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2016-12-13 Tuesday Team Meeting

Dundee: Petr, Kenny, Gus, David W, Mark, June, Jean-Marie, Simon, Dominik, Will, Balaji, Simone, Ola, Josh, Helen, Seb, Jason, Jaime, Chris, Roger,

Remote: David, Harald, Eleanor, Emil, Melissa,

  1. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Files/Formats/OME Files (Sebastien)
        • 5.3.0 release yesterday!
        • No “congrats” e-mail from Jason!?!
        • Already being used in the wild!
        • OME-files discussions with Multimot
        • Wrap in python, handle heterogenous metadata etc.
      2. Metadata (Josh)
        • Josh: IDR solutions for Multimot
        • use ‘data’ package to read csv. Don’t need Perl etc, just Python
        • IDR paper: positive feedback from community
        • More fixes to come before holidays
      3. OMERO 5.3.0
        1. 5.2.7 release
          • Less CI infrastructure on 5.2 line now - more work to release
        2. Fixing legacy ome-model/omero mismatch: color, name.
          • Need to discuss update script to handle color under some conditions
        3. Web Api
          • Breaking down PRs into bit-size chunks
          • trying to remove hand-coded queries; making them more configurable
          • what configurations of omero-marshal/web-api/etc will we support?
      4. Outreach
        • Looking at another course in Cambridge in June/July
        • Bangalore microscopy course
        • Okinawa
        • Australia
        • Jason: scaling up road-show/workshops: need setup in ‘cloud’.

    2. Other releases/upgrades:

      1. Figure
      2. Iviewer
        • CI deployment in progress. Install node etc.
        • First round of testing done.
      3. Learning
      4. Sysadmin
        • Storage work on nightshade this morning
        • Testing migration to openStack in progress
      5. Website redevelopment/redesign (Liza)
        • Will merge Liza’s branch
        • Then work on content
      6. Smuggler (Montpellier)
        • Deployed & waiting on IT

    3. Glencoe Update (Chris)

      • CellProfiler on cluster feedback
      • OHSU interested in this too
      • Issues with scaling of processing,

  2. Talk - Jaime Pilusky "bioimg"

    • Bioimg platform for annotating storing and sharing BioImgaging Data
    • 80 microscopes across campus, 1300 users, 20 k new files a day
    • Bimg1, bimg2… bimgn (5) servers with mirrored storage
    • Automatic data transfer every 2 hours
    • Access-point to access servers via web interface
    • SAMBA access for analysis - don’t need to upload/download data
    • Mandatory annotation of data with Project name etc. Auto detect un-annotated data
    • Can share externally by email
    • Copy data to another server outside firewall
    • Unique hash in url to access data
    • Don’t do metadata extraction on upload. Doesn’t contain exp metadata - can parse files for acquisition metadata later if needed.
    • Would like to add OMERO interface
    • Looking at eduGAIN for login
    • Josh: script that does the upload & e-mail could also notify OMERO / import etc
    • But, annotations and other DB data not shared
    • Chris: Options 1) Don’t copy annotations 2) try to copy in both directions 3) display only
    • Josh: Federated, use web apis to combine data from different resources
    • Chris: tricky with authentication & authorisation.
    • Jason: data transfer workflow
    • Jaime: put data in “your” folder on microscope. Auto uploaded
    • Then, go to web-ui, browse by experiment type, date etc.
    • All data is saved, even if experiment didn’t work etc.
    • Thumbnails generated via BioFormats using Perl script
    • Generate 1 thumbnail per ‘experiment’ which may be many images
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