1. A system for training a visual prosthesis comprising: a) a processor configured to i) present a non-visual reference stimulus corresponding to a reference image to a user having a visual prosthesis via a reference image presentation tool; ii) output a series of stimulation patterns to the user to induce corresponding user perceived images; and iii) receive a series of user perception inputs corresponding to the respective user perceived images including features of the respective perceived images, wherein at least one stimulation pattern in the series of stimulation patterns is determined at least in part based on a fitness function optimization algorithm and at least one previously received user perception input in the series of user perception inputs; and b) a user input for providing the user perception inputs to the processor.