2023-10-17

Attending: Will, Frances, Dom, June, David, Petr, Melissa, Seb, Khaled, Maadhav, Andreas, David S,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • NGFF (Will) - mkngff sql scripts in github, applied to all filesets on idr-testing: see https://idr-testing.openmicroscopy.org/webclient/usertags/?show=tag-38280641. Memo file generated for first fileset from each study.
  • Now I’ve updated mkngff and the sql scripts to set clientpath for every file to the corresponding s3 URL
  • ZarrReader https://github.com/ome/ZarrReader/pull/64 Performace improvements works with mkngff but breaks import.
  • TODO (for release): PR merge (idr-utils, ZarrReader), testing (e.g. performance), validation, memo file regeneration
  • TODO (post release) cleanup/delete from s3 etc, documentation
  • Q: what is the future workflow for NGFF data? Use mkngff (not working for idr0125) OR import metadata-only (without chunks, then symlink)
  • ZarrReader: need to figure out what changes needed to enable import AND Performance improvements.
• OMERO
  • Andreas: omero-web release in due course, couple of questions for Will
  • Petr & Khaled: RHEL9 testing of deployment. Server and web (with nginx) deployed 3 times. Running fine.
    • SELinux issues with services
    • Seb: production system soon (end of year)? Petr yes
    • Seb: GPFS is next big “beast”
• Bio-Formats (David)
  • 7.0.1 patch release yesterday. Announcements today.

• NGFF

• GerBI

• Glencoe
  • Kevin: permissions checking improvements - will need testing
  • Seb: building ice binaries across various platforms, including Mac for dev
  • Looking at python 3.11 support. E.g. Ubuntu LTS April next year.
• Community
  • Barcelona 7th-8th

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)