27th January, 2021

Attendees: Josh Moore, Matthias Bussonnier, Ryan Williams, Martin Duran, Jackson Brown, Jon Kirkham. Martin Durant

• Ryan: Interim report due Sunday or Monday.

  • 2 month extension from CZI.

• Having Josh or Jon have their subcontractor hat.

  • Do that via Glencoe

    (Commercial arm of OME) if for a Java implementation of Zarr V3?

• Jackson: spec/impl discussion (Tiffs as Zarr)

  • I got a question for you all as to how to handle a spec

    implementation. I am not sure if it’s a tifffile aszarr, dask from_zarr issue, or a general “the spec is still undetermined issue”

  • Work on

    aicsimageio in free time

  • Preparing to support pyramids

  • https://github.com/AllenCellModeling/aicsimageio/issues/140

  • Josh: only “spec” I know of is

    https://ngff.openmicroscopy.org/

  • John:

    ZarrTiffStore issue from Trevor: https://github.com/cgohlke/tifffile/issues/56

  • Josh: see also:

    https://github.com/pydata/xarray/issues/4118

• Martin:

  • NB: Jackson: thanks for fsspec

  • Maybe interest in

    intake_informaticslab (some logic for parsing paths)

    • Zarr for accessing chunks that are each HDF5.
    • Can additionally save zarr locally as cache
    • Something to backport? Cache as a wrapper

  • For fsspec-reference-maker, need various new codecs: szip, jpeg…

    • needed in numcodecs
    • Josh: https://git.embl.de/balazs/B3D
    • Martin: also true for GRIB files. DICOM.
    • Josh: need for “functions”. Martin: see templating method.
    • Also JSON isn’t overly efficient. Zarr itself. Even if tuple-like….

• Matthias:

  • Ramping up on napari

  • Partial read from andrew has been merged

  • I’m working on reenabling flake /mypy in CI (Josh: merged)

    • May need to go back to 120 line length

  • Rebasing my basestore PR.

  • Also looking at numcodecs, release, and then migrate to blosc

    wheels

    • Jackson: can look. Dropping overhead. (Czaki)
    • Wheels are the future? so ok. ci-buildwheel marks per platform. (Sub-optimal)

• Misc

  • General worries on Python 3.x release schedule….

  • Matthias: Jupyter folks are thinking of writing rust and

    compiling to Python, JS

    • Jackson: dask in rust. Martin: that’s difficult

    • https://github.com/aschampion/rust-n5 (and rust-pyn5)

    • John: limited number of compressors.

    • Matthias: https://github.com/PyO3/pyo3 very simple.

      • https://github.com/PyO3/maturin