Comprehensive cellular-resolution atlas of the adult human brain

Song Lin Ding; Joshua J. Royall; Susan M. Sunkin; Lydia Ng; Benjamin A.C. Facer; Phil Lesnar; Angie Guillozet-Bongaarts; Bergen McMurray; Aaron Szafer; Tim A. Dolbeare; Allison Stevens; Lee Tirrell; Thomas Benner; Shiella Caldejon; Rachel A. Dalley; Nick Dee; Christopher Lau; Julie Nyhus; Melissa Reding; Zackery L. Riley; David Sandman; Elaine Shen; Andre van der Kouwe; Ani Varjabedian; Michelle Write; Lilla Zollei; Chinh Dang; James A. Knowles; Christof Koch; John W. Phillips; Nenad Sestan; Paul Wohnoutka; H. Ronald Zielke; John G. Hohmann; Allan R. Jones; Amy Bernard; Michael J. Hawrylycz; Patrick R. Hof; Bruce Fischl; Ed S. Lein

doi:10.1002/cne.24080

Comprehensive cellular-resolution atlas of the adult human brain

Song Lin Ding, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A.C. Facer, Phil Lesnar, Angie Guillozet-Bongaarts, Bergen McMurray, Aaron Szafer, Tim A. Dolbeare, Allison Stevens, Lee Tirrell, Thomas Benner, Shiella Caldejon, Rachel A. Dalley, Nick Dee, Christopher Lau, Julie Nyhus, Melissa Reding, Zackery L. RileyDavid Sandman, Elaine Shen, Andre van der Kouwe, Ani Varjabedian, Michelle Write, Lilla Zollei, Chinh Dang, James A. Knowles, Christof Koch, John W. Phillips, Nenad Sestan, Paul Wohnoutka, H. Ronald Zielke, John G. Hohmann, Allan R. Jones, Amy Bernard, Michael J. Hawrylycz, Patrick R. Hof, Bruce Fischl, Ed S. Lein

Research output: Contribution to journal › Article › peer-review

244 Scopus citations

Abstract

Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016.

Original language	English
Pages (from-to)	3127-3481
Number of pages	355
Journal	Journal of Comparative Neurology
Volume	524
Issue number	16
DOIs	https://doi.org/10.1002/cne.24080
State	Published - 1 Nov 2016

Keywords

AB_2314904
DWI
MRI
RRIDs: AB_10000343
SCR_014329
amygdala
brain atlas
brainstem
cerebellum
cerebral cortex
cytoarchitecture
hippocampal formation
hypothalamus
neurofilament protein
parvalbumin
thalamus

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10.1002/cne.24080

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Ding, S. L., Royall, J. J., Sunkin, S. M., Ng, L., Facer, B. A. C., Lesnar, P., Guillozet-Bongaarts, A., McMurray, B., Szafer, A., Dolbeare, T. A., Stevens, A., Tirrell, L., Benner, T., Caldejon, S., Dalley, R. A., Dee, N., Lau, C., Nyhus, J., Reding, M., ... Lein, E. S. (2016). Comprehensive cellular-resolution atlas of the adult human brain. Journal of Comparative Neurology, 524(16), 3127-3481. https://doi.org/10.1002/cne.24080

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title = "Comprehensive cellular-resolution atlas of the adult human brain",

abstract = "Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016.",

keywords = "AB_2314904, DWI, MRI, RRIDs: AB_10000343, SCR_014329, amygdala, brain atlas, brainstem, cerebellum, cerebral cortex, cytoarchitecture, hippocampal formation, hypothalamus, neurofilament protein, parvalbumin, thalamus",

author = "Ding, {Song Lin} and Royall, {Joshua J.} and Sunkin, {Susan M.} and Lydia Ng and Facer, {Benjamin A.C.} and Phil Lesnar and Angie Guillozet-Bongaarts and Bergen McMurray and Aaron Szafer and Dolbeare, {Tim A.} and Allison Stevens and Lee Tirrell and Thomas Benner and Shiella Caldejon and Dalley, {Rachel A.} and Nick Dee and Christopher Lau and Julie Nyhus and Melissa Reding and Riley, {Zackery L.} and David Sandman and Elaine Shen and {van der Kouwe}, Andre and Ani Varjabedian and Michelle Write and Lilla Zollei and Chinh Dang and Knowles, {James A.} and Christof Koch and Phillips, {John W.} and Nenad Sestan and Paul Wohnoutka and Zielke, {H. Ronald} and Hohmann, {John G.} and Jones, {Allan R.} and Amy Bernard and Hawrylycz, {Michael J.} and Hof, {Patrick R.} and Bruce Fischl and Lein, {Ed S.}",

