Quantifying mesoscale neuroanatomy using X-ray microtomography

TL;DR

This paper demonstrates the use of synchrotron X-ray microtomography to rapidly produce mesoscale 3D brain maps from millimeter-scale mouse brain samples, offering a non-destructive alternative to traditional slicing methods.

Contribution

It introduces a comprehensive pipeline combining sample prep, imaging, automated segmentation, and analysis for mesoscale brain mapping using X-ray microtomography.

Findings

Achieved 1 μm^3 resolution in large brain volumes.

Provided rapid, non-destructive 3D brain mapping.

Showed potential to complement existing connectomics methods.

Abstract

Methods for resolving the 3D microstructure of the brain typically start by thinly slicing and staining the brain, and then imaging each individual section with visible light photons or electrons. In contrast, X-rays can be used to image thick samples, providing a rapid approach for producing large 3D brain maps without sectioning. Here we demonstrate the use of synchrotron X-ray microtomography ($\mu$CT) for producing mesoscale $(1~\mu m^3)$ resolution brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for $\mu$CT-based brain mapping that combines methods for sample preparation, imaging, automated segmentation of image volumes into cells and blood vessels, and statistical analysis of the resulting brain structures. Our results demonstrate that X-ray tomography promises rapid quantification of large brain volumes, complementing other brain mapping and connectomics efforts.