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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.

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

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AbstractFullPdf
Sep 20173307
Oct 20174981048318
Nov 2017164300144
Dec 201710148189
Total 20177961829558
Jan 20188218266
Feb 20186721555
Mar 20185320555
Apr 20187216366
May 201871222107
Jun 20184216681
Jul 20183214269
Aug 20184520687
Sep 20182414151
Oct 20183727957
Nov 20184229261
Dec 20182119342
Total 20185882406797
Jan 20191823265
Feb 20191522539
Mar 2019729136
Apr 2019621743
May 2019620643
Jun 2019513742
Jul 2019924339
Aug 2019937145
Oct 2019736539
Nov 2019923029
Dec 2019515626
Total 2019962673446
Jan 202067223
Feb 202036725
Mar 202035311
May 202017216
Jun 202058321
Jul 202055719
Aug 202035310
Sep 2020710242
Oct 2020414925
Nov 202047315
Dec 2020814329
Total 202049924236
Jan 2021312012
Feb 2021812415
Mar 2021413231
Apr 2021313421
May 2021710917
Jun 2021311123
Jul 202139128
Aug 202157829
Sep 202138815
Oct 2021211448
Nov 202108931
Dec 2021310033
Total 2021441290303
Jan 202209725
Feb 202235912
Mar 2022218329
Apr 2022010318
May 202228323
Jun 202217810
Jul 202216511
Aug 202245319
Sep 202216022
Oct 202206011
Nov 2022210321
Dec 202238116
Total 2022191025217
Jan 202307421
Feb 202325812
Mar 20232467
Total 2023417840
Total1596103252597
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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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