  We propose an efficient algorithm to analyze $3D$ atomic resolution crystal
images based on a fast $3D$ synchrosqueezed wave packet transform. The proposed
algorithm can automatically extract microscopic information from $3D$ atomic
resolution crystal images, e.g., crystal orientation, defects, and deformation,
which are important information for characterizing material properties. The
effectiveness of our algorithms is illustrated by experiments of synthetic
datasets and real $3$D microscopic colloidal images.
