Comprehensive cellular‐resolution atlas of the adult human brain

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. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

• Publication year

  2016

• Venue

  The Journal of comparative neurology

• Publication date

  2016-09-15

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1002/cne.24080PMID 27418273PMCID 5054943
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture

  2016influential reference
• A multi-modal parcellation of human cerebral cortex

  2016cited by this paper
• The MNI data-sharing and processing ecosystem

  2016cited by this paper
• Chapter 18 – High-Resolution Fiber and Fiber Tract Imaging Using Polarized Light Microscopy in the Human, Monkey, Rat, and Mouse Brain

  2016influential reference
• A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI

  2015cited by this paper
• Detailed segmentation of human hippocampal and subicular subfields using a combined approach

  2015cited by this paper
• Optical coherence tomography visualizes neurons in human entorhinal cortex

  2015influential reference
• Large-scale brain networks of the human left temporal pole: a functional connectivity MRI study.

  2015cited by this paper
• Organization and detailed parcellation of human hippocampal head and body regions based on a combined analysis of Cyto‐ and chemoarchitecture

  2015cited by this paper
• In search of the definitive Brodmann's map of cortical areas in human

  2015cited by this paper
• MRI parcellation of ex vivo medial temporal lobe

  2014cited by this paper
• Transcriptional Landscape of the Prenatal Human Brain

  2014cited by this paper
• Interoperable atlases of the human brain

  2014cited by this paper
• Waxholm Space atlas of the Sprague Dawley rat brain

  2014cited by this paper
• Blockface histology with optical coherence tomography: A comparison with Nissl staining

  2014cited by this paper
• Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

  2014cited by this paper
• Cross-validation of serial optical coherence scanning and diffusion tensor imaging: A study on neural fiber maps in human medulla oblongata

  2014cited by this paper
• Individual variability is not noise.

  2013cited by this paper
• A volumetric comparison of the insular cortex and its subregions in primates.

  2013cited by this paper
• The human insula: Architectonic organization and postmortem MRI registration.

  2013cited by this paper
• Cingulate area 32 homologies in mouse, rat, macaque and human: Cytoarchitecture and receptor architecture

  2013cited by this paper
• Predicting the location of human perirhinal cortex, Brodmann's area 35, from MRI

  2013cited by this paper
• Bridging Neuroanatomy, Neuroradiology and Neurology: Three-Dimensional Interactive Atlas of Neurological Disorders

  2013cited by this paper
• Comparative anatomy of the prosubiculum, subiculum, presubiculum, postsubiculum, and parasubiculum in human, monkey, and rodent

  2013cited by this paper
• BigBrain: An Ultrahigh-Resolution 3D Human Brain Model

  2013cited by this paper
• Microstructural grey matter parcellation and its relevance for connectome analyses

  2013influential reference
• An anatomically comprehensive atlas of the adult human brain transcriptome

  2012cited by this paper
• Diffusion tractography of post-mortem human brains: Optimization and comparison of spin echo and steady-state free precession techniques

  2012cited by this paper
• Chapter 25 – Cingulate Cortex

  2012cited by this paper
• Brain templates and atlases

  2012influential reference
• Organization of the Human Inferior Parietal Lobule Based on Receptor Architectonics

  2012influential reference
• Multi-voxel pattern analysis in human hippocampal subfields

  2012cited by this paper
• A specialized area in limbic cortex for fast analysis of peripheral vision.

  2012cited by this paper
• Organization of Brainstem Nuclei

  2012cited by this paper
• Chapter 37 – Visual System

  2012cited by this paper
• Entorhinal verrucae geometry is coincident and correlates with Alzheimer’s lesions: a combined neuropathology and high-resolution ex vivo MRI analysis

  2011cited by this paper
• The Human Cerebral Cortex: An MRI Atlas of the Sulci and Gyri in MNI Stereotaxic Space

  2011cited by this paper
• A dynamic 4D probabilistic atlas of the developing brain

  2011cited by this paper
• Stratum radiatum of CA2 is an additional target of the perforant path in humans and monkeys

  2010cited by this paper
• Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature

  2010cited by this paper
• Borders, extent, and topography of human perirhinal cortex as revealed using multiple modern neuroanatomical and pathological markers

