Synchrotron X‐ray micro‐CT as a validation dataset for diffusion MRI in whole mouse brain

Abstract

Purpose: To introduce synchrotron X-ray microcomputed tomography (microCT) and demonstrate its use as a natively isotropic, nondestructive, 3D validation modality for diffusion MRI in whole, fixed mouse brain. Methods: Postmortem diffusion MRI and microCT data were acquired of the same whole mouse brain. Diffusion data were processed using constrained spherical deconvolution. Synchrotron data were acquired at an isotropic voxel size of 1.17 μm.Structure tensor analysis was used to calculate fiber orientation distribution functions from the microCT data. A pipeline was developed to spatially register the 2 datasets in order to perform qualitative comparisons of fiber geometries represented by fiber orientation distribution functions. Fiber orientations from both modalities were used to perform whole-brain deterministic tractography to demonstrate validation of longrange white matter pathways. Results: Fiber orientation distribution functions were able to be extracted throughout the entire microCT dataset, with spatial registration to diffusion MRI simplified due to the whole brain extent of the microCT data. Fiber orientations and tract pathways showed good agreement between modalities. Conclusion: Synchrotron microCT is a potentially valuable new tool for future multi-scale diffusion MRI validation studies, providing comparable value to optical histology validation methods while addressing some key limitations in data acquisition and ease of processing.

Comparative hard x-ray tomography for virtual histology of zebrafish larva, human tooth cementum, and porcine nerve

“…Previous work has shown that microtomography has excellent correlation with the conventional histology of embedded tissue slices, 14 , 24 , 26 , 74 and so x-ray microtomography can be referred to as virtual histology. This imaging technique is also compatible with prior MRI-techniques, e.g., diffusion MRI, 76 or subsequent electron microscopy. 77 Furthermore, volumetric virtual histology provides a third dimension for histopathological investigation that has typically relied on irreversible, sparse, two-dimensional sectioning.…”

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

“…Micron-scale synchrotron x-ray computed tomography (microCT) is a non-destructive, 3D imaging technique that can provide micron resolution images of thick (~1cm cubed) tissue blocks ( Foxley et al, 2020 ; Trinkle et al 2021 ; Andersson et al, 2021 ). Here, osmium-stained tissue is rotated through a synchrotron x-ray beam, after which a high-resolution 3D volume is reconstructed from a series of 2D back-projections.…”

“…Consequently, nanometer EM techniques are limited to characterizing small tissue blocks (50-100 μ m 3 ), which are sparsely sampled throughout the brain. The penetration of chemicals for tissue clearing currently limits the field of view in fluorescence imaging, as does the osmium-stain penetration in microCT ( Trinkle et al, 2021 ). If the imaged block is not representative of the larger MRI voxel from which it is sampled, this may bias the comparison.…”

A scalable and modular computational pipeline for axonal connectomics: automated tracing and assembly of axons across serial sections

“…For each subregion, the orientation distribution function was estimated (Fig. 5B, left) based on the tangent vectors of skeleton segments within that region (Trinkle et al 2021).…”