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Tissue Simulation Toolkit

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.

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What Tissue Simulation Toolkit can do for you

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)
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</>Source code

Participating organisations

Leiden University
Netherlands eScience Center
Utrecht University

Contributors

Related projects

TissueOpt

Optimizing the Tissue Simulation Toolkit

Updated 1 week ago
Finished