2020-08-18

Attending: Will, Petr, Jason, Jean-Marie, Mark, June, Wilma, Simon, Andreas, Kevin, Melissa, Josh, David, Erin, Emil, Seb (14:17)

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR

  • New data upload mechanism:

  • IDR 0.8.5 released: two new 3D mouse studies

  • IDR 0.8.6: WSI data: a new histopathology study with lung cancer

    images + 1000 new HPA antibodies

• NGFF

  • S3 fun (CORS, public, private, clients, etc.)

    • Some testing this morning - OK. Fast(ish) but not as fast as

      Aspera

  • Visualization clients

  • EBI feedback. JavaScript apps using EBI s3 failed because of

    CORS.

    • Current workaround needs local copy etc.

  • Simon: using Amazon JS viewer to browse idr-upload

  • Need a web upload client via minio

  • Simon: re-use OMERO.dropbox? Josh: yes, possible using minio

    events

  • [Masks in

    omero-ms-zarr</u>](https://github.com/ome/omero-ms-zarr/pull/60): overlapping

    • Updating other repos: ome-zarr-py, omero-cli-zarr

  • Pushing on the final breaking changes (“labels/”)

    • Python easy update, Java harder

  • Next steps: handle multi-resolution zarr.

    • JM - already had issues with this being missing

  • Use cases, drivers, etc.

  • JM: Cellprofiler (python2) issues with zarr - need to test again

  • Jason: will provide datasets to test, with masks.

  • Viv (Trevor) aims to add labels support

• OMERO 5:

  • deep copy (Mark)

    • burrowing into repository and DAO code

  • chown (Will/Petr)

    • Will: chown is quite conservative, not wanting to end up in

      a situation where hierarchies belong to different users (at least in R-O and R-A). The webclient, however, allows you to create such hierarchies by dragging things from one container to another. The discrepancy leads to links being cut.

      • Change the server? Change chown? Handle it in the

        client?

    • Petr: “chown … will cut the link on me” isn’t how I

      understood it. Instead:

      • From a low-level, when you talk to OMERO permissions

        people are shutting off. They don’t want to hear “link is cut”. → “Why?!” (They don’t care about R-O or R-A) The more complex the rules the deeper the hole we are digging for ourselves. Intuitive expectation: “everything will stay the same except what I want to move.“

    • Jason: links shouldn’t be cut?

    • Petr: exactly! NO links should ever be cut.

      • Deep copy work very high priority to fix this issue

        between groups.

    • Mark: received wisdom was P/D/I groups were ‘same owner’

    • Josh: chown should fail. And give user options for how to

      fix it: unlink, deep-copy

    • Mark: ability to query which links will be broken during

      change ownership, before running the chown command

  • anything else? (component releases?)

• SA: Josh: pgslave is growing

• Glencoe: Emil

  • n5/zarr looking at open-cv for downsampling

  • Tile-db instead of pytables?

  • Omero microservices for 3D analysis, imput from s3 buckets

  • Josh: what do you want to try

  • Emil: labelled masks, WSI. Can convert slides and create masks

• Community

  • CLA and Code of Conduct in Draft

  • Sanger proposal funded - single cell imaging/analysis

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)