1. A method for processing a biological sample, comprising (a) contacting a biological sample with an agent or combination of agents that stains the biological sample for objects of interest and at least one fluorescent agent that interacts with an at least one molecule in the biological sample, wherein the at least one molecule is associated with the object of interest, and wherein the at least one fluorescents agent comprises a fluorescent indicator; (b) acquiring a plurality of images of the biological sample at a plurality of locations/coordinates in transmitted light; (c) processing the plurality of images to identify a stained object of interest; (d) determining a coordinate for each identified stained object of interest; (e) storing each of the determined coordinates corresponding to each identified stained object of interest; (f) applying an excitation light to the biological sample thereby causing the fluorescent indicator of the at least one fluorescent agent to fluoresce; (g) acquiring a fluorescent images at each of the identified coordinates; and (h) processing the fluorescent images to identify a fluorescently labeled at least one molecule.