2018-11-06

Dundee: N/A

Remote: Simon, Chris, Mark, JM, Kenny, Frances, Andreas, Petr, Josh, Jason, David, Melissa, Dom, Wilma, Riad, Liza

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• Data-In:

  • Simon: S3 imports working on east-ci. Imported internal minio

    mirror of czi.starfish.data.public/browse/raw/20180820/merfish_u2os into east-ci

  • Josh: primarily focusing on Sanger/Harmony dataset (see

    \#ome-sanger). Performance issues may point to parallelization. SpaceTX-OMERO work.

• Data-Out

  • Mark: For omero-downloader now pushed simple usage instructions

    to README and drafted test scenario. Focus shifting to launcher/wrapper and testing.

  • J-M:

    • Fixing Fiji workflows issue for next trainings

    • Ongoing R work for Cambridge training (December)

    • Helping to update Smuggler, potential training session next

      year

• Glencoe (Chris):

  • Formats work

    • Fixing bugs, more PRs coming

  • OMERO work

    • Fixing up microservice bugs

  • Customer updates

  • iCAIRD and PathLAKE (Jason):

    • Funding from Innovate UK for 5 digital pathology hubs,

      Glencoe involved in two.

• Community

  • Kobe/SSBD Summary

    • Jason:

      • OMERO workshop: ~37 participants from different

        institutions across Japan

      • Webinar: Technical side worked well apart from

        screen-sharing Fiji

      • Okinawa workshop: ~20 participants from across Asia

      • Consider promoting other analytical/exploratory tools

        (e.g. Parade or Figure instead of just ImageJ), and data resources in future workshops

      • CellProfiler currently has limited maintainers, Broad

        moving to Cyto-AI (http://cyto.ai) instead

    • Josh:

      • SSBD is a single instance, not going to pursue running

        multiple SSBDs as a platform for storing ROIs or tracks

      • Will be collaborating on linking OMERO objects to

        external resources

  • FYI

    • EBIB/Heidelberg: Wed/Thurs (Seb/Josh)

      • Presentations available on downloads

    • IDR talk/Basel: Nov 19. (Josh)

    • I2K/Heidelberg: Dec. 5-8

1. AOB

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

• Kenny/Network (Dundee-only): volunteer yourself for switching your

  switch. No change for externals.

  • Separate issue with the VPN (Frances/Cisco client)
• Presentation at IDR 10 am call Aubin/Wei presenting on CNN for

  segmentation

1. Main Topic

(20-25 minutes plus 15 minutes questions max)