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You are here: Home Community Minutes Conference Calls 2016 2016-04-26 Tuesday Team Meeting

2016-04-26 Tuesday Team Meeting

Dundee: Petr, Will, Simon, Mark C, Jean-Marie, Gus, Dominik, Colin, Simone, Ola, June, Kenny, Balaji, Helen, Jason, Roger Remote: Ian, Josh M, Melissa, Sebastien B, Kelli, Liza, Andrea, Chris, Eleanor, Stick, Wilma

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)
        • OMERO PR freeze now in effect
        • further testing with Ice 3.6 this morning, working fine
        • RC later this week to test changes with downloads page, etc.
          • if testing goes well, full release early next week
      2. Model (Sebastien)
        • reviewed board to check last breaking changes
          • will need to discuss a couple of cards with David
          • ensure OMERO can consume them
        • cleaning up Insight after issues from demo
        • created new OMERO 5.3.x board in addition to the 5.3.0 board
          • "buckets" become columns
          • after coming OMERO release scoping should begin in earnest
            • may report progress at these meetings
      3. Metadata (Josh M)
        1. Tagged IDR 0.0.4 build (OMERO 5.2), deployed on a couple of servers
        2. Beginning re-import of mitocheck as well as testing of new datasets.
          • docker, openstack
        3. Testing new caching configuration and preparing for web-proxy migration
        4. No pressing need known for IDR to be on OMERO 5.3
    2. Other releases/upgrades - 14:39 UK

      1. Figure
        • Will: minor release last week
        • Jean-Marie: planning/scoping for further work? (ROI, tag...)
        • Jason: put them in an inbox column to make them all explicit
      2. ImageJ
      3. Learning
      4. Sysadmin
        • Kenny: nginx upgrade on haddock and nightshade, trying to increase consistency
        • Kenny: EasyDNS renewal done
        • Josh M: recent reliability issues with docker, suggests move to OpenStack
    3. Glencoe Update (Chris) - 14:44 UK

      • working with Harald on unit / marshal issues, making progress
        • also looking at masks
      • hoping to share ROI code soon
    4. The Great Demise of Jabber (Jason) - 14:45 UK

      • considering switching to Slack, speak up soon if you have a strong opinion
    5. OME Mtg Update (Jason & June) - 14:49 UK

      • June: 55 people registered (32 externals), closes this Friday so needs a last push to remind people to register
      • Jean-Marie: could remind local people, e.g., Ninewells
    6. Social media update (Kelli) - 14:52 UK

      • Kelli in US over May, back in June
        • Facebook, LinkedIn on hiatus
        • Helen to do announcements, Josh handling interesting links, etc.
    7. nDimension presentation by Roger - 14:54 UK

      • Mark: allowing open naming of dimensions raises community issue of same people using same dimension name for different things
      • Roger: imglib2 may be interesting to study in how they handle storage
      • Ian: requesting pixels in not their storage order could mean reading the whole file many times
        • Roger: yes, storage order can make a big difference, though that order is available to caller so they can optimize accordingly; also region copies can be optimized by the library where a set of memcpy could be done
      • Simon: could it help with acquisition in allowing microscope to stream in any order?
        • Roger: is already flexible by IFD layout in TIFF
      • Will: could allow sparse arrays?
        • Roger: possibly, as an implementation detail
        • Roger: for higher-dimensional data sparseness may more probably arise (samples aren't over exactly a hyperrectangle)
      • Jason: helps correlative / micro-magellan / non-contiguous sampling
        • Josh M: not really
      • Jason: avian? (expose Java to C++) prefer not to reimplement imglib2
        • Roger: probably wouldn't allow low/zero-copy, etc., so performance would suffer; would be useful for wrapping existing readers
        • Roger: imglib2 would probably be worth looking at for a Java implementation
        • Jason: check out vigra
        • Roger: still need to do the model part anyway
          • Josh: good to compare with others' nDim approaches
          • Roger: would be pleasant surprise to find any offering PixelBuffer for patterning data for consumption by OpenGL, etc., etc.
      • Roger: proposed C++ code generalizes Boost multi-array library
    8. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:45 UK

      • CTIR Scientific Advisory Boards (Dundee only)
        • SAB visit on May 9th
        • open series of talks by PIs
        • opportunity for Dundee OME team to meet Søren Brunak, our SAB member
        • not mandatory but useful and encouraged

Done 15:53 UK

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