The CompuCell 3D Visualization Engine is a small tool which allows for the viewing of image data files in the format specified. It has been used to create most of the images on this page, as well the images used in the multi-time stepped animated GIF.

• Download the Visualization Engine documentation
• Download the Windows executable
• Download the source and installation instructions for *nix installation.

3D Examples with Visualization Engine

3D simulations of limb bud

3D limb bud simulations. Submodels used: Potts for cell dynamics, RD for TGF-beta, Cell state automaton for RO, ROC, medium states, Fibronectin ODE's. RD prepattern is shown below. Initial number of cells ~2500. Iterations = 600, time~12 hours.

RD Simulation Movie can be viewed HERE. NOTE: This is a large animated GIF!

The change from one bone to two bones. For this simulation, the ratio between width and length is 2:7(2 in y-direction and 7 in x-direction), and the actual length in x-direction is taken to be 3.0. The grid size of the whole domain is 20 by 70 by 210. The parameters for Schnakenberg kinetics are: a=0.017, b=1.015, d=7.1

Ratio 2:7, Length=3.0, diffusion=7.1

Acknowledgments
This research is supported in part by
a National Science Foundation Biocomplexity grant PHY-0083653
a National Science Foundation ACI CAREER award ACI 01-35195
an Arthur J. Schmitt Fellowship
and the Center For Applied Mathematics at the University of Notre Dame