TopoStats: Batch Processing Atomic Force Microscopy (AFM) Images

Sylvia Whittle, Max Gamill, Laura Wiggins, Neil Shephard, Toby Allwood, Tobias Firth, Mingxue Du, Joseph G. Beton, Robert Turner, Thomas E Catley & Alice Pyne

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.

To use this resource go to the resource landing page.

This resource is part of the TopoStats and AFMDB: Resources for Atomic Force Microscopy (AFM) Image Analysis resource theme.

Further Information

TopoStats Github Documentation

Deep Learning-Enhanced TopoStats for the Automated Quantification of DNA and Complex Biomolecular Structures

Publisher

PSDI

Access

Open Access

Licenses

LGPL-3.0

GNU General Public License v3.0 only

Contact

https://github.com/AFM-SPM/TopoStats/issues

Citation

Please cite: 'Whittle, S., Firth, T. A., Gamill, M. C., Wiggins, L., Shephard, N., Allwood, T., Catley, T. E., Pyne, A. L. B., (2026). Deep Learning-Enhanced TopoStats for the Automated Quantification of DNA and Complex Biomolecular Structures. bioRxiv 2026.05.06.723223. https://doi.org/10.64898/2026.05.06.723223' and 'Beton, J. G., Moorehead, R., Helfmann, L., Gray, R., Hoogenboom, B. W., Joseph, A. P., Topf, M., & Pyne, A. L. (2021). TopoStats - A program for automated tracing of biomolecules from AFM images. Methods, 193, 68-79. https://doi.org/10.1016/j.ymeth.2021.01.008'