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<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I tried using the new OMER 5.0 beta to import flex files from the PerkinElmer Opera.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I configure a CIA in the import.ini file and it starts to import correctly but then fails on importing the metadata.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I then used Insight -> Import and selected the corresponding .mea file. Then I clicked Import.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here is an excerpt from the log file.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:15:53,280 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:15:53,280 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values:
<a href="file:///\\10.79.2.101\hcs\OperaArchiveCol">\\10.79.2.101\hcs\OperaArchiveCol</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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'.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:15:53,385 DEBUG [penmicroscopy.shoola.util.NetworkChecker] ( Thread-22) Network status: true (in 99 ms.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:15:54,383 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:15:54,383 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values:
<a href="file:///\\10.79.2.101\hcs\OperaArchiveCol">\\10.79.2.101\hcs\OperaArchiveCol</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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'.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:01,674 DEBUG [ ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:01,980 INFO [ ome.formats.importer.ImportConfig] ( Thread-22) OMERO Version: 5.0.0-beta1-ice33-b3470<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:01,980 INFO [ ome.formats.importer.util.IniFileLoader] ( Thread-22) Raw Flex reader map values:
<a href="file:///\\10.79.2.101\hcs\OperaArchiveCol">\\10.79.2.101\hcs\OperaArchiveCol</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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'.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:01,986 INFO [ ome.formats.importer.ImportCandidates] ( Thread-22) Depth: 4 Metadata Level: MINIMUM<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:02,008 DEBUG [ ome.scifio.io.Location] ( Thread-22) Location.mapFile: embedded-stream.raw -> null<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] ( Thread-22) Reading contents of .mea file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:02,183 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing XML from .mea file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:03,094 INFO [ loci.formats.FormatHandler] ( Thread-22) Looking for corresponding .res file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:03,208 INFO [ loci.formats.FormatHandler] ( Thread-22) Grouping together files in the same dataset<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:34,782 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing IFDs for well D6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:35,084 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing .flex file (well D6)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:35,086 INFO [ loci.formats.FormatHandler] ( Thread-22) Parsing XML in .flex file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] ( Thread-22) Populating core metadata for well row 3, column 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:35,090 INFO [ loci.formats.FormatHandler] ( Thread-22) Populating pixel scaling factors<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Courier New"">2013-11-12 18:16:35,090 WARN [ loci.formats.FormatHandler] ( Thread-22<b><span style="background:yellow;mso-highlight:yellow">) mismatch between image count, names and factors (count=9,
names=3, factors=3)</span></b><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any help on this might be very helpful as I think I’m missing something here…<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for your help.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-add-space:auto">
<b><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:gray">................................................................................<o:p></o:p></span></b></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-add-space:auto">
<b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:gray">Dipl.-Ing. Christophe TREFOIS</span></b><span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:gray"><br>
<i>Ing. Sys. Com. Dipl. EPF <o:p></o:p></i></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-add-space:auto">
<span style="font-size:9.0pt;font-family:"Arial","sans-serif";color:gray">PhD Candidate<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><span style="font-size:7.5pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray;mso-fareast-language:FR-LU">Université du Luxembourg | University of Luxembourg<o:p></o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray;mso-fareast-language:FR-LU">Campus Belval | House of Biomedicine<o:p></o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span lang="FR-LU" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray;mso-fareast-language:FR-LU">7, avenue des Hauts-Fourneaux<o:p></o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span lang="FR-LU" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray;mso-fareast-language:FR-LU">L-4362 Esch-sur-Alzette<o:p></o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span lang="FR-LU" style="font-size:8.0pt;font-family:"Arial","sans-serif";color:gray;mso-fareast-language:FR-LU">T +352 46 66 44 6124<br>
F +352 46 66 44 6949<br>
<a href="http://www.uni.lu/lcsb"><span style="color:blue">www.uni.lu/lcsb</span></a><o:p></o:p></span></p>
<p class="MsoNormalCxSpMiddle" style="mso-margin-top-alt:auto;margin-bottom:3.0pt;mso-add-space:auto">
<span lang="FR-CH" style="font-size:7.5pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:gray">This message is confidential and may contain privileged information.
<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:gray">It is intended for the named recipient only.
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial","sans-serif";color:gray">If you receive it in error please notify me and permanently delete the original message and any copies.</span></b><b><span style="font-size:7.5pt;font-family:"Times New Roman","serif";color:gray"><o:p></o:p></span></b></p>
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