2023-05-16

Attending: Will, Josh, Frances, Petr, Khaled, Jean-Marie, Maadhav, Seb, Richard, Chris, June, Andreas, Tom, Kyle, David, Melissa, Jason, Kevin, David Stirling,

Start: 2:00 pm UK

Accepting minutes from last meeting

• Review location of meeting minutes and upda

Project Status

(2-3 minutes each)

• IDR (Frances):
  • Globus connection issues - ongoing work with EBI
  • Format reader issues - idr0088 and idr0044
  • Search engine permissions meeting - just IDR, then wider to include Glencoe
  • Will: progress with NGFF Fileset swapping, working with idr0012
  • Jason: how long till we can release something?
  • Will: Not till all studies done - quite a long time
  • JM: NB: this still requires psql steps - since not supported by API
• OMERO:
  • Cookies settings PR for web
  • JM: Django 4.0 support: can’t test on merge-ci (python3.6) - lots of work to update. Need to decide on priority to spend time to upgrade. Busy till early June. Need to organise a discussion then
  • Seb: Glencoe testing with Django 4.0 is looking good. Could release omero-web and/or apps as working with Django 3.2.
  • Jason: plan time soon
• Bio-Formats (David)
  • idr work (see above)
  • 2 large external PRs - new/updated Readers Nikon, and Zeiss reader rewrite to fix perf issue
• NGFF (Josh)
  • Papers - all submitted except 1 (later this week)
    • contact from Nature journalist…
  • HMS presentation - Vitessce etc
  • Resources (website, etc)
    • Meeting on Fridays
    • Logo in time for paper?
  • Specifications
    • 0.5.0 - calls with Kevin & John on their PRs
    • Beyond (Zarr V3)
      • Spec agreed on
      • Movement started on various implementations, e.g Rust
      • OME will need to decide when to adopt
• GerBI (Tom)
  • webtagging
    • No response from Douglas
    • fork -> tag search & auto-tagging apps
    • JM: try David Pinto?
  • pico-quant - work to support OMERO import
• Glencoe
  • OMERO/SSL/Ciphers
    • https://github.com/ome/omero-server-docker/pull/78
    • https://github.com/ome/omero-documentation/pull/2315
    • End of CentOS7 support needs to be discussed
    • Preparing to end new installs
    • Rocky 8 or 9 for new RHEL targets
    • Ubuntu also possible, not used by OME
    • JM: lot of work to move off CentOS7
    • Chris: 13 months till CentOS7 EOL
  • ABRF meeting went well - lots of interest in NGFF by commercial and others
  • BioIT world this week
• Community
  • Frances: Ongoing prep for next week EBI imaging course (Monday, presenting Thurs/Fri) and ICOPs workshop (EOSC related) on Ontologies (related to https://open-phytoliths.github.io/FAIR-phytoliths/).
  • JM presenting end of June - notebooks. Related to https://open-phytoliths.github.io/FAIR-phytoliths/
  • Petr: Defragmentation workshop last week - cloud computing, Jupyter notebooks with NGFF, OMERO etc.
  • University of Gadja Mada - Indonesia, training pathologists. Petr tending to demo.
  • AHRI and SATVI/UCT
    • large scale pathology work on TB

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)