note = "Publisher Copyright: Copyright {\textcopyright} 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.",

year = "2016",

month = nov,

day = "1",

doi = "10.1002/cne.24080",

language = "English",

volume = "524",

pages = "3127--3481",

journal = "Journal of Comparative Neurology",

issn = "0021-9967",

publisher = "Wiley-Liss Inc.",

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Ding, SL, Royall, JJ, Sunkin, SM, Ng, L, Facer, BAC, Lesnar, P, Guillozet-Bongaarts, A, McMurray, B, Szafer, A, Dolbeare, TA, Stevens, A, Tirrell, L, Benner, T, Caldejon, S, Dalley, RA, Dee, N, Lau, C, Nyhus, J, Reding, M, Riley, ZL, Sandman, D, Shen, E, van der Kouwe, A, Varjabedian, A, Write, M, Zollei, L, Dang, C, Knowles, JA, Koch, C, Phillips, JW, Sestan, N, Wohnoutka, P, Zielke, HR, Hohmann, JG, Jones, AR, Bernard, A, Hawrylycz, MJ, Hof, PR, Fischl, B & Lein, ES 2016, 'Comprehensive cellular-resolution atlas of the adult human brain', Journal of Comparative Neurology, vol. 524, no. 16, pp. 3127-3481. https://doi.org/10.1002/cne.24080

TY - JOUR

T1 - Comprehensive cellular-resolution atlas of the adult human brain

AU - Ding, Song Lin

AU - Royall, Joshua J.

AU - Sunkin, Susan M.

AU - Ng, Lydia

AU - Facer, Benjamin A.C.

AU - Lesnar, Phil

AU - Guillozet-Bongaarts, Angie

AU - McMurray, Bergen

AU - Szafer, Aaron

AU - Dolbeare, Tim A.

AU - Stevens, Allison

AU - Tirrell, Lee

AU - Benner, Thomas

AU - Caldejon, Shiella

AU - Dalley, Rachel A.

AU - Dee, Nick

AU - Lau, Christopher

AU - Nyhus, Julie

AU - Reding, Melissa

AU - Riley, Zackery L.

AU - Sandman, David

AU - Shen, Elaine

AU - van der Kouwe, Andre

AU - Varjabedian, Ani

AU - Write, Michelle

AU - Zollei, Lilla

AU - Dang, Chinh

AU - Knowles, James A.

AU - Koch, Christof

AU - Phillips, John W.

AU - Sestan, Nenad

AU - Wohnoutka, Paul

AU - Zielke, H. Ronald

AU - Hohmann, John G.

AU - Jones, Allan R.

AU - Bernard, Amy

AU - Hawrylycz, Michael J.

AU - Hof, Patrick R.

AU - Fischl, Bruce

AU - Lein, Ed S.

PY - 2016/11/1

Y1 - 2016/11/1

N2 - Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016.

AB - Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole-brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high-resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and 1,356 large-format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto- and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016.

KW - AB_2314904

KW - DWI

KW - MRI

KW - RRIDs: AB_10000343

KW - SCR_014329

KW - amygdala

KW - brain atlas

KW - brainstem

KW - cerebellum

KW - cerebral cortex

KW - cytoarchitecture

KW - hippocampal formation

KW - hypothalamus

KW - neurofilament protein

KW - parvalbumin

KW - thalamus

UR - http://www.scopus.com/inward/record.url?scp=84987906293&partnerID=8YFLogxK

U2 - 10.1002/cne.24080

DO - 10.1002/cne.24080

M3 - Article

C2 - 27418273

AN - SCOPUS:84987906293

SN - 0021-9967

VL - 524

SP - 3127

EP - 3481

JO - Journal of Comparative Neurology

JF - Journal of Comparative Neurology

IS - 16

ER -

Comprehensive cellular-resolution atlas of the adult human brain

Abstract

Keywords

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