An algorithm for extracting the network geometry of three-dimensional collagen gels

Abstract

The geometric structure of a biopolymer network impacts its mechanical and biological properties. In this paper, we develop an algorithm for extracting the network architecture of three-dimensional (3d) fluorescently labeled collagen gels, building on the initial work of Wu et al., (2003) . Using artificially generated images, the network extraction algorithm is then validated for its ability to reconstruct the correct bulk properties of the network, including fiber length, persistence length, cross-link density, and shear modulus.