This title appears in the Scientific Report : 2014 

Simulation and Modeling for the Reconstruction of Nerve Fibers in the Brain by 3D Polarized Light Imaging
Menzel, Miriam (Corresponding Author)
Strukturelle und funktionelle Organisation des Gehirns; INM-1
Jülich Supercomputing Center; JSC
v, 165
RWTH Aachen, Masterarbeit, 2014
Master Thesis
ohne Topic
Three-dimensional Polarized Light Imaging (3D-PLI) is a neuroimaging technique that is able to reconstruct the pathways of nerve fibers in post-mortem brains at the micrometer scale: By transmitting polarized light through histological brain sections in a polarimeter, the birefringence of the nerve fibers is measured, thus revealing their spatial orientations. Although 3D-PLI is a well-established imaging technique which has been applied successfully in recent years, the reconstruction of the nerve fiber orientations is based on a simplified macroscopic model whoselimitations have not been investigated to date.In this thesis, different analytical methods and numerical simulations are employed to better understand the physical mechanisms and processes behind 3D-PLI and to justify the use of the simplified model. In order to validate the nerve fiber reconstruction, two complementary simulation approaches are developed which simulate different fiber constellations and compare the derived fiber orientations with the underlying fiber model: The intrinsic birefringence of the nerve myelin sheaths is modeled with the Jones matrix calculus; other optical tissue properties are modeled with a Maxwell Solver that computes the propagation of the polarized light wave through a tissue sample based on a finite-difference time-domain(FDTD) algorithm.The limitations of the simplified model are studied with the Jones matrix calculus. Simulations of different fiber constellations and different optical resolutions show that the simplified model of uniaxial birefringence ensures a reliable estimation of the fiber orientations as long as the polarimeter does not resolve structures smaller than the fiber diameter. Furthermore, it is demonstrated that the derived fiber orientation can be improved considerably by including the local myelin thickness into the calculation of the fiber inclination.The FDTD simulations show that different fiber arrangements exhibit form birefringence, scattering, and diattenuation which provide additional information about the spatial ber orientation. The diattenuation effect is also investigated in an experimental study. In this context, a method is developed that eliminates the diattenuation effect from the measured birefringence signal and illustrates how vertical and crossing fiber arrangements could be distinguished.