tags: Tuesday —

2025-05-27

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

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • prod128 - 2 new studies idr0151. Drosophilia idr0166 - myelin basic protein - brain images. Broken image to be re-uploaded
  • searchengine testing ongoing.
• OMERO
  • OMERO.server (Seb)
    • Dependencies upgraded to address several CVEs with critical severity
    • Looking into upgrades for CVEs with high severity and general cleanup of unnecessary dependencies
    • Proposed next steps
      • Merge CodeQL workflows across all omero-* Java components by EOB
      • Start releasing Java components after the inclusion of Bio-Formats 8.2.0 in omero-model
      • Draft advisories for critical CVEs not applicable to OMERO
      • Release of OMERO components to follow up-coming Bio-Formats release
  • OMERO.web (Andreas)
    • two new PRs to be reviewed from David and Seb
• Bio-Formats
  • 8.2.0 release planned for today. Will talk to Seb after
• NGFF (Josh)
  • Javascript discussion with Trevor: Zod work up for maintainership. vizarr future uncertain
    • ITK being further developed
  • Python discussion:
    • ome-zarr-models-py: hopefully a minimal version (no pydantic and zarr v3 dependency)
    • ngff-zarr: full support for up to 0.5
    • Will: ome-zarr-py can now read 0.5. Writing is limited to 0.4. -#404 - Use zarr v3, read OME-Zarr v0.4 and v0.5 but ONLY write v0.4.
      • Propose to get an RC with the breaking change out
  • Java discussion (Dom)
    • https://central.sonatype.org/news/20250326_ossrh_sunset/#what-does-this-mean
    • Dom/JM: Import workflows set up on merge-ci using zarr-pixel buffer
    • Working on supporting zarr without ome.xml metadata file and file stored on AWS. Create ome.xml first from zarr.
    • Josh: source.coop various issues:
      • no CORS or range-requests and 502s rather than 404s
• GerBI (Josh)
  • Metadata discussions: NFDI working group. Hackathon work on omero-marshal.
  • GerBI OMERO server for testing prototypes, e.g. like gallery. Munster hosted, public.

• Glencoe - see above

• Community
  • ELMI (4th June 14:30)
  • India trip - VMs provided by Kobe
  • Brno training - repeat of last year

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)