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 (μCT) for producing mesoscale (1μm3) resolution brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for μCT-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.
@article{arxiv.1604.03629,
title = {Quantifying mesoscale neuroanatomy using X-ray microtomography},
author = {Eva L. Dyer and William Gray Roncal and Hugo L. Fernandes and Doga Gürsoy and Vincent De Andrade and Rafael Vescovi and Kamel Fezzaa and Xianghui Xiao and Joshua T. Vogelstein and Chris Jacobsen and Konrad P. Körding and Narayanan Kasthuri},
journal= {arXiv preprint arXiv:1604.03629},
year = {2016}
}