1. A functional imaging system comprising an acquisition system, a reconstruction system, and a display system, wherein the functional imaging system is selectively optimizable for use with a molecular agent, and wherein the molecular imaging system further includes: an interface that receives an external input indicative of a desired molecular imaging agent; a processor that automatically adjusts at least a reconstruction parameter of the reconstruction system wherein the reconstruction system employs the reconstruction parameter to reconstruct an image based on the desired molecular agent wherein the reconstruction parameter includes count optimization through a dual match filter.