2023-11-14

Attending: Will, Dom, Petr, Josh, JM, David, Frances, Muhanad, Melissa, Seb, Khaled, Kyle, Andreas, June, David S, Chris, Erin,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • Frances: public EBI folder now unblocked. Transfer in progress
  • Will: Seb ran memo file generation on idr-testing last week. Found a bunch of failures, mostly due to a missed sql statements (now fixed) but also 8 NGFF plates that are missing files on EBI s3. Re-running the conversion for these now… Also memo file generation is re-running due to memo cache not working on readonly-X proxy servers.
  • Decided to push NGFF release to early next year
• OMERO
  • issue with omero-py building on Windows see std: binary function - don’t block release, create an issue to keep track
  • ansible roles: a handful to be released.
  • OMERO.web UI customization support: https://github.com/ome/omero-web/issues/510 feedback welcome!
• Bio-Formats
  • ZarrReader - last few fixes
  • Bio-Formats PR reviews, aim for 7.1.0 release mid December
• NGFF
  • Hackathon (stream / website)
    • Summary forthcoming (image.sc) but tl;dr
    • Presentations: nextflow, galaxy, spark, slurm, fractal, cellprofiler, as well as pydantic and spatialdata
    • Breakout groups:
      • Converters (mcd, MD Image Xpress, Cellvoyager, etc.) –> GitHub topics
        • all in python.
      • First nextflow workflows with OME-Zarr
      • OME-Zarrs in PyTorch
      • validators and hierarchical modelling (pydantic/linkml)
      • Features (“NGFFF”)
      • OME-Zarrs in Galaxy
      • NGFF reader/writer review
    • Common place to work: https://github.com/bioimagetools
      • review of various tools/python libs -gdoc
  • NGFF spec discussions
    • Proposed RFC like process. General agreement. Next steps.
    • Extensions: Let us put other stuff into OME-Zarr
    • Transforms: F-Order (computer vis libs) vv C-order (numpy)
      • e.g. n5, itk and Matlab? are F-Order
• GerBI
  • Training docs & a few repos (Tom?)
    • Zenodo https://zenodo.org/records/8323588 and YouTube links
    • Working on https://github.com/German-BioImaging/omero-scripts/tree/xtnd_support_kvpairs
  • Hackathons (Josh)
    • Cologne November and Bielefeld December
    • Discussing importing & exporting from & to OMERO
    • ARC, BIDS, RDF.
    • Interest in more advanced annotation namespace usages

• Glencoe

• Community
  • Good Feedback and engagement from Barcelona workshop https://docs.google.com/document/d/1j5YcLq86lEYHit-kC6jbC67A60kF-SwDVm8dVTR0L0Q/edit . Colour-blind support

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)