zarrmony

Convert any bioimage file to OME-Zarr v0.5, preserving metadata.

Zarrmony reads proprietary microscopy formats (CZI, LIF, ND2, OME-TIFF, ...) via bioio and writes them as OME-Zarr v0.5 in the bioformats2raw.layout shape, with a configurable user-metadata gate, mean-pool pyramid generation, and a full audit trail of the conversion.

Status: v0.1 in active development. API and metadata schema are not yet stable.

Install

pip install zarrmony

Optional extras:

Extra	Adds	When you need it
gcs	gcsfs	Writing output to gs:// URIs
s3	s3fs	Writing output to s3:// URIs
nd2	bioio-nd2	Reading Nikon ND2 input
ome-tiff	bioio-ome-tiff	Reading OME-TIFF input
all	All of the above
dev	pytest, ruff, pre-commit	Contributing

CZI and LIF reader plugins are included by default.

Usage

CLI

zarrmony convert input.czi output.ome.zarr --metadata-file metadata.json
zarrmony inspect input.czi
zarrmony schema dump > zarrmony-metadata.schema.json

Library

from zarrmony import convert, UserMetadata

audit = convert(
    "input.lif",
    "output.ome.zarr",
    metadata=UserMetadata(...),
)

License

Apache-2.0. See LICENSE.