A scanning transmission electron microscope for imaging a specimen includes an electron beam source to generate an electron beam. Beam optics are provided to converge the electron beam. A stage is provided to hold a specimen in the path of the electron beam. A beam scanner scans the electron beam across the specimen. A controller may define one or more scanning areas corresponding to locations of the specimen, and control one or more of the beam scanner and stage to selectively scan the electron beam in the scanning areas. A detector is provided to detect electrons transmitted through the specimen to generate an image. The controller may generate a sub-image for each of the scanning areas, and stitch together the sub-images for the scanning areas to generate a stitched-together image. The controller may also analyze the stitched-together image to determine information regarding the specimen.