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You are here: Home Community Minutes Conference Calls 2016 2016-02-16 Tuesday Team Meeting

2016-02-16 Tuesday Team Meeting

Dundee: Petr, Kenny, Mark C, Gus, Dominik, Simon, Jean-Marie, June, Ola, Roger, Simone, Jason Remote: Sebastien B, Josh M, Luca L, Ian, Chris A, Helen, Andreas, Harald, David, Melissa, Wilma, Eleanor, Balaji, Emil

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Project Timelines (2-3 minutes each)

    1. Spaces - 14:31 UK

      1. Mainline (J-m)
        • card updated re. Ola updating documentation re. download
        • posted on ZeroC forum re. Ice
        • PR freeze this Friday
          • maybe units/scalebar PR coming from Will
        • not as much infrastructure / generation progress made as hoped but will seem the same from outside
        • Josh: general ticket cleanup going on, especially moving into milestones that correspond to boards/topics
        • Balaji did 5.1.8 release of Bio-Formats
      2. Model (Sebastien)
        • Mark: has been making small Shape model changes and collecting comments on others for discussion
        • open PR freeze for m1, Bio-Formats should be done this week
        • on OMERO side still design decisions / mockups to finalize scope of m1 for next week’s demo
        • ongoing discussions to decide backend content of m2, will also need to choose end-user use cases
      3. Metadata (Josh)
        • working on generating WND-CHARM features
        • scaling issues again rearing their head
          • may need to look at Django session backend
        • Eleanor: working on another dataset, small study represented as HCS but without screening (more “analysis” of plates)
        • Simon: has installed gpfs
    2. Other releases/upgrades: - 14:39 UK

      1. Figure
      2. FLIMfit/OPT (Ian)
        • about to release from new CI setup (based in Australia)
      3. ImageJ
        • Josh: discussed with Ian and Curtis; Alison Walker has been working on table stuff, so need to manage work with respect to other current table work
      4. Learning
      5. Sysadmin
        • Josh: now have a production docker, looking ahead to migrating data from beluga to minke, then Jenkins can run jobs on beluga
          • should start up a testing server now, some bugs may appear after longer uptimes
        • Jason: useful to know soon if more hardware resources would help
          • Josh: alas not all six of IDR servers yet up; maybe extending something?
          • Simon: good to work back from what we actually want to use the hardware for
    3. Glencoe Update (Chris) - 14:46 UK

      • helping Ola with deployment with new workers
      • opened some small PRs (marshalling, viewer configuration, etc.), probably the last for 5.2.2
      • now shipping 5.1 patches for physical size bugs so speak up if there are any issues with the proposed fix
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 14:49 UK

    • Jean-Marie: at Montpellier got their off-line import to work with our clients
    • Jason: attended advanced imaging methods meeting in Berkeley
      • OMERO well appreciated
      • Damir described usage at OHSU
      • also visited UCSF, OMERO may solve some issues there
    • Jason: Wellcome Trust grant due at the end of the month, grateful for ideas for getting letters of support
    • Jason: thanks to those who updated the upgrade / statistics databases
      • in 2015 worldwide around 100,000 starts of Bio-Formats per day
      • C++ upgrade check statistics would be useful
      • still many BF 4.x users
  4. Presentation on Openseadragon and OMERO by Luca Lianas of CRS4 - 14:53 UK

    • Jason: so, hybridized image server?
      • Luca: yes; currently uses only one rendering engine or the other at once, but working on increasing flexibility
    • Jean-Marie: students can save their drawn ROIs to the server?
      • Luca: yes, then later teacher in Moodle can review answers
    • Jean-Marie: what kinds of shape?
      • Luca: circles by students, ellipses, rectangles, etc. by teachers, but also working on that
    • Jean-Marie: are the ROIs annotated, by text, etc.?
      • Luca: teachers can add text but not currently using OMERO annotations
    • Jean-Marie: some ROIs visible or not, where is that visibility stored?
      • Luca: in Moodle, it is part of the data that defines the question
    • Jason: any OME work we should prioritize to help you?
      • Luca: not high priority
    • Chris: issues when tile sizes are not powers of two or not square or images with odd-numbered dimensions, like with part-tiles at edges, are those still issues?
      • Luca: tile size is a problem, but with SVS OMERO and openslide can give a portion of a tile
      • Luca: many aspects do seem now to work fine on various formats but more testing to be done
    • Jason: when does it go into production?
      • Luca: since end of last December, since bug-fixing, etc., yet to test scaling with large student class
    • Jean-Marie: how difficult was integration with Moodle, etc.
      • Luca: quite easy, arranged as a few plug-ins
    • Harald: has seen other examples of systems giving the zoom level, tile, etc. that is wanted, adapting stored image accordingly; is very nice

Done 15:30 UK

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