fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI

Abstract

3D Polarized Light Imaging (3D-PLI) is a microscopic neuroimaging technique used to study the nerve fiber architecture in unstained histological brain sections at the micrometer scale (Axer et al., 2011). It provides image contrast for fibers and fiber tracts, and ultimately enables reconstruction of 3D nerve fiber orientations. The physical effect behind 3D-PLI is the optical property of the nerve fibers called birefringence. Due to this intrinsic birefringence, it is possible to use polarized light, pass it through a thin brain section and observe the change of the polarization state of light. This change is directly related to the 3D orientation of the fibers and also provides strong contrasts between fibers and other tissue components.