1. A method of registering an analytical image of a microsphere array comprising: a) providing a microsphere array, wherein said microsphere array comprises: i) a substrate with a surface comprising discrete sites; and ii) a population of microspheres comprising at least a first and a second subpopulation each comprising a bioactive agent; wherein said micropsheres are distributed on said surface such that each of said discrete sites contain no more than 1 microsphere; b) decoding said microsphere array so that the location of each bioactive agent is elucidated; c) computing a registration grid based on known locations of said bioactive agents from information obtained from step b; d) contacting said array with a sample comprising target analytes; e) acquiring a hybridization intensity image of said microsphere array, wherein said hybridization intensity image further comprises at least two bright bead types to serve as a fiducials; f) overlaying a registration grid to said hybridization intensity image; g) aligning the registration grid with the hybridization intensity image; and h) identifying the intensity at each grid location for each bead type within said array.