zarrmony 0.3.4

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

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, with a configurable user-metadata gate, mean-pool pyramid generation, and a full audit trail of the conversion.

By default (--layout auto) the writer is chosen from the reader's layout_hint: a flat reader writes one self-describing <scene>.ome.zarr store per scene under the output directory; a plate-shaped reader writes a single OME-NGFF HCS plate store at the output. The legacy bundled bioformats2raw.layout shape is opt-in via --layout bf2raw (CLI) or layout="bf2raw" (library).

Status: v0.3 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
ome-tiff	bioio-ome-tiff	Reading OME-TIFF input
all	All of the above
dev	pytest, ruff, pre-commit	Contributing

CZI, LIF, and ND2 reader plugins are included by default.

Usage

CLI

# Auto (default): dispatches on the reader's layout_hint.
#   flat readers (CZI, LIF, ND2, OME-TIFF) → per-scene stores under OUTPUT
#   plate-shaped readers (e.g. zarrmony-phenix) → a single HCS plate store at OUTPUT
zarrmony convert input.czi output_dir/ --metadata-file metadata.json

# Force per-scene (one <scene>.ome.zarr store per scene under OUTPUT).
zarrmony convert input.czi output_dir/ --layout per-scene --metadata-file metadata.json

# Force HCS plate (one <plate>.ome.zarr store at OUTPUT). Requires a
# plate-shaped reader; flat readers raise LayoutMismatchError.
zarrmony convert phenix-acquisition/ output.ome.zarr --layout plate --metadata-file metadata.json

# Bundled bioformats2raw.layout (opt-in): writes a single store at OUTPUT.
zarrmony convert input.czi output.ome.zarr --layout bf2raw --metadata-file metadata.json

zarrmony inspect input.czi
zarrmony schema dump > zarrmony-metadata.schema.json

Library

from zarrmony import convert, UserMetadata

# Auto (default): for a flat reader, returns {"input": ..., "stores": [...]};
# for a plate-shaped reader, returns the single plate audit dict (schema 3,
# with "fields" and a top-level "plate" block). Switch on audit["layout"].
result = convert(
    "input.lif",
    "output_dir/",
    metadata=UserMetadata(...),
)

# Bundled: returns the single bundle's audit dict.
audit = convert(
    "input.lif",
    "output.ome.zarr",
    layout="bf2raw",
    metadata=UserMetadata(...),
)

# HCS plate: writes one OME-NGFF plate store at OUTPUT.
audit = convert(
    "phenix-acquisition/",
    "output.ome.zarr",
    layout="plate",
    metadata=UserMetadata(...),
    per_well_metadata={"B04": {"treatment": "control"}, "C05": {"treatment": "drug-X"}},
)

Extending zarrmony

Add support for a new bioimage format by writing a reader plugin. See Writing a zarrmony reader plugin for the Reader Protocol, matcher conventions, entry-point registration, and a worked example.

License

Apache-2.0. See LICENSE.