Write OME-ZARR images

The principle entry-point for writing OME-NGFF images is ome_zarr.writer.write_image(). This takes an n-dimensional numpy array or dask array and writes it to the specified zarr group according to the OME-NGFF specification. By default, a pyramid of resolution levels will be created by down-sampling the data by a factor of 2 in the X and Y dimensions. For more custom control over the pyramid, see the more in-depth example on scaling functions and scale factors.

import numpy as np

from ome_zarr.writer import write_image

path = "test_ngff_image.ome.zarr"

size_xy = 128
size_z = 10
rng = np.random.default_rng(0)
data = rng.poisson(lam=10, size=(size_z, size_xy, size_xy)).astype(np.uint8)

write_image(
    data, path, axes="zyx",scale={"z": 1.0, "y": 0.5, "x": 0.5},
    axes_units={"z": "micrometer", "y": "micrometer", "x": "micrometer"},
    )

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Alternatively, the ome_zarr.writer.write_multiscale() can be used, which takes a “pyramid” of pre-computed numpy arrays.

The default version of OME-NGFF is v0.5, which is based on Zarr v3. A zarr v3 group and store is created by zarr.open_group() below. To write OME-NGFF v0.4 (Zarr v2), add the fmt=FormatV04() argument.

from ome_zarr.format import FormatV04

path = "test_ngff_image_v2.ome.zarr"
write_image(data, path, axes="zyx", fmt=FormatV04())

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To view the image, see tutorial on viewing images.