Examples

Each example is a short script in the repository's Examples/ folder. The first six generate their own tissue (foams of Voronoi cells, or a doublet at equilibrium whose answer is known), so they need nothing but foambryo; each writes its outputs in a folder of the current directory.

example	what it shows	time
Anisotropic voxels	spacing, the resampling to cubic voxels, what forgetting the spacing does	under a minute
Cropped tissue	crop faces, cut cells, nan pressures, a pressure method that refuses	under a minute
Seed ensembles	eight seeds, the relative spread, the flags, the caveat	under a minute
Large tissue	the cost estimate, sparse and dense solves, the diagnostics table	about a minute
The command line	foambryo mesh, infer, view, infer-over-seeds, --no-pressures, --diagnostics	under a minute
The Polyscope viewer	the viewer from Python, saved figures, a seed ensemble, the window that starts from a mask	under a minute
Second-order angle reading	angle_reading="quadric" on a benchmark mesh	seconds
Folded trijunction observations	the wedge-refusal policies	seconds
Junction relocation	what delaunay-watershed-3d's relocation changes, on your own mask	seconds

The introductory notebook walks through the API on a benchmark aggregate; its data are downloaded separately (see data/alternative_link_to_data). The napari plugin has its own examples: a quick start on benchmark case 000, and From a segmentation plugin to foambryo.

Times were measured on one machine (Apple M3 Max); the Polyscope examples need a display.