The operation of Diffuse! is largely self-explanatory. The operation of each individual page is described under the help pages for the Setup, Run, and View pages respectively. What is not discussed in those sections will be highlighted here.
Program parameters for Diffuse! can be edited through the Paramaters|Mathematical menu and the Parameters|Simulation menu. The mathematical parameters are those involved in the diffusion equation itself, namely kappa, tau, and h. When adjusting these parameters, be sure to heed the warning given on the page that the product of kappa and tau divided by the square of h must be less than one half for the simulation to be stable.
The simulation parameters control the speed and size of the simulation. More specifically, they allow the user to adjust the rate at which successive matrix calculations are made and how many calculations are made per screen rendering. The user can also modify the size of the matrix in this menu. Take note that while increasing the size of the matrix makes for better representations on the checker plot of the shapes drawn on the graph, it also slows the programís execution exponentially.