Finite-Difference Time-Domain Simulation for Three-dimensional Polarized Light Imaging

Three-dimensional Polarized Light Imaging (3D-PLI) is a promising technique to reconstruct the nerve fiber architecture of human post-mortem brains from birefringence measurements of histological brain sections with micrometer resolution. To better understand how the reconstructed fiber orientations are related to the underlying fiber structure, numerical simulations are employed. Here, we present two complementary simulation approaches that reproduce the entire 3D-PLI analysis: First, we give a short review on a simulation approach that uses the Jones matrix calculus to model the birefringent myelin sheaths. Afterwards, we introduce a more sophisticated simulation tool: a 3D Maxwell solver based on a Finite-Difference Time-Domain algorithm that simulates the propagation of the electromagnetic light wave through the brain tissue. We demonstrate that the Maxwell solver is a valuable tool to better understand the interaction of polarized light with brain tissue and to enhance the accuracy of the fiber orientations extracted by 3D-PLI.Comment: 13 pages, 5 figure

Diattenuation of Brain Tissue and its Impact on 3D Polarized Light Imaging

3D-Polarized Light Imaging (3D-PLI) reconstructs nerve fibers in histological brain sections by measuring their birefringence. This study investigates another effect caused by the optical anisotropy of brain tissue - diattenuation. Based on numerical and experimental studies and a complete analytical description of the optical system, the diattenuation was determined to be below 4 % in rat brain tissue. It was demonstrated that the diattenuation effect has negligible impact on the fiber orientations derived by 3D-PLI. The diattenuation signal, however, was found to highlight different anatomical structures that cannot be distinguished with current imaging techniques, which makes Diattenuation Imaging a promising extension to 3D-PLI.Comment: 32 pages, 15 figure

Microstructural Analysis of Human White Matter Architecture Using Polarized Light Imaging: Views from Neuroanatomy

To date, there are several methods for mapping connectivity, ranging from the macroscopic to molecular scales. However, it is difficult to integrate this multiply-scaled data into one concept. Polarized light imaging (PLI) is a method to quantify fiber orientation in gross histological brain sections based on the birefringent properties of the myelin sheaths. The method is capable of imaging fiber orientation of larger-scale architectural patterns with higher detail than diffusion MRI of the human brain. PLI analyses light transmission through a gross histological section of a human brain under rotation of a polarization filter combination. Estimates of the angle of fiber direction and the angle of fiber inclination are automatically calculated at every point of the imaged section. Multiple sections can be assembled into a 3D volume. We describe the principles of PLI and present several studies of fiber anatomy as a synopsis of PLI: six brainstems were serially sectioned, imaged with PLI, and 3D reconstructed. Pyramidal tract and lemniscus medialis were segmented in the PLI datasets. PLI data from the internal capsule was related to results from confocal laser scanning microscopy, which is a method of smaller scale fiber anatomy. PLI fiber architecture of the extreme capsule was compared to macroscopical dissection, which represents a method of larger-scale anatomy. The microstructure of the anterior human cingulum bundle was analyzed in serial sections of six human brains. PLI can generate highly resolved 3D datasets of fiber orientation of the human brain and has high comparability to diffusion MR. To get additional information regarding axon structure and density, PLI can also be combined with classical histological stains. It brings the directional aspects of diffusion MRI into the range of histology and may represent a promising tool to close the gap between larger-scale diffusion orientation and microstructural histological analysis of connectivity

A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue

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 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.Comment: 20 pages, 8 figure

Insight into the fundamental trade-offs of diffusion MRI from polarization-sensitive optical coherence tomography in ex vivo human brain

In the first study comparing high angular resolution diffusion MRI (dMRI) in the human brain to axonal orientation measurements from polarization-sensitive optical coherence tomography (PSOCT), we compare the accuracy of orientation estimates from various dMRI sampling schemes and reconstruction methods. We find that, if the reconstruction approach is chosen carefully, single-shell dMRI data can yield the same accuracy as multi-shell data, and only moderately lower accuracy than a full Cartesian-grid sampling scheme. Our results suggest that current dMRI reconstruction approaches do not benefit substantially from ultra-high b-values or from very large numbers of diffusion-encoding directions. We also show that accuracy remains stable across dMRI voxel sizes of 1 ​mm or smaller but degrades at 2 ​mm, particularly in areas of complex white-matter architecture. We also show that, as the spatial resolution is reduced, axonal configurations in a dMRI voxel can no longer be modeled as a small set of distinct axon populations, violating an assumption that is sometimes made by dMRI reconstruction techniques. Our findings have implications for in vivo studies and illustrate the value of PSOCT as a source of ground-truth measurements of white-matter organization that does not suffer from the distortions typical of histological techniques.Published versio

3D Polarized Light Imaging Portrayed: Visualization of Fiber Architecture Derived from 3D-PLI

