tags: Tuesday —

2025-08-12

Attending: Will, Petr, Josh, Jason, Khaled, Frances, Seb, Kevin, Melissa, Tom, Kyle, Chris, Andreas,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • released prod129 last week with idr0170: OME-Zarr converted by submitter. First usage of omero-zarr-pixel-buffer. Also using BioFile Finder to provide access to s3 URLs. Posted on bsky. TODO: post on LinkedIn
• OMERO (Andreas)
  • OMERO.web security release prepared for tomorrow 1pm
• Bio-Formats (Melissa)
  • 8.3.0 released, prep 8.4.0 started
• NGFF
  • Will
    • BioNGFF: omero-import-utils: import OME/METADATA.ome.xml
      • • In progress: moving register.py to omero-cli-zarr so we can add integration tests etc.
    • testing searchengine cotainer_bff_data - reported at https://github.com/ome/omero_search_engine/pull/114#issuecomment-3174141682 - Load ALL images from an IDR study into BioFile Finder from searchengine. 300k images is OK, 900k times-out
      • Jason: Is 500k an acceptable compromise?
    • ome-zarr-py RC last week: https://github.com/ome/ome-zarr-py/releases/tag/v0.12rc1 with OME-Zarr v0.5 support
  • Josh
    • RFC-4 (orientation): response submitted; approved by Juan
    • RFC-5 (transforms): plan for 0.6.dev2
      • Johannes to start work on schema & spec
      • SpatialData transforms: https://github.com/BioImageTools/ngff-transformations
    • ZEP10 (extensions) Lachlan Deacon: approaching concensus
    • Zarr Summit in Rome: https://github.com/zarr-developers/community/issues/74 Oct 13-17
      • Attendees etc. Josh attending https://github.com/cloudnativegeo/community-events/issues/9
      • Feature flag in ngff-zarr to support e.g. transforms etc. We may want to do something similiar
• GerBI
  • Josh: interviews this week
  • Tom: attending MiFoBio in France, to present
    • https://imabio-cnrs.fr/introduction-to-mifobio2025/
• Glencoe (Chris)
  • OMERO logo PR: https://github.com/ome/www.openmicroscopy.org/pull/813 Approved - ready to merge? Will to look
  • omero-py cleanup, SSL upgrade etc
  • Chris away for 2 weeks tomorrow
• Community

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)