2024-02-06

Attending: Will, Dom, Petr, Frances, Muhanad, Andreas, JM, June, David, Josh, Khaled, Seb, Kyle, Kevin, Jason, Melissa, Chris, David S, Maadhaav

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR (Frances):
  • Looking at 2 fixes for NGFF perf
    • configuration changes:
    • large memory usage when loading NGFF data
    • e.g. 20 Threads of 1GB memory each
    • Ice threads and DB connections. e.g:
    • config set – omero.db.poolsize 40
    • config set – Ice.ThreadPool.Server.SizeMax 25
    • config set – Ice.ThreadPool.Client.SizeMax 25
    • When Django gives up (timeout) server doesn’t give up, then Django tries again!
  • Also looking at microservices deployment
  • BioFormats - David looking at sizes of memo files but minimal space for improvements. E.g. some memos 100MB. 95% of what’s stored is ome.xml
  • Jason: target publication dates? Frances: some pressing dates coming up. Feb release would be nice.
  • Won’t add any more studies to the 2 new ones in this release.
• OMERO:
  • waiting on omero-web python 3.12 changes before full testing with omero-py
  • RHEL9 - preparing switch of ci infrastructure
• Bio-Formats (David):
  • 7.2.0 release should go ahead this week on Thursday
• NGFF (Josh):
  • Zarr v3 status: zarr-python v3 branch is active. Major review coming up. Any users should have a look. Try to get blog post on changes for users.
  • Movement on other ZEPs. Zep4 on conventions.
  • Unidata update (netCDF etc) devs left.
  • Will: started looking at v0.5 support for ome-ngff-validator…
• GerBI
  • Conferences, etc.
• Glencoe (Chris):
  • python 3.12 (see above)
  • Erin presenting tables etc at SLAS in Boston. Will add poster to website
• Community (Petr):
  • Karolinska workshop 14th Feb
  • Wellcome BioImaging

AOB

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

Main Topic

(20-25 minutes plus 15 minutes questions max)