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You are here: Home Community Minutes Conference Calls 2014 2014-11-25 Tuesday Team Meeting

2014-11-25 Tuesday Team Meeting

Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

Dundee: Will, Kenny, Petr, Emil, Chris, June, JM, Dominik, Helen, Graeme, Colin, Simon, Mark, Andrew, Jason, Balaji, Remote: Seb B, Josh, Gus, Kelli, Josh B, Ian, Douglas

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Project Status (15 minutes max)

    1. Mainline (5 minutes)

      • 5.1.0-m2

        • units (Petr)

        • Mostly all done. Bio-Formats issue just fixed by JM.

        • Other PRs won’t be in m2 (E.g. 5.0.6 rebase).

        • Blockers all fixed.

        • Seb: artifacts built and tagged.

        • Need to decide if we’re happy with tag.

        • JM: few items remaining on trello board, but these can go to m3.

        • Josh: m2 tag allows us to get all builds green again.

        • Hopefully keep everything green during future work.

          • tagged build, testing
      • 5.1.0

        • Mark: reworking generally working pretty well. Couple of bugs - should be fixed & PR soon.
        • graphs reimplementation Trac #11779 (Mark)
          • integration tests pass
          • several broken integration tests fixed and a few tests added
          • several bug tickets fixed
          • performance improved
            • could be better, see Trac #11084 (not graphs, but related)
          • discovered yesterday that new chgrp has bug, Trac #9610
            • should be able to fix this week, then open PR for all work
          • looking to reproduce Trac #12023, is probably already fixed
        • maps: PR for discussion open and in breaking
        • conversion of units on DB upgrade (if we decide to do it)
        • rendering, timezone, etc. forthcoming
        • Andrew: hope to finish model by end of week.
          • Have outline of objects now, just need attributes, compile fixes etc.
        • Group sudo (breaking PR open).
        • various other internal efforts (necromancer, docs, hiring etc.)
        • Josh: probably about 4 weeks behind where we wanted to be wrt model & DB changes.
    2. Glencoe Update (5 minutes)

      • Chris: series of PRs to bring back to OME. All based on 5.0
      • Import PR opening soon. Can port forward to develop after.
      • Other BF work mostly based on develop.
      • Jason: no plans to backport everything - but Glencoe work already tested etc.
  3. Consortium Update

    • Ian: currently bugfixing FLIMFIT. Not working on 5.1 yet.
    • Douglas: jsTree testing feedback - most issues fixed. Waiting on Hibernate fixes for perms projections.
    • Not much imaging covered in conference
    • Should OMERO be installable by anyone in the lab? Is this a good idea? How to make it easier?
    • Mark H. Fiji fixes in progress. Been busy paper writing etc.
    • Seb S. been away
    • Dallas update from Sebastien:
      • Very cold!
      • Lab: biologists, instrumentation team, ‘dry lab’ image processing & analysis pipeline
      • dry lab: git training. uTrack bug fixes coming soon.
      • 3D tracking, processing etc is next big thing, using their own cluster.
      • Not currently using OMERO, but BF is highly used for analysis on cluster etc.
      • Fileformat discussions: ND2. 200-300 GB files. Reader not very performant on large files
      • Memoiser fixes effectively solves these issues. Open in 1 second.
      • Want to use it in ImageJ/Fiji.
      • OME-tiff generated by custom LightSheet microscope.
      • Subcontract acquisition to Labview software -> OME-tif.
      • 1 tiff per z-stack. Bugs in headers.
      • Our sample files are hard to find.
      • Needs to be easier to find specific examples.
      • Will soon hit very large files (TB)
  4. Bio-Formats - next steps, development planning

    • Trying to understand how much BF effort is needed
    • Tricky to see the status, quite cumbersome etc.
    • Decoupling: independent B-F and OMERO releases possible?
    • 5.1 timeline (early spring) - need to limit coding accordingly
    • Need to improve internal work-flow, docs etc. E.g. for new hires.
    • Chris - Glencoe work has been increasingly B-F focussed.
      • Highly inefficient at the moment and difficult for open-source team to get involved.
      • Need to share knowledge, workflow use-cases etc with OME team.
      • Complex use-cases from digital pathology etc. Metadata critical. E.g. Zoom
      • Real world use requires better performance than we typically test with.
    • Jason: - larger datasets, performance critical
      • E.g. ND2 or czi are complex formats with heterogenous internal structure
      • Sheer scale of BF usage, including OMERO and other applications
      • All of this is too much for Melissa - needs more of team involved.
      • Data Model doesn’t cover a lot of metadata from various formats, E.g. DICOM.
    • Melissa - big tasks - can’t do all at once. Preference:
      • Docs & samples
      • Decoupling BF & OMERO releases
      • IO / memoizer
    • Chris: 1 - 2 months per component (3 - 4 people).
      • Remove submodule, update build system, testing fixes, model decoupled.
      • Possibly stop adding file formats between now and 5.1 release?
    • JM: scope docs work and gather info needed by 17th Dec workshop (after meeting).
    • Melissa: this may not leave us enough time before 5.1 release (3-4 wks in Jan).
    • Chris: fixing BF bugs is still the priority.
    • Chris will add more detail to trello card on Decoupling
  5. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    • Can we manage a docs afternoon before xmas holidays? If so, possible dates? Friday afternoon with drinks and snacks?
      • Helen: maybe too busy before Christmas?
      • Josh: Not necessarily! Depends on how many people we need.
      • JM: Maybe after Tues 17th meeting?
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