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Dear Jens,
<div class=""><br class="">
</div>
<div class="">thanks for reporting the error. The stack trace looks very similar to what has been</div>
<div class="">reported on the image.sc forum [1] as well as the Micro-Manager mailing list [2].</div>
<div class=""><br class="">
</div>
<div class="">For Micro-Manager 2.0.0-beta3 datasets, currently unsupported by Bio-Formats, we</div>
<div class="">are aware that the metadata format has been through several breaking changes,</div>
<div class="">including the IJType field which is the cause of the Bio-Formats parsing failure below.</div>
<div class=""><br class="">
</div>
<div class="">For Micro-Manager 1.4.23 datasets, it might be this constitutes a variant of the</div>
<div class="">Micro-Manager 1.4 metadata format [3]. But we have no representative datasets</div>
<div class="">showing the issue so far. Would it be possible for you to upload sampled data at</div>
<div class=""><a href="http://qa.openmicroscopy.org.uk/qa/upload/?" class="">http://qa.openmicroscopy.org.uk/qa/upload/?</a></div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://forum.image.sc/t/exception-thrown-when-importing-micro-manager-dataset-with-bioformats/11068" class="">https://forum.image.sc/t/exception-thrown-when-importing-micro-manager-dataset-with-bioformats/11068</a></div>
<div class="">[2] <a href="http://micro-manager.3463995.n2.nabble.com/Exception-thrown-when-importing-Micro-Manager-2-0-dataset-with-Bioformats-td7589436.html" class="">http://micro-manager.3463995.n2.nabble.com/Exception-thrown-when-importing-Micro-Manager-2-0-dataset-with-Bioformats-td7589436.html</a></div>
<div class="">[3] <a href="https://micro-manager.org/wiki/Files_and_Metadata" class="">https://micro-manager.org/wiki/Files_and_Metadata</a> </div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 19 Nov 2018, at 15:13, Jens Eriksson <<a href="mailto:jenseri@gmail.com" class="">jenseri@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">I have been saving the metadata.txt with the ome-tifs, but now I realize there has been an unnoticed error at the import step. We normally import the folders and not the files directly, so there has not been any indications of this error
to the user. If I import ome-tif + metadata.txt files directly, I discovered that the metadata.txt files are not processed correctly by BioFormats. The following error is logged in the OMERO-insight64 importer:
<div class="">
<div class=""><br class="">
</div>
<div class="">
<div class=""><font size="1" face="monospace" class="">java.lang.NumberFormatException: For input string: ""</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.NumberFormatException.forInputString(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Integer.parseInt(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Integer.parseInt(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:765)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:441)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:305)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.FormatReader.setId(FormatReader.java:1397)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ImageReader.setId(ImageReader.java:842)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.Memoizer.setId(Memoizer.java:662)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1070)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Thread.run(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><br class="">
</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.util.Status.update(Status.java:594)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1070)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Thread.run(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class="">Caused by: java.lang.NumberFormatException: For input string: ""</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.NumberFormatException.forInputString(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Integer.parseInt(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at java.lang.Integer.parseInt(Unknown Source)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:765)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:441)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:305)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.FormatReader.setId(FormatReader.java:1397)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ImageReader.setId(ImageReader.java:842)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.Memoizer.setId(Memoizer.java:662)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)</font></div>
<div class=""><font size="1" face="monospace" class=""><span style="white-space:pre-wrap" class=""></span>... 16 more</font></div>
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<div class="">This error is given by both MM 1.4.23-nightly & MM 2.0-beta3-nightly metadata.txt files. ome-tifs from these import without errors.</div>
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<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Jens<br class="">
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">On Thu, Nov 15, 2018 at 3:13 PM Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank" class="">s.besson@dundee.ac.uk</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Hi Jens,
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</div>
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<blockquote type="cite" class="">
<div class="">On 13 Nov 2018, at 14:42, Jens Eriksson <<a href="mailto:jenseri@gmail.com" target="_blank" class="">jenseri@gmail.com</a>> wrote:</div>
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<blockquote type="cite" class="">
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<div class="">I recently finished implementing an OMERO.server with a OMERO.web interface, together with the OMERO.figure & OMERO.iviewer apps (good job BTW, users and PIs LOVE these!).</div>
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<div class="">Thanks for the positive feedback. Always appreciated.</div>
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<div class="">However, neither OMERO.viewer or OMERO.figure display correct time points on timelapse data we generate.</div>
