TopoStats is our in-house free and open-source AFM image analysis software. It is a high-throughput, open-source Python package that automates the analysis of AFM image datasets, producing processed, clean AFM images, and extracting quantitative information. TopoStats is designed to reduce the burden of user oversight including the processing of single images one-at-a-time for downstream analysis. It reads and analyses raw AFM data, automating image segmentation, analysis of surface features, and extracting statistical information from complex datasets using traditional and machine learning algorithms. Some exemplar applications of this software are shown below.