2022-05-03

Attending: Will, Frances, Seb, Dom, Jean-Marie, Josh, David, Khaled, Andreas, Petr, Susanne, Melissa, Chris, David S, Wilma, Mina, Kyle

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

• IDR:
  • Next release - 3 viruses and time-lapse study, and histology sections (5 studies).
  • Release on Thursday. But, embassy upgrade still ongoing… Assume OK for now.
  • 2 new videos for “showcase”. IDR analytical workflow on Analysis section on IDR front page
  • Search ongoing. Seb: next target is June incl. search
• OMERO (JM)
  • FYI: Working on alternative to replace the CI jobs
  • Doc to rtd.PR 2195 - priority since release is currently painful
    • Naming / urls on rtd
    • More flexible release of docs when e.g. omero-web / omero-py releases
  • Artifacts to GitHub PR 6318
• Bio-Formats (Bio-Formats)
  • ZarrReader testing etc
  • https://github.com/ome/ZarrReader/issues/32
• NGFF
  • image.name
    • poorly named from ZarrReader. Could use OME.xml. Needs discussion.
    • https://github.com/ome/design/issues/57
  • OME-XML testing & v0.2-v0.4
  • bf2raw rcs? Maven rc? conda?
  • polygons & extensions to metadata
    • Polygons may clash with OME.xml
    • Seb: deprecating OME-XML’s mask? “Use labels”
    • J-m: going back to label itself. Loss of context.
  • Scifio metadata
  • dask writing - see PR
  • zarr 2.12 release soon (zarr v3), governance, etc.
  • J-m: Catalog & Showcases
    • How comfortable to start highlighting converted data?
    • E.g. on the website.Have notebooks, workshops, etc.
• Glencoe (Chris):
  • Using NGFF labels with OMERO & masks. ZarrReader support
  • Adding lots of annotations to ROIs, e.g. KVpairs, modifiable etc. Encode this in OME.xml or just NGFF? Andreas: push more logic to server
  • Extensions, labels min/max, histograms etc.
  • Plate metadata duplicated between OME.xml and NGFF. precedence?
  • Image names - OME.xml from s3 or Azure - poorly named images
  • Insight sessions issue
• Community
  • I2K coming soon. Some team attending
  • EBI course week on 16th May

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)