In the summer of 2009, working from a single 6502, we exposed the silicon die, photographed its surface at high resolution and also photographed its substrate. Using these two highly detailed aligned photographs, we created vector polygon models of each of the chip's physical components - about 20,000 of them in total for the 6502. These components form circuits in a few simple ways according to how they contact each other, so by intersecting our polygons, we were able to create a complete digital model and transistor-level simulation of the chip.
This model is very accurate and can run classic 6502 programs, including Atari games. By rendering our polygons with colors corresponding to their 'high' or 'low' logic state, we can show, visually, exactly how the chip operates: how it reads data and instructions from memory, how its registers and internal busses operate, and how toggling a single input pin (the 'clock') on and off drives the entire chip to step through a program and get things done.
This my jaw on the floor.