mwatershed

mwatershed

A rusty mutex watershed

See docs here

Installation

pip install mwatershed

Features

• A mutex watershed implementation for affinities
• Should handle up to 6 dimensional arrays of fragments (7 dimensions if you include offsets in affinities) but only tested on 2 and 3 dimensions

Usage

components = mwatershed.agglom(
    affinities: NDArray[np.float64],
    offsets: list[list[int]],
    seeds: NDArray[np.uint64],
    edges: Optional[list[tuple[usize, usize, f64]]] = None,
)

where:

• affinities is a k+1 dimensional array of non nan affinities with leading dimension having size n
• offsets is a list of length n of offset tuples of k integers
• seeds is a k dimensional array of fragment ids. Note seeds.shape must be equal to affinities.shape[1:]. Any entry not equal to 0 is guaranteed to stay that way, any entry equal to zero has no priors.
• edges is a list of (u, v, aff) tuples to insert arbitrary extra affinities between fragment ids