pmplewa / ome-ngff-types

pydantic models for OME-NGFF metadata

OME-NGFF Types

This package contains pydantic models to represent and validate OME-NGFF metadata, according to version 0.4 of the NGFF specification.

The included models cover the axes, coordinateTransformations, multiscales, omero, labels, image-label, plate, and well metadata. They implement all requirements from the specification, as well as the following constraints that are slightly more restrictive than the original versions.

Axis Metadata

• The value of the field type MUST be one of space, time or channel.
• The value of the field unit MUST be one of the UDUNITS-2 units.

Coordinate Transformation Metadata

• Both translation vectors and scale vectors MUST be specified as a list of floats.

Installation

To install the latest development version, run:

pip install git+https://github.com/pmplewa/ome-ngff-types.git

Examples

import zarr

from ome_ngff_types.v0_4 import Metadata

group = zarr.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0044A/4007801.zarr")
metadata = Metadata.model_validate(group.attrs)

assert metadata.multiscales is not None
multiscales = metadata.multiscales[0]
assert multiscales.version == "0.4"

Sample Data

The sample data for testing this package has been aggregated from the specification itself, as well as the following public datasets:

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0044A/4007801.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0047A/4496763.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0048A/9846152.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0054A/5025551.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0054A/5025552.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0054A/5025553.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001247.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0073A/9798462.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0076A/10501752.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0083A/9822152.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr
https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457539.zarr