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Hi Jens,
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<div class="">On 13 Nov 2018, at 14:42, Jens Eriksson <<a href="mailto:jenseri@gmail.com" class="">jenseri@gmail.com</a>> wrote:</div>
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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>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>There are different types of metadata and file representations created by Micro-Manager. For</div>
<div>versions 1.4.x, we tried to summarise the representation of the various scenarios in the table</div>
<div>at the bottom of this documentation page [1].</div>
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<div>As you mentioned Micro-Manager captures extensive metadata which is stored within a TIFF tag.</div>
<div>This metadata can optionally be saved as a separate text file. Additionally, a subset is also</div>
<div>converted into OME metadata and stored in the ImageDescription tag as per the OME-TIFF</div>
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<div>To maximise the acquisition metadata, our current recommendation is to create companion files</div>
<div>at acquisition containing the MM metadata and use this file when importing the data into OMERO.</div>
<div>This should result in the data being available as Original Metadata in the right-hand panel - see</div>
<div>screenshots below for an example with a sample dataset [2] created with the demo configuration.</div>
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<div>[1] <a href="http://docs.openmicroscopy.org/bio-formats/5.9.2/users/micromanager/index.html" class="">http://docs.openmicroscopy.org/bio-formats/5.9.2/users/micromanager/index.html</a> </div>
<div>[2] <font color="#0069d9" class=""><span style="caret-color: rgb(0, 105, 217);" class=""><u class=""><a href="http://downloads.openmicroscopy.org/images/Micro-Manager/1.4.22/thomas/test/test2_stack/" 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="">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>If you cannot get the data in the representation described above or if you have data already</div>
<div>imported, the expectationfrom the Micro-Manager file format specification [3] is that the</div>
<div>extra metadata should be stored in the private TIFF tag 51123. </div>
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<div>[3] <a href="https://micro-manager.org/wiki/Micro-Manager_File_Formats#Image_File_Directories" 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>All agreed. Micro-manager datasets are certainly a very interesting example of imaging data</div>
<div>where the overall metadata is stored according to various models (OME, ImageJ, MM-JSON)</div>
<div>and in different places. Preliminary discussion have been engaged on how to reconcile these</div>
<div>various sources of metadata when reading the files [4]. In the short run, the suggestion described</div>
<div>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" class="">https://github.com/openmicroscopy/bioformats/pull/2213</a> </div>
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<div>Best,</div>
<div>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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