tags: Tuesday —

2025-06-03

Attending: Will, JM, Dom, Frances, Khaled, Kevin, Jason, Melissa, Kyle, Seb, Andreas, Chris

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances)
  • prod128 work ongoing
  • searchengine testing of re-indexing done (JM) and merged.
  • landing pages ongoing, deployed on idr-testing
• OMERO
  • OMERO.server (Seb)
    • omero-model 5.7.3 released incl. Bio-Formats 8.2.0 and other dependencies upgrade e.g. Spring Framework 4.3.30
    • next components (next few days): omero-common, omero-romio, omero-renderer, omero-serve, omero-blitz, omero-gateway-java
    • TBD: when to release OMERO.server bundle
    • Next major dependency effort to be scoped post Summer: Spring/Hibernate. Large body of work, needs scoping.
  • OMERO.web (Andreas)
    • no updates this week
• Bio-Formats (Melissa)
  • 8.2.0 released last week. Moving towards 8.3.0…
• NGFF
  • Techdev update:
    • 3a (import) JM: Python-only import “register” the zarr image. Create image using API using sizes and pixelType, then set ExternalInfo. No Fileset created.
      • Next: need to add support for non-5D images (for e.g. idr0167) to omero-zarr-pixel-buffer and support for EBI Embassy s3
      • Looking into Python only options to “import” ome-zarr files.
    • 3c (BioFile Finder): Discussed possible use in IDR workflow submission: combine list of zarrs from BIA with annotation.csv to create BFF file that might be useful for validation? Will: see idr0125 in BFF from csv_to_biofilefinder.py.
      • Jason: @will broken for me.
    • 3b/3d (python libs): Will: more positive feedback received on ome-zarr-py zarr v3 PR. I think it’s ready for release of v 0.12.0rc1. Looks like a tag will trigger Pypi publish: publish_pypi.yml
    • Jason on a massive Plate export escapade with omero-cli-zarr
  • Next OME NGFF Community Call June 24, 09:00 CEST and 17:00 CEST

• GerBI

• Glencoe (Chris)
  • see dependency updates above
  • Django 5.2 compatibility testing upcoming
  • Erin: SBI2 and other meetings later
• Community
  • Reminder: OME Annual Meetings Talks
  • Petr at ELMI

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)