fastPLI is an open source toolbox based on Python and C++ for modeling myelinated axons, i.e. nerve fibers and simulating the results of measurement of fiber orientations with a polarization microscope using 3D Polarized Light Imaging (3D-PLI). The fastPLI package includes the following modules: 1. Fiber Modelling Modules: A detailed 3D modelling of nerve fibers at the micrometer level is essential as input for the measurement simulation. In order to recreate biological tissue as a model, it is important that the nerve fibers do not spatially overlap. We have decided to implement a solver module that takes any configuration of fiber bundles as input and converts it over several iterations into a collision-free configuration. In order to generate collision free fiber arrangements, a dedicated algorithm to prohibit such overlaps has been developed. 2. Simulation Module: The 3D-PLI simulation is based on Stokes vector and Müller matrix approaches. For the simulation the polarimetric setup can be equipped with a tiltable specimen stage. By this means the brain section can be scanned from oblique views which adds important information to unambiguously analyze the 3D fiber orientation. 3. Analysis Module: The resulting simulated measurements (i.e., image stacks of a section acquired at different polarizing filter rotation angles and, optionally, at different oblique views) can be processed similarly to the real, experimental 3D-PLI.

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  1. Felix Matuschke; Katrin Amunts; Markus Axer: fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI (2021) not zbMATH