<div class="">It seems like OMERO/Bio-Formats is not correctly reading (or utilizing) TimeIncrement & TimeIncrementUnit from Micro-Manager generated files, even though the deltaT value for each image is displayed correctly.</div>
<div class="">We are running both MM 1.4.23-nightly and 2.0-beta-nightly to control our microscope, depending on user preference.</div>
<div class="">I occasionally upgrade the nightlies, but the problems I describe are common for all versions tested.</div>
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<div class="">How can I get correct TimeIncrement & TimeIncrementUnit values set for my existing Micromanager generated data in the OMERO.server/web environment?</div>
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<div class="">Question 2:</div>
<div class="">During the setup of the MM configuration files I have been very systematic and thorough, so that all relevant data (filter bandpass, product numbers, objective NAs, etc...) is captured in the Micro-Manager metadata through informative device and
property names.</div>
<div class="">As a facility manager it would be very helpful for me and my users to have easy access to this data through OMERO.</div>
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<div class="">There are different types of metadata and file representations created by Micro-Manager. For</div>
<div class="">versions 1.4.x, we tried to summarise the representation of the various scenarios in the table</div>
<div class="">at the bottom of this documentation page [1].</div>
<div class=""><br class="">
</div>
<div class="">As you mentioned Micro-Manager captures extensive metadata which is stored within a TIFF tag.</div>
<div class="">This metadata can optionally be saved as a separate text file. Additionally, a subset is also</div>
<div class="">converted into OME metadata and stored in the ImageDescription tag as per the OME-TIFF</div>
<div class="">specification.</div>
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<div class="">To maximise the acquisition metadata, our current recommendation is to create companion files</div>
<div class="">at acquisition containing the MM metadata and use this file when importing the data into OMERO.</div>
<div class="">This should result in the data being available as Original Metadata in the right-hand panel - see</div>
<div class="">screenshots below for an example with a sample dataset [2] created with the demo configuration.</div>
</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="http://docs.openmicroscopy.org/bio-formats/5.9.2/users/micromanager/index.html" target="_blank" class="">http://docs.openmicroscopy.org/bio-formats/5.9.2/users/micromanager/index.html</a> </div>
<div class="">[2] <font color="#0069d9" class=""><span class=""><u class=""><a href="http://downloads.openmicroscopy.org/images/Micro-Manager/1.4.22/thomas/test/test2_stack/" target="_blank" class="">http://downloads.openmicroscopy.org/images/Micro-Manager/1.4.22/thomas/test/test2_stack/</a></u></span></font></div>
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<div class=""><img id="m_2977828888505119788m_2889380162356099707D802730A-08D4-4BA2-9F86-7312DC5A2F2E" class=""></div>
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<div class="">Is there some plugin/app/script that makes the Micro-Manager metadata accessible on the OMERO.server, or at least viewable from the web interface?</div>
<div class="">If not, I can try to implement one. I have spent some time reading through tif-tags and MM metadata for other projects, but there is no need to reinvent the wheel if there is something out there.</div>
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<div class="">If you cannot get the data in the representation described above or if you have data already</div>
<div class="">imported, the expectationfrom the Micro-Manager file format specification [3] is that the</div>
<div class="">extra metadata should be stored in the private TIFF tag 51123. </div>
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<div class="">[3] <a href="https://micro-manager.org/wiki/Micro-Manager_File_Formats#Image_File_Directories" target="_blank" class="">https://micro-manager.org/wiki/Micro-Manager_File_Formats#Image_File_Directories</a></div>
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<div class="">It has always annoyed me that MM ome-tiff files won't display a correct frame interval when drag&dropped into ImageJ/FIJI.</div>
<div class="">On the other hand, if images are instead opened through the Bio-Formats Importer, then they loose their LUTs (but gain the lost frame intervals).</div>
<div class="">The lost LUTs is also a (minor) issue when importing MM data to OMERO.server.</div>
<div class="">I suspect that this is because ImageJ has its own TIF-tag that stores imageJ-metadata, and that there is some inconsistencies in how MM writes the tif tags here.</div>
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<div class="">Anyway, thanks for great softwares everyone, let's make them even better!</div>
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<div class="">All agreed. Micro-manager datasets are certainly a very interesting example of imaging data</div>
<div class="">where the overall metadata is stored according to various models (OME, ImageJ, MM-JSON)</div>
<div class="">and in different places. Preliminary discussion have been engaged on how to reconcile these</div>
<div class="">various sources of metadata when reading the files [4]. In the short run, the suggestion described</div>
<div class="">above is the one that hopefully should offer the maximal preservation of the original metadata.</div>
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[4] <a href="https://github.com/openmicroscopy/bioformats/pull/2213" target="_blank" class="">https://github.com/openmicroscopy/bioformats/pull/2213</a> </div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">Dr. Jens Eriksson, manager</div>
<div class="">Sellin Imaging Platform</div>
<div class="">Dep. Medical Biohecmistry and Microbiology</div>
<div class="">Uppsala University</div>
<div class="">Sweden</div>
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