2024-03-05

Attending: Will, David, Dom, June, Frances, Khaled, Oumou, Muhanad, Kyle, David S, Melissa, Seb, Kevin, Chris, Erin,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • prod120: idr0154, idr0155 release later today
  • Will: testing perf of NGFF on idr-testing:
    • Rendering images is much faster when data is on local disk (~0.4 secs) compared with S3 (~2 secs).
  • David looking at reading from s3 directly
• OMERO
  • Chris: preparing security blog post
• Bio-Formats
  • Melissa: Java 21 tests now running, surprisingly passing!

• NGFF

• GerBI

• Glencoe (Chris)
  • OMERO.web items ongoing:
  • HCS thumbnail refreshing
  • OMERO.figure - no prevention of max-intensity projection
  • single sign-on
  • Erin: Webknosses chunking discussion blog post https://www.glencoesoftware.com/blog/2024/03/01/data-structure-ome-zarr.html
  • poster https://www.glencoesoftware.com/blog/2024/03/04/SLAS.html
• Community
  • Indonesia trip in progress!
  • OME meeting planning ongoing. Dates TBC

AOB

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

Main Topic

Microscope metrics: Julio Mateos Langerak, Oumou

• Imaging to check health of the microscope
• Data is often kept in inaccessible locations
• Idea is to use OMERO to store this data
• Now have finance to implement this
• Ease of use, FAIRness etc
• Encourage core facility staff to use OMERO for their own data
• Benefits of training etc
• Packages:
  • microscope-metrics: algorithms
  • schema: Link-ml
  • microscope-metrics-omero: Interface with OMEREO
• Seb: who will want to access the data? Users?
  • Julio: yes. Publish QC data alongside experimental data
• Mapping:
  • OMERO group -> microscope
  • Project -> analysis over time
  • Dataset