  2010cited by this paper
• Direct Visualization of the Perforant Pathway in the Human Brain with Ex Vivo Diffusion Tensor Imaging

  2010cited by this paper
• Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping

  2010cited by this paper
• Centenary of Brodmann's map — conception and fate

  2010cited by this paper
• Receptor mapping: architecture of the human cerebral cortex

  2009cited by this paper
• Duvernoy's Atlas of the Human Brain Stem and Cerebellum

  2009cited by this paper
• Predicting the location of entorhinal cortex from MRI

  2009cited by this paper
• Overlapping functional anatomy for working memory and visual search

  2009cited by this paper
• Parcellation of human temporal polar cortex: A combined analysis of multiple cytoarchitectonic, chemoarchitectonic, and pathological markers

  2009influential reference
• Medical imaging: MRI rides the wave

  2009cited by this paper
• A probabilistic MR atlas of the human cerebellum

  2009cited by this paper
• Construction of a 3D probabilistic atlas of human cortical structures

  2008cited by this paper
• Stereotactic Atlas of the Human Thalamus and Basal Ganglia, A. Morel. Informa Healthcare, New York (2007), Price: US$ 229.95

  2008cited by this paper
• Probabilistic maps, morphometry, and variability of cytoarchitectonic areas in the human superior parietal cortex.

  2008cited by this paper
• Amygdala

  2008cited by this paper
• A combined MRI and histology atlas of the rhesus monkey brain in stereotaxic coordinates

  2007cited by this paper
• Cytoarchitecture of the cerebral cortex - More than localization

  2007cited by this paper
• Distribution of the dopamine innervation in the macaque and human thalamus

  2007cited by this paper
• Cortical Folding Patterns and Predicting Cytoarchitecture

  2007cited by this paper
• Volumes, spatial extents and a probabilistic atlas of the human basal ganglia and thalamus

  2007cited by this paper
• Genome-wide atlas of gene expression in the adult mouse brain

  2007cited by this paper
• Towards multimodal atlases of the human brain

  2006influential reference
• Detection of entorhinal layer II using 7Tesla [corrected] magnetic resonance imaging.

  2005cited by this paper
• Consequences of large interindividual variability for human brain atlases: converging macroscopical imaging and microscopical neuroanatomy

  2005cited by this paper
• Detection of entorhinal layer II using Tesla magnetic resonance imaging

  2005cited by this paper
• Automatically parcellating the human cerebral cortex.

  2004cited by this paper
• CHAPTER 22 – Amygdala

  2004cited by this paper
• Topography, cytoarchitecture, and cellular phenotypes of cortical areas that form the cingulo‐parahippocampal isthmus and adjoining retrocalcarine areas in the monkey

  2003cited by this paper
• Three‐dimensional maximum probability atlas of the human brain, with particular reference to the temporal lobe

  2003cited by this paper
• Architectonic subdivision of the human orbital and medial prefrontal cortex

  2003cited by this paper
• Cytoarchitecture of the human cerebral cortex: MR microscopy of excised specimens at 9.4 Tesla.

  2002influential reference
• A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM).

  2001cited by this paper
• Cytology of human caudomedial cingulate, retrosplenial, and caudal parahippocampal cortices

  2001cited by this paper
• Mapping visual cortex in monkeys and humans using surface-based atlases.

  2001cited by this paper
• A global optimisation method for robust affine registration of brain images

  2001cited by this paper
• Localization of area prostriata and its projection to the cingulate motor cortex in the rhesus monkey.

  2000cited by this paper
• Three‐dimensional tracking of axonal projections in the brain by magnetic resonance imaging

  1999cited by this paper
• Cellular distribution of the calcium-binding proteins parvalbumin, calbindin, and calretinin in the neocortex of mammals: phylogenetic and developmental patterns.

