1. A spectroscopic microscope including: a. a specimen stage bearing a specimen; b. a light source situated to supply light to the specimen; c. a detector situated to receive light from the specimen; d. a video camera capturing an image of the specimen; e. a movable aperture stage interposed between the detector and the specimen stage, the aperture stage having an aperture of adjustable size therein; f. a processor: (1) receiving the image of the specimen, the image being formed of a set of pixels; (2) isolating sets of adjacent pixels within the image wherein the pixels have similar contrast, with each such set defining an image region; (3) moving the aperture stage to align the aperture: (a) between the specimen and the detector, and (b) to a portion of the specimen corresponding to one of the image regions, with this portion of the specimen defining a specimen region; (4) obtaining a region spectrum of the specimen region through the aperture; (5) identifying one or more substances from the region spectrum; g. a display showing: (1) the image of the specimen, and (2) an output of the identified substances.