An algorithm for extracting the network geometry of three-dimensional collagen gels
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Updated: Jun 27, 2026
Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo
Published on: May 9, 2016
Andrew M Stein1, David A Vader, Louise M Jawerth
1Institute for Mathematics and its Applications, University of Minnesota, Minneapolis, MN 55403, USA, +astein@ima.umn.edu+
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.
