[ome-users] LSM import failed.
Melissa Linkert
melissa at glencoesoftware.com
Mon Nov 29 16:20:30 GMT 2010
Hi Jerome,
Thank you for sending additional information.
> I've attached the DEBUG and OUTPUT logs from OMERO.importer... See the previous emails for the ERROR prompt and the JavaIO error generated.
One thing I noticed is that the version information in your output.txt
seems a bit off - the revision number and build date in the first few
lines indicate that you are using a version of the importer from over 2
years ago. If that really is the case, then it would almost certainly
explain why the files cannot be imported.
> I also tried loading one of the LSM files (first one) from that folder, with FIJI with the trunk of bioformats and get the same error.. Full stack trace from FIJI found below:
That stack trace indicates that at least one of the .lsm files is empty.
Can you please confirm whether or not this is the case?
The latest trunk build of Bio-Formats (r7260) should properly skip over
empty .lsm files, so with any luck the problem is now fixed. Note that
to use the very latest trunk build in Fiji, you need to update either by using
"Plugins > LOCI > Update LOCI Plugins" or by manually downloading a new
loci_tools.jar from http://loci.wisc.edu/bio-formats/downloads and
placing it in your Fiji plugins directory.
Regards,
-Melissa
On Thu, Nov 25, 2010 at 12:13:46PM +0000, Jerome Avondo wrote:
>
>
> Hi Melissa,
>
> Here are the MDB/LDB files and the first LSM:
> http://cmpdartsvr1.cmp.uea.ac.uk/downloads/data/Tubulin_101108.mdb/
>
> Here is the exact original folder contents:
>
> All_tub_40_25min_01__Sum0.lsm
> All_tub_40_25min_01__Sum.lsm
> All_tub_40_25min_02__Sum.lsm
> All_tub_40_25min_03__Sum0.lsm
> All_tub_40_25min_03__Sum1.lsmAll_tub_40_25min_03__Sum.lsm
> All_tub_40_25min_07__Sum0.lsm
> All_tub_40_25min_07__Sum1.lsm
> All_tub_40_25min_07__Sum2.lsm
> All_tub_40_25min_07__Sum3.lsm
> All_tub_40_25min_07__Sum4.lsm
> All_tub_40_25min_07__Sum5.lsm
> All_tub_40_25min_07__Sum.lsm
> All_tub_40_25min_15__Sum.lsm
> kimkong_z15.lsm
> MT_z05_thurs.lsm
> Tubulin_101108.ldb
> Tubulin_101108.mdb
>
> Total is about 20GB so not easy to make them all available to you... Though you might not need everything anyways... Full error log from OMERO.importer attached.
> I've attached the DEBUG and OUTPUT logs from OMERO.importer... See the previous emails for the ERROR prompt and the JavaIO error generated.
>
> I also tried loading one of the LSM files (first one) from that folder, with FIJI with the trunk of bioformats and get the same error.. Full stack trace from FIJI found below:
>
> java.io.EOFException: Attempting to read beyond end of file.
> at loci.common.NIOFileHandle.readByte(NIOFileHandle.java:219)
> at loci.common.RandomAccessInputStream.readByte(RandomAccessInputStream.java:286)
> at loci.common.RandomAccessInputStream.read(RandomAccessInputStream.java:403)
> at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:351)
> at loci.formats.FormatReader.setId(FormatReader.java:1067)
> at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:328)
> at loci.formats.FormatReader.setId(FormatReader.java:1067)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:432)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:136)
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> at loci.plugins.in.Importer.run(Importer.java:77)
> at loci.plugins.LociImporter.run(LociImporter.java:77)
> at ij.IJ.runUserPlugIn(IJ.java:193)
> at ij.IJ.runPlugIn(IJ.java:154)
> at ij.Executer.runCommand(Executer.java:147)
> at ij.Executer.run(Executer.java:78)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: java.nio.BufferUnderflowException
> at java.nio.Buffer.nextGetIndex(Buffer.java:474)
> at java.nio.HeapByteBuffer.get(HeapByteBuffer.java:117)
> at loci.common.NIOFileHandle.readByte(NIOFileHandle.java:217)
> ... 16 more
>
> Let me know if you need anything else,
> And thanks for your time/help!!
