Data-driven traction force microscopy in 3D collagen hydrogels

Jorge Barrasa Fano; Laurens Kimps; Alejandro Apolinar–Fernández; Débora do Carmo Linhares; Iain Muntz; Elías Núñez-Ortega; Nele Vaes; Apeksha Shapeti; Ruth Cardinaels; Gijsje Hendrika Koenderink; Jose A. Sanz‐Herrera; Hans Van Oosterwyck

doi:10.1101/2025.11.17.688772

BiophysicsbioRxivNov 17, 2025

Preprint

Data-driven traction force microscopy in 3D collagen hydrogels

Jorge Barrasa Fano iD, Laurens Kimps iD, Alejandro Apolinar–Fernández iD, Débora do Carmo Linhares iD, Iain Muntz iD, Elías Núñez-Ortega iD, Nele Vaes, Apeksha Shapeti iD, Ruth Cardinaels iD, Gijsje Hendrika Koenderink iD, Jose A. Sanz‐Herrera iD, Hans Van Oosterwyck iD

Abstract

Three-dimensional traction force microscopy (3DTFM) in fibrillar hydrogels typically models the extracellular matrix as a continuum. We present data-driven 3DTFM (DD-TFM), which reconstructs fiber networks from confocal images and models them as discrete fiber networks mechanically calibrated by shear rheology. We validate DD-TFM in silico and apply it to endothelial cells, quantifying cell-generated forces and matrix stresses at the fiber level. Compared with continuum TFM DD-TFM reveals network-guided matrix deformations, shifting 3DTFM toward fiber-resolved force calculation.

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