title: Parameter-free binarization and skeletonization of fiber networks from confocal image stacks.
abstract: We present a method to reconstruct a disordered network of thin biopolymers, such as collagen gels, from three-dimensional (3D) image stacks recorded with a confocal microscope. The method is based on a template matching algorithm that simultaneously performs a binarization and skeletonization of the network. The size and intensity pattern of the template is automatically adapted to the input data so that the method is scale invariant and generic. Furthermore, the template matching threshold is iteratively optimized to ensure that the final skeletonized network obeys a universal property of voxelized random line networks, namely, solid-phase voxels have most likely three solid-phase neighbors in a 3 x 3 x 3 neighborhood. This optimization criterion makes our method free of user-defined parameters and the output exceptionally robust against imaging noise.
authors.affiliation: Department of Physics, Biophysics Group, Friedrich-Alexander University, Erlangen, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Krauss
authors.forename: Claus
authors.initials: C
authors.lastname: Metzner
authors.forename: Janina
authors.initials: J
authors.lastname: Lange
authors.forename: Nadine
authors.initials: N
authors.lastname: Lang
authors.forename: Ben
authors.initials: B
authors.lastname: Fabry
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry*; D003094:Collagen / Q000737:chemistry; D003198:Computer Simulation; D005782:Gels; D021621:Imaging, Three-Dimensional / Q000379:methods* / Q000706:statistics & numerical data; D018613:Microscopy, Confocal / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D001704:Biopolymers; D005782:Gels; D003094:Collagen