title: Rapid three-dimensional quantification of voxel-wise collagen fiber orientation.
abstract: Defining fiber orientation at each voxel within a 3D biomedical image stack is potentially useful for a variety of applications, including cancer, wound healing and tissue regeneration. Current methods are typically computationally intensive or inaccurate. Herein, we present a 3D weighted orientation vector summation algorithm, which is a generalization of a previously reported 2D vector summation technique aimed at quantifying collagen fiber orientations simultaneously at each voxel of an image stack. As a result, voxel-wise fiber orientation information with 4° to 5° accuracy can be determined, and the computational time required to analyze a typical stack with the size of 512x512x100 voxels is less than 5 min. Thus, this technique enables the practical extraction of voxel-specific orientation data for characterizing structural anisotropy in 3D specimens. As examples, we use this approach to characterize the fiber organization in an excised mouse mammary gland and a 3D breast tissue model.
authors.affiliation: Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
authors.forename: Kyle P
authors.initials: KP
authors.lastname: Quinn
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Lucia
authors.initials: L
authors.lastname: Speroni
authors.affiliation: Department of Anatomy and Cell Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Arendt
authors.affiliation: Department of Anatomy and Cell Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Kuperwasser
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Carlos
authors.initials: C
authors.lastname: Sonnenschein
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Soto
authors.affiliation: Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA.
authors.forename: Irene
authors.initials: I
authors.lastname: Georgakoudi
keywords: (100.2960) Image analysis; (100.6950) Tomographic image processing; (180.4315) Nonlinear microscopy