TopoStats and AFMDB: Resources for Atomic Force Microscopy (AFM) Image Analysis

AFMDB is a centralised collection of Atomic Force Microscopy (AFM) data covering a range of physical and biological materials, hosted within the PSDI Community Data Collections. Each entry includes the original AFM files along with a processed image generated during analysis. Initial examples demonstrate the output from our open-source tool TopoStats which has been used to process images and standardised the data output. By making these datasets openly available, AFMDB supports good data sharing practices and provides high quality, standardised examples that can be used to train and evaluate deep learning methods for enhanced AFM analysis. Researchers are encouraged to contribute AFM data from their publications and to test TopoStats, helping refine the tool through community feedback.

TopoStats is a Python toolkit that automates the processing and analysis of Atomic Force Microscopy (AFM) data. It batch processes raw AFM files to identify molecules or other features, trace their shapes, and generate image outputs at each stage of the workflow. The software produces rich quantitative measurements in both tabular and graphical formats, and is developed in line with FAIR research software principles to support transparent, reproducible AFM analysis.