[ome-users] OMERO 5 Flex Import Problem

Tue Nov 12 17:47:58 GMT 2013

Dear all,

I tried using the new OMER 5.0 beta to import flex files from the PerkinElmer Opera.

I configure a CIA in the import.ini file and it starts to import correctly but then fails on importing the metadata.

I then used Insight -> Import and selected the corresponding .mea file. Then I clicked Import.

Here is an excerpt from the log file.

2013-11-12 18:15:53,280 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
2013-11-12 18:15:53,280 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
2013-11-12 18:15:53,285 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-12 18:15:53,285 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
2013-11-12 18:15:53,385 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-22) Network status: true (in 99 ms.)
2013-11-12 18:15:54,383 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
2013-11-12 18:15:54,383 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
2013-11-12 18:15:54,386 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-12 18:15:54,386 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
2013-11-12 18:16:01,674 DEBUG [                  ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null
2013-11-12 18:16:01,980 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470
2013-11-12 18:16:01,980 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values: \\10.79.2.101\hcs\OperaArchiveCol<file:///\\10.79.2.101\hcs\OperaArchiveCol>
2013-11-12 18:16:01,984 INFO  [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Added Flex reader server map 'CIA-1' = '\\10.79.2.101\hcs\OperaArchiveCol'.
2013-11-12 18:16:01,984 INFO  [       ome.formats.importer.ImportConfig] ( Thread-22) Bioformats version: 5.0.0-beta1 revision: 3a84df1 date: 19 June 2013
2013-11-12 18:16:01,986 INFO  [   ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM
2013-11-12 18:16:02,008 DEBUG [                  ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null
2013-11-12 18:16:02,182 INFO  [                loci.formats.ImageReader] ( Thread-22) FlexReader initializing V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
2013-11-12 18:16:02,183 INFO  [              loci.formats.FormatHandler] ( Thread-22) Reading contents of .mea file
2013-11-12 18:16:02,183 INFO  [              loci.formats.FormatHandler] ( Thread-22) Parsing XML from .mea file
2013-11-12 18:16:03,094 INFO  [              loci.formats.FormatHandler] ( Thread-22) Looking for corresponding .res file
2013-11-12 18:16:03,094 INFO  [              loci.formats.FormatHandler] ( Thread-22) Looking for files that are in the same dataset as V:\OperaDB_Backups\2013\2013_11\OperaDB_2013_Nov\Christophe Trefois\CT 2013.11.08_Rotenone_Paraquat\Settings\Beads control\CT 20131109_BeadsControl\Meas_01\Meas_01(2013-11-09_13-13-12).mea
2013-11-12 18:16:03,208 INFO  [              loci.formats.FormatHandler] ( Thread-22) Grouping together files in the same dataset
2013-11-12 18:16:34,782 INFO  [              loci.formats.FormatHandler] ( Thread-22) Parsing IFDs for well D6
2013-11-12 18:16:35,084 INFO  [              loci.formats.FormatHandler] ( Thread-22) Parsing .flex file (well D6)
2013-11-12 18:16:35,086 INFO  [              loci.formats.FormatHandler] ( Thread-22) Parsing XML in .flex file
2013-11-12 18:16:35,090 INFO  [              loci.formats.FormatHandler] ( Thread-22) Populating core metadata for well row 3, column 5
2013-11-12 18:16:35,090 INFO  [              loci.formats.FormatHandler] ( Thread-22) Populating pixel scaling factors
2013-11-12 18:16:35,090 WARN  [              loci.formats.FormatHandler] ( Thread-22) mismatch between image count, names and factors (count=9, names=3, factors=3)

Any help on this might be very helpful as I think I'm missing something here...

Thank you for your help.

................................................................................

Dipl.-Ing. Christophe TREFOIS
Ing. Sys. Com. Dipl. EPF

PhD Candidate

Université du Luxembourg | University of Luxembourg

Campus Belval | House of Biomedicine

7, avenue des Hauts-Fourneaux

L-4362 Esch-sur-Alzette

T +352 46 66 44 6124
F +352 46 66 44 6949
www.uni.lu/lcsb<http://www.uni.lu/lcsb>

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