2020-04-14

Attending: Frances, Will, Josh, Dominik, Mark, Petr, Sebastien, June, Jason, Jean-Marie, Simon, Wilma, David, Melissa, Liza, Chris, Kevin, Andreas, Ola, Emil,

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR: waiting for idr-next to be available again,

  • Releasing idr0064 next

  • However disks for our NFS haven’t been shipped yet!

  • Discuss - upload direct to production?

  • Seb: need to upgrade idr-contrib thread. (“big issue with

    storage”)

• IO:

  • See notes from this morning.

  • How to get all the parts together?

  • Break TODOs into chunks so we know who’s doing what?

  • Discuss on Thursday

• SA (learning/mail)

  • GPFS/VMWare: nothing new on pricing.

  • E-mail: Prioritizing migration in case necromancer dies

    • Looking into abilities of Google Suite

    • And using Outlook for any remaining items.

  • Upcoming questions about outstanding hosts.

    • Simon hopes to get rid of ~90% of them.

• Glencoe:

  • Looking at Bio-Formats to raw use-cases.

  • Test with HCS datasets

  • Isyntax -> raw -> OME-TIFF - fixing chunking issues

    • Small chunk sizes are expensive for large amounts of data

    • E.g. rgb as 3 chunks can be e.g 15% slower.

    • Josh: zarr PR fs-spec - Use UI to pick where to store stuff.

    • Might need tests to check output of n5, read by zarr etc.

• Community

  • Ola: imjoy integration

    (https://imjoy.io)

    • Javascript based image platform

    • Based on jupyter

    • Useful for machine learning (e.g. to build ground truth)

    • JRS: discussed several times. Nice application. Very

      powerful for demonstrating. Have looked into repositories for AI training.

    • Use case: primarily giving ground truths (ROIs) to users.

      Josh: other tools worth looking into are Ilastik or QuPath.

      • Chris: also some tooling for converting QuPath regions

        back into OMERO (https://github.com/glencoesoftware/ome-omero-roitool)

      • J-M: existing integrations for Ilastik/QuPath

        • https://omero-guides.readthedocs.io/en/latest/

  • Funding Ops

    • EOSC-Life (9-12 months)

    • A few other EU projects….

  • Community Meeting

    • Amended virtual

      agenda

    • Use recorded content except for Jason, JM & Keynote.

    • What to do with Videos? Speakers happy for them to be

      public? (youtube)? Hosting ourselves? (more work).

    • Workshops?

    • Seb: watch videos *before* meeting. Then discussion on the

      day?

      • Jason: yes. We will record the speakers.

    • (Trello Joy)

    • Zoom Joy

1. AOB

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

1. Main Topic

(20-25 minutes plus 15 minutes questions max)