2018-07-31

Dundee: Dom, Simon, Mark, Kenny, JM, June,

Remote: Seb, Josh, Andreas, Chris, David, Emil, Melissa, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

• Josh: “several big image fixes ASAP”?

  • J-M: figure related bugs. Not OMERO version bump: check.

1. Project Status

(2-3 minutes each)

• Summer epics

  • Secvuln retrospective

    • Minor bumps in process but nothing too bad

    • CVE being applied for

  • Import

    • Mark: Noticed that many-tiny-file uploads take much longer

      than I would have expected. Not yet clear that there are any easy solutions. Also learned to include sync in timing filesystem writes!

      • Mark: Might be improved by parallel imports but root

        cause is unknown

      • Chris: Metadata creation is likely to be the main

        slowdown

  • ITR

    • VAE 0.5.1 released by end of next week as minimal showcase

      (ITR linked to live notebooks)

    • Notebooks with CellProfiler, R and ImageJ (“static” only

      jython script available this time)

    • Docker Image: Migrate R and CP installation from

      training-notebooks now that the refactoring is finished

    • JupyterLab bug means we’ll use old notebooks UI links for

      now

  • Apps release schedule

    • Figure: several open PRs being reviewed (release 4.0.1)

    • FPBioImage

      • Anatole is interested in displaying cropped ROIs in

        FPBioImage

    • Parade: next

• Glencoe

  • GS 5.4.7 in progress

  • Improvements to PathViewer due to be released soon

  • More microservice work, including work on ingesting very large

    (multi GB) metadata files

  • Refinements to ND2 format handling

• Community

  • HCA (Josh): see extended

    notes

    • report on SpaceTx file format decisions

      • Decided to maintain their own file format after

        considering others

      • Ingest process is still to be developed, depends on

        long-term plan for format

    • Metadata meeting tomorrow

    • Regular weekly “starfish sync” meetings on Thursdays to

      discuss SpaceTx format, others welcome to join

    • Also some motion on the

      “scoreboard” front: meeting either today or on the 7th

      • Support for “challenge” platforms where researchers can

        compare their algorithms, others welcome to join.

1. AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

1. Main Topic

(20-25 minutes plus 15 minutes questions max)