2020-06-09 | Open Microscopy Environment (OME)

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margin-left: 10px;">Explore</a></li> <li class="show-for-small-only"><a href="/explore/">Explore</a></li> </ul> </div> </div>  <a name="top-of-page"></a>  <div class="callout large primary" id="bg-image-announcements"> <div class="row column text-center"> <h1>2020-06-09</h1> <p></p> </div> </div> <hr class="invisible"> <div class="text-center"> <a id="back-to-top" href="/announcements/"><i class="fa fa-arrow-left"></i> back to Announcements</a> </div> <hr class="invisible"> <div class="row"> <div class="columns"> <p>Attending: Dom, Seb, June, Petr, Frances, Mark, Melissa, Will, Josh, Wilma, Andreas, Jason, Jean-Marie, Chris</p> <p>Start: 2:00 pm</p> <ol> <li> <h2 id="accepting-minutes-from-last-meeting">Accepting minutes from <a href="https://drive.google.com/open?id=0B9Xg53EhqUycZEVHclBwRHNFRGM"><u>last meeting</u></a></h2> </li> </ol> <p>N/A</p> <ol> <li> <h2 id="project-status">Project Status</h2> </li> </ol> <p>(2-3 minutes each)</p> <ul> <li> <p>IDR</p> <ul> <li> <p>Frances: good. Working on next release (3 datasets in testing).</p> <ul> <li>Josh: should be first release back on EBI Embassy</li> </ul> </li> </ul> </li> <li> <p>SA (learning/mail)</p> <ul> <li>Mark: Google Groups looking promising, offering archiving and <blockquote> <p>moderation.</p> </blockquote> <ul> <li>Can subscribe users without them receiving mail, useful to <blockquote> <p>let automated systems submit notifications to list.</p> </blockquote> </li> <li>Can coax subscription lists out of necromancer鈥檚 Mailman by <blockquote> <p>unpickling list config and can bulk-subscribe in Google.</p> </blockquote> </li> <li>Can fake list submissions without needing MX record <blockquote> <p>switched.</p> </blockquote> </li> <li> <p>Any final objections?</p> </li> <li> <p>Seb: migration timelines and any need for testing?</p> <ul> <li>Mark: still polishing the expected migration plan, get <blockquote> <p>procedure in place then circulate for feedback. Some list specificities need to be accounted for</p> </blockquote> </li> <li>Have other people joining for testing might come next</li> </ul> </li> </ul> </li> </ul> </li> <li> <p>Glencoe</p> <ul> <li>Chris: bioformats2raw and raw2ometiff issues. Might need to <blockquote> <p>write tutorials next.</p> </blockquote> <ul> <li>Josh: material available. Question is where does it live <blockquote> <p>given both repositories.</p> </blockquote> </li> <li> <p>Chris: considering single external location.</p> </li> <li>J-M: NGFF workshop guide migration? Josh: primarily waiting <blockquote> <p>on the renaming.</p> </blockquote> </li> <li>J-M: also more and more material specific to IDR</li> </ul> </li> </ul> </li> <li> <p>Community</p> <ul> <li>Jason: Community Survey went out yesterday. Responses largely <blockquote> <p>positive. Appreciative of the work. Lots of feedback. Do not edit!</p> </blockquote> <ul> <li> <p>Remote aspect of the meeting was very much appreciated</p> </li> <li> <p>Looking forward to the future (still to be defined)</p> </li> <li> <p>Missing in-person discussion</p> </li> </ul> </li> <li>Grant reviews available. Overall positive and acknowledging <blockquote> <p>great work.</p> </blockquote> </li> </ul> </li> </ul> <ol> <li> <h2 id="aob">AOB</h2> </li> </ol> <p>(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)</p> <ol> <li> <p>Dundee ongoing WFH arrangements.</p> <ol> <li></li> </ol> </li> <li> <h2 id="main-topic">Main Topic</h2> </li> </ol> <p>(20-25 minutes plus 15 minutes questions max)</p> <ul> <li> <p>Jason: points to more general directions.</p> <ul> <li> <p>Good response to new data vessels & workflows.</p> </li> <li> <p>Opportunities to bring this forward e.g. import</p> </li> <li> <p>Also metadata for correlative imaging, storing ROIs etc</p> </li> <li> <p>Moving into Summer with decreased team velocity (annual leave)</p> </li> <li> <p>Continue the trajectory of NGFF started in April. Metadata</p> <blockquote> <p>specifications</p> </blockquote> </li> </ul> </li> <li>Josh e.g. what if ROIs are no longer in the DB? How does that affect <blockquote> <p>our APIs like the iviewer issue above</p> </blockquote> <ul> <li>Start from IDR datasets, store ROIs in Zarr and use this define <blockquote> <p>new APIs</p> </blockquote> </li> <li>J-M: also applies to results generated for an image e.g. Ilastik <blockquote> <p>probability maps</p> </blockquote> </li> </ul> </li> <li>Jason: IDR datasets are great use cases for exercising these <blockquote> <p>directions</p> </blockquote> <ul> <li>Could we get all behind getting data imported in IDR? Distribute <blockquote> <p>datasets?