We have designed and built an improved, dedicated analytical scanning transmission electron microscope (STEM). A novel feature of this microscope is a magnetic lens above the accelerating gun, allowing the specimen probe to achieve very high current densities while retaining the high spatial resolution of the STEM. Integrated with this microscope, we have also implemented an image processing system which allows rapid analysis of the digitized microscope output signals. This processing system also allows the graphic simulation of planar materials (such as intercalated graphite) to derive diffraction pattern simulations for comparison with the experimental data. An image database system allows over 2000 images to be easily managed.