FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain.

PURPOSE: The technique 3D polarized light imaging (3D-PLI) allows to reconstruct nerve fiber orientations of postmortem brains with ultra-high resolution. To better understand the physical principles behind 3D-PLI and improve the accuracy and reliability of the reconstructed fiber orientations, numerical simulations are employed which use synthetic nerve fiber models as input. As the generation of fiber models can be challenging and very time-consuming, we have developed the open source FAConstructor tool which enables a fast and efficient generation of synthetic fiber models for 3D-PLI simulations. METHODS: The program was developed as an interactive tool, allowing the user to define fiber pathways with interpolation methods or parametric functions and providing visual feedback. RESULTS: Performance tests showed that most processes scale almost linearly with the amount of fiber points in FAConstructor. Fiber models consisting of < 1.6 million data points retain a frame rate of more than 30 frames per second, which guarantees a stable and fluent workflow. The applicability of FAConstructor was demonstrated on a well-defined fiber model (Fiber Cup phantom) for two different simulation approaches, reproducing effects known from 3D-PLI measurements. CONCLUSION: We have implemented a user-friendly and efficient tool that enables an interactive and fast generation of synthetic nerve fiber configurations for 3D-PLI simulations. Already existing fiber models can easily be modified, allowing to simulate many different fiber models in a reasonable amount of time.

MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres.

A GPU-based tool to generate realistic phantoms of the brain microstructure is presented. Using a spherical meshing technique which decomposes each microstructural item into a set of overlapping spheres, the phantom construction is made very fast while reliably avoiding the collisions between items in the scene. This novel method is applied to the construction of human brain white matter microstructural components, namely axonal fibers, oligodendrocytes and astrocytes. The algorithm reaches high values of packing density and angular dispersion for the axonal fibers, even in the case of multiple white matter fiber populations and enables the construction of complex biomimicking geometries including myelinated axons, beaded axons, and glial cells. The method can be readily adapted to model gray matter microstructure.