</p> </blockquote> </li> <li>E.g. idr0081 (adenovirus) has lots of interesting metadata that <blockquote> <p>could be used e.g. for parade</p> </blockquote> </li> </ul> </li> <li>J-M: feedback from workshop also pointed towards making short videos <blockquote> <p>available (<20min)</p> </blockquote> <ul> <li>Jason: appreciation of video content for the meeting (despite <blockquote> <p>timing & accessibility issues)</p> </blockquote> </li> </ul> </li> <li>Josh: discuss IDR datasets post standup? Similar process to what <blockquote> <p>happened while discussing the conversion of 7 specific images ahead of the meeting</p> </blockquote> <ul> <li>Possible topics: rendering, acquisition, plate, ROIs,</li> </ul> </li> <li>Will: Follow-up discussion on linking to ROIs in iviewer <blockquote> <p><a href="https://github.com/ome/omero-iviewer/issues/308"><u>https://github.com/ome/omero-iviewer/issues/308</u></a></p> </blockquote> <ul> <li>For single-shape ROI use case, open the image, left-hand panel <blockquote> <p>does not change (full image thumbnails, images in dataset and/or well)</p> </blockquote> </li> <li> <p>How to construct the query with other parameters</p> <ul> <li>Generally scalability problem with creating a URL after <blockquote> <p>selecting N ROIs</p> </blockquote> </li> <li>Jean-Marie: question of sharing the same view e.g. <blockquote> <p>resolution level</p> </blockquote> </li> <li>Jason: are ROIs transmitted when clicking on viewport <blockquote> <p>settings?</p> </blockquote> </li> <li>Josh: example of COVID datasets (single ROIs for each <blockquote> <p>figure).</p> </blockquote> </li> <li>Chris: similar exposure with Pathviewer. Quickly get into <blockquote> <p>weeds when replicating what鈥檚 in the UI esp. When considering active/inactive</p> </blockquote> </li> <li>For single ROI case, capturing viewport is a good <blockquote> <p>workaround. Does not solve the bigger issue</p> </blockquote> </li> <li>In pathviewer either show viewport or link to ROI and do not <blockquote> <p>allow configuration</p> </blockquote> </li> <li>Will: main thing remaining is the control of the Zoom. Seb: <blockquote> <p>expand zoom level using bounding box of the ROI</p> </blockquote> </li> </ul> </li> <li> <p>Multiple ROIs?</p> <ul> <li>Chris: do not allow unless you are ready to explain why some <blockquote> <p>of them are not showed</p> </blockquote> </li> <li>Current implementation with multiple ROIs queries all images <blockquote> <p>associated with each ROI and displays them in the left-hand panel</p> </blockquote> </li> <li> <p>J-M: issue of creating duplicate thumbnails</p> </li> <li>Jason: would not break thumbnail/image paradigm in left-hand <blockquote> <p>panel</p> </blockquote> </li> <li>If multiple ROIs are part of the same image, this loses the <blockquote> <p>ability to see all the selected ROIs at once</p> </blockquote> </li> <li>Petr: cf feedback from EDI workshop with similar requests, <blockquote> <p>interested in group of ROIs. Chris: built Pathviewer grid with that use case in mind, took > 1 year. Very hard to build generic solutions that are application-agnostic</p> </blockquote> </li> <li>Jason: not even thinking how this would scale in the HCS <blockquote> <p>domain</p> </blockquote> </li> </ul> </li> <li> <p>Seb: might need to solve 1 ROI/N shape problem</p> <ul> <li>Josh: do it iteratively, i.e. get rois=xxx first then <blockquote> <p>shapes==xxx</p> </blockquote> </li> <li>Will: effectively the implementation is working on shapes at <blockquote> <p>the moment</p> </blockquote> </li> <li> <p>Chris: Support both URLs styles when selecting object</p> </li> <li>When selecting a ROI, return rois or shapes?</li> </ul> </li> <li> <p>Petr: question of shape propagation through Z</p> <ul> <li>Jason: important but separate question. People in need for <blockquote> <p>this functionality.</p> </blockquote> </li> <li>Chris: concepts around multi-shaped ROIs very loosely <blockquote> <p>defined.