RT Journal Article SR Electronic T1 Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography JF eneuro JO eNeuro FD Society for Neuroscience SP ENEURO.0195-17.2017 DO 10.1523/ENEURO.0195-17.2017 VO 4 IS 5 A1 Dyer, Eva L. A1 Gray Roncal, William A1 Prasad, Judy A. A1 Fernandes, Hugo L. A1 Gürsoy, Doga A1 De Andrade, Vincent A1 Fezzaa, Kamel A1 Xiao, Xianghui A1 Vogelstein, Joshua T. A1 Jacobsen, Chris A1 Körding, Konrad P. A1 Kasthuri, Narayanan YR 2017 UL http://www.eneuro.org/content/4/5/ENEURO.0195-17.2017.abstract AB Methods for resolving the three-dimensional (3D) microstructure of the brain typically start by thinly slicing and staining the brain, followed by imaging numerous individual sections 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 (∼1 µm 3 resolution) brain maps from millimeter-scale volumes of mouse brain. We introduce a pipeline for µCT-based brain mapping that develops and integrates methods for sample preparation, imaging, and automated segmentation of cells, blood vessels, and myelinated axons, in addition to statistical analyses of these brain structures. Our results demonstrate that X-ray tomography achieves rapid quantification of large brain volumes, complementing other brain mapping and connectomics efforts.