Cited by 475Advanced Neuroimaging Techniques and ApplicationsAnatomy and Medical TechnologyMedical Image Segmentation Techniques

The DOI matches its Crossref record; 90 of the 91 references it cites were found in a registry or an index; none of the 60 sources its claims cite is checked for support yet.

Comprehensive cellular‐resolution atlas of the adult human brain

Open access

Ding, Song‐Lin, Royall, Joshua J., Sunkin, Susan M., Ng, Lydia, Facer, Benjamin A.C., Lesnar, Phil, Guillozet‐Bongaarts, Angie, McMurray, Bergen, Szafer, Aaron, Dolbeare, Tim A., Stevens, Allison, Tirrell, Lee, Benner, Thomas, Caldejon, Shiella, Dalley, Rachel A., Dee, Nick, Lau, Christopher, Nyhus, Julie, Reding, Melissa, Riley, Zackery L., Sandman, David, Shen, Elaine, van der Kouwe, Andre, Varjabedian, Ani, Write, Michelle, Zollei, Lilla, Dang, Chinh, Knowles, James A., Koch, Christof, Phillips, John W., Sestan, Nenad, Wohnoutka, Paul, Zielke, H. Ronald, Hohmann, John G., Jones, Allan R., Bernard, Amy, Hawrylycz, Michael J., Hof, Patrick R., Fischl, Bruce, Lein, Ed S.·2016·Journal of Comparative Neurology

DOI 10.1002/cne.24080PMC PMC5054943

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

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TL;DR

The paper presents a digital adult human brain atlas combining ex vivo MRI, DWI, and high-resolution histology from a complete adult female brain, with 1,356 cellular-resolution anatomical plates and 862 annotated structures. It is publicly accessible, interactive, and integrated with existing Allen Institute human brain gene expression atlases.

Key findings

The atlas includes MRI, DWI, and 1,356 large-format cellular-resolution (1 µm/pixel) Nissl and immunohistochemistry plates from the same adult female brain; 106 Nissl-stained sections were annotated for 862 structures using 11,398 polygons, including 117 white matter tracts.
Annotations cover modified Brodmann areas, sulci/gyri, subcortical nuclei, brainstem, and cerebellum, and identify novel or newly detailed structures/subdivisions such as MDam in the thalamus, BMm in the amygdala, the lateral olfactory area (LOA), area prostriata (APro), and the basal interstitial nucleus of the cerebellum (BIcb).
Correlated histology and MRI allowed feature extraction and transfer: the medial geniculate nucleus showed high signal intensity and the dorsal lateral geniculate nucleus low signal intensity, enabling identification in MRI from other Allen Human Brain Atlas cases; 76 coronal MRI slices at 2-mm intervals were annotated.
The resource is freely accessible online and linked to adult and developing human brain transcriptional atlases.

Methods

Single 34-year-old female donor with no history of neurological disease; brain was fixed, scanned ex vivo with 7 T structural MRI and 3 T DWI, bisected, slabbed, and sectioned coronally at 50 µm. Of 2,716 total sections, 679 were Nissl-stained (200-µm interval), 339 NFP-immunostained (400-µm interval), and 338 PV-immunostained (400-µm interval); 1,356 sections were digitized at 1 µm/pixel.
Anatomical delineation used 106 selected Nissl sections with sampling intervals of 0.4–3.4 mm, combined with adjacent NFP and PV sections; outlines were drawn on printouts, converted to digital polygons, and linked to a hierarchical whole-brain ontology.
MRI annotations were made on 76 coronal slices at 2-mm intervals; DWI tractography used the FACT algorithm with a 60° angular threshold, tracts longer than 20 mm, and 90% skip applied.

Limitations

Stated: the atlas is based on a single representative brain specimen, and the authors note that interindividual variability makes it unrealistic to map histological annotations from one specimen directly into a probabilistic reference space.
Stated: transposing Nissl-based delineations into full 3D annotations registered to MRI is challenging because of incomplete and nonuniform sampling of the annotated plates.
Stated: sectioning and mounting produced artifacts including large cracks and smaller tears in some sections; evident from the text, the resource is descriptive and single-donor, with no group-level statistical validation, and annotations are manual and could be reannotated by other researchers.

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Integrity signals

Registry

Crossref · 10.1002/cne.24080

Cites

90 of 90 references verified0 citation errors · 0 not checkable

Statistics

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Claims the paper makes

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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
Load-bearingStrength:plain· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: A single adult female brain without neurological disease is representative of the adult human brain for the purpose of a reference atlas.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The atlas is comprehensively annotated for 862 structures”
- Also stated in: § Digital atlas design and annotation · plain
  “In total, 862 brain structures were digitally annotated on the 106 whole‐hemisphere images using 11,398 polygons.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
Load-bearingStrength:plain· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- Rests on an assumption: A single adult female brain without neurological disease is representative of the adult human brain for the purpose of a reference atlas.
None of the sources cited for this claim have been checked yet.
In the paper
“Another example of modification of Brodmann's areas is the orbitofrontal cortex, where Brodmann's large area 11 was replaced with smaller areas 14, 11, and 13 according to a few modern anatomical studies in human (Hof et al., 1995a; Öngür et al., 2003) and our own investigation of Nissl preparations and PV‐ and NFP‐immunostained sections.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Creation of a unified structural brain ontology
What the sources say
- Not checked yetcites Hof et al., 1995a
- Not checked yetcites Öngür et al., 2003
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes

Show all 58 claims

Probably not a substantial claim. 33
It may state two separate claims as one. 34

None of the sources cited for this claim have been checked yet.
In the paper
“Finally, for the insular cortex that was not numbered by Brodmann in human (1909; see Simić and Hof, 2015), three major subdivisions were delineated and these included agranular, dysgranular, and granular insula (e.g., Bauernfeind et al., 2013; Morel et al., 2013), with the latter two further divided into rostral and caudal parts.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Creation of a unified structural brain ontology
What the sources say
- Not checked yetcites Bauernfeind et al., 2013
- Not checked yetcites Morel et al., 2013
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“We created a whole‐brain ontology spanning all adult structures (Table 3) and including a developmental axis for transient structures observed during the specification and cytoarchitectural maturation (Miller et al. 2014).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Creation of a unified structural brain ontology
What the sources say
- Not checked yetcites Miller et al. 2014
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: Anatomical delineations and annotations based on this one brain can be transferred to MRI data from other brains.
None of the sources cited for this claim have been checked yet.
In the paper
“Interpretation of these data relies heavily on anatomical reference atlases for localization of underlying anatomical partitions, which also provides a common framework for communicating within and across allied disciplines”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Mazziotta et al., 2001
- Not checked yetcites Toga et al., 2006
- Not checked yetcites Evans et al., 2012
Load-bearingStrength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
In the paper
“While neuroimaging data are typically registered to probabilistic reference frameworks (Das et al., 2016) to deal with interindividual variation”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