Quantifying mesoscale neuroanatomy using X-ray microtomography

Eva L. Dyer*, William Gray Roncal, Judy A. Prasad, Hugo L. Fernandes, Doga Gürsoy, Vincent De Andrade, Kamel Fezzaa, Xianghui Xiao, Joshua T. Vogelstein, Chris Jacobsen, Konrad P. Körding, Narayanan Kasthuri

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


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 μm3 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.

Original languageEnglish (US)
Article numbere0195-17.2017
Issue number5
StatePublished - Sep 1 2017


  • Automated segmentation
  • Cell counting
  • Electron microscopy
  • Neocortex
  • Neuroanatomy
  • X-ray Microtomography

ASJC Scopus subject areas

  • Neuroscience(all)

Fingerprint Dive into the research topics of 'Quantifying mesoscale neuroanatomy using X-ray microtomography'. Together they form a unique fingerprint.

Cite this