The geometry of 3D collagen networks is a key factor that#N#influences the behavior of live cells within extracellular#N#matrices. This paper presents a hybrid, two-step method for#N#fully automatic quantification of the 3D collagen network#N#geometry at fiber resolution in confocal reflection microscopy#N#images. First, a coarse binary mask of the entire network is#N#obtained using steerable filtering and local Otsu thresholding.#N#Second, individual collagen fibers are reconstructed by~tracing#N#maximum ridges in the Euclidean distance map of the binary#N#mask. The proposed method, validated in a novel framework using#N#3D collagen gels with various collagen and Matrigel#N#concentrations, reveal that Matrigel affects the collagen#N#network geometry by decreasing the network pore size while#N#preserving the fiber length and fiber persistence length.
['Martin Maška', 'Cristina Ederra', 'Javier Fernández-Marqués', 'Arrate Muñoz-Barrutia', 'Michal Kozubek', 'Carlos Ortiz-de-Solorzano']
Quantification of the 3D collagen network geometry in confocal reflection microscopy