SimCortex Home Page

Much experimental data exists concerning the development of the cerebral cortex. There is a need for a common vehicle to integrate this data, and to allow the testing of hypotheses concerning development. Computer simulation and visualization is a powerful mechanism for hypothesis testing. Our long-term goal is to create a robust, extensible, portable tool for simulation and visualization of cortical development to serve both research and educational purposes.

We have implemented a simulation, SimCortex, which models the early stages of development of the cerebral cortex. Version 1.0 of SimCortex models the proliferation of progenitor cells in the pseudo-stratified ventricular epithelium (PVE), and the generation of young neurons and their migration into the cortical plate, the forerunner of layers II through VI of the mature cortex. Future versions will include layer I and glial cells, and will allow the user to begin to test hypotheses concerning such important variables as cell death, and cell-cell interactions during development. The speed of the simulation will increase in future versions, and edge effects that result in a somewhat 'bumpy' cortex will be addressed.

The black rectangle represents a section of the developing cerebral cortex. Upon clicking "Go", gray cells representing progenitor cells in the PVE appear on the right hand side of the rectangle. The progenitor cells divide, giving rise to more progenitor cells, and then to young neurons destined for layer 6 (pink cells), which migrate into the cortical plate (to the left of the rectangle). As the simulation progresses, young neurons representing layer 5 (red) arise; cells destined for later layers follow. Several counters at the right of the simulation keep track of real time (D HH:MM), current number of cells in the simulation, current number of progenitors and progeny, and Q (the probability of a daughter cell from a division becoming a post-mitotic neuron and migration into the cortical plate). Clicking on an individual cell provides information on that cell at the bottom of the screen. To obtain graphical information, click "Stop", and choose the desired graph next to the "Graph" button; then click "Graph". To return to the simulation, click "Simulation" and then "Go". Hit Shift-Reload to restart the simulation. For further information, contact or To download a copy of the code, click here