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    TopoStats – a program for automated tracing of biomolecules from AFM images

    Beton, Joseph and Moorehead, R. and Helfmann, L. and Gray, R. and Hoogenboom, B.W. and Praveen Joseph, Agnel and Topf, Maya and Pyne, A.L.B. (2021) TopoStats – a program for automated tracing of biomolecules from AFM images. Methods 193 , pp. 68-79. ISSN 1046-2023.

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    We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, ~90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub ( and is intended to be modified and adapted for use if required.


    Item Type: Article
    Keyword(s) / Subject(s): Atomic Force Microscopy (AFM), Single-molecule imaging, Image analysis, Python scripting, Biomolecular structure, DNA
    Depositing User: Administrator
    Date Deposited: 05 Mar 2021 13:32
    Last Modified: 10 Nov 2022 18:06


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