Tissue Simulation Toolkit (TST) 2.0 is an efficient C++ library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993). It is suitable for simulations with live visualization as well as batch simulations on clusters.
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)