A multimodal computational pipeline for 3D histology of the human brain

Abstract

Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors. Motivation. One of the major challenges in the quest to understand the human brain as a complex system is characterizing its multiscale organization. From a macroscopic anatomical perspective, the brain is subdivided into distinct structures and presents well-defined landmarks, for instance its gyri and sulci. At a much finer scale, neurons are interconnected to form complex circuits. These circuits give rise to features at coarser scales, e.g., the laminar organization of the cortex 1. Although these distinct levels of organization may seem separate, they are, in fact, deeply linked and mutually influential. One clear example is given by Alzheimer's disease, which can be described by the interactions between proteinopathy at the microscale and distributed, network-level disruptions at the macroscale 2. Understanding these multi-scale mechanisms requires a multi-scale map of the brain. However, the current concept of brain mapping is closely linked to the specific tool used to construct cartographic representations, and thus to the spatial scale of the tool. As a result, the different organizational principles can only be observed in a scale-specific fashion with dedicated tools 3. Multi-scale imaging of the human brain is therefore necessarily multimodal, as different modalities are needed to study different scales. While a macroscopic anatomical picture of the brain is easily acquired non invasively or ex vivo with magnetic resonance imaging (MRI), finer characterization requires histological procedures and microscopy. Histology and MRI are highly complementary modalities: histology produces excellent contrast at the microscopic scale using dedicated stains that target different microanatomical or cytoarchitectural features, but it is a 2D modality that also inevitably introduces distortions in the tissue during blocking and sectioning. MRI does not yield microscopic resolution, but produces undistorted 3D volumes. Therefore, the combination of these two modalities offers a solution to the problem of imaging the human brain at high resolution in 3D.

Middle Frontal Gyrus and Area 55b: Perioperative Mapping and Language Outcomes

“… Tractography. Diffusion and T1-weighted data were pre-processed using the framework described by Mancini et al ( 62 ). Multi-fiber orientations were estimated using single-shell two-tissue constrained spherical deconvolution using order l max = 8 ( 63 ).…”

“…Probabilistic tractography was done using Second-order integration over Fiber Orientation Distributions (iFOD2) ( 63 ) and seeding randomly from the white-matter/grey-matter interface, both to reconstruct whole-brain (FOD amplitude cut-off = 0.05 and total_streamlines = 10 million) and region-of-interest (ROI) based tractography (FOD amplitude cut-off = 0.05 and total_streamlines = 1,000). ROI-based tractography relied on reconstructing the arcuate fasciculus (AF) tract from the left side of the brain based on similar pipeline introduced in ( 62 ). The posterior MFG was used to filter the reconstructed AF and its connectivity analysis.…”

Tissue expansion of ‘cleared’ whole brains reduces contrast in ex vivo MRI

“…Polymerized brains were actively cleared in electrophoretic tissue clearing (ETC) solution containing 200 mM boric acid and 4% (wt/vol) SDS (pH 8.5) (C13001, Logos Biosystems) by the Tissue Clearing System (C10001, Logos Biosystems). uDISCO: Whole brains were dehydrated by sequential immersion in incrementing concentrations of tert-Butanol (30,50,70,80,90,96, and 100 % vol in DDW; 360538, Sigma-Aldrich) for 4-12 hrs in each solution with gentle shaking at 34 °C. Samples were delipidated in Dichloromethane (DCM; 270997, Sigma-Aldrich) for 1 h. The RI-matching solution mix included 1:2 benzyl alcohol and benzyl benzoate solution (BABB solution; 24122 and B6630, Sigma-Aldrich) added with DPE (67334, Sigma aldrich) at 15:1 BABB to DPE ratio, and 0.4 % vol DL-alpha-tocopherol (Vitamin E; A17039, Alfa Aesar), as previously described 41 .…”

“…ECi: Whole brains were dehydrated by sequential immersion in incrementing concentrations of ethanol solutions (30,50,70, 100 % vol in DDW, 30, 50 and 70 % were adjusted to pH 9) supplemented with 2 % Tween-20 (P1379, Sigma-Aldrich) for 12-24 hrs in each solution with gentle shaking at 4 °C. Samples were delipidated in 100 % ECi (112372, Sigma-Aldrich) for at least 24 hrs until achieving transparency, as previously described 44 .…”

“…Despite these advantages, dual LM-ex vivo MRI is not common (more common are in vivo MRI followed by ex vivo LM 24,26,30 ). In fact, it has been recently shown that several clearing methods, notably CLARITY, produce samples with no contrast when imaged by ex vivo MRI 5,14,[31][32][33] .…”