Quickstart

End-to-end workflow

1. Prepare a mesh — Start from a closed triangle mesh.

2. Generate or obtain a skeleton — See Skeletonization for options.

3. Load inputs — Load the mesh with MeshManager and the skeleton with from_txt().

4. Fit a morphology graph — Use CableFitter with FitOptions.

5. Optionally optimize the morphology basis — Configure BasisOptimizerOptions via FitOptions.basis_optimizer_options.

6. Validate and export — Inspect results, optionally scale radii, and export to SWC.

Full example

from mascaf import (
    BasisOptimizerOptions,
    CableFitter,
    FitOptions,
    MeshManager,
    SkeletonGraph,
)

mesh_mgr = MeshManager(mesh_path="neuron.obj")
skeleton = SkeletonGraph.from_txt("neuron.polylines.txt")

fit_options = FitOptions(
    max_edge_length=1.0,
    radius_strategy="equivalent_area",
    basis_optimizer_options=BasisOptimizerOptions(
        do_snapping=True,
        do_forcing=True,
        max_iterations=50,
        smoothing_weight=0.5,
    ),
)

fitter = CableFitter(fit_options)
morphology = fitter.fit(mesh_mgr, skeleton)

morphology.scale_radii_to_match_mesh(mesh_mgr, metric="surface_area")
morphology.to_swc_file("neuron.swc")

Minimal example

If you already have a skeleton and do not want basis optimization:

from mascaf import CableFitter, FitOptions, MeshManager, SkeletonGraph

mesh_mgr = MeshManager(mesh_path="shape.obj")
skel = SkeletonGraph.from_txt("shape.polylines.txt")
fitter = CableFitter(FitOptions(max_edge_length=0.5))
morph = fitter.fit(mesh_mgr, skel)
morph.to_swc_file("shape.swc")

Radius strategies

Supported values for FitOptions.radius_strategy:

• equivalent_area (recommended) — r = sqrt(A/π) from cross-section area.

• equivalent_perimeter — r = L/(2π) from boundary length.

• section_median — median ray-to-boundary distance in the section plane.

• section_circle_fit — algebraic circle fit (Kasa) to the section boundary.

• nearest_surface — distance from sample point to nearest mesh surface.