title: A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue.
abstract: The neuroimaging technique three-dimensional polarized light imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres—consisting of an axon and a surrounding myelin sheath—are uniaxial birefringent and that the measured optic axis is oriented in the direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve structures smaller than the diameter of single fibres. In the case of fibre bundles, polarimeters with even higher resolutions can be used without losing reliability. When taking the myelin density into account, the derived fibre orientations are considerably improved.
authors.affiliation: Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich 52425, Germany m.menzel@fz-juelich.de.
authors.forename: M
authors.initials: M
authors.lastname: Menzel
authors.affiliation: Jülich Supercomputing Centre, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich 52425, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Michielsen
authors.affiliation: Department of Applied Physics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands.
authors.forename: H
authors.initials: H
authors.lastname: De Raedt
authors.affiliation: Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich 52425, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Reckfort
authors.affiliation: Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich 52425, Germany Cécile and Oskar Vogt Institute of Brain Research, University of Düsseldorf, Düsseldorf 40204, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Amunts
authors.affiliation: Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich 52425, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Axer
mesh_terms: D000465:Algorithms; D001369:Axons / Q000502:physiology*; D001718:Birefringence; D001921:Brain / Q000502:physiology*; D003198:Computer Simulation; D006801:Humans; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008027:Light; D008962:Models, Theoretical; D009186:Myelin Sheath / Q000502:physiology*; D009412:Nerve Fibers / Q000502:physiology*; D059906:Neuroimaging / Q000379:methods*; D055095:Optics and Photonics
keywords: Jones matrix calculus; birefringence; computer simulation; nerve fibre architecture; optics; polarized light imaging