Agenda - 2:30pm Start

1. Accepting minutes from last meeting

   • accepted

2. Project Status/Testing Update - 14:31 UK

   • Petr: working on permissions testing, concentrating on move
     • creating tables of permissions focusing on specific combinations matching stories
     • not sure what should happen, Balaji helping to determine what does happen
     • checking that client and server behavior match
     • move stories include various objects annotated
   • Jean-Marie: considering further format testing
   • Mark: will try to match permissions tables against ongoing graph traversal work
   • Mark: will try to understand BasicACLVoter and explain to Petr
   • Gus: report of ROI intensity analysis slower if drawn on 5.0
   • Jean-Marie: work on evaluating client on iPad and Android
     • Gus has started evaluating iPad
   • Petr: deployment of Squash is surprisingly easy
     • Kenny: will work on it
   • Jean-Marie: intent to release consortium tools two weeks after 5.0.0

3. Glencoe Update - 14:38 UK

   • Josh B: search stuff being rebased from dev_5_0 to dev_5_1
   • Josh B: looking at rebasing firehose
   • Seb B: Carlos opened PR against dev_4_4: intentional?
     • Carlos: yes, should also go against 5, easy rebase
     • Seb B: will talk to Kenny, may reactivate some dev_4_4 CI jobs
     • Jean-Marie: will then be in if we have to do another 4.4 release
     • Will/Simon: worth the effort to test at this time?
     • Jean-Marie: could leave dev_4_4 PR open for now
     • Carlos: could open dev_5_0 PR for testing

4. Consortium Update (every month) - 14:43 UK

   • Seb B: meeting in Edinburgh
     • progress with integrating clients with OMERO.insight
       • FLIMfit, Michael’s tools
     • FLIMfit, U-track now available from downloads site
       • OMERO.figure should also live there
       • also could do OMERO.searcher, webtagging, Michael’s tools
     • many ready to go, or nearly so, main pending question is Michael’s tools, including its name
       • Jean-Marie: can talk to Michael
       • Jean-Marie: Applications trello board
   • Jean-Marie: using breaking tag from Seb B, now a couple of CI jobs
   • Ian: in this release do we plan to harmonize Matlab versions?
     • Chris: no
     • Jean-Marie: indicate how to switch between MCR, as it is tricky
     • Jean-Marie: in longer term, version in Dundee will be used for testing
   • Jean-Marie: must decide on parameters

5. Upcoming meetings/conferences/outreach visits - 14:52 UK

   • Will: Alex in Sussex requests postponing visit, now discussing
   • Jean-Marie: Helen submitted abstract for Manchester meeting following workshop
   • Gus: submitting poster for Crieff meeting
     • Jean-Marie: can check poster over and print
     • Chris: note that printing service will be busy just beforehand

6. Simon Li: OMERO.searcher update - 14:55 UK

   • image-based search
     • currently optimized for sub-cellular localization, from CMU’s work (Murphy Lab)
       • similarity based on distribution within cell
     • features calculated with script and stored outside OMERO DB as OMERO.tables is too slow
     • images compared pairwise with distance metric
     • search results ordered by degree of similarity
       • scores are useful for relative ranking, not significant as absolute values or ratios
       • spreadsheet export includes rank column
   • proof of concept, intended to be easy to use, not aimed at machine learning experts
   • user interface is prototype, plenty of review yet to be done
   • Jean-Marie: CMU develops analysis algorithms, Simon integrates into OMERO
   • Balaji: what confidence have we that the search has useful accuracy?
     • Simon: works well on CMU’s dataset, probably will on ones that look similar
   • not scale-invariant, not obvious how to approach differently sized images
   • Jean-Marie: OMERO.tables issues?
     • Simon: partly speed in transferring much data over Ice, with data conversions, etc.
   • ongoing discussions with Lee K, et al.
     • API and generality over analysis algorithms / feature representation and storage, e.g. hstore columns
   • Balaji: some existing relevant work from EMBL on PCA to determine relevant features of microscopy images

7. Any other business (<5 mins) - 15:29 UK

   • Will: may show public-facing gallery web app

Done 15:30 UK