AbstractWe develop an algorithm for feature extraction based on structural similarity and demonstrate its application for atom and pattern finding in high-resolution electron and scanning probe microscopy images. The use of the combined local identifiers formed from an image subset and appended Fourier, or other transform, allows tuning selectivity to specific patterns based on the nature of the recognition task. The proposed algorithm is implemented in Pycroscopy, a community-driven scientific data analysis package, and is accessible through an interactive Jupyter notebook available on GitHub.