files are not being imported together, the the program refuses, giving the above error. If they are imported together then they are imported several times each.

Okay. Can you upload the third one to the QA system then please?