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 mean-pool pyramid generation and a full audit trail of the conversion. User-supplied metadata (study/treatment/etc.) is not handled by zarrmony — it is owned by aperture-backend, which associates OME-Zarr stores to a separate metadata database.

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/

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

# 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

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

# LIF-specific: write one OME-Zarr per mosaic tile (with stage positions in
# <Plane>) instead of bioio-lif's auto-stitched 1-pixel-overlap output.
# See docs/adr/0005-lif-mosaic-write-strategy.md.
zarrmony convert mosaic.lif output_dir/ --lif-mosaic per-tile

zarrmony inspect input.czi

Library

from zarrmony import convert

# 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/")

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

# HCS plate: writes one OME-NGFF plate store at OUTPUT.
audit = convert("phenix-acquisition/", "output.ome.zarr", layout="plate")

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.