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You are here: Home Community Minutes Conference Calls 2017 2017-04-18 Tuesday Team Meeting

2017-04-18 Tuesday Team Meeting

Dundee: Petr, June, Dom, Balaji, JM, Mark C, Simone, Ola, Simon, Kenny, Jason, Roger Remote: Josh, Seb, Eleanor, Kevin E., Wilma, Liza, Will, Melissa, Andreas, Curtis, Alison, Chris

Agenda - 2:00pm Start

  1. Accepting minutes from last meeting

  2. Alison Walter (UW Madison) - converting ROI from ImageJ to OMERO

    • Masters at LOCI
    • 1) Add ROIs to ImgLib2
    • 2) ImageJ-OMERO ROI support
    • ImgLib2 ROIs. Add OMERO equivalent ROIs.
    • Use Real space
    • Binary/Unary operations, affine transforms
    • Contains() implementation
    • Currently visible in BigDataViewer without needing major changes
    • Curtis: ImgLib2 hackathon discussed ROIs. Good progress
    • Wrap OMERO ROIs in IJ.
    • Saving to OMERO - simply add new ROIs instead of updating existing ROIs
    • Consistent boundary behavior - OMERO doesn’t specify behavior. Insight (awt) inconsistent.
    • Could configure options for inclusion algorithm.
    • IJ -> OMERO ROIs - add annotations to document inclusion behavior
    • Jason: IJ inclusion behaviour inconsistent (different plugins)?
    • Alison: no
    • Curtis: e.g. ‘Open rectangle’ in IJ -> OMERO with annotation to specify ‘open’
    • Chris: transforms in real space. Need consistent handling of edges with affine transform.
    • Implementation-dependent wrt performance.
    • Alison: ImgLib2 does have consistent handling of affine transforms
    • Curtis: use cases don’t need to go back and forth Integer space <-> real space.
    • Won’t support OMERO label shapes initially
    • Jason: can use this on IDR data?
    • Josh: e.g. mitocheck 50000 polygons in timelapse movie.
    • IDR has 1.2 million polygons
    • Curtis: see trackmate for high performance handling of many ROIs
    • Chris: would be useful to select shapes within region of an image (big images).
    • Alison: probably doable with image ops
    • Curtis: BigDataViewer only loads ROIs as needed for viewed region/resolution.
    • Josh: OMERO can have extra metadata/annotations - how to handle this in IJ ROIs? E.g. filter ROI display by metadata.
    • Curtis: will point us to code etc when ready for testing etc.
  3. Project Timelines (2-3 minutes each)

    1. Spaces

      1. Files/Formats/OME Files (Sebastien)
        • OIR testing of new reader (Balaji)
        • Assess this week to decide on next steps/release
        • Paper discussion -
        • 5.4.1 release last week, bug fixes and docs
        • Discussing bringing tiling API in C++ (same as for Java)
      2. Metadata (Josh)
        • Paper needs to be in by Friday
        • Demo 35 released today (1 new dataset - need to fix rendering settings before tweeting).
        • Would be nice to allow authors to set settings (without sending yaml files)
        • Wnd-Charm features being generated for users’ meeting
        • Several PRs rebased to OMERO 5.3. But maybe target 5.4.
        • IDR testing server available with public login
      3. OMERO 5.3.1 (J-M)
        • Major share bug
        • Release scheduled for Thursday 20/04
        • Include other smaller bugfixes
        • Pushed 5.3.2 release to 16/05, include thumbnails work
      4. OMERO 5.4.0-m1 (Mark)
        • can* methods work done
          • fixed Petr's failing can* test
          • Mark added canChgrp, canChown
        • still to improve performance
          • the triggers approach of OMERO5.4DEV__1 database could be extended to move more permissions checking code from Java to PL/pgSQL
          • in server code could cache more with session
        • in OmeroWeb integration tests a couple of failures
          • Will to help Mark understand them
        • rare group-related flakiness in import
          • may preexist roles work but could be triggered more by it
          • thorny issue, may require Josh's help to diagnose
          • trying another optimistic fix in tomorrow's merge build
        • Jason: want to try a demo of clients to highlight remaining issues?
        • Petr: happy to do one, but clients are looking pretty good
      5. Outreach
        • Planning nightshade user training with new features, analysis tools
    2. Other releases/upgrades:

      1. Figure
        • release 3.0.0 scheduled 19/04
        • Testing deployment from testPypi today
        • Will try new commercial tool for pypi testing & release after release
      2. Iviewer
        • Browser testing - issues in IE
      3. new website
        • Liza working on graphics, team working on content
        • Liza has added the new navigation to allow extra pages in the OMERO developer section
        • next content priorities are developer focused and marked with orange labels on the 'content to dos' list of the new website trello board, anyone should feel free to contribute, there's a gdoc for drafting 'Getting Started' suggestions
      4. Sysadmin (current board and recent PRs)
        • Nightshade major version upgrade.
        • Pre-upgrade check delayed due to web de-coupling investigation
        • 5.3.0 upgrade planned for this evening
        • OMERO.web running from separate VM, stable. Ready for upgrade this evening.
        • Mark: docs could be improved.
    3. Glencoe Update (Chris)

      • Olympus work up now for review
      • couple PRs related to session handling up for review in the next couple of days
      • Working on preparing for OMERO Plus 5.3 / Bio-Formats 5.4
      • webinar at the end of the month.
    4. User meeting update

      • Workshop confirmations
      • Will need to start prepping soon
      • First night at DCA, with chairs!
      • 2nd night - wine tasting in “The Street” with food.
  4. AOB (5 mins max - technical discussions should be highlighted to relevant people and rescheduled)

    • Curtis: would be good to have OME presence at IJ hackathon - several coming up
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