ArticleMethods (San Diego, Calif.)2021
TopoStats - A program for automated tracing of biomolecules from AFM images.
Article in Methods (San Diego, Calif.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Automating Model Building for SPM Images of Biomolecules Using MISO.Journal of chemical information and modeling · 2026Article
- Imaging and mechanism of DNA-DNA recognition mediated by divalent ions.Nucleic acids research · 2026Article
- SEM mapping of sequence-specific protein-DNA interactions on long DNA molecules.Nucleic acids research · 2026Article
- Mapping the Conformational Landscape of DNA Minicircles Through Atomic Force Microscopy and Shape Space Analysis.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- A modular framework for automated segmentation and analysis of AFM imaging of chromatin organization.Nucleic acids research · 2026Article
- Optimising DNA origami assembly by reducing off-target interactions.Nature communications · 2026Article
- Article
- Synthetic data-driven deep learning for label-free autonomous atomic force microscopy.Nature communications · 2026Article
- G-quadruplexes self-assembled from nucleotide monomers as stable prepolymer scaffolds in aqueous environments.Scientific reports · 2026Article
- PS Poly: A chain tracing algorithm to determine persistence length and categorize complex polymers by shape.PloS one · 2026Article
- Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis.Nature communications · 2025Article
- A trackable trinuclear platinum complex for breast cancer treatment.Nucleic acids research · 2025Article
- Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.Nature communications · 2025Article
- Design and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease.Nucleic acids research · 2025Article
- Complement-mediated killing of Escherichia coli by mechanical destabilization of the cell envelope.The EMBO journal · 2024Article
- Two codependent routes lead to high-level MRSA.Science (New York, N.Y.) · 2024Article
- High-speed atomic force microscopy: extracting high-resolution information through image analysis.Biophysical reviews · 2023Article
- Simulating structurally variable nuclear pore complexes for microscopy.Bioinformatics (Oxford, England) · 2023Article
- Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.Nature communications · 2023Article
- BioAFMviewer software for simulation atomic force microscopy of molecular structures and conformational dynamics.Journal of structural biology: X · 2023Review
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Authors and funding
8 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.