1. A computer system comprising: one or more processors; one or more user input devices; a display capable of displaying an image and associated information in particular ways responsive to input signals from one or more of the input devices and signals from one or more of the processors, wherein the image comprises an external representation of at least a portion of an object superimposed with a light representation, the light representation corresponding to the location and magnitude of electro-magnetic radiation emitted from an internal portion of the object; and a graphical user interface running on one or more of the processors and providing the image and one or more tools for defining a region of interest on the image, wherein when the computer system receives input via the one or more tools to define a region of interest, the computer system can calculate information about a portion of the image within the defined region of interest.