Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography

eNeuro. 2017 Oct 16;4(5):ENEURO.0195-17.2017. doi: 10.1523/ENEURO.0195-17.2017. eCollection 2017 Sep-Oct.


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.

Keywords: Automated segmentation; X-ray microtomography; cell counting; electron microscopy; neocortex; neuroanatomy.

Publication types

  • Video-Audio Media
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Blood Vessels / anatomy & histology
  • Blood Vessels / diagnostic imaging
  • Brain / anatomy & histology*
  • Brain / diagnostic imaging*
  • Female
  • Imaging, Three-Dimensional
  • Mice, Inbred BALB C
  • Myelin Sheath
  • Neurons / cytology
  • Pattern Recognition, Automated
  • Reproducibility of Results
  • Software
  • X-Ray Microtomography* / instrumentation
  • X-Ray Microtomography* / methods