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

Beton, JG; Moorehead, R; Helfmann, L; Gray, R; Hoogenboom, BW; Praveen Joseph, A; Topf, M; (2021) TopoStats - a program for automated tracing of biomolecules from AFM images. Methods 10.1016/j.ymeth.2021.01.008. (In press). Green open access

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Abstract

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 (https://github.com/afm-spm/TopoStats) and is intended to be modified and adapted for use if required.

Type: Article
Title: TopoStats - a program for automated tracing of biomolecules from AFM images
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ymeth.2021.01.008
Publisher version: https://doi.org/10.1016/j.ymeth.2021.01.008
Language: English
Additional information: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Atomic Force Microscopy (AFM), DNA, biomolecular structure, image analysis, python scripting, single-molecule imaging
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Physics and Astronomy
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > London Centre for Nanotechnology
URI: https://discovery.ucl.ac.uk/id/eprint/10121535
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