2023-03-07

Attending: Will, Dom, JM, Petr, Josh, Frances, Tom B, David, Khaled, Melissa, Seb, Richard, Kevin, Kyle, David Stirling, Muhanad

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • SSBD visit last week.
    • lots of discussion comparing SSBD and IDR, potential bridges, common terms etc.
    • IDR search for use in SSBD etc.
  • Conversion of datasets to NGFF ongoing (for server upgrade)
• OMERO (JM)
  • releasing omero-* Java components. Adjustments made to the release process.
    • starting with omero-model
    • omero-server discussion wrt indexing PR
  • Kevin: please comment on rendering PR if any more TODOs
  • Josh: https://github.com/Qureator/omero-acquisition-transfer
    • need to make this extensible/reusable
    • Keep an eye out for other community forks
    • https://github.com/ome/omero-cli-transfer/pull/43 (accident)
• Bio-Formats (David)
  • focus back on ZarrReader, dealing with issues from conversions above
  • chunk API for openbytes - PR open against Bio-Formats
    • https://github.com/ome/bioformats/pull/3794
• NGFF
  • 0.4/Paper
    • not heard from submission - waiting on reviewer:
    • Add authors: RIKEN (data), DKFZ/Helmholtz (tools), SciLifeLab (generation)
    • scilifelab generating NGFF data from microscope (https://github.com/kasasxav/ImSwitch)
  • 0.5/Tables:
    • BDZ - tracking data in AnnData tables, view in napari Validator, etc
    • Tables PR - discussion upcoming to check on progress
  • 0.6+/Metadata: Chat next Wed. Requirements, etc.
    • other binary files?
• GerBI
  • Tom: TIM meeting in 2 weeks
    • OMERO install on Hive looking good, with in-place import, 5TB of space, users created for all participants.
    • Any config improvements for performance etc?
    • Zarr in-place import not worked, but not needed for workshop
    • Most users expected to use Insight
  • I3D: first meeting
    • ongoing training material creation. How to collaborate?
    • cf. RDMKit and progress for submission
    • discuss after TiM?
  • Josh: NFDI launch. NGFF position.
    • started. hiring people. Ad for position around ngff to go out later this month. Easier if based in Germany but not a must
    • First meeting April
• Glencoe
  • Erin: Chris at meeting
  • Running OMERO.plus release. Lot of testing. including Bio-Formats and OMERO updates.
  • Compatibility testing with plugins and OMERO.web 5.18 went well. Happy to share notes.
  • New version of bioformats2raw and raw2ometiff (~2 weeks ago)
    • https://github.com/glencoesoftware/bioformats2raw/releases/tag/v0.6.1
    • https://github.com/glencoesoftware/raw2ometiff/releases/tag/v0.4.1
  • Attending ABRF in Boston (Erin and Stick) and JupyterCon in Paris (Emil and David)
  • OMERO search indexing needs a resolution. https://github.com/ome/omero-server/pull/156
• Community
  • Training at TiM
  • Talks from J-m
  • EuBI workshop at the end of the month
  • Richard: to be approaching regarding OMERO/IDR training (in-person slightly preferable to remote) later in the year. Petr: first come first serve :smile:

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)