  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.