</p> </blockquote> </li> </ul> </li> </ul> </li> <li></li> </ul> </div> </div> <div class="row"> <div class="column"> <p class="text-right"> — <i></i> </p> </div> </div>   <div class="text-center"> <a id="back-to-top" href="#top-of-page"><i class="fa fa-arrow-up"></i> back to top</a> </div>  <hr class="whitespace"> <div id="footer" class="callout large secondary"> <div class="row"> <div class="small-12 medium-4 columns"> <div class="medium-4"><a href="/index.html"><img class="footer-logo" src="/img/logos/ome-main-nav.svg" alt="OME logo" /></a></div> <p>© 2005-2024 University of Dundee & Open Microscopy Environment. <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International License</a></p> <p>OME source code is available under the <a href="https://www.gnu.org/copyleft/gpl.html">GNU General public license</a> or more permissive open source licenses, or through commercial license from <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a><br/>OME, Bio-Formats, OMERO, IDR and their associated logos are trademarks of <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a>, which holds these marks to protect them on behalf of the OME community.</p> <p class="tiny-print" style="float:left;">[ <a href="/site-map/">Site Map</a> ]</p> <p class="tiny-print" style="float:right;">Version: 2024.11.21</p> </div> <div class="medium-2 columns"> <h6>Learn About Us</h6> <ul class="menu vertical"> <li><a href="/about/">Who We Are</a></li> <li><a href="/teams/">Our Team</a></li> <li><a href="/explore/">What We Can Do</a></li> <li><a href="/news/">What We鈥檙e Up To</a></li> <li><a href="/events/ome-community-meeting-2024/">OME 2024</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Try Our Products</h6> <ul class="menu vertical"> <li><a href="/omero/downloads/">OMERO <span class="badge">Download</span></a></li> <li><a href="/bio-formats/downloads">Bio-Formats <span class="badge">Download</span></a></li> <li><a href="/ome-files/downloads">OME Files <span class="badge">Download</span></a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Knowledge Base</h6> <ul class="menu vertical"> <li><a href="/support/">Support</a></li> <li><a href="/docs/">Documentation</a></li> <li><a href="https://omero-guides.readthedocs.io/">User Guides</a></li> <li><a href="https://www.openmicroscopy.org/forums">Forum</a></li> <li><a href="https://www.openmicroscopy.org/security/advisories/">Security Advisories</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns end"> <h6>OME Public</h6> <ul class="menu vertical"> <li><a href="https://twitter.com/openmicroscopy" target="_blank"><i class="fa fa-fw fa-twitter"></i> Twitter</a></li> <li><a href="https://www.linkedin.com/company/ome---open-microscopy-environment" target="_blank"><i class="fa fa-fw fa-linkedin"></i> LinkedIn</a></li> <li><a href="https://www.facebook.com/openmicroscopy" target="_blank"><i class="fa fa-fw fa-facebook"></i> Facebook</a></li>  <li><a href="/on-the-web/" target="_blank"><i class="fa fa-globe"></i> On the Web</a></li> <li class="hide-for-large-only"> </li> </ul> </div> </div> </div> <script src="https://code.jquery.com/jquery-2.1.4.min.js"></script> <script src="/js/vendor/jquery.js"></script> <script src="/js/vendor/what-input.js"></script> <script src="/js/vendor/foundation.js"></script> <script src="/js/app.js"></script> <script src="/js/responsive-tables.js"></script> <script> $(document).foundation(); try { // helper function to filter out empty paths (trailing slash) var omitEmpty = function(el) { return el.trim() !== ''}; // extract last path bit from url var paths = document.location.pathname.split('/').filter(omitEmpty); var path = paths[paths.length-1]; // helper function to find and set active option var setActiveNavOption = function(el) { var subPaths = el.href.split('/').filter(omitEmpty); var subPath = subPaths[subPaths.length-1]; if (subPath === path) { $(el).addClass('is-active'); return true } return false; } // check if we have a .header-subnav match? var hasSubMenu = false; $(".header-subnav li a").each(function(i, el) { var isMatch = setActiveNavOption(el); if (isMatch) { hasSubMenu = true; return false; } }); // find corresponding path bit for .menu-subnav option if (hasSubMenu && paths.length > 1) { var parentPath = paths[paths.length-2]; if (parentPath !== 'omero') path = parentPath; } // set .menu-subnav option $(".menu-subnav li a").each(function(i, el) { if (setActiveNavOption(el)) return false; }); } catch(ignored) {} </script> </body> </html>

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2020-06-09 | Open Microscopy Environment (OME)