Skip to content

Add ome-tiff and ome-zarr writers #21

@TimMonko

Description

@TimMonko

🚀 Feature

Add writers to ndevio. They will use bioio-ome-tiff.writers.OmeTiffWriter and bioio-ome-zarr. In particular, these will focus on creating a round trip: ndevio-writers to ndevio-readers experience.

Motivation

There exists no good (IMO) I<->O in napari yet. In addition, because this maintains metadata via Bioio, then we can keep pace with the metadata lifecycle it provides, which has thus far been sufficient for napari.
Furthermore, we should be able to provide some kind of metadata, like "is_label" to confer to napari that this data should be represented as a certain layer, and write bespoke interpretations if needed; to start off this means image and labels layers. Hopefully later a shapes/points IO operation can be added, though I'm not sure these OME formats would be best for it.

Pitch

  1. a napari writer pathway for one of ome-tiff or ome-zarr
  2. individual classes subclassing the BioIO writers for use in ndevio
  3. convenience methods on nImage for quick saving by just specifiying a path

Start with a MWP for Zarr, in particular, but use the work in napari-ndev for setting up the Ome-tiff writing. However, there is considerable ome-tiff writing duplication across the files, so it will need centralized.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions