TopoStats

TopoStats automates identification and tracing of individual molecules in Atomic Force Microscopy (AFM) images to quantify molecular conformations and contour lengths.

Key Features:

• Automated identification and tracing: Detects and traces individual molecules, including circular and linear conformations such as DNA minicircles, DNA origami rings, and pore-forming proteins, without prior image processing.
• High accuracy: Produces contour lengths typically within 10 nm of predicted values and successfully identifies and traces approximately 90% of individual molecules and assemblies across a wide field of view.
• Versatility across molecular types: Handles mixed samples containing both linear and enclosed circular molecules for consistent detection and tracing.

Scientific Applications:

• Molecular structure characterization: Quantifies conformations and contour lengths of biomolecules from AFM images for structural analysis.
• DNA nanotechnology: Analyzes DNA minicircles and DNA origami rings to assess topology and assembly outcomes.
• Protein pore analysis: Characterizes pore-forming proteins in AFM datasets to evaluate topology and distribution.
• Nanotechnology and materials science: Processes large AFM datasets to support studies of nanoscale structures and materials assemblies.

Methodology:

Python implementation employing image-processing algorithms for automated identification and tracing of molecular structures in AFM images, operating without prior image manipulation and eliminating manual input.