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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Caterina and David-<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thanks much for this communication and in particular for all the work on this. We first discussed this work with David at our 2018 Annual Users Meeting and it’s great to see the ideas mature into
working specs.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Overall , we like the idea of a tiered approach to the spec—this provides the flexibility required for real-world scientific environments (we couldn’t help wondering if you are going to provide an
award for the first validated “Virtuoso” implementation </span><span style="font-family:"Segoe UI Emoji",sans-serif;mso-fareast-language:EN-US">😉</span><span style="mso-fareast-language:EN-US">). In addition, it’s very clear that the original modelling OME
published in 2005 (Goldberg et al, <a href="https://doi.org/10.1186/gb-2005-6-5-r47">
https://doi.org/10.1186/gb-2005-6-5-r47</a>) has to be expanded to over other critical concepts around optical and illumination calibration that are required for transmitting and interpreting modern imaging modalities. We have been considering how to evolve
the Instrument model for some time—there are now many implementations of “light microscopy” in the just the biological sciences, so modelling becomes quite challenging. Regardless, intensity calibration seemed less important in 2005, it’s now quite critical.
We appreciate the effort you’ve put into this and your willingness to open the discussion on how we capture the diversity and details required for modern quantitative light microscopy.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Just so everyone is up to date, the work from Caterina and David dovetails with work from Norio Kobayashi (</span><a href="https://gitlab.com/openmicroscopy/incubator/ome-owl/">https://gitlab.com/openmicroscopy/incubator/ome-owl/</a>)
and a few others. If at all possible, we want to ensure all these efforts are at least are aware of each other and if possible, align.<span style="mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">We’re working towards a major OMERO release, so must focus on that over the next few weeks. We’ll follow up with more detailed comments in the next couple of weeks.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Thanks again for the great work.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Jason<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> ome-devel <ome-devel-bounces@lists.openmicroscopy.org.uk>
<b>On Behalf Of </b>Strambio, Caterina<br>
<b>Sent:</b> 11 April 2019 22:48<br>
<b>To:</b> ome-devel@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> [ome-devel] Proposal for 4D Nucleome Microscopy Metadata Guidelines based on the OME data model<o:p></o:p></span></p>
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<p class="MsoNormal">Dear All<br>
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the 4D Nucleome Imaging Standards Working Group would like to solicit feedback on proposed guidelines we are putting forwards for a metadata standard for describing:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) MICROSCOPE HARDWARE Specifications<o:p></o:p></p>
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<p class="MsoNormal">2) IMAGE ACQUISITION Settings<o:p></o:p></p>
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<p class="MsoNormal">3) OPTICAL, FIELD, EXCITATION POWER and WAVELENGTH, and DETECTOR CALIBRATION Procedures<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">used to document imaging experiments and foster their reproducibility.<br>
<br>
The guidelines incorporate and update the OME data model and aim at increasing data fidelity, easing future analysis and facilitating objective comparison of different imaging datasets and imaging experiments setups.<br>
<br>
The proposed 4DN-OME guidelines have the following distinctive features:<br>
<br>
1) Based on the premise that not all imaging experiments are “created equal” and that different reporting guidelines might be required depending upon the experimental intent, we propose a Tiered system of guidelines that specify what kind of metadata is required
for different kind of imaging experiments.<br>
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2) Attempt to transition the OME data model towards a clear set of community standards that could serve as a basis for an “Encode”-like standard for imaging.
<br>
<br>
3) Help to guide different stake holders, including manufacturers, experimental and computational biologists, peer reviewers, publishers and funding agencies in evaluating of the performance, quality and uncertainty associated with specific microscope setups.<br>
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The current version of the metadata model and tier system description can be found on GitHub at the following address:<br>
<br>
<a href="https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines">https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines</a>
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Please feel free to contact us for any question, concern, comment, (constructive) criticism.<br>
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Cheers<br>
<br>
Caterina Strambio De Castillia and David Grunwald<br>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Avenir-Book",serif;color:black">----------------</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Avenir-Book",serif;color:black">Caterina Strambio De Castillia, Ph.D. | Chan Zuckerberg Initiative Imaging Scientist |</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Avenir-Book",serif;color:black">Assistant Professor, Program in Molecular Medicine |</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Avenir-Book",serif;color:black">The University of Massachusetts Medical School | 373 Plantation Street, Biotech II, Suite 114<br>
Worcester, MA 01605, USA |</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Avenir-Book",serif;color:black">+ 1 857-288-9331 |
<a href="mailto:caterina.strambio@umassmed.edu">caterina.strambio@umassmed.edu</a> |
<a href="http://big.umassmed.edu/omegaweb/">http://big.umassmed.edu/omegaweb/</a> | @StrambioLab</span><span style="color:black"><o:p></o:p></span></p>
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