>
> Jerome.
>
> > Date: Wed, 24 Nov 2010 11:52:18 -0600
> > From: melissa at glencoesoftware.com
> > To: jeromeavondo at msn.com
> > CC: j.burel at dundee.ac.uk; ome-users at lists.openmicroscopy.org.uk
> > Subject: Re: [ome-users] LSM import failed.
> >
> > Hi Jerome,
> >
> > > That file is from a user's directory that contains more then one LSM in it (raw data and projections) and an .mdb file...
> > > If I add all the LSM files and ignore the .mdb file to the import queue in OMERO.importer, and try an import that is when it fails.
> >
> > That's certainly something we can fix, but we'll need to see the .mdb file in
> > order to do so. Could you please send the corresponding .mdb file and perhaps
> > the full text of the error message? If you need somewhere to upload it, just
> > let me know and I can send you our SFTP server information off-list.
> >
> > > So, OMERO.importer is still reading the mdb file even if I don't select it for import. Would it not be better to read the mdb file only if selected? If I don't select something for import I would excpect that to be the outcome.... But again there might be good reasons for you to do what you do... :)
> >
> > The .mdb file is always included if it references one of the selected LSM files.
> > It should not be included if you only select LSM files that are not referenced
> > by the .mdb file.
> >
> > Regards,
> > -Melissa
> >
> > On Tue, Nov 23, 2010 at 02:49:58PM +0000, Jerome Avondo wrote:
> > >
> > > Hi Jmarie,
> > >
> > > Right I have understood what is going on...
> > >
> > > That file is from a user's directory that contains more then one LSM in it (raw data and projections) and an .mdb file...
> > > If I add all the LSM files and ignore the .mdb file to the import queue in OMERO.importer, and try an import that is when it fails.
> > >
> > > If I move all the LSM files to a new directory, without the .mdb file, then the import succeeds....
> > >
> > > So, OMERO.importer is still reading the mdb file even if I don't select it for import. Would it not be better to read the mdb file only if selected? If I don't select something for import I would excpect that to be the outcome.... But again there might be good reasons for you to do what you do... :)
> > >
> > > I think the problem we have with the current approach is that users like to create their data by some imaging runs, so lots of LSMs and the mdb, then also produce projections for this data, so there are further LSMs not associated to the .mdb and all of these are stored in the same experiment folder....
> > >
> > > J.
> > >
> > >
> > >
> > > Date: Tue, 23 Nov 2010 13:14:39 +0000
> > > From: j.burel at dundee.ac.uk
> > > To: jeromeavondo at msn.com
> > > CC: ome-users at lists.openmicroscopy.org.uk
> > > Subject: Re: [ome-users] LSM import failed.
> > >
> > >
> > >
> > > Hi Jerome
> > >
> > > If you use the released version 4.2.1, it should work.
> > > I have just imported the LSM file.
> > >
> > > http://www.openmicroscopy.org.uk/site/support/omero4/downloads
> > >
> > >
> > > Jmarie
> > >
> > >
> > > ************************************************************
> > > Please consider the environment. Do you really need to print this email?
> > >
> > >
> > >
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
>
> 2010-11-25 12:03:35,363 22428 [ Thread-6] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to omero.nbi.bbsrc.ac.uk:4064
> 2010-11-25 12:03:38,772 25837 [ Thread-6] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
> 2010-11-25 12:03:39,179 26244 [ Thread-6] ERROR ome.formats.OMEROMetadataStoreClient - Can't modify the current group.
