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2015-10-13 Tuesday Team Meeting

Dundee: Kenny, Gus, Simon, June, Will, Jean-Marie, Graeme, Balaji, Dominik, Petr, Roger, Colin, Jason, Simone, Helen, Remote: Josh M, David G, Kelli G, Andreas K, Emil R., Melissa L., Eleanor W., Ian M., Chris A., Curtis R, Ola T. (14:41)

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. OMERO

      1. 5.2.0 (J-m) Django upgrade from 1.6 to 1.8. Testing on-going Admins will install version of choice How long with Ice 3.5 be supported? Roger: they say they are still supporting it Chris: could change New PRs for web and Insight for right panel. PR deadline by next Monday in time for Nov 2nd release For 5.2.x, Deprecate ROI service - introduce ROI container (not on Regions branch)
      2. Regions v2 (Josh) Changes for first DB upgrade merged. Other work on space can continue. Josh: Where does Regions branch from BF get back into OMERO? (5.2.0?)

    2. Bio-Formats

      1. Java: 5.1.5 out today(Seb in absentia)
      2. C++: 5.1.5 to follow (S.i.a) Superbuild tomorrow or Thursday. A couple of minor issues.
      3. Work on multi-version in Registry to start next week (S.i.a) Work will start in next few days
      4. Datasets / New formats (see below)

    3. Glencoe Update (Chris) Upgrading to 5.1 ROI work etc.

    4. Repositories

      1. Virtual Microscope/teaching
      2. IDR Project (see below)

    5. FLIMfit/OPT (Ian)

      • Been pulled back to FLIMfit this week - following IC sever finally being updated.
      • Ready for release next week, depending on plates (new data from plate reader)

    6. Other consortium timelines (5 minutes) ImageJ ops making good progress

  3. IDR review/demo (20-25 minutes plus 15 mins questions max)

    • Josh: for Seeing is Believing, we compiled numbers E.g. 1500 plates, 10.5 TB imported
    • Sysgro: complicated / corrupt data
    • Secretion screen: 900 plates - not all imported
    • Getting individual plates in “painful”.
    • Tara: 84 plates, 6 chambers (only 2 complete - each with 400 fields) Instead turned these into 396-well plates
    • Large number of files per plate - 4 hours import
    • Mitocheck: HDF5 reduces number of files but very complex data - long import times
    • Melissa created screen-reader 2.0. Use multiple patterns in ini file to describe assembly of multiple files on disk into plate (extension of existing ‘pattern’ functionality).
    • Do we want to support ini files in future? Is HDF file a better approach.
    • 40000 readers needed - opening file can take 20 minutes.
    • Propose “cacheDirectory” for Memoizer to directly access HDFCellReader
    • Fixed issues (could go into 5.2.x)
    • Import targets on CLI
    • CLI: csv files to OMERO.tables / map annotations. Improved searching
    • Various performance issues
    • Other work needs planning:
    • Importing into existing plate (instead of starting long import from scratch)
    • Caching in web server. Too much caching (e.g. of right panel) causes bugs
    • Federation of multiple servers
    • Context & State - loss of selection in jsTree. Problem when working on big plates
    • JM: Some other points captured during testing. Petr has notes. Context & State
    • Jason: Slides of Gabriella are available.
    • Different studies have never had data all in the same system
    • Tara, HMS Beagle-based ocean sampling.
    • 4 major studies currently in IDR - more coming.
    • Ontology annotations - will be able to link out to OLS etc.
    • Using current vanilla OMERO.web UI
    • ‘BioStudies’ registry
    • 13 Studies loaded so far. 7 on the way.
    • 10.7 TB so far. 80 TB to come
    • All studies have experimental metadata
    • http://idr-demo.openmicroscopy.org takes you to 11 studies (screens)
    • OMERO.tables metadata shown in right panel. Subset of key-value pairs picked -> Map annotations (searchable)
    • Mitocheck is in different server for convenience (large) Cell h5
    • 35 TB total - 10% loaded so far. More in progress
    • Tara study: lots of key-value pairs on Plates - links to PDFs for experimental cards
    • Vanilla web UI not optimised for various different studies but generally works
    • Lots of value for these studies in querying and visualising data.
    • Plan to release url to OME lists soon, then Confocal lists.

  4. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    1. Social Media review (Kelli) Currently going well, but more coordination and planning required for future E.g. announcing IDR resources Plan to start weekly meetings soon Jason: twitter engagement good. Could do more with microscope pony. Blog posts in preparation on improved BF support Become more vocal on commercial adoption?
    2. Conf
      1. Quantitative BioImaging conf
      2. SMG
    3. Also Facility Managers’ meeting in January
    4. CVs needed for grants:
      • By next Tuesday.
      • CVs should be in MS-Word, two pages, Arial, Font size 11
    5. Holidays: keep an eye on holiday allocation - none carried over to next year
      • 2 weeks off - longer needs a month’s notice
      • 4pm 24th Dec - 5th Jan is University holiday period
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