I have a Perl script that goes through time data from my simulations and develops what are commonly known as isochronal maps or activation maps. They show a color-coded snapshot of which parts of the model were activated by time, usually in "bins" of several milliseconds. Here's a sample isochronal map from one of our papers: Anyway, these maps take about 10-30 seconds of processing for my 2D regional ischemia model. For my new, larger model, it takes about 28 minutes.