Command line

Installing patchworks also installs a patchworks command: the same building blocks as the Python API, for a one-off run without writing a script or a Snakemake config.

# Convert anything bioio reads (or an existing store) to a pyramidal OME-ZARR
patchworks convert scan.czi scan.zarr

# Segment it; labels go into scan.zarr/labels/labels
patchworks segment scan.zarr --method cellpose --model cyto3 --diameter 30 --gpu

# What is in the store: levels, chunks, codecs, calibration, label images
patchworks info scan.zarr

# Did the tiling leave marks in the labels?
patchworks seams scan.zarr/labels/labels --tile-shape 16,1024,1024

# Look at the result (needs patchworks[napari])
patchworks view scan.zarr

Segmentation methods

--method	What it does	Main flags
threshold (default)	one global threshold (Otsu over the image unless --threshold), then connected components	--threshold
cellpose	Cellpose	--model, --diameter, --do-3d, --gpu
dog	difference of Gaussians	--low-sigma, --high-sigma, --threshold
custom	any importable function	--fn module:function, --fn-kwargs '{"k": 1}'

Cellpose's anisotropy and the DoG plugin's voxel size are read from the store's own calibration, at the level being segmented.

Tiling and stitching take the same options as tile_process: --tile-shape (z,y,x, auto or none), --overlap (N or z,y,x), --stitch iou, --resume, --skip-empty, --level, --channel (an index, or none for every channel), --compression. Run patchworks <command> --help for the full list.