  1999cited by this paper
• The Human Brain

  1999cited by this paper
• High‐resolution intersubject averaging and a coordinate system for the cortical surface

  1999cited by this paper
• Neurofilament and calcium‐binding proteins in the human cingulate cortex

  1997cited by this paper
• Theory and application of array coils in MR spectroscopy

  1997cited by this paper
• Human orbitofrontal cortex: Cytoarchitecture and quantitative immunohistochemical parcellation

  1995influential reference
• Neurochemical phenotype of corticocortical connections in the macaque monkey: Quantitative analysis of a subset of neurofilament protein‐immunoreactive projection neurons in frontal, parietal, temporal, and cingulate cortices

  1995influential reference
• Human cingulate cortex: Surface features, flat maps, and cytoarchitecture

  1995cited by this paper
• Human Brain Anatomy in Computerized Images

  1995cited by this paper
• The NMR phased array

  1990cited by this paper
• Co-Planar Stereotaxic Atlas of the Human Brain—3-Dimensional Proportional System: An Approach to Cerebral Imaging, J. Talairach, P. Tournoux. Georg Thieme Verlag, New York (1988), 122 pp., 130 figs. DM 268

  1990cited by this paper
• Monoclonal antibody to neurofilament protein (SMI‐32) labels a subpopulation of pyramidal neurons in the human and monkey neocortex

  1989cited by this paper
• Monoclonal antibodies directed against the calcium binding protein parvalbumin.

  1988cited by this paper
• Monoclonal antibodies distinguish phosphorylated and nonphosphorylated forms of neurofilaments in situ.

  1983cited by this paper
• Book Review: Atlas of the Human Brain

  1971cited by this paper
• ON THE THALAMUS *

  1905cited by this paper
• Die Cytoarchitektonik der Hirnrinde des erwachsenen Menschen.

  year unknowninfluential reference

• Multi-modal brain data exploration software for imaging transcriptomics: A comparative evaluation and future directions

  2026cites this paper
• A Tiered Approach to Human Synapse Proteomics: Optimized LC-MS/MS Analysis of Whole-Tissue and Synaptosome Preparations from Frozen Post-Mortem Brain Samples

  2026cites this paper
• Histology-guided spatial lipidomics and proteomics of the trisynaptic circuit in the human hippocampus.

  2026cites this paper
• Investigating central sensitization in women with primary dysmenorrhea: A narrative review

  2026cites this paper
• CytoCLIP: Learning Cytoarchitectural Characteristics in Developing Human Brain Using Contrastive Language Image Pre-Training

  2026cites this paper
• Fixel-based analysis reveals detailed white matter changes in semantic dementia

  2026cites this paper
• Autoregressive deep learning for real-time simulation of soft tissue dynamics during virtual neurosurgery

  2026cites this paper
• Convergent molecular pathways to inherited Parkinson's disease.

  2026cites this paper
• Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

  2026cites this paper
• Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling

  2026cites this paper
• Spatially-resolved molecular sex differences at single cell resolution in the adult human ventromedial and arcuate hypothalamus

  2026cites this paper
• A precise atlas of the human subcortex

  2026cites this paper
• Stereotactic rodent-to-human approximation of the mesencephalic cuneiform nucleus to guide deep brain stimulation.

  2026cites this paper
• Spatial multiomics dissects the SARS-CoV-2-induced disruption of cell adhesion and immune dynamics in the human hippocampus.

  2026cites this paper
• Cortical white matter: no longer a silent partner

  2026cites this paper
• Comparing Gallyas and AT8 staining for quantification of tau pathology in subregions of the human hippocampus.

  2026cites this paper
• Whole-Brain Cell-Cell Interaction Axes Explaining Tissue Vulnerability Across the Neurodegenerative Spectrum

  2026influential citation
• Stereological analysis of cholinergic neurons within bilateral pedunculopontine nuclei in health and when affected by Parkinson's disease

  2025cites this paper
• Cross-species dissection of the modular role of the ventral tegmental area in depressive disorders.

