2022-02-01

Attending: Will, Petr, JM, June, Seb, David, Kevin, Jason, Frances, Khaled, David Stirling, Chris, Andreas, Wilma, Melissa, Muhanad, Erin, Mina, Josh,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR:
  • next release: 2 new studies
  • idr0127 (timelapse bacteria), idr0123 (FISH-omics)
  • Khaled: search - deployed for testing
• NGFF
  • OME-NGFF 0.4
    • Good community calls last week
    • Final spec updates (transformations, clarifications)
    • JSON schemas / samples
    • reading/writing implementations (Python, Java)
  • Hackathon (Zulip, image.sc gather.town)
    • squid-py compatibility
• Releases
  • Jenkins update See summary
    • Upgrade prior to moving to python 3.8, CentOS7
• Glencoe
  • Updating Gradle, Java LTS versions 17 etc
• Community
  • Global bioimaging workshop last week
    • wide range of participants - global
    • enthusistic chat
    • OMERO and IDR workshops - went well
  • Next week: Karolinska Institute
  • OME meeting

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max) Glencoe software:

• deploy with microservices
• Use shared storage for Zarr data in well-defined format (Fileset IDs etc.)
  • Data duplicated
  • Different pyramid structure from raw data
• Make OMERO.server aware of shared storage
  • run bioformats2raw
  • import OME.xml - get Image ID
  • tell microservice Image ID and path/to/zarr
• Previous investigation from Simon https://gitlab.com/openmicroscopy/incubator/bioformats-urlreader