IDR-NGFF-2020-10-01

--- tags: NGFF --- # IDR-NGFF-2020-10-01 - Dataset (idr0033) - https://github.com/IDR/idr-notebooks/pull/34 "useless" (unless Anatole can find something) - https://trello.com/c/YLm8GJG4/3-rois-idr0033-rohban - PNG image data, 1080 x 1080, 8-bit grayscale, non-interlaced Mask pattern is [0-9]+/[a-z]+[0-9]+_s[0-9]+_(Cell|Nuclei)Outlines.png [plate-id, well, site] - [elife](https://github.com/elifesciences-publications/2016_rohban_submitted) apparently has R scripts, etc. - Would we want the ROIs in a pre-NGFF release? - J-m: happy to start on ROIs, and would like to see them in IDR and Zarr. - Starting to work on notebooks. - Need new connection method for binderhub - Simon: thought we fell back to websockets automatically - Seb: masks look straight-forward from PNG masks. Ground-truth in OMERO. - Simon: creating polyline for contour of region. Good for overlaying. - Simon: already attached? Don't know. Seb: should we? Maybe, useful to have access for mybinder. Seb: will look at connecting them. - Clients - Will: do we have features? Yes. Per cell (ROI) and per well. J-m: thinking about looking at Parade V2 (prototype)? Yes. - see [napari comment](https://openmicroscopy.slack.com/archives/C0K5EED3R/p1601479615331300) - Grid layout of plate in omero-napari - Can load Data from OMERO - simple: show 1 image per Well. But idea to show other fields via a slider etc. Or via zoom. - Will: could imagine a pyramid of the plate itself with dask - Seb: https://github.com/ome/ome-model/issues/62 Cf the overview image mentioned here (from Tischer) - Simon: similar to overview or "index" image from NDPI - Josh: call with Tischer on mobie - J-m: Ugis said he tried it but it was slow - Will: https://github.com/will-moore/omero-openwith-url - Josh: for loading from S3? - Will: yes, let's you register vitesse as a URL opener with the image ID. - Josh (NB) working on registry of all the zarr - Josh: are any of us planning on working on vizarr? - Simon: Wei is being doing development on vizarr... using imjoy?! - Josh: big question -- what client for HCS from zarr are we working on first? - Will: If we support plate-as-a-big-image, then anything can support it. - Simon: we want it to look like highest resolution but likely not in zarr. - Microservices - https://github.com/manics/docker-example-omero-microservices - http://localhost:10080 for the proxy - omero-ms-thumbnail service runs, picks up the web session - Doesn't return thumbnails 😢 (HTTP 403) - Josh: 3 types of existing micro-services: client, server, PSQL (and also backbone i.e. talk to the server) - See Slack starting from https://openmicroscopy.slack.com/archives/C0K5WAD8A/p1601460543257800 - maybe 4th type could exist that only talks to Zarr - thumbnail-ms very client-focused i.e. creates session and cannot use the API - imageRegion-ms is server, has access to the internals e.g. renderer - if thumbnail-ms become type 2, can use renderer - could even teach renderer to work directly from Zarr - supported by Chris' statement in Slack (current assumption requires Hibernate interaction but could be changed if downsampled data is precomputed) - J-M: similar to Insight. Main downside might be duplication of code - possible extraction of common code for rendering data that could use different loaders - Simon: some initial thoughts from Andrea https://github.com/ome/omero-ms-queue/issues/8 - Josh: can one micro-service be of 2 types (client & server) - Format - Josh: to start looking into Zarr specification - currently. each series is split - Seb: PlateAcquisition may be a complexity. (Derived image solution?) - Simon: make acquisition mandatory (runs)? Certainly one option. - Seb: please implement in bf2raw first - immediate need for this - ZarrReader: start using it in bioformat2raw. David to open everything for Bio-Formats 6.6 - Communication - Seb: general channel? idr? - J-M: stick to general. Keep idr for upcoming publications - Josh: ngff also available. Main caveat is accessibility for externals - Seb: for externals, alternative is weekly digest. Josh: to some extent, this can happen on Tuesday - Potentially move notes publicly - Simon: some links might not be working e.g. Slack. Probably not overly critical - No immediate action but something to look into in the future