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Methods/New Tools, Novel Tools and Methods

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 and Narayanan Kasthuri
eNeuro 25 September 2017, ENEURO.0195-17.2017; https://doi.org/10.1523/ENEURO.0195-17.2017
Eva L. Dyer
1Department of Biomedical Engineering, Georgia Institute of Technology & Emory University
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William Gray Roncal
2The Johns Hopkins University Applied Physics Laboratory
3Department of Computer Science, the Johns Hopkins University
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Judy A. Prasad
4Department of Neurobiology, University of Chicago
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Hugo L. Fernandes
5Department of Physical Medicine and Rehabilitation, Northwestern University
6Sensory Motor Performance Program, Rehabilitation Institute of Chicago
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Doga Gürsoy
7Advanced Photon Source, Argonne National Laboratory
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Vincent De Andrade
7Advanced Photon Source, Argonne National Laboratory
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Kamel Fezzaa
7Advanced Photon Source, Argonne National Laboratory
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Xianghui Xiao
7Advanced Photon Source, Argonne National Laboratory
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Joshua T. Vogelstein
8Department of Biomedical Engineering, the Johns Hopkins University
9Institute of Computational Medicine, the Johns Hopkins University
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Chris Jacobsen
7Advanced Photon Source, Argonne National Laboratory
10Department of Physics and Astronomy, Northwestern University
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Konrad P. Körding
5Department of Physical Medicine and Rehabilitation, Northwestern University
6Sensory Motor Performance Program, Rehabilitation Institute of Chicago
11Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA
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Narayanan Kasthuri
4Department of Neurobiology, University of Chicago
12Center for Nanoscale Materials, Argonne National Laboratory
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Abstract

Methods for resolving the three-dimensional microstructure of the brain typically start by thinly slicing and staining the brain, followed by the imaging of 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 (approximately 1μm 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.

Significance Statement Reconstructing neuroanatomical samples in three dimensions (3D) is challenging, as traditional methods require fine sectioning of tissue and alignment of these sections into a 3D volume. In this manuscript, we present a pipeline for quantifying neuroanatomy with synchrotron X-ray microtomography (μCT), a method that achieves micron resolution over thick millimeter-scale intact samples. As brain tissue can be imaged with μCT without damaging the integrity of the sample, electron microscopy was applied to survey higher-resolution structures. We introduce this data analysis pipeline for blood vessel segmentation and cell detection, as well as producing estimates of cell densities and spatial relationships among cells and blood vessels. These methods promise efficient imaging, reconstruction, and analysis of brain structures using μCT.

  • Automated Segmentation
  • Cell Counting
  • Electron Microscopy
  • Neocortex
  • Neuroanatomy
  • X-Ray Microtomography

Footnotes

  • Authors report no conflict of interest.

  • HHS | National Institutes of Health (NIH) [NIH U01MH109100]; DOD | Defense Advanced Research Projects Agency (DARPA) [N66001-15-C-4041].

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license, which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

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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
eNeuro 25 September 2017, ENEURO.0195-17.2017; DOI: 10.1523/ENEURO.0195-17.2017

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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
eNeuro 25 September 2017, ENEURO.0195-17.2017; DOI: 10.1523/ENEURO.0195-17.2017
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Keywords

  • Automated Segmentation
  • cell counting
  • electron microscopy
  • neocortex
  • neuroanatomy
  • X-Ray Microtomography

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