2020-09-01

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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)

  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)

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

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