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)

Select a repo