In a spectroscopic microscope, a video image of a specimen is analyzed to identify regions having different appearances, and thus presumptively different properties. The sizes and locations of the identified regions are then used to position the specimen to align each region with an aperture, and to set the aperture to a size appropriate for collecting a spectrum from the region in question. The spectra can then be analyzed to identify the substances present within each region of the specimen. Information on the identified substances can then be presented to the user along with the image of the specimen.