>
>
> 2010-11-25 12:03:39,758 26823 [ Thread-6] ERROR ome.formats.OMEROMetadataStoreClient - Can't modify the current group.
>
>
> 2010-11-25 12:03:39,883 26948 [ Thread-6] INFO ome.formats.importer.gui.LoginHandler - Login successful!
> 2010-11-25 12:03:39,914 26979 [ Thread-6] ERROR e.formats.importer.gui.HistoryTableStore - Error retrieving base list from Thu Nov 25 00:00:00 GMT 2010 to Thu Nov 25 23:59:59 GMT 2010.
> 2010-11-25 12:03:39,914 26979 [ Thread-6] ERROR e.formats.importer.gui.HistoryTableStore - Error retrieving base list from Wed Nov 24 00:00:00 GMT 2010 to Wed Nov 24 23:59:59 GMT 2010.
> 2010-11-25 12:03:39,914 26979 [ Thread-6] ERROR e.formats.importer.gui.HistoryTableStore - Error retrieving base list from Sat Nov 20 00:00:00 GMT 2010 to Thu Nov 25 23:59:59 GMT 2010.
> 2010-11-25 12:03:39,914 26979 [ Thread-6] ERROR e.formats.importer.gui.HistoryTableStore - Error retrieving base list from Sat Nov 13 00:00:00 GMT 2010 to Sat Nov 20 23:59:59 GMT 2010.
> 2010-11-25 12:03:39,914 26979 [ Thread-6] ERROR e.formats.importer.gui.HistoryTableStore - Error retrieving base list from Sun Oct 31 00:00:00 BST 2010 to Thu Nov 25 23:59:59 GMT 2010.
> 2010-11-25 12:03:44,747 31812 [ Thread-14] WARN e.formats.importer.gui.HistoryTableStore - History tables service Disabled.
> 2010-11-25 12:03:53,349 40414 [entQueue-0] INFO me.formats.importer.gui.FileQueueHandler - Scheduling candidate calculations(1)=[C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_02__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum1.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum.lsm, C:\Documents and Settings\avo
> ndoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum1.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum2.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum3.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum4.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum5.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_15__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\kimkong_z15.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_10
> 1108.mdb\MT_z05_thurs.lsm]
> 2010-11-25 12:03:53,349 40414 [entQueue-0] INFO me.formats.importer.gui.FileQueueHandler - Handling import containers(1)=[C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_02__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum1.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum.lsm, C:\Documents and Settings\avondoj\De
> sktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum0.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum1.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum2.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum3.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum4.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum5.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_15__Sum.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\kimkong_z15.lsm, C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.md
> b\MT_z05_thurs.lsm]
> 2010-11-25 12:04:01,857 48922 [2-thread-1] INFO ome.formats.importer.gui.ImportHandler - Background: Importing images
> 2010-11-25 12:04:01,857 48922 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:01,857 48922 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_01__Sum.lsm
> 2010-11-25 12:04:01,919 48984 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:02,795 49860 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,171 50236 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum.lsm
> 2010-11-25 12:04:03,186 50251 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum.lsm
> 2010-11-25 12:04:03,186 50251 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,186 50251 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:03,202 50267 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:03,202 50267 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_01__Sum0.lsm
> 2010-11-25 12:04:03,374 50439 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,468 50533 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,577 50642 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum0.lsm
> 2010-11-25 12:04:03,593 50658 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum0.lsm
> 2010-11-25 12:04:03,593 50658 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,609 50674 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:03,609 50674 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:03,609 50674 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_02__Sum.lsm
> 2010-11-25 12:04:03,640 50705 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,749 50814 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,859 50924 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_02__Sum.lsm
> 2010-11-25 12:04:03,874 50939 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_02__Sum.lsm
> 2010-11-25 12:04:03,874 50939 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:03,890 50955 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:03,890 50955 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:03,890 50955 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_03__Sum.lsm
> 2010-11-25 12:04:03,937 51002 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,031 51096 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,156 51221 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum.lsm
> 2010-11-25 12:04:04,156 51221 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum.lsm
> 2010-11-25 12:04:04,156 51221 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,172 51237 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:04,172 51237 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:04,172 51237 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_03__Sum0.lsm
> 2010-11-25 12:04:04,203 51268 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,312 51377 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,422 51487 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum0.lsm
> 2010-11-25 12:04:04,437 51502 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum0.lsm
> 2010-11-25 12:04:04,437 51502 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,437 51502 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:04,453 51518 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:04,453 51518 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_03__Sum1.lsm
> 2010-11-25 12:04:04,500 51565 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,610 51675 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,735 51800 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum1.lsm
