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You are here: Home Community Minutes Conference Calls 2015 2015-12-01 Tuesday Team Meeting

2015-12-01 Tuesday Team Meeting

Dundee: Dominik, Kenny, Petr, Mark C, Jean-Marie, Simone, Will, Gus, June, Helen, Roger, Balaji Remote: Sebastien B, Kelli, Colin, David, Wilma, Melissa, Ian, Curtis

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

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

    1. OMERO - 14:30 UK

      1. 5.2.1 (J-m)
        • starting to clean up the documentation, including Windows and web deployment
          • alternative to SCL on CentOS 6
          • nightshade upgrade revealed problems
            • Kenny: added to nightshade card
            • Jean-Marie: link from deployment column
            • Kenny/Will: e-mail to warn people?
              • Helen: already told CentOS 6 people to hold off for now
          • also WSGI / Apache issue
          • may need troubleshooting page for our documentation
            • Roger: already a CentOS 6 page
            • Kenny: issue needs to be more obvious from sysadmin upgrade page
        • some PRs open, was focusing on deployment issues before merging further changes
        • Mac OS X docs have been taking shape
      2. Metadata
        • Colin: with Simon now rebasing PRs from metadata to develop
        • Simone: working on metadata Python repository (idr-metadata repo, Josh M has been trying it out), driven by MULTIMOT work
    2. Bio-Formats - 14:39 UK

      1. 5.1.7 (Melissa)
        • now under PR freeze
        • need to make jobs green so may have to push release date to Monday
      2. 5.2.0
        1. Folders
          • Mark: Start with a Folder that can contain just ROIs, maybe Images? Or a Folder that can contain any top-level object, or maybe exclude Screen, Project, Dataset from that? Comments welcome on ROI Folders.
          • general consensus seems okay with starting with just ROIs and Images as Folder contents
            • Jean-Marie: risk of including too much too soon and having it misused
          • Mark: slowed down by unexpected code generation issues on both Bio-Formats (recursive elements) and OMERO (significant ordering), and by the merging of regions into develop on Bio-Formats, but will be able to push branches by the end of the week if nothing else
          • Roger: Mask and BinData generation progress?
            • David: coming along, still some to-do’s
    3. Other releases/upgrades: - 14:51 UK

      1. Figure
        • Will: now released, could look at release process improvements
        • Kenny: mention Pillow version on install instructions?
          • Will: absolutely, but is probably a more general OMERO scripts issue than just Figure
          • Jean-Marie: in longer term could improve testing to catch these issues
      2. FLIMfit/OPT (Ian)
        • I'm now working on upgrading the Localization Microscopy work to be compatible with 5.2.
        • demonstrating next Tuesday
      3. IDR Project
      4. ImageJ
      5. Learning
      6. Sysadmin (Kenny)
        • nightshade is back on its feet and users can log in
        • a few files seem corrupt, but appear to have been that way for a long time, will investigate
        • PostgreSQL indexes rebuilt
        • Chris suggests providing post-mortem details in a blog post (using import logs, checksums in DB, etc.)
        • Jean-Marie: black thumbnails?
          • Kenny/Gus: nothing further known
          • Petr: some still exist on nightshade
            • Jean-Marie: sent out e-mail with workaround
            • Petr: there could be an easier way for users to regenerate thumbnails in bulk
            • Roger: also pyramids
            • Roger: server probably still doesn’t requeue aborted jobs on restart
    4. Glencoe Update (Wilma) - 15:01 UK

      • webinar just started
      • attending digital pathology meeting at end of week
  3. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled) - 15:03 UK

    • June: David and Jason off to workshop in Cambridge next week, Simon to attend light microscopy managers’ meeting
    • Simone: anything about signing up for MULTIMOT meeting in March?
      • June: will find out
    • June: still waiting for plenty of OSAR forms back

Done 15:05 UK

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