2024-02-13

Attending: Will, Dom, Petr, Frances, Josh, June, JM, Kevin, Jason, David S, Chris, Tom, Khaled, David, Maadhav, Melissa, Andreas, Kyle,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • NGFF issues: Khaled installing microservices working on idr-testing.
    • Need to regenerate cache. Will: Deleting first…
    • Chris: Just move it first, then can delete later
  • David working on ZarrReader memo file generation
    • e.g. idr0090 has large memo files ~110M slow to load.
    • Lots of structured annotations from nd2 file
    • Stripping back annotations gives smaller file and this appears faster to load (testing with idr0090)
  • zipkin.io tracing used by Glencoe for microservices
    • Needs quite a bit of work to function properly
    • Josh: would like low-cost option to improve situation
    • Chris: can be more trouble than it’s worth
    • Kevin: then you need prometheus & grafana to aggregate. Big ecosystem! Maintenance admin burden.
    • Chris: limited opensource tools. Better solutions have costs.
• OMERO
  • testing Python https://docs.google.com/spreadsheets/d/1zI3vlcTLp7okz_Mi2LHK40NxwCkGXUGHgDqgCd7jP_A/edit#gid=1254367109 (omero-py and omero-web python 3.12 support). Needs more testers (see sheet and add name).
  • Aim for Thursday? Using merge-ci server.
  • When done, can migrate merge-ci to RHEL9.
  • Petr: can test async - don’t need to be on same call.
  • JM: add name to sheet, and test in your own time.
• Bio-Formats
  • 7.2.0 released last week. svs and czi changes.
• NGFF (Josh)
  • NGFF office hours on Wednesdays
  • NGFF RFC status update. RFC1 (current) and RFC0 (previous)
  • zarr-python: discord :arrow_right: zulip - common hosting
  • https://github.com/ome/ome-ngff-validator/pull/32 - implementing transforms etc ahead of spec being finalised
    • JM: automated testing of validator?
• GerBI (Tom)
  • Analysing histology data in Fiji use-case. Pierre Pouchin. Failing to load all data into memory. Trying to load regions
    • https://github.com/GReD-Clermont/omero_macro-extensions/pull/19
    • JM: good to add this to our guides
• Glencoe (Chris)
  • Bio-Formats working with regions of interest is tricky.
  • Single sign-on with light Admin - web with sudo’d sessions.
    • poor handling of long usernames and passwords.
  • TileDB research with OMERO.tables. Preparing data on s3. Links to come
• Community
  • Jason: The wonderful OME Community Meeting. Community interested. Limited room availability. Checking dates around end of May.

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)