2022-06-21

Attending: Will, Dom, Petr, Frances, Jean-Marie, Seb, Josh, Khaled, David, Kyle, Melissa, Kevin, Suzanne K, Chris,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • planning to release today but issues:
    • search indexing…
    • released Dataset: well annotations
  • Search
    • Josh feedback: facet search & cross-indexing
      • packages available for facet search. May need different indexing
      • Do we need study metadata on Images and vice versa? For grouping (like mapr “give me Projects which contain Images with matching Key/Value”). But explosion in index size.
      • Jason: No (not for IDR). Start with “find me studies with these keywords”
      • Chris: ES not designed to do many-to-many joins with queries in both directions. Need to enforce e.g. Image in 1 Dataset
      • JM: can do this with IDR, but not so generic for other OMERO use-cases
• Bio-Formats
  • ZarrReader integration - dependency discrepancies between OMERO and BioFormats. Will look at this till Thursday. If no solution, will not include in next OMERO release
• OMERO
  • Build system investigation on-going.
    • Not working as expected with ZarrReader
• NGFF
  • Neuroglancer: https://bit.ly/3MQtk7y (code)
  • Quarep & the metadata backdoor:
    • generate metadata (OME.xml) file and store alongside data
    • Jason: validation?
  • FFMPEG (other movie formats) -> OME-NGFF conversion
    • Chris: output will be much larger
  • John Bogovic will host next NGFF call (v0.5, transformations)
• Glencoe
  • Ongoing min/max calculation, NGFF work…
  • layout spec
• Community
  • SLS workshop
    • follow up meeting with user cf. analysis
    • Small numbers but very engaged users
  • ELMI feedback (Josh)
    • iRODS - well received
    • NGFF & VR (Warwick)
    • Protocols.io OMERO widget (omero-web app?)
    • MoBIE projects in OMERO (attach metadata to Project/Dataset)
    • https://twitter.com/MicroscopyDB training community
  • Suzanne: how to forward/delegate help requests to appropriate experts: i3D:bio or OME team?
    • Meeting to discuss?
    • many users reluctant to ask questions publicly (image.sc)
    • Jason: hard to move an established discussion into public, best to start in public.
  • OME meeting (virtual) looking like week of 14th November

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)