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You are here: Home Community Minutes Conference Calls 2015 2015-02-10 Tuesday Team Meeting

2015-02-10 Tuesday Team Meeting

Dundee: Mark, Will, Kenny, Chris, Petr, Emil, Ola, Jean-Marie, June, Simon, Roger, Dominik, Helen, Jason, Balaji Remote: Colin, Sebastien B, Ian, Kelli, Josh M, Wilma, Melissa, Andreas, Curtis, Josh B, Sebastien S, Liza

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

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

    1. Core (incl. CI & QA) - 14:30 UK

      • Units/Maps/Namespaces - getting to developer documentation time (cf. MPorter), also some last UI changes
        • mtools as a test run? Nothing’s broken so far.
          • Jean-Marie: Petr will be doing some testing on Friday
        • Roger: but new methods may be needed to keep things forward-compatible
      • Rendering - in progress, PR opened by Melissa
        • Josh: some tricky issues, will try to work them out, so not yet time for client work
      • libbioformats (Roger) - finishing up OME-TIFF reader; almost complete now
      • Windows testing (Simon)
        • Simon: would welcome any available help, getting CI server up and running, etc.
        • Kenny: we have a Windows Server 2012R2
        • Jason: would be good to know soon if will be ready for 5.1.0 testing
          • Simon: probably not, integration tests haven’t yet even run on Windows
          • Josh: would be good to know what is broken, e.g., recent tables fix
          • Roger: the Bio-Formats tests pass on Windows
          • Chris: has at least been improving over time
          • Jason: so, no we won’t
          • Roger: note that in usage statistics, 10% of servers are on Windows
      • Next steps?
        • m4 this week if possible
        • Finish up Upcoming cards, then start tackling tickets (goal?)
          • around another month of development time left to make changes usable
        • Weekly-ish latest deploys with a "m5" in 2 weeks
        • 5.1.0 board
          • can add cards to first column if nowhere better, to make sure they get done for 5.1.0
          • include cards noting what new testing must be done
        • developer documentation of changes
      • Josh: necromancer to be largely replaced in six days
        • many services being migrated
        • be patient regarding other sysadmin work
    2. Glencoe Update (Chris) - 14:48 UK

      • various HCS improvements in Bio-Formats and OMERO
        • PRs coming in due course, maybe not next week
          • already deployed by Glencoe in production
        • populate_metadata, populate_roi, etc.: scripts not often tested, and awkward to test, so will be trying to simplify and make more robust
      • working with some very large plates, pushing limits, including graphical client / UX
      • Jason: attending digital pathology session at conference
        • many vendors, so perhaps many more image formats
    3. Virtual Microscope/teaching (Ola) - 14:56 UK

      • successfully upgraded to m3, next will be m4 (ndpi, etc.)
      • meeting another doctor from Ninewell’s on Friday
      • received tissuegnostics scanner data, so can try importing
        • Melissa: prediction: it’s not going to work
    4. FLIMfit/OPT (Ian) - 14:58 UK

      • Continuing Matlab 2014b upgrade work
      • working through critical bugs, hoping to release before too long
        • 5.1 will probably have to wait for a while yet
    5. Bio-Formats large file sets (Sebastien B) - 14:59 UK

      • Woolz libraries finally compiled and set up on all CI nodes/servers
      • also Woolz testing scenario under ome-internal
      • questions from Dallas on how to properly check generated OME-TIFF w/ Fiji
        • will ask for more information and point at the documentation
        • also looking at setting up some QA process for generated OME-TIFF
    6. Other consortium timelines (5 minutes) - 15:01 UK

      • Jean-Marie: discussion with Curtis about ImageJ OMERO
        • Balaji now has it running, Curtis will help him get going with issues
        • Curtis: planned modularization of Insight will help
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:03 UK

    1. Meeting report/Heidelberg: CellH5, ontologies, and much much more.
      • Jason: attended two consecutive meetings with Josh
        • large phenotypic screening effort, HCS metadata standards
          • OME-TIFF / SPW model generally accepted
            • also CellH5, though noted that HDF5 is not self-describing
          • given variety of image formats, Bio-Formats generally accepted as interface to data
          • issues somewhat repeat those Alvis Brazma worked on with microarray data management
          • interest in annotating various model objects, especially ROIs
          • interest in ontological terms
            • Josh: including environmental factor ontology
        • second meeting included various efforts to address familiar problems
  4. OMERO.figure update - Will - 15:17 UK

Done 15:56 UK

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