2022-09-13

Attending: Will, Dom, David, Frances, Chris, Seb, Melissa, June, Khaled, Kevin, Kyle, Wilma, Josh, J-m, Erin, Gina, Petr

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • Datasets still testing
  • Search UI phase 1 mostly there - testing ongoing
  • Release aiming for end of September (dataset and search)
  • Storage: FIRE testing with HPA data ongoing
• OMERO:
  • omero-py release last week
  • wait for next release of BioFormats before updating in OMERO (J-M explained process to Petr)
• Bio-Formats:
  • release planned for week after next 6.11.0 (instead of patch release as previously planned)
• NGFF
  • Chunks in OMERO:
    • Bug: https://github.com/ome/ZarrReader/issues/40 from idr-0125
    • Possible fix: https://github.com/ome/ZarrReader/pull/41 - ignore chunks at import time
    • Workaround: manually “in-place” chunks after import?
  • Fiji/N5 hackathon in Praque
    • See https://imagesc.zulipchat.com/#narrow/stream/329366-.5B2022-09.5D-Fiji.2BNGFF-Prague-hackathon
    • Teams interested in a low-level Java jar from github.com/ome which provides generated model classes
  • :warning: bioformats2raw.layout work is currently blocked bioformats2raw 0.5.0
    • Gathering & reviewing all PRs this week. Feedback & help welcome.
  • Will: acquisitions handling https://github.com/ome/ome-zarr-py/issues/225
    • How do users want to see acquisitions? slider? stacked as multiple channels? (cf. CyCIF)
    • Chris: depends on the use case. e.g. PerkinElmer for multiple day spaces between acquisitions
    • Will: then almost like an extra dimension
    • Chris: don’t currently allow declaring how you want them displayed. for the moment, make a choice when writing the data
    • Seb: from issue, no problem from spec & impl. layer. but more how do you consume them? napari issue? (all clients)
      • are they asking for more metadata about display? (part of the rendering work?)
    • Josh: do we encourage them to write their own plugin?
    • Chris: try to extend the plugin so someone could extend

• GerBI

• Glencoe (Chris):
  • BioFormats and bioformats2raw updates in progress (PRs open) to be in 0.5.0.
  • OMERO plus releases
  • bioformats2raw metadata: rendering settings etc.
• Community (Petr):
  • TIM 2023 discussion: they will set up an OMERO server (Tom B)
  • EastBio masterclass in November (week)
  • JM to London on Friday for BioImaging UK Meeting

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)