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You are here: Home Community Minutes Conference Calls 2016 2016-10-04 Tuesday Team Meeting

2016-10-04 Tuesday Team Meeting

Dundee: Gus, Mark, Simone, Dominik, Helen, Simon, Roger, Jean-Marie, June, Petr, Balaji, Will, Ola, Jason, Chris Remote: Eleanor, Josh, Seb, Liza, David, Wilma, Andrea F., Melissa, Dominik, Andreas, Emil

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. Project Timelines (2-3 minutes each)

    1. Spaces - 14:04 UK

      1. Files/Formats/OME Files (Sebastien)
        1. Bio-Formats 5.2.3 status
          • about to release 5.2.3, waiting for last PR, builds this afternoon
          • will try to get Boost PR into tag for Roger
        2. OME Files 0.2.2 status
          • Roger working on last piece of code for inclusion in release
        3. Bio-Formats 5.3.0 plan
          • new minor series 5.3.x, propose to move to semantic versioning hereon
          • rearchitect Bio-Formats components / dependencies
          • APIs: tiling, options
            • options because difficult to know which getters/setters are offered by underlying readers
            • Roger: options down to OME-Files too?
              • Sebastien: maybe
              • Roger: would be a big win
          • Mark: semver for OMERO too? or be very clear about difference
            • Chris: may not yet need to announce change in policy
            • Jason: good where we can to have others maintain sets of things like ontology terms; such concerns affect even API for configuring Bio-Formats
            • Chris: as well as our enumerations possibly not being exhaustive, there is also a separate issue of defining backward compatibility, definitely an issue in the ontology community
            • Roger: also issue of code-generated enums maybe not being enums in the programming language to make changes less breaking
      2. Metadata (Josh)
        • working on draft paper, nearly ready for submission
        • getting demo-2 good for Jason's coming demo in Singapore
        • trying to stabilize mapr UI for demo-3
        • some Jupyter-based computational resource coming within next few days
      3. OMERO 5.3.0 (Jean-Marie)
        • 5.2.6 now released
        • new screenshots out, more coming (new viewer, etc.)
      4. Outreach (Jean-Marie)
        • Balaji still producing videos, useful for coming training, next in November
    2. Other releases/upgrades - 14:32 UK

      1. Figure
        • Jean-Marie: announcing renaming of repository
        • Ola: try with web-error first so as to work through checklist and see what breaks in renaming
      2. ImageJ
      3. Learning
      4. Sysadmin (Josh)
        • cowfish still a problem, doubtful about octopus
        • web-prod timeouts, already tried resetting plone
        • notifications about embassy
      5. Website redevelopment/redesign (Liza)
        • working on Bio-Formats content
      6. Smuggler (Montpellier) (Andrea)
        • quick presentation on proposed project for students
          • funded six-month masters student
          • idea: machine health report via analysis of acquired images
            • want certain scripts available only to facility managers
          • idea: integration of analysis scripts, extending Balaji's work
            • including sandbox for analysis applications, directly accessing managed repository while respecting OMERO permissions
              • Josh: tricky
              • Jason: Douglas (Harvard) showed OMERO.forms which somehow respects OMERO permissions and is for annotating images
            • analysis is a big selling point for OMERO
          • Josh: idea: single sign-on, bit tricky though
          • Josh: idea: generalize Smuggler as compute resource, cf. our celery work
        • can now batch multiple imports into single submission
        • may get to introduce Toulouse to OMERO / Smuggler
    3. Glencoe Update (Chris) - 14:56 UK

      • finishing JPEG-XR work
      • sorting out Windows build stuff
      • working on PerkinElmer formats
        • image naming, plate naming, etc.
        • Jean-Marie: also issue of well naming now annotations being exposed in GUI
      • work on Python BF stack as shim in CellProfiler
      • PathViewer 1.1 coming soon
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:01 UK

    • Jason: HMS visit next week: stitching 27-channel images, may be relevant to tiling API
    • Jason: seek Orbit demo from Basel
    • Jason: make sure all have done security survey
    • Jason: HDF5-based file format emerging in EM tomography

Done 15:07 UK

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