© 2018 Society for Industrial and Applied Mathematics. Recent developments of imaging techniques enable researchers to visualize materials at atomic resolution to better understand the microscopic structures of materials. This paper aims at automatic and quantitative characterization of potentially complicated microscopic crystal images, providing feedback to tweak theories and improve synthesis in materials science. As such, an efficient phase-space sketching method is proposed to encode microscopic crystal images in a translation, rotation, illumination, and scale invariant representation, which is also stable with respect to small deformations. Based on the phase-space sketching, we generalize our previous analysis framework for crystal images with simple structures to those with complicated geometry.