2020-09-01

Attending: Will, Jason, Jean-Marie, June, Mark, Melissa, Petr, Frances, Seb, Josh, David, Dom,

Kevin, Erin, Wilma, Chris, Emil

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR:

  • Seb: release planned for tomorrow. 3 studies.

    • Idr0082 pathology, mouse (idr0092), HPA

    • But: Antibody annotations in incompatible state - fix tested

      on pilot - looking good for release tomorrow.

• NGFF:

  • Josh: few PRs opened recently

    • Can discuss after this meeting

    • Color handling proposals - see

      omero-ms-zarr issue

  • OME-TIFF ‘slow’ (image.sc discussions)

    • https://forum.image.sc/t/bio-formats-clij-compatibility/42157/5

• OMERO 5

  • Josh: omero-py / omero-web releases upcoming?

    • Omero-py release when Simon is back

    • Omero-web - fix for Qupath - need wider feedback on response

      code change

      • Seb: big changes coming. If this is a bug-fix (small

        impact) then should get it out. Will can drive release.

    • Jason: good to get schedule defined

  • Mark: Deep copy PR is open

    • Josh: tried to build whole OMERO stack in Docker using open

      PRs -

    • Much more work? Mark: not a whole lot. But lots of scenarios

      to test

    • Currently only testable via the CLI & API. May conflict with

      web chown work.

    • Concern over testing deep-copy on merge-ci - make snapshot

• SA

• Glencoe:

  • TileDB stuff being pushed to bioformats2raw

    • Some upstream changes requested to improve portability

• Community

1. AOB

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

• Scheduling of next week’s team meeting.

• HPA talk at 2pm next Tuesday.

• Go for 4pm - 4.30pm try to keep it short

1. Main Topic

(20-25 minutes plus 15 minutes questions max)

Usage Stats: upgrade checks - total vv unique IPs

Zarr fun if desired

- All PRs in ‘sets of 3’ omero-ms-zarr (spec), ome-zarr-py & omero-cli-zarr,

- ome-zarr-py #45 lots of changes. Black formatting etc. pre-commit file.

- mypi - specify return types. Work to add, but useful for refactoring

- conda environment.yml - not many versions pinned yet. Might be needed.

- testing qt via github actions is hard. OS-specific.

- ome-zarr create - to create sample data. Avoid hitting s3 in testing

- Main change: graph traversal API. entry point: parse_url()

- also split out napari logic.

- separate our metadata from napari spec. E.g. ‘contrast_limits’

- Chris: we’ve had issues with graph traversal on s3 - xarray any use?

- Josh: that’s using fsspec. Could support /add that in our api

- Layer (from napari) hard to know what’s in the tuples.

- need to add labels ‘on top’ - layer opacity allows other layers below

- Other types possible - e.g. image-image links.

- Need a name for hierarchy of data ‘layers’ with metadata

- Hierarchy is converted into ordered list of layers, retaining the relationships between them.

- Reader class - uses ‘yeild’ generators everywhere, but not used anywhere yet - napari wants everything up front.

- Scaler class - used for downsampling. Used by omero-cli-zarr so that it saves downsampled labels.

- Can now download any image with labels (both as pyramids) and open in napari.

- naming needs deciding on: e.g. labels layers are identified by ‘color’ metadata.

Expect more discussions in public when released.

Bio-Formats Total

Bio-Formats Unique

OMERO Clients Total

OMERO Clients Unique

OMERO server Unique