  2025cites this paper
• Preoperative Cholinergic Signatures Drive Segregated Brain Architecture in Postoperative Delirium

  2025cites this paper
• Comparison of thalamic atlases and segmentation techniques in defining motor and sensory nuclei for deep brain stimulation targeting in essential tremor

  2025cites this paper
• Limits of Vibrating Microtomy

  2025cites this paper
• Microglial glycolytic reprogramming in alzheimer’s disease: association with impaired phagocytic function and altered vascular proximity

  2025cites this paper
• Distribution of Serotonergic Transporter Innervation in the Nucleus Accumbens and Ventral Pallidum Is Highly Conserved Among Primates

  2025cites this paper
• The histological development of the fetal human inferior colliculus during the second trimester

  2025cites this paper
• A Combined Neuroanatomy, Ex Vivo Imaging, and Immunohistochemistry Defined MRI Mask for the Human Paraventricular Nucleus of the Thalamus

  2025cites this paper
• India Gets a Seat at the Table of Human Brain Cartography

  2025cites this paper
• Revealing layer-specific cortical activity in human M1 using high-resolution line-scanning fMRI

  2025cites this paper
• DHARANI: A 3D Developing Human‐Brain Atlas Resource to Advance Neuroscience Internationally Integrated Multimodal Imaging and High‐Resolution Histology of the Second Trimester

  2025cites this paper
• Conservation of glial density and cell-type ratios within a brain region across mammals

  2025cites this paper
• Alpha-synuclein deposition patterns in Alzheimer’s disease: association with cortical amyloid beta and variable tau load

  2025cites this paper
• Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans

  2025cites this paper
• Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity

  2025cites this paper
• Thalamus and consciousness: a systematic review on thalamic nuclei associated with consciousness

  2025cites this paper
• Magnetic Resonance Imaging and Anatomical Correlation of Human Temporal Lobe Landmarks in 3D Euclidean Space: A Study of Control and Epilepsy Disease Subjects

  2025cites this paper
• BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics

  2025cites this paper
• Accurate spatial localization of Allen Human Brain Atlas gene expression data for human neuroimaging

  2025cites this paper
• Yale Brain Atlas to interactively explore multimodal structural and functional neuroimaging data

  2025cites this paper
• Localization and connections of the tail of caudate and caudal putamen in mouse brain

  2025cites this paper
• Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration.

  2025cites this paper
• Reduced synaptic vesicle protein 2A in extracellular vesicles and brains of Alzheimer’s disease: associations with Aβ, tau, synaptic proteins and APOE ε4

  2025cites this paper
• The expression of repulsive guidance molecule a in the rat brain and the diffusion tensor imaging evaluation for crossed cerebellar diaschisis

  2025cites this paper
• Intracranial electrophysiological biomarkers of compulsivity in obsessive–compulsive disorder

  2025cites this paper
• Visualizing cortical laminar architecture in the living human brain using next-generation ultra-high-gradient diffusion MRI

  2025cites this paper
• Translating the Transcriptome: A Connectomics Approach for Gene-Network Mapping and Clinical Application

  2025cites this paper
• A unified 3D reconstruction of microscopy and MRI in a brain showing Alzheimer's disease‐related neuropathology

  2025cites this paper
• Medframealign: 3D Histological Reconstructions Using Video Frame Interpolation Techniques

  2025cites this paper
• Fixel-Based Analysis Reveals Detailed White Matter Changes in Semantic Dementia

  2025cites this paper
• Brain-wide connections of the parvicellular subdivision of the basolateral and basomedial amygdaloid nuclei in the rats

  2025cites this paper
• Psychedelic studies in nonhuman primates: Past and future

  2025cites this paper
• A combined neuroanatomy, ex vivo imaging and immunohistochemistry defined MRI mask for the human paraventricular nucleus of the thalamus

  2025cites this paper
• Blunted Ventral Striatal Reactivity to Social Reward Is Associated with More Severe Motivation and Pleasure Deficits in Psychosis.

  2025cites this paper
• Translating Brain Anatomy and Disease from Mouse to Human in Latent Gene Expression Space

  2025cites this paper
• Basolateral amygdala volume in affective disorders using 7T MRI in vivo

  2025cites this paper
• From fibers to cells: Fourier-based registration enables virtual Cresyl violet staining from 3D polarized light imaging

  2025cites this paper
• Comparative lipidomic alterations in the anterior cingulate cortex in schizophrenia and major depression.