> 2010-11-25 12:04:04,750 51815 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum1.lsm
> 2010-11-25 12:04:04,750 51815 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,750 51815 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:04,750 51815 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:04,750 51815 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum.lsm
> 2010-11-25 12:04:04,797 51862 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:04,907 51972 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,016 52081 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum.lsm
> 2010-11-25 12:04:05,032 52097 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum.lsm
> 2010-11-25 12:04:05,032 52097 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,047 52112 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:05,047 52112 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:05,047 52112 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum0.lsm
> 2010-11-25 12:04:05,079 52144 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,282 52347 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,407 52472 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum0.lsm
> 2010-11-25 12:04:05,423 52488 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum0.lsm
> 2010-11-25 12:04:05,423 52488 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,423 52488 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:05,423 52488 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:05,423 52488 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum1.lsm
> 2010-11-25 12:04:05,438 52503 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,532 52597 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,657 52722 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum1.lsm
> 2010-11-25 12:04:05,657 52722 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum1.lsm
> 2010-11-25 12:04:05,673 52738 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,673 52738 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:05,673 52738 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:05,673 52738 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum2.lsm
> 2010-11-25 12:04:05,783 52848 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,876 52941 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:05,986 53051 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum2.lsm
> 2010-11-25 12:04:06,001 53066 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum2.lsm
> 2010-11-25 12:04:06,017 53082 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,017 53082 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:06,017 53082 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:06,017 53082 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum3.lsm
> 2010-11-25 12:04:06,189 53254 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,283 53348 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,392 53457 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum3.lsm
> 2010-11-25 12:04:06,408 53473 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum3.lsm
> 2010-11-25 12:04:06,408 53473 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,408 53473 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:06,408 53473 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:06,408 53473 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum4.lsm
> 2010-11-25 12:04:06,502 53567 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,596 53661 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,721 53786 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum4.lsm
> 2010-11-25 12:04:06,737 53802 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum4.lsm
> 2010-11-25 12:04:06,737 53802 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,737 53802 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:06,737 53802 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:06,737 53802 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_07__Sum5.lsm
> 2010-11-25 12:04:06,846 53911 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:06,940 54005 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,049 54114 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum5.lsm
> 2010-11-25 12:04:07,081 54146 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum5.lsm
> 2010-11-25 12:04:07,081 54146 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,081 54146 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:07,081 54146 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:07,081 54146 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: All_tub_40_25min_15__Sum.lsm
> 2010-11-25 12:04:07,174 54239 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,268 54333 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,378 54443 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_15__Sum.lsm
> 2010-11-25 12:04:07,409 54474 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_15__Sum.lsm
> 2010-11-25 12:04:07,409 54474 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,409 54474 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:07,409 54474 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:07,409 54474 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: kimkong_z15.lsm
> 2010-11-25 12:04:07,472 54537 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,581 54646 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,691 54756 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\kimkong_z15.lsm
> 2010-11-25 12:04:07,706 54771 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\kimkong_z15.lsm
> 2010-11-25 12:04:07,706 54771 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,722 54787 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:07,722 54787 [2-thread-1] INFO ome.formats.importer.ImportLibrary - Metadata only import? false
> 2010-11-25 12:04:07,722 54787 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - LOADING_IMAGE: MT_z05_thurs.lsm
> 2010-11-25 12:04:07,784 54849 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:07,894 54959 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:08,003 55068 [2-thread-1] INFO ormats.importer.gui.LoggingImportMonitor - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\MT_z05_thurs.lsm
> 2010-11-25 12:04:08,019 55084 [2-thread-1] ERROR importer.gui.ErrorHandler$MyErrorHandler - FILE_EXCEPTION: C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\MT_z05_thurs.lsm
> 2010-11-25 12:04:08,019 55084 [2-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - Creating root!
