title: SOAX: a software for quantification of 3D biopolymer networks.
abstract: Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called "SOAX", which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint.
authors.affiliation: Department of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Ting
authors.initials: T
authors.lastname: Xu
authors.affiliation: Department of Physics, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Vavylonis
authors.affiliation: FOM Institute AMOLF, Systems Biophysics department, Amsterdam, The Netherlands.
authors.forename: Feng-Ching
authors.initials: FC
authors.lastname: Tsai
authors.affiliation: FOM Institute AMOLF, Systems Biophysics department, Amsterdam, The Netherlands.
authors.forename: Gijsje H
authors.initials: GH
authors.lastname: Koenderink
authors.affiliation: Department of Physics, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Nie
authors.affiliation: 1] Department of Physics, Lehigh University, Bethlehem, Pennsylvania, USA [2] Surya College of Education, SURE Center, Tangerang, Indonesia [3] IPH Schools, Surabaya, Indonesia.
authors.forename: Eddy
authors.initials: E
authors.lastname: Yusuf
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA.
authors.lastname: I-Ju Lee
authors.affiliation: Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA.
authors.forename: Jian-Qiu
authors.initials: JQ
authors.lastname: Wu
authors.affiliation: Department of Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Huang
mesh_terms: D000199:Actins / Q000737:chemistry / Q000378:metabolism; D001704:Biopolymers / Q000737:chemistry* / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D021621:Imaging, Three-Dimensional; D018613:Microscopy, Confocal; D008870:Microtubules / Q000737:chemistry / Q000378:metabolism; D060066:Protein Interaction Maps; D012568:Schizosaccharomyces; D012984:Software
chemical_list: D000199:Actins; D001704:Biopolymers