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

Quantifying Mesoscale Neuroanatomy Using X-Ray Microtomography.

Author information

1
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332.
2
The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, 20723.
3
Dept. of Computer Science, The Johns Hopkins University, Baltimore, MD, 21218.
4
Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637.
5
Dept. of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611.
6
Sensory Motor Performance Program, Rehabilitation Institute of Chicago, Chicago, IL, 60611.
7
Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439.
8
Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205.
9
Institute of Computational Medicine, The Johns Hopkins University, Baltimore, MD, 21218.
10
Department of Physics and Astronomy, Northwestern University, Chicago, IL, 60208.
11
Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA, 19104.
12
Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439.

Abstract

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

PMID:
29085899
PMCID:
PMC5659258
DOI:
10.1523/ENEURO.0195-17.2017
[Indexed for MEDLINE]
Free PMC Article

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