Code collection - Snooping helices: The elastic path–finding algorithm of growing of hyphae

Collection of Python scripts for the analysis and modeling of filamentous biological structures, with a focus on fungal hyphae. Associated with the publication Snooping helices: The elastic path–finding algorithm of growing of hyphae in PNAS.

It combines four independant components:

• Timelapse processing pipeline based on SAM2 for segmentation, tracking, skeletonization, and extraction of dynamical observables (trajectories, kymographs, spectral analysis).

• 3D skeleton analysis tools to compute geometric properties such as curvature, torsion, and tangent correlations from filament centerlines.

• Images processing pipeline to compute tangent correlations from filament centerlines.

• Physical simulation framework for modeling filament growth as an elastic rod under constraints, enabling exploration of emergent behaviors.

Model, movie, image, and stack analysis are separated in four independant folders. More details can be found in each project's REAME.md file.