The University of Sheffield
Browse (9.25 MB)

TopoStats - an automated tracing program for AFM images

Download (9.25 MB)
Version 3 2021-06-06, 22:52
Version 2 2021-02-01, 12:48
Version 1 2020-11-01, 00:56
posted on 2021-06-06, 22:52 authored by Joseph Beton, Alice PyneAlice Pyne, Agnel Praveen Joseph, Maya Topf

This is a downloadable version of TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program includes identification and tracing of individual molecules in both circular and linear conformations without user input. The program is freely available via GitHub (, and is intended to be modified and adapted for use if required. TopoStats can identify individual molecules and molecular assemblies within a wide field of view, without the need for prior processing. We demonstrate its power by identifying and tracing individual biomolecules, including DNA origami, pore-forming proteins, and DNA molecules in both closed circular and linear form.


Targeting Twist: Single-molecule insights into supercoiled DNA-topoisomerase interactions for drug discovery

Medical Research Council

Find out more...

Timestamping Integrative Approach to Understand Secondary Envelopment of Human Cytomegalovirus

Wellcome Trust

Find out more...

An integrative approach to deciphering the entry process in Herpesviruses

Medical Research Council

Find out more...



  • There is no personal data or any that requires ethical approval


  • The data complies with the institution and funders' policies on access and sharing

Sharing and access restrictions

  • The data can be shared openly

Data description

  • The file formats are open or commonly used

Methodology, headings and units

  • There is a readme.txt file describing the methodology, headings and units

Usage metrics

    Department of Materials Science and Engineering



    Ref. manager