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You are here: Home Community Minutes Conference Calls 2016 2016-06-14 Tuesday Team Meeting

2016-06-14 Tuesday Team Meeting

Dundee: Will, Kenny, Gus, Helen, Simon, Colin, Simone, Roger, Balaji, Jean-Marie, June, Ola, Kenny, Petr, Jason, Remote: Josh, Andrea, Melissa, David, Kelli, Eleanor, Seb, Andreas, Ian, Wilma, Chris,

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

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

  2. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Model (Sebastien)
        • 5-10min presentation on 2016-06 model
        • Changes proposed for 2016-06 from last 6-8 months, Mark, David, Roger
        • Namespace unification. Single namespace instead of SAs BinaryFile etc
        • Class Hierarchies.
          • LightSource, Shape and Map are now ComplexType. E.g. use instead of
          • MapPairs dropped
          • ROI Properties dropped: namespace, line ending enums etc
        • Folders - top level element - Contains ROIs, Images
        • What’s next
          • June - release 2016-06 schema
          • July - release OME Files C++ 0.2.0
          • Aug/Sept - release BF 5.2.0
        • Chris: LineCap enums - what’s lost?
          • Seb: existing Circle Square linecaps not supported
          • These have never been implemented in our clients
          • Chris: Need to check if Aperio & Hammamatsu would use these?
        • Andreas: Can Folders contain Datasets? Seb: No. But can have tree of Folders
          • Andreas: Users ask for custom hierarchy.
          • Sebastien: 5.3.0 clients will not support Folder hierarchy for images.
      2. Metadata (Josh)
        • IDR priorities - prototype for tag export, feature calculation for 2 studies,
        • Into OMERO tables. Make available to Jupyter analyses.
        • More data going in.
        • Jason: discussing UI changes for IDR and writing up current work (Thursday)
        • IRP from eurobioimaging - (visitors next week)
      3. 5.3.x Scoping and 5.3.0 (J-M)
        • Database change PR opened
        • Histogram PR opened for web
        • Web api and omero-marshal progress restarted
        • Conservatively moving cards to 5.3.0 board
      4. Outreach (Colin)
        • Thanks for presentation videos - more please!
        • Helen: unconference notes being organised into pdfs. Preparing blog post
        • Colin: Preparing for user training days in Cambridge & Oxford
        • May also do some Sysadmin training in Oxford or elsewhere
    2. Other releases/upgrades:

      1. Figure
      2. Learning
      3. Sysadmin Lifesci IT provisioned remote processing storage for nightshade.
        • Josh: OpenStack training started
      4. Smuggler (Montpellier)
        • Writing docs.
        • Thinking of grant for work on splitting imports, as discussed at POTN data pipeline session
        • JM: deployment? Andreas: on a few workstations but session timeout too short. Admin wants testing with longer timeout to check on thread counts
    3. Glencoe Update (Chris)

      • omero-marshal :more objects mapped
      • Key-value search in web
  3. Remove CodomainMapContext from 5.3 OMERO model?

    • To be discussed elsewhere
  4. ImageJ backend demo by Balaji

    • Use ImageJ on the OMERO server for batch processing of images
    • Use OMERO.insight IJ plugin
    • Open image - start recorder - threshold image - create ROIs etc.
    • Save Macro locally - upload to OMERO as attachment to Datase
    • Select Dataset and pick attachment - run script..
    • Results are attached to Dataset and user is sent e-mail
    • Script creates temp folder, adds images (OME-TIFF) and macro, runs Fiji headless
    • Jason: ImageJ “doesn’t scale” (E.g SPW) but still very useful to many users who run ImageJ manually.
    • Josh: no security / sand-boxing. Can’t let users run “any macro”.
    • Andreas: Many plugins don’t run headless.
      • We would put together macros - don’t let biologists write them
      • Is it possible to offload processing to cluster?
    • Balaji: looking into this.
    • Roger: create a “scripts user” with limited permissions on the server to provide sandbox security?
    • Josh: tricky to create a generic solution.
    • Jason: we could write up various approaches.
    • Gus: users want various permissions for different scripts
    • Simon: direct access to data / without ice? Josh: discussed at POTN
    • Jason: lets work with a couple of local ImageJ use cases.
    • Will: upload new images as new Images in OMERO?
    • Balaji - not yet. Just handle new files as attachments.
    • Will: Can user choose parameters as inputs for macros?
    • Balaji: Not currently - considered a ‘black box’
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