Cellpose 2-D

Segment every z-slice independently: each tile is one plane (1, y, x).

pip install "patchworks[cellpose,gpu]"

from functools import partial
from patchworks import auto_tile_shape_cellpose, tile_process
from patchworks.plugins.cellpose import cellpose_fn

tile_process(
    "image.zarr",
    cellpose_fn("cyto3", gpu=True, diameter=30),
    channel=0,
    tile_shape=partial(auto_tile_shape_cellpose, diameter=30, use_gpu=True),  # fits the VRAM
    overlap=20,        # about one cell diameter
    skip_empty=True,
)

Cellpose arguments not listed in cellpose_fn's signature (flow_threshold, cellprob_threshold, ...) are passed through. A cyto stain with a nuclear channel: on the cluster, set nuclei_channel: (Options worth knowing).