For development the circuit was designed as two modules. A LED lighting module and a micro-controller module.
Eagle Schematic: https://projects.cecs.pdx.edu/projects/fa2012ece411-operationawesome/repository/revisions/master/changes/Circuits/MicrocontrollerModule.sch
LED Lighting module
Eagle Schematic: https://projects.cecs.pdx.edu/projects/fa2012ece411-operationawesome/repository/revisions/master/changes/Circuits/LightingModule.sch
The LED design was influenced by the way raster display refresh by rows. In this circuit there is a strobe signal that increments the row to be updated. There are also three signal lines RGB that control whether a color is pulsed during it's time slot. With a high enough strobing frequency dithering and blending are possible.