ConvertToOmeZarr

ConvertToOmeZarr reads an image file and converts it to a single-scale, uncompressed OME-Zarr v2 directory. It is intentionally lightweight and useful for smoke-tested workflow demos, simple local handoffs, and validating that downstream tools can consume an NGFF-like directory.

For production multiscale pyramids, chunk tuning, compression, or very large datasets, use a future BioIO or ome-zarr-backed converter instead.

Inputs

• input_image: image file to convert.

Outputs

• output_image: converted OME-Zarr directory, defaulting to {input_image.stem}.ome.zarr.

Dependencies and Core Libraries

BioImageFlow core APIs, imageio for reading, NumPy, and the package’s minimal OME-Zarr v2 writer.

Assumptions

The input image is small enough for the lightweight single-scale writer and has already been sliced to the desired array. This converter creates a minimal OME-Zarr v2 directory for deterministic workflow exchange, not a production multiscale NGFF export.

Minimal Example

from bioimageflow_core import Arguments
from bioimageflow_io_tools import ConvertToOmeZarr

ConvertToOmeZarr().process_row(
    Arguments(input_image="selected_plane.tif", output_image="selected_plane.ome.zarr")
)

Expected Results

The output directory contains .zgroup, .zattrs, a 0/.zarray metadata file, and the first array chunk. Metadata includes a single multiscales entry.

Failure Modes

Unreadable inputs and filesystem write failures stop execution. The converter does not build pyramids, compression, or chunk layouts optimized for large production data.