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You are here: Home Community Minutes Conference Calls 2014 2014-06-17 Tuesday Team Meeting

2014-06-17 Tuesday Team Meeting

Attending: Dundee: Kenny, Simon, Chris, Gus, Andrew, Balaji, Dominik, Emil, Mark, Petr, Graeme, Blazej, Ola, Roger, Colin, June, Jason, Simone Remote: Josh, Ian, Andreas, Mark H, Melissa, Seb S, Seb B, Sunil Kumar, Kelli, Liza, Douglas

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Project Status (15 minutes max)

    1. Mainline (5 minutes) - 14:31 UK

      • Josh: search card is main one in flight
      • Josh: looking at speeding up back end but won’t be making major changes now so people won’t need to re-index their database
      • Balaji: is going to look at the nightshade ROIs with mtools
      • Melissa: two tickets solved with open PR, other tickets remain
      • Josh: import ticket needs to be picked up
      • Josh: milestone 5.0.3 still has 115 tickets open, 74 bugs.
      • Jason: 5.0.3 goal is to make search work with documentation, server, clients much as they are now
        • also good ideas from Will, Gus, Douglas, etc. for future work for 5.1
      • Sebastien/DOCS: with Helen away, need to take this on.
    2. Glencoe Update (Chris) (5 minutes) - 14:39 UK

      • Andreas has been fixing bugs
      • also work with Douglas on tagging, jsTree
      • Carlos will be away for a while
    3. Consortium Update (5 minutes) - 14:41 UK

      • Jason: Simone Leo from CRS4 is joining us in Dundee for the summer
      • Sebastien B: will be trying to teach git to Texans
      • Douglas: working with Chris on JavaScript third-party library version updates
        • jsTree will be wholly JSON and perform faster
        • Jason: targeting 5.1? Douglas: yes, too much for 5.0.3
        • Jason: impact on others working on web plugins, etc.?
          • Douglas: can use library to assist backward compatibility for jQuery
          • Chris: generally need to review how we are using jQuery and jQuery UI
          • Jason: changes needed by Douglas may also benefit others
  3. OPT and OMERO - Ian Munro and Sunil Kumar from Imperial (20-25 minutes plus 15 mins questions max) - 14:47 UK

    • problem of acquiring images of sample at different angles, then needing to extract sinograms from those planes where each needs data from every plane
      • original images have camera aimed perpendicular to axis of rotation, but users will request planes that are perpendicular to the axis of rotation
    • Chris/Jason: may be most easily solved with more storage in hardware rather than effort in optimizing software
    • Sunil: Yuriy wonders if sinograms can be annotated with a corresponding more-viewable image easily accessed from client
      • Chris: strips along other dimensions available but puts greater burden on server
    • Sunil: possible to show a thumbnail that isn’t a XY plane from the image?
      • Chris: not at present, but contributions welcome
    • Ian: could custom Bio-Formats reader help?
      • Chris: need to store as scan-line or tile, then reading the other way will be slow
      • Sunil: scan-line may make most sense given sinograms
      • Chris: reader examples from Bio-Formats open bytes on web, showing extraction of parts of planes
      • Roger: currently limited by dimension ordering always starting X, Y
        • Jason: could perhaps be okay to be less general depending on conventions accepted in tomography
          • Sunil: X-ray CT would be analogous, they may well also use sinograms
          • Sunil: will cause others to ask around about conventions
            • Jason: also note that people are doing micro CT and HREM
    • Jason: what metadata do you need to store?
      • Sunil: angular spacing is important for reconstruction algorithm, may not be equally stepped
        • Roger: use modulo Z as rotation? is okay even if Z is the physical Z dimension
          • Sunil: and rotation will be in Y Roger: but no modulo Y yet
          • Chris: clients probably won’t be great at handling using modulo like this
            • Melissa: be cautious though Bio-Formats may not work if modulo annotations are misused
            • Chris: so use Z as angle of rotation
  4. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:58 UK

    • Jason: Seating: OME team will be in “goldfish bowl” and in nearby seating in larger area, Java people from other groups nearby
    • Paris Video Content (Dundee only)
      • Chris: video is poor, Emil has experimented with using audio with presentation slides
      • Jason: post the video chopped into talks, make the presentation slides available alongside?
      • Jason: experiment with Jason’s talk, synchronizing slide video with talk audio, see if anybody looks at it
        • Emil: already half-done anyway
        • Jason: cautious about engineering media of other people’s work
        • Andrew: will check if anybody downloads the speakers' slides PDFs

Done 16:18 UK

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