1. A scanning transmission electron microscope for imaging a specimen, the microscope comprising: an electron beam source to generate an electron beam; beam optics to converge the electron beam; a stage to hold a specimen in the path of the electron beam; a beam scanner to scan the electron beam across the specimen; a detector to detect electrons transmitted through the specimen to generate an image; and a controller to (1) define one or more scanning areas corresponding to locations of the specimen, (2) control one or more of the beam scanner and stage to selectively scan the electron beam in the scanning areas, (3) generate a sub-image for each of the scanning areas, (4) stitch together the sub-images for the scanning areas to generate a stitched-together image, and (5) analyze the stitched-together image to determine information regarding the specimen.