High-content-screening plates

PlateWriter writes a plate as the plate/<row>/<column>/<field> layout defined by the OME-Zarr 0.5 spec. Each field of view is an ordinary multiscale image written with Writer, so it accepts the same options.

import numpy as np
from ome_zarr_io import PlateWriter

units = {"y": "micrometer", "x": "micrometer"}

with PlateWriter(
    "screen.ome.zarr",
    rows=["A", "B"],
    columns=["1", "2", "3"],
    name="Screen 1",
    acquisitions=[{"id": 0, "name": "t0"}],  # optional
) as plate:
    for row, column in [("A", "1"), ("A", "2"), ("B", "3")]:
        for _ in range(2):  # two fields of view per well
            image = np.random.randint(0, 255, size=(2, 256, 256), dtype=np.uint8)
            plate.add_field(
                row, column, image, dims=["c", "y", "x"], axis_units=units,
                channels=["DAPI", "GFP"], downscale_levels=2, acquisition=0,
            )

  • Rows and columns are declared up front. Their order sets each well’s rowIndex and columnIndex.

  • add_field takes the same keyword arguments as Writer (except overwrite, which belongs to the plate). It creates the row and well groups as needed. field= sets the field index; by default the next free one is used.

  • If you declare more than one acquisition, every add_field call must say which one it belongs to (acquisition=), as the spec requires.

  • The well and plate metadata are rewritten after every field, so an interrupted run leaves a valid partial plate. The plate metadata first appears with the first field, because the spec requires at least one well.

  • By default every field must match the first one in dims, axes and channels. Pass check_consistency=False to allow mixed fields.

  • add_field returns the field’s Writer, so you can attach labels with add_labels.

  • Leaving the with block validates the plate and all wells against the schemas. Without with, call plate.close().

  • overwrite=True replaces an existing plate.