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Research ArticleMethods/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, 4 (5) ENEURO.0195-17.2017; DOI: https://doi.org/10.1523/ENEURO.0195-17.2017
Eva L. Dyer
1Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332
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William Gray Roncal
2The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, 20723
3Dept. of Computer Science, The Johns Hopkins University, Baltimore, MD, 21218
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Judy A. Prasad
4Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637
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Hugo L. Fernandes
5Dept. of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611
6Sensory Motor Performance Program, Rehabilitation Institute of Chicago, Chicago, IL, 60611
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Doga Gürsoy
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
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Vincent De Andrade
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
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Kamel Fezzaa
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
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Xianghui Xiao
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
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Joshua T. Vogelstein
8Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205
9Institute of Computational Medicine, The Johns Hopkins University, Baltimore, MD, 21218
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Chris Jacobsen
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
10Department of Physics and Astronomy, Northwestern University, Chicago, IL, 60208
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Konrad P. Körding
11Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA, 19104
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Narayanan Kasthuri
4Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637
12Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439
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Article Information

DOI 
https://doi.org/10.1523/ENEURO.0195-17.2017
PubMed 
29085899
Published By 
Society for Neuroscience
History 
  • Received June 2, 2017
  • Revision received August 2, 2017
  • Accepted August 23, 2017
  • Published online September 25, 2017.
Copyright & Usage 
Copyright © 2017 Dyer et al. 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.

Author Information

  1. Eva L. Dyer1,
  2. William Gray Roncal2,3,
  3. Judy A. Prasad4,
  4. Hugo L. Fernandes5,6,
  5. Doga Gürsoy7,
  6. Vincent De Andrade7,
  7. Kamel Fezzaa7,
  8. Xianghui Xiao7,
  9. Joshua T. Vogelstein8,9,
  10. Chris Jacobsen7,10,
  11. Konrad P. Körding11,* and
  12. Narayanan Kasthuri4,12,*
  1. 1Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332
  2. 2The Johns Hopkins University Applied Physics Laboratory, Laurel, MD, 20723
  3. 3Dept. of Computer Science, The Johns Hopkins University, Baltimore, MD, 21218
  4. 4Dept. of Neurobiology, University of Chicago, Chicago, IL, 60637
  5. 5Dept. of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL, 60611
  6. 6Sensory Motor Performance Program, Rehabilitation Institute of Chicago, Chicago, IL, 60611
  7. 7Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439
  8. 8Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, 21205
  9. 9Institute of Computational Medicine, The Johns Hopkins University, Baltimore, MD, 21218
  10. 10Department of Physics and Astronomy, Northwestern University, Chicago, IL, 60208
  11. 11Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA, 19104
  12. 12Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439
  1. 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{at}gatech.edu; or Narayanan Kasthuri. E-mail: bobbykasthuri{at}anl.gov.
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Author contributions

  1. 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.

  2. ↵* K.P.K. and N.K. contributed equally to this paper.

View Abstract

Disclosures

  • Authors report no conflict of interest.

  • 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.

Funding

  • HHS | National Institutes of Health (NIH)

    NIH U01MH109100
  • DOD | Defense Advanced Research Projects Agency (DARPA)

    N66001-15-C-4041
  • DOD | Defense Advanced Research Projects Agency (DARPA)

    N66001-14-1-4028

Other Version

  • previous version (September 25, 2017).
  • You are viewing the most recent version of this article.

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Sep 2017535096
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Total 201712981829647
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Feb 20186721555
Mar 20185320555
Apr 20187216366
May 201871222107
Jun 20184216681
Jul 20183214269
Aug 20184520687
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Apr 2019621743
May 2019620643
Jun 2019513742
Jul 2019924339
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Sep 2019736232
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Total 20191033035478
Jan 202067223
Feb 202036725
Mar 202035311
Apr 202088625
May 202017216
Jun 202058321
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Aug 202035511
Sep 2020710242
Oct 2020414925
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Total 2020571012262
Jan 20213696
Total 20213696
Total204983512190
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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, 4 (5) 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, 4 (5) 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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