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 journalArticlepeer-review

213 Scopus citations


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 languageEnglish
Pages (from-to)3127-3481
Number of pages355
JournalJournal of Comparative Neurology
Issue number16
StatePublished - 1 Nov 2016


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


Dive into the research topics of 'Comprehensive cellular-resolution atlas of the adult human brain'. Together they form a unique fingerprint.

Cite this