CellularPotts.jl

Link to Documentation
Author RobertGregg
Popularity
11 Stars
Updated Last
11 Months Ago
Started In
November 2020

CellularPotts.jl

The goal of this package is to develop a Cellular Potts modeling approach in Julia using a network-based approach. Currently, other software exists to simulate these types of models, but they have a number of limitations:

  • They are written in a low-level language (e.g. C++) with a GUI or python frontend
    • This separates developers from users, complicates the code base, and makes customization difficult
  • They rely on a grid approach instead of a network based approach
    • Representing the model as a graph allows access to decades of graph theory research, for example:
      • calculating articulation points to avoid cells disconnecting
      • using graph partitioning algorithms to simulate cellular division
      • avoiding cumbersome boundary conditions by simply adding edges that loop around
      • using graphical laplacians to simulate diffusion
  • They cannot take advantage of how composable Julia packages are with one another. For example, we can use state-of-the-art differential equation solving techniques from DifferentialEquations.jl.
    • Most CPM software relies on Runge-Kutta or even simple Euler Methods

Researchers and developers have been able to accomplish a lot with their respective softwares and I would urge anyone to check them out. My favorites are Morpheus, Artistoo, and CompuCell3D. This package takes a lot of inspiration from their design and pedagogical examples.

Careful attention has been taken to ensure this package is as performant as I can possibly make it, however, if you spot something egregious in the package, feel free to raise an issue or pull request.

Also of note, this package is still in major development and is not currently recommended for general use. I'm still working out how to best organize datastructures and functionally. However, still feel free to try it if you're curious.

Simple Example

#Install the package
using Pkg; Pkg.add("CellularPotts")

#Load in the package
using CellularPotts

#Create a space (50×50) for cells to exist in
space = CellSpace(50,50; isPeriodic=true, neighborhood=:moore)

#Describe the cells in the model
initialCellState = CellTable(
    [:Epithelial], #names
    [500],         #sizes
    [1])           #counts

#Add penalties to the model
penalties = [
    AdhesionPenalty([0 20;
                     20 0]),
    VolumePenalty([5])
    ]

#Create a model object
cpm = CellPotts(space, initialCellState, penalties)

#Record a simulation of the model
recordCPM("ReadMeExample.gif", cpm)

Major Improvements

  • Introduce more cell properties

    • Division
    • Death
    • Active movement
    • Movement up gradients
  • Integrate hybrid modeling schemes

    • ODE Modeling (intracellular)

    • PDE Modeling (extracellular)

    • Maybe use Neural networks to speed up the PDE computation?

    • Stochastic jumps?

  • Create an Examples folder

  • How to save output?

    • Save the data into a dictionary of dataframes
    • Needs to be made more efficient
  • Implement different ways to initialize cell locations

    • Image input
    • specify locations with property
  • Allow cells to have different properties (used NamedTuple)

  • Use automatic differentiation to calculate cellular forces from the Hamiltonian

  • Add a correction factor to adhesion to deal with boundaries.

Minor Improvements

  • Allow user defined parameters to cells (used NamedTuple)
  • Allow cells of the same type to be different sizes (?)
    • Just specify different desired volumes
  • Could get a big speed improvement if you don't loop through all cells to update articulation points
    • Need to be clever about updating articulation points locally (is this possible?)
    • rewrote Tarjan's algoirthm to find articulation points which is O(V+E)
  • Adding cell borders is slow for large spaces
    • fixed by using NA
  • Use abstract typing (e.g. AbstractVector vs Vector) without creating type instability
  • Do we even need to track to total energy? (nope!)
  • Use SVectors to store graph edges? 🤔
    • Only useful for spaces where all nodes are identical (e.g., periodic boundaries)
  • Add more tests and CI badge