  2025cites this paper
• A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

  2025cites this paper
• UC Irvine’s Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project

  2025cites this paper
• Targeting Kinin B1R Attenuates Hypertension Through AT1R-Dependent Mechanisms

  2025cites this paper
• Automated Segmentation of the Pituitary and Pineal Glands

  2025cites this paper
• Effects of KCNQ potassium channel modulation on ventral tegmental area activity and connectivity in individuals with depression and anhedonia

  2025cites this paper
• Integration of polygenic risk with single cell methylation profiles for depression

  2025influential citation
• Distinct Longitudinal Clinical‐Neuroanatomical Trajectories in Parkinson's Disease Clinical Subtypes: Insight toward Precision Medicine

  2025cites this paper
• Topographic Variation in Human Neurotransmitter Receptor Densities Explains Differences in Intracranial EEG Spectra

  2025cites this paper
• A Shared Threat-Anticipation Circuit Is Dynamically Engaged at Different Moments by Certain and Uncertain Threat

  2025cites this paper
• The nonsteroidal anti-inflammatory drug meclofenamate mitigates kainic acid–induced seizures via TRPM4 inhibition

  2025cites this paper
• Integrating multimodal data to understand cortical circuit architecture and function

  2025cites this paper
• A probabilistic histological atlas of the human brain for MRI segmentation

  2025cites this paper
• A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation

  2024cites this paper
• Molecular signatures of cortical expansion in the human fetal brain

  2024cites this paper
• BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

  2024cites this paper
• Integrated multimodal cell atlas of Alzheimer’s disease

  2024cites this paper
• Fetal development of the human amygdala

  2024cites this paper
• A role for the cerebellum in motor-triggered alleviation of anxiety.

  2024cites this paper
• MiR-128-3p – a gray eminence of the human central nervous system

  2024cites this paper
• Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories

  2024cites this paper
• Topographic variation in neurotransmitter receptor densities explains differences in intracranial EEG spectra

  2024cites this paper
• Integrated platform for multi-scale molecular imaging and phenotyping of the human brain

  2024cites this paper
• A general strategy for generating expert-guided, simplified views of ontologies

  2024cites this paper
• The role of the motor thalamus in deep brain stimulation for essential tremor

  2024cites this paper
• Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity

  2024cites this paper
• Prior‐guided individualized thalamic parcellation based on local diffusion characteristics

  2024influential citation
• A Contrast‐Agnostic Method for Ultra‐High Resolution Claustrum Segmentation

  2024cites this paper
• On the cusp of x-ray tomographic mapping of the human brain and its 1011 cells

  2024cites this paper
• Elevated tau in the piriform cortex in Alzheimer's but not Parkinson's disease using PET‐MR

  2024cites this paper
• A human brain network linked to restoration of consciousness after deep brain stimulation

  2024cites this paper
• Alterations of subcortical structure volume in pediatric bipolar disorder patients with manic or depressive first-episode

  2024cites this paper
• Molecular signatures of cortical expansion in the human foetal brain

  2024cites this paper
• Intracranial Voltage Profiles from Untangled Human Deep Sources Reveal Multisource Composition and Source Allocation Bias

  2024cites this paper
• st-DenseViT: A Weakly Supervised Spatiotemporal Vision Transformer for Dense Prediction of Dynamic Brain Networks

  2024cites this paper
• Structural brain preservation: a potential bridge to future medical technologies

  2024cites this paper
• A tomography slice through the entire human brain with less than three micrometer voxels

  2024cites this paper
• Segmentation of supragranular and infragranular layers in ultra-high-resolution 7T ex vivo MRI of the human cerebral cortex.

  2024cites this paper
• A shared threat-anticipation circuit is dynamically engaged at different moments by certain and uncertain threat

  2024cites this paper
• Oxytocin and vasopressin 1a receptor alterations in the superior temporal sulcus and hypothalamus in schizophrenia

  2024cites this paper
• Identification of Intrinsic Features for Cortical Separability of Human and Mouse Neurons

  2024cites this paper
• Quantitative susceptibility mapping in the brain reflects spatial expression of genes involved in iron homeostasis and myelination

  2024cites this paper
• Blunted ventral striatal reactivity to social reward is associated with more severe motivation and pleasure deficits in psychosis

  2024influential citation
• Neuromodulation strategies in developmental and epileptic encephalopathies.

  2024cites this paper
• eLemur: A cellular-resolution 3D atlas of the mouse lemur brain

  2024cites this paper