Tissue Simulation Toolkit

Welcome to Tissue Simulation Toolkit (TST) 2.0, a library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993).

TST 2.0 is an efficient C++ library for two-dimensional Cellular Potts Simulations. It is suitable for simulations with live visualization as well as batch simulations on clusters.

TST 2.0 provides many recent extensions to the CPM, including

• Efficient edgelist algorithm
• Infinite number of PDE layers (forward Euler)
• A reaction diffusion solver on the CPU and on CUDA
• Interaction of CPM cells and PDE (secretion, absorption)
• Chemotaxis
• Length and connectivity constraints
• Act-CPM model (Niculescu et al., PLOS Comput Biol 2015)
• Discrete fibrous extracellular matrix (molecular dynamics)

The current version of the TST includes example programs for the following published simulations:

• Differential adhesion driven cell sorting (Glazier and Graner, 1993)
• Cell elongation dependent vasculogenesis (blood vessel growth) (Merks et al., 2006)
• Contact-inhibition dependent vasculogenesis and angiogenesis (Merks and Glazier, 2005; Merks and Glazier, 2006; Merks et al, PLoS Comput Biol 2008)
• Hybrid cellular Potts and bead-spring modeling of cells in fibrous extracellular matrix (Tsingos and Bakker et al, Biophys J. 2023)

and visualization of:

• Cells, according to cell type or anything you wish
• Chemical fields, using color ramps and contour lines (level sets)