Parameter-Free Binarization and Skeletonization of Fiber Networks from Confocal Image Stacks

  • 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 neighborWe 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 neighborhood. This optimization criterion makes our method free of user-defined parameters and the output exceptionally robust against imaging noise.show moreshow less

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Metadaten
Author:Patrick Krauss, Claus Metzner, Janina Lange, Nadine Lang, Ben Fabry
URN:urn:nbn:de:bvb:29-opus-35900
Document Type:Article
Language:English
Date of Publication (online):2012/10/10
Publishing Institution:Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Release Date:2012/10/10
SWD-Keyword:-
Original publication:PLoS ONE 7.5 (2012): 10.10.2012 <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036575>
Institutes:Naturwissenschaftliche Fakultät -ohne weitere Spezifikation-
Dewey Decimal Classification:530 Physik
Collections:Von der FAU geförderte Open Access Artikel 2012

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