2020-09-15

Attending: Petr, Josh, Simon, Frances, J-m, June, Mark, Seb, Melissa, David, =10

Kevin, Wilma, Chris, Will, Jason, Emil, Erin, Ola

Start: 2:00 pm

1. Accepting minutes from last meeting

2. Project Status

(2-3 minutes each)

• IDR:

  • Release planned for end of month.

    • 1 screen in and ready

    • 2 more studies planned. Both in progress: idr0089 and

      idr0094 (big covid screen)

    • Some data missing from idr0094. Lots of compounds handling.

    • Using PubChem

      identifiers as standard. Some cleanup needed after publication

    • First submission using OME-TIFF for HCS data. Bigger example

      to follow…

    • Lots of challenges with e.g. 1TB of data.

    • Jason: idr0094 - first phenotypic screen of covid infection

      in Human cells with drugs.

    • Chemical annotation is challenging. Commercial compound

      library.

    • EMBL (ChEMBL?) also involved

    • JM: we are encouraged to use this open data for training

    • Seb: see also

      https://www.ebi.ac.uk/unichem/

• NGFF

  • S3 status:

    • CORS- fixed thanks to Simon - proxy server

      idr-s3.openmicroscopy.org

      • Vivesse:

        +1, neuroglancer: unknown

      • Nginx adding headers for all responses, including

        errors.

    • FIRE (production s3) - no change.

  • Spec status: merged, uploaded data, one bug, then issue

    • Versioning issue

    • Bug in public access

    • Do we transform all masks into new spec before getting

      feedback from community?

    • May create sub-directory of data in different versions

  • EMBL Heidelberg call - after global bio-imaging meeting

    • Imaris writer.

    • Tags, calls, etc.

    • HDF5

    • Ilastik also compatible format. Dominic Kutra

    • Emil: Use Ilastik for segmentation, CellProfiler for feature

      extraction.

• OMERO 5

  • [Simon] OMERO.py: [One PR

    remaining</u>](https://github.com/ome/omero-py/pull/251), 5.8.0 release tomorrow?

  • Will merge after this meeting.

  • Release along with omero-web.

  • OMERO deep-copy PR ready to merge.

  • Good to merge. Error message improvement can be follow-up.

  • CLI allows various options for different workflows.

  • Needs good docs for CLI and UI work to expose optimal workflows

    in webclient.

  • Seb: announce py/web with duplicate server release?

  • Josh: yes, but don’t delay releases

• SA

  • Okay to have UoD-IT [decommission

    necromancer</u>](https://github.com/openmicroscopy/management_tools/issues/1266)?

  • Josh: users.openmicroscopy.org.uk

    http://users.openmicroscopy.org.uk/\~wmoore

• Glencoe Chris:

  • TileDB and zarr work ongoing.

  • Looking at tools for spatial indexing from Geo-spatial community

  • re: Pete Bankhead /Qupath. GeoIs, Shapely (python).

  • Need to store large amounts of shapes and query by coordinates.

• Community

  • [Code of

    Conduct</u>](https://docs.google.com/document/d/1bYa82C7ZN3z9bHGzFzCeeru2CS__yeTGeBBsenOoBv4/edit#)

1. AOB

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

• Returning to the OME Fishbowl

1. Main Topic

(20-25 minutes plus 15 minutes questions max)