3D polarized light imaging (3D-PLI) is a neuroimaging technique that has recently opened up new avenues to study the complex architecture of nerve fibers in postmortem brains at microscopic scales. In a specific voxel-based analysis, each voxel is assigned a single 3D fiber orientation vector. This leads to comprehensive 3D vector fields. In order to inspect and analyze such high-resolution fiber orientation vector field, also in combination with complementary microscopy measurements, appropriate visualization techniques are essential to overcome several challenges, such as the massive data sizes, the large amount of both unique and redundant information at different scales, or the occlusion issues of inner structures by outer layers. Here, we introduce a comprehensive software tool that is able to visualize all information of a typical 3D-PLI dataset in an adequate and sophisticated manner. This includes the visualization of (i) anatomic structural and fiber architectonic data in one representation, (ii) a large-scale fiber orientation vector field, and (iii) a clustered version of the field. Alignment of a 3D-PLI dataset to an appropriate brain atlas provides expert-based delineation, segmentation, and, ultimately, visualization of selected anatomical structures. By means of these techniques, a detailed analysis of the complex fiber architecture in 3D is feasible

Scattered Light Imaging: Resolving the substructure of nerve fiber crossings in whole brain sections with micrometer resolution

For developing a detailed network model of the brain based on image reconstructions, it is necessary to spatially resolve crossing nerve fibers. The accuracy hereby depends on many factors, including the spatial resolution of the imaging technique. 3D Polarized Light Imaging (3D-PLI) allows the three-dimensional reconstruction of nerve fiber tracts in whole brain sections with micrometer in-plane resolution, but leaves uncertainties in pixels containing crossing fibers. Here we introduce Scattered Light Imaging (SLI) to resolve the substructure of nerve fiber crossings. The measurement is performed on the same unstained histological brain sections as in 3D-PLI. By illuminating the brain sections from different angles and measuring the transmitted (scattered) light under normal incidence, SLI provides information about the underlying nerve fiber structure. A fully automated evaluation of the resulting light intensity profiles has been developed, allowing the user to extract various characteristics, like the individual directions of in-plane crossing nerve fibers, for each image pixel at once. We validate the reconstructed nerve fiber directions against results from previous simulation studies, scatterometry measurements, and fiber directions obtained from 3D-PLI. We demonstrate in different brain samples (human optic tracts, vervet monkey brain, rat brain) that the 2D fiber directions can be reliably reconstructed for up to three crossing nerve fiber bundles in each image pixel with an in-plane resolution of up to 6.5 $\mu$m. We show that SLI also yields reliable fiber directions in brain regions with low 3D-PLI signals coming from regions with a low density of myelinated nerve fibers or out-of-plane fibers. In combination with 3D-PLI, the technique can be used for a full reconstruction of the three-dimensional nerve fiber architecture in the brain.Comment: 30 pages, 16 figure

Dense Fiber Modeling for 3D-Polarized Light Imaging Simulations

3D-Polarized Light Imaging (3D-PLI) is a neuroimaging technique used to study the structural connectivity of the human brain at the meso- and microscale. In 3D-PLI, the complex nerve fiber architecture of the brain is characterized by 3D orientation vector fields that are derived from birefringence measurements of unstained histological brain sections by means of an effective physical model. To optimize the physical model and to better understand the underlying microstructure, numerical simulations are essential tools to optimize the used physical model and to understand the underlying microstructure in detail. The simulations rely on predefined configurations of nerve fiber models (e.g. crossing, kissing, or complex intermingling), their physical properties, as well as the physical properties of the employed optical system to model the entire 3D-PLI measurement. By comparing the simulation and experimental results, possible misinterpretations in the fiber reconstruction process of 3D-PLI can be identified. Here, we focus on fiber modeling with a specific emphasize on the generation of dense fiber distributions as found in the human brain's white matter. A new algorithm will be introduced that allows to control possible intersections of computationally grown fiber structures

Towards Ultra-High Resolution Fibre Tract Mapping of the Human Brain – Registration of Polarised Light Images and Reorientation of Fibre Vectors

Polarised light imaging (PLI) utilises the birefringence of the myelin sheaths in order to visualise the orientation of nerve fibres in microtome sections of adult human post-mortem brains at ultra-high spatial resolution. The preparation of post-mortem brains for PLI involves fixation, freezing and cutting into 100-μm-thick sections. Hence, geometrical distortions of histological sections are inevitable and have to be removed for 3D reconstruction and subsequent fibre tracking. We here present a processing pipeline for 3D reconstruction of these sections using PLI derived multimodal images of post-mortem brains. Blockface images of the brains were obtained during cutting; they serve as reference data for alignment and elimination of distortion artefacts. In addition to the spatial image transformation, fibre orientation vectors were reoriented using the transformation fields, which consider both affine and subsequent non-linear registration. The application of this registration and reorientation approach results in a smooth fibre vector field, which reflects brain morphology. PLI combined with 3D reconstruction and fibre tracking is a powerful tool for human brain mapping. It can also serve as an independent method for evaluating in vivo fibre tractography