> 2010-11-25 12:04:08,035 55100 [2-thread-1] ERROR ome.formats.importer.gui.ImportHandler - I/O error while importing image.
> 2010-11-25 12:04:39,815 86880 [4-thread-1] DEBUG ome.formats.OMEROMetadataStoreClient - KeepAlive ping.
> > Starting the importer (revision 2524).
> > Build date: 2008-06-23 10:29:21 +0100 (Mon, 23 Jun 2008)
> > Release date: 2008-06-16 16:18:13 +0100 (Mon, 16 Jun 2008)
> > Login Successful.
> > Starting import at: 2010-11-25 12:04
>
> > [0] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum.lsm"
> > [0] Loading image "All_tub_40_25min_01__Sum.lsm"...
> > [0] Failure importing.
> > [1] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_01__Sum0.lsm"
> > [1] Loading image "All_tub_40_25min_01__Sum0.lsm"...
> > [1] Failure importing.
> > [2] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_02__Sum.lsm"
> > [2] Loading image "All_tub_40_25min_02__Sum.lsm"...
> > [2] Failure importing.
> > [3] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum.lsm"
> > [3] Loading image "All_tub_40_25min_03__Sum.lsm"...
> > [3] Failure importing.
> > [4] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum0.lsm"
> > [4] Loading image "All_tub_40_25min_03__Sum0.lsm"...
> > [4] Failure importing.
> > [5] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_03__Sum1.lsm"
> > [5] Loading image "All_tub_40_25min_03__Sum1.lsm"...
> > [5] Failure importing.
> > [6] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum.lsm"
> > [6] Loading image "All_tub_40_25min_07__Sum.lsm"...
> > [6] Failure importing.
> > [7] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum0.lsm"
> > [7] Loading image "All_tub_40_25min_07__Sum0.lsm"...
> > [7] Failure importing.
> > [8] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum1.lsm"
> > [8] Loading image "All_tub_40_25min_07__Sum1.lsm"...
> > [8] Failure importing.
> > [9] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum2.lsm"
> > [9] Loading image "All_tub_40_25min_07__Sum2.lsm"...
> > [9] Failure importing.
> > [10] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum3.lsm"
> > [10] Loading image "All_tub_40_25min_07__Sum3.lsm"...
> > [10] Failure importing.
> > [11] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum4.lsm"
> > [11] Loading image "All_tub_40_25min_07__Sum4.lsm"...
> > [11] Failure importing.
> > [12] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_07__Sum5.lsm"
> > [12] Loading image "All_tub_40_25min_07__Sum5.lsm"...
> > [12] Failure importing.
> > [13] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\All_tub_40_25min_15__Sum.lsm"
> > [13] Loading image "All_tub_40_25min_15__Sum.lsm"...
> > [13] Failure importing.
> > [14] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\kimkong_z15.lsm"
> > [14] Loading image "kimkong_z15.lsm"...
> > [14] Failure importing.
> > [15] Importing "C:\Documents and Settings\avondoj\Desktop\ExpID-1283\temporaryProcessing\Tubulin_101108.mdb\MT_z05_thurs.lsm"
> > [15] Loading image "MT_z05_thurs.lsm"...
> > [15] Failure importing.
> > Total import time: 0 hour(s), 0 minute(s), 6 second(s).
> > Image import completed!
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