Tight Spaces

In this example we use a matrix of zeros and ones to denote valid locations that cells may occupy. This example blocks out a square in the middle of the space where cell cannot move to.

More complex geometrics (2D and 3D) could be created by modifying the spaceImage defined below.

using CellularPotts
using Plots


#Make a space that looks like a box frame
spaceImage = ones(Int, 100,100)
spaceImage[10:90,10:90] .= 0

space = CellSpace(spaceImage; periodic=false, diagonal=true)

initialCellState = CellState(:Epithelial, 500, 1; positions = (5,5));

penalties = [
    AdhesionPenalty([0 30;
                    30  0]),
    VolumePenalty([10]),
    MigrationPenalty(100, [100], size(space))
    ]

cpm = CellPotts(space, initialCellState, penalties)


(rows,columns) = size(cpm.space)

anim = @animate for t in 0:1000

    plotObject = heatmap(
        cpm.space.nodeIDs',
        c = cgrad(:tol_light, rev=true),
        grid=false,
        axis=nothing,
        legend=:none,
        framestyle=:box,
        aspect_ratio=:equal,
        size = (600,600),
        xlims=(0.5, rows+0.5),
        ylims=(0.5, columns+0.5)
        )

    plot!(plotObject,[9.5, 9.5],[9.5, 90.5], color=:black)
    plot!(plotObject,[90.5, 90.5],[9.5, 90.5], color=:black)
    plot!(plotObject,[9.5, 90.5],[9.5, 9.5], color=:black)
    plot!(plotObject,[9.5, 90.5],[90.5, 90.5], color=:black)

    cellborders!(plotObject, cpm.space)

    cellmovement!(plotObject,cpm)

    ModelStep!(cpm)

    plotObject
end

gif(anim, "TightSpaces.gif", fps = 30)

This page was generated using Literate.jl.