2020-10-27

Attending:

Will, Petr, Dominik, Simon, Frances, Josh, David, Sebastien, Jean-Marie, Jason, Melissa, Chris, Erin,

Start: 2:00 pm UK

Accepting minutes from last meeting

Project Status

(2-3 minutes each)

• IDR:
  • Next release idr0088 - big drug screen, and idr0095.
  • Expect to release next week
  • CSHL - 2 posters and 2 talks accepted on IDR and NGFF.
    • Posters to be uploaded tomorrow, feedback by EOB today
• NGFF
  • HCS status (releasing etc. for Thursday)
    • Performance issues in python and dask - viewing in napari
    • Next: port issue to spec.md
  • Zarr v3 spec RFC
    • Open for feedback
    • Draft implementation expected in Dec/Jan
  • Zarr/CloudVolume/Numpy twitter threads
    • PanGeo asking about working with CloudVolume (format from neuroglancer) - lots of features.
    • Also zarr
    • Encouraged to use existing formats
  • See “Main Topic” as well
  • Paper drafting - on gdoc
    • Metrics. Is new thing better/faster than existing solutions?
• Releases
  • No big release planned. Maybe iviewer ROIs loading?
• SA
  • Quotes for new hardware
  • Improving access to minio etc for zarr dataset export/publication
• Glencoe
  • ROI processing, masks with TileDB
  • Good progress with masks microservices, OMERO.tables, in pathviewer
  • Missing features in web API for tables
    • e.g. get rows with offset
    • Using tables linked to Image, instead of Plate, Screen etc.
  • Josh: example data of masks with multiple resolutions?
    • Chris: yes - 8k x 8k images. Stardist segmentations. 7 levels.
• Community
  • 4DNucleome project funded.
  • Sanger project funded. Human embryonic tissue imaging
  • EastBio workshop, Nov 3 - see OME calendar
  • MacGill workshop,
  • Global BioImaging - same content as I2K workshop.

AOB

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

Main Topic - NGFF meeting on Oct 29th - Thursday

(20-25 minutes plus 15 minutes questions max)

• 2 Sessons 11am and 5pm. Everyone’s welcome
• Will: demo.
  • Seb: # of requests? Should only be 4x well.
  • JM: Discrepancy in channel names.
  • Display of field of views?
  • Chris: Nice demonstrator. For HCS user, it will need lots of features. Not (yet) the point.
    • Possibly open a field-view on double-click? (If they exist)
  • Chris: number of calls is incredibly high. Cascade of failures.
    • Also looks like all calls are at the same time.
    • Slowing down viv and/or deck.gl?
    • Seb: new assumption on their side of thousands of images
    • Chris: our code is adding the tiles? Yes, but as a react callback for created layers. Chris: guess this is the same for an image that’s zoomed out with very small tile size.