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

Abstract

Abstract3D 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

“…Due to the similar setup (illuminating unstained histological brain sections and measuring the transmitted light), the SLI measurement can be easily combined with a 3D-PLI measurement (by using removable polarizing filters in the 3D-PLI setup), which significantly improves the high-resolution 3D-reconstruction of the nerve fibers: As SLI and 3D-PLI have different sources of error, SLI can serve as cross-validation for 3D-PLI, also when using a tiltable specimen stage. When performing SLI and 3D-PLI measurements on several consecutive brain sections, registering the resulting images onto each other (as described in Section 2.4 ), and combining the 2D vector field from SLI (containing up to three crossing fiber directions in each image pixel) with the 3D vector field from 3D-PLI (containing one three-dimensional fiber orientation for each image pixel), streamline-based tractography can be performed on the three-dimensional brain volume Schubert et al. (2018) .…”

Post mortem mapping of connectional anatomy for the validation of diffusion MRI

“…The use of PLI to image brain tissue has been demonstrated in human (Axer et al, 2011a,b; Caspers et al, 2015; Mollink et al, 2017; Zeineh et al, 2017; Henssen et al, 2019), seal (Dohmen et al, 2015), rat (Schubert et al, 2016, 2018), pigeon (Herold et al, 2018; Stacho et al, 2020), and vervet monkey (Takemura et al, 2020). Examples of the detailed visualizations of cortical and white-matter fiber architecture that can be achieved by PLI are shown in Fig.…”

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

“…The orientation of the vectors are color-coded. Visualization has been realized with in-house developed software [24]. b FDTD simulations of the three selected regions (fiber crossings) in the collision-free Fiber Cup phantom shown in ( a ).…”