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You are here: Home Community Minutes Conference Calls 2014 2014-03-04 Tuesday Team Meeting

2014-03-04 Tuesday Team Meeting

Dundee: Simon, Chris, Kenny, Petr, Emil, Mark, Jean-Marie, Blazej, Gus, Colin, Balaji, Andrew, Dominik, June, Will Remote: Douglas, Kelli, Mark H, Sebastien S, Sebastien B, Andreas, Ian, Roger, Curtis, Melissa, Josh B, Carlos

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: 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

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