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Author Notes:

Correspondence should be addressed to either of the following: Eva L. Dyer, Georgia Institute of Technology 313 Ferst Drive NW Atlanta, GA 30332. E-mail: evadyer@gatech.edu; or Narayanan Kasthuri. E-mail: bobbykasthuri@anl.gov.

Author contributions: E.L.D., C.J., K.P.K., and N.K. designed research

E.L.D., W.G.R., D.G., X.X., and N.K. performed research

E.L.D., W.G.R., J.A.P., H.F., V.d.A., K.F., J.T.V., and N.K. contributed unpublished reagents/analytic tools

E.L.D., W.G.R., and D.G. analyzed data

E.L.D., J.A.P., K.P.K., and N.K. wrote the paper.

Acknowledgments: We thank Jordan Matelsky from The JHU Applied Physics Laboratory for his assistance with data access and creating 3D visualizations of our results.

We also thank Norman Clark and Olivia Grebski for their assistance in annotating some of the training volumes.

A big thanks to Francesco De Carlo (Argonne) and Pavan Ramkumar (Northwestern) for useful discussions regarding this work.

Authors report no conflict of interest.


Research Funding:

This research used resources from the US Department of Energy (DOE) Office of Science User Facilities operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357.

Support was provided by NIH U01MH109100 (E.L.D., H.L.F., D.G., X.X., C.J., N.K., and K.P.K.), the IARPA MICRONS project under IARPA Contract D16PC0002 (N.K.), an educational Fellowship from the Johns Hopkins University Applied Physics Laboratory (W.G.R.), the Defense Advanced Research Projects Agency (DARPA) SIMPLEX program through SPAWAR contract N66001-15-C-4041, and DARPA GRAPHS N66001-14-1-4028.


  • q-bio.QM
  • q-bio.QM
  • cs.CV

Quantifying mesoscale neuroanatomy using X-ray microtomography

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Journal Title:



Volume 4, Number 5


, Pages ENEURO.0195-17.2017-ENEURO.0195-17.2017

Type of Work:

Article | Final Publisher PDF


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.

Copyright information:

© 2017 Dyer et al.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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