2020-10-06

Attending: Seb, Andreas, Dominik, Frances, June, Mark, Petr, Wilma, David, Jean-Marie, Simon, Melissa, Jason, Erin, Chris, Emil

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR
  • Frances: prod89 released today incl. 2 new studies:
    • idr0094 second Sars-COV-2 dataset. Upcoming press release
    • idr0091 bacterial time-lapse imaging study
• NGFF
  • Seb: Trying to ramp up on a set features
    • HCS metadata layout/spec for OME-Zarr
    • Notebooks with a parallelizable analysis
    • Thumbnail microservice in IDR
    • Some form of visualization of the plate layout
    • Export of the images
  • Dataset: idr0033
    • Demo by end of November
• OMERO 5
  • Mark: OMERO 5.6.3 released last week
• Bio-Formats 6.6
  • Seb: most API changes opened for inclusion in minor release. Focusing on testing and identifying blockers
    • memoization for sub-readers requires more investigation/discussion. Pushed to a follow-up minor release.
    • post release considerations: OMERO, IDR, bioformats2raw
  • David: starting to finalize next week.
    • ETA: end of next week or the week after
  • Simon: can the IDR Bio-Formats fork be dropped?
    • Seb: further reducing the divergence (a few readers). Still a few places (memoization, Screen)
  • Jason: outside IDR use case, worth looking into ways to communicate the API value to Bio-Formats consumers
    • Seb: few examples demonstrating the usage of these concepts.
    • Look into something to complement the detailed release notes e.g. blog post or similar
• SA
  • Simon: nightshade upgrade incl. GPFS upgrade
    • Seb: also fix the temp file filling up as part of downtime?
    • Simon: originally tried to reduce the impact of files download. Other paths might be involved
• Glencoe
  • Chris: fixing series of issues in bioformat2raw.
• Community
  • Petr: Likely two workshops at the end of November
    • McGill and Goteborg: want shorter workshops (user-targetted)
  • Jason: NIH Funding for 4DN project
    • UI integrating OMERO with genomics, loci, in-situ
    • 5 years of 80% FTE
    • Need to work out communication.
  • Petr: series of workshops will happen next year

AOB

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

• Mark’s last Tuesday meeting!

Main Topic

(20-25 minutes plus 15 minutes questions max)