2023-05-02

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

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • Searchengine permissions: see notes: https://docs.google.com/document/d/1hOtnUrI2CZH0OwrR0U2xvvRwqqH_vPQu7IOuBavOqHs/edit
    • Any further comments - please add
    • Schedule meeting to discuss
  • NGFF conversion (Will)
    • Each dataset seems to have a different issue
    • Have scripts in place to swap the in-place symlinks
      • Doesn’t work with idr0010 for some reason
      • Perhaps due to bioformatscache?
      • Must look at one image in a plate before updating (but doesn’t help with idr0010)
      • Dom: perhaps due to skip all? Possibly.
    • Re-ordering fix now in ZarrReader
      • Previously imported NGFF plate now broken
    • Next steps?
      • David looking at ZarrReader
      • Josh will read the idr0010 thread
  • IDR application for Global Core Data Resource
    • Folder
• OMERO
  • Django 4.2 update for omero-web
    • Chris: can release compatibility for Django 4.2 without actually bumping the dependency (will work with Django 3 and 4)
    • Can decide on schedule for bumping
    • Andreas: Also need to update web apps
  • JM: remove portalocker first
  • Discussion on version naming.
    • docs for users on what versions of omero-web are compatible with OMERO.server versions
• Bio-Formats (David)
  • 6.13 was planned for last week, but issues with new deployment (now fixed)
    • build, deployed & tested.
    • release later today or tomorrow
• NGFF
  • Josh: re-entry
  • Zarr: 2.15 release
  • Zarr v3 - RFC till end of the week (plus SciPy)
  • 10 weeks (July) to prepare ppt, logo, use-cases
  • NGFF-related Papers (see CZI single cell insights)
    • SpatialData
    • NGFF paper nearly done
    • Zarr trademark - call scheduled
  • EOSC meeting
    • good vibe on OME-Zarr
    • Zeiss & Leica present
    • devs looking to update OR have already adopted
    • Richard: Nanostring?
      • Jason: have had discussions with Nanostring on OME-NGFF and OME-TIFF.
• GerBI (Tom)
  • webtagging PR to add Well support
    • webtagging not actively maintained - GebBI to take over?
    • Split auto-tagging from tag-search (2 apps)?
    • JM: OME merge-ci can install/test a fork
• Glencoe (Chris)
  • Seb: sessions not cleaned on web upgrade. Needs fix/docs update. Crosslink web and server docs
  • Chris: sessions won’t be compatible Django 3 -> 4
• Community
  • NEUBIAS meeting ‘defragmentation’ next week
  • EBI microscopy course - later in May

AOB

• Jason: Notes above
• OME Team: Rest Day on May 8 - meetings cancelled

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

Main Topic

(20-25 minutes plus 15 minutes questions max)