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You are here: Home Community Minutes Conference Calls 2017 2017-01-24 Tuesday Team Meeting

2017-01-24 Tuesday Team Meeting

Dundee: Will, Jean-Marie, June, Mark, Balaji, Kenny, Dom, Simone, Simon, Ola, Remote: Sebastien, Josh, Eleanor, Ian, Andreas, David, Melissa, Wilma, (later) Chris, Jason

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces - 14:00 UK

      1. Files/Formats/OME Files (Sebastien)
        • Stable line 0-2-x performance tests on Windows. Linux next.
        • Roger back soon. Need to finish by end of next week
        • Python bindings for OME files (Simone) nearly done
        • BF 5.3 more bug fixes.
        • Writing OME-tiff with BigTiff fixed (David) being used by Emil
      2. Metadata (Josh)
        1. Upcoming MULTIMOT meeting (Thurs. travel)
          • Simone, Seb, Josh - back on Sunday
          • ‘Selling OME files’. Also OMERO.
          • MIACA? Minimum recording exp
        2. Demo32 released on Wednesday (i.e. IPs swapped) - openstack
          • Tweet mentioned openstack. Present in openstack summit in Boston in summer?
        3. Demo33 in-progress with a focus on ‘tricky’ re-annotation
      3. OMERO 5.3.0 (J-M)
        1. Possible DB change
          • No DB changes required. To consider in next major release
          • ARGB update testing (Mark’s script)
        2. Web API
        3. FYI:Java 1.9
          1. failure with javadoc (code OK)
          2. Test CentOS7 in devspace.
        4. New Roles (Mark)
          • last week's work was:
            • split WriteFile privilege out separately for WriteOfficialScript, also Write privileges out from Delete privileges
            • map OriginalFile.repo into OMERO object model but prohibit changing it
          • this week's work is: focus on on user management privileges: create group, add to group, etc.
          • added to 5.3.0 work: prefix light administrator privilege names in Experimenter configuration so as to clearly separate them from other configuration settings
          • Will expose some of this in webadmin UI. Need to decide on subset.
      4. Outreach
        • Possible date for summer training in Cambridge 29-30/06/2017
          • NEUBIAS - Feb. Graham, Anatole, Josh
          • March - aiming for IDR meeting in Dundee
    2. Other releases/upgrades

      1. Figure Balaji’s PR re-opened
      2. Iviewer
        • OpenLayer update.
        • Open small images without tiling.
        • ARGB fix/handling
      3. Learning
      4. Sysadmin
      5. Website redevelopment/redesign (Liza)
        • no update until mid-February
      6. Smuggler (Montpellier)
    3. Glencoe Update (Chris)

      • Web api & omero-marshal progress
      • OME-TIFF writing setups working: 64bit tiffs
      • Design issues for read-only & scalability
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    • comment on formal design proposals by next Tuesday
    • Some updates to proposed template… Any more?
    • OME meeting: 31st May - 1st June (+ 2nd June)
  4. Ian's presentation

    • Single molecule microscopy on cluster
    • SMLM processing, localisation using cluster, ThunderSTORM
    • Use low concentration of fluorophores - active a subset - acquire image - repeat…
    • ThunderSTORM - IJ plugin to process raw images ‘blinking movie’ -> image
    • 30 - 60 mins on Desktop for 2D. 10 x Longer for 3D
    • Can’t see result until experiment is finished (can’t fix errors etc)
    • Need ‘real time’ results
    • Run on cluster.
    • ThunderSTORM is preferred app for users.
    • But, ThunderSTORM won’t run headless
    • Each user has their own preferred version of ThunderSTORM
    • Last release 4 years ago.
    • Use ‘vanilla’ ThunderSTORM
    • VNC to provide ‘virtual’ graphics for each node.
    • Parallel is easy - work on subset of frames each.
    • Need to load frames separately.
    • Later frames quicker to process (fewer points - bleached)
    • Upload, Localisation, Merging .csv, Visualisation - 6 mins total (2D data)
    • Post-processing by user interactive using VNC on login node (don’t have to move data).
    • Skilled manual process.
    • Some automatic tasks possible - E.g. drift correction.
    • Future work: Parallelising “Visualisation” step.
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