Potts.jl

Cellular Potts models written as equations, in the style of ModelingToolkit, and solved with SciML-style problems, solvers and solutions, on the CPU or a GPU.

using Potts, PottsModels, MakiePotts, CairoMakie

σ0, k0 = graner_glazier_state()                      # a 64-cell aggregate of two kinds
gg = GranerGlazier(; name = :gg, lattice = size(σ0)) # Graner & Glazier (1992) cell sorting
prob = PottsProblem(gg, [ownership => σ0, kind => k0], (0, 200); seed = 1)
sol = solve(prob, SequentialCPM(); saveat = 2)
record_potts("cell_sorting.mp4", sol; framerate = 15) # a video of the sorting

This repository holds four Julia packages:

Package	Path	What it is
Potts	/	The modelling language: @potts_model, PottsProblem, layouts, components
CorePotts	lib/CorePotts	The numerical layer: lattices, SequentialCPM and CheckerboardCPM, solutions, ensembles, callbacks, GPU kernels
PottsModels	lib/PottsModels	Published models as ordinary @potts_model constructors, with reproductions
MakiePotts	lib/MakiePotts	Plotting of states and solutions with Makie

Install

The packages are not registered yet. With Julia 1.12:

git clone https://github.com/PraneethMerugu/Potts.jl

using Pkg
Pkg.develop([PackageSpec(path = "Potts.jl/lib/CorePotts"), PackageSpec(path = "Potts.jl"),
             PackageSpec(path = "Potts.jl/lib/PottsModels"), PackageSpec(path = "Potts.jl/lib/MakiePotts")])
Pkg.add("CairoMakie")   # a Makie backend, for figures and videos

GPU runs use any KernelAbstractions backend (Metal is tested): load the backend package and pass backend = MetalBackend() to solve.

Documentation

Build the documentation locally:

julia --project=docs -e 'using Pkg; Pkg.instantiate()'
julia --project=docs docs/make.jl

and open docs/build/index.html. It covers getting started, tutorials, the modelling language, and the published models, each built step by step from its public constructor.

History

This repository replaces the earlier CorePotts.jl, MakiePotts.jl and PottsModels.jl repositories (now archived) and the previous contents of this one. Their histories stay reachable: the old main is an ancestor of this branch, and every earlier branch is kept as an archive/* or legacy/* tag in its repository.