Command line

The patchworks command runs the same building blocks as the Python API, without a script or a workflow 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

# One row per object; which cell each nucleus is in
patchworks tables scan.zarr --relate nuclei:cells

# Look at the likely mistakes one by one and fix them (napari)
patchworks review scan.zarr --expect cells:nuclei=1

# Bring a store written by an older patchworks up to the OME-Zarr spec
patchworks fix-metadata scan.zarr

fix-metadata only touches metadata, in place, and is safe to run twice. review also runs without a window: --summary, --export DIR, --workbooks DIR, --write-labels NAME (see Reviewing).

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}'

Voxel sizes (Cellpose's anisotropy, the DoG sigmas, a custom function's voxel_size) come from the store's calibration. The membrane plugins fill space, so they need --stitch iou: --method custom --fn patchworks.plugins.plantseg:segment --stitch iou. --denoise MODEL denoises tiles first (Denoising).

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.