29th January, 2020

Plans to attend: RyanW

Attending: RyanW, Josh, Jackson Maxfield Brown, Jamie, Ward,

  • Standing items

    • Introductions: new joinees should feel welcome to introduce

      themselves and their interest in zarr/n5.

    • Jackson+Jamie: Allen Institute for Cell Science, deal with

      “Zeiss” CZI files, have python bindings to “libczi”, integrating with Dask, interested in Zarr for storage.

    • Ward: Unidata (Boulder, CO); team lead for netcdf-c

      (netcdf-java folks v interested in Java-based Zarr impl)

    • Ryan: Mount Sinai School of Medicine in NYC; scRNA-seq biofx

      → Zarr

    • John: HHMI→Nvidia, lots of image data work → Zarr
  • NumFOCUS / Quansight

    • discussing Quansight doing contract work related to EOSS grant

      • James Bourbeau (dask) may be taking this on, but his time is limited
      • But looking for someone to focus on the v3 spec in 2020
    • Zarr is now a NumFOCUS project!

  • Zarr v2: any open and/or blocked PRs?

    • Jamie: what features are being added?

    • John: less adding things and more removing things. E.g. Zarr in

      Python allows you to store objects

    • Josh: smaller core with an extension mechanism

    • [*Zarr v3

      update*](https://zarr-developers.github.io/zarr/specs/2019/06/19/zarr-v3-update.html) (June 2019)

  • Goal: have OME move a huge amount of archival data to Zarr

    • today: OME-TIFF; more features desired

    • some issues keeping XML aligned w/ TIFFs today; possible to put

      relevant metadata into Zarr, avoid extra level of metadata indirection around Zarr?

    • recently launched tool for converting out of proprietary formats

      • Zarr/N5 produced as intermediates
      • might be interesting to use those as 1st-class
  • NetCDF:

    • merged 1st code from nc-zarr dev fork into main branch

      (NCZarr; nczarr-merge.wif branch)

    • Ward hopefully speaking at [*EGU in Vienna in


    • John: does it make sense for people writing bindings to look at

      it before release?

    • Ward: not sure without speaking to Dennis. Perhaps the next

      month or two.

  • Opportunities for contributions from Allen Institute folks?

    • interest in Zarr from C(++)

    • see: z5 (“Lightweight

      C++ and Python interface for datasets in zarr and N5 format”)

    • [*zarr-python


    • Josh: bioformats2”raw” & metadata pain points

    • Using it in production and migrating as necessary
  • AOB (Any Other Business)

    • Josh: Shared gdoc folder. John: use NumFOCUS folder? RyanW: not

      sure it’s shared. Start off by adding people to the current folder.

    • [*Here’s a “community” gdrive

      folder*](https://drive.google.com/drive/folders/144M9w9LQElyu7gMGeT5tpqGvibqZKCJe?usp=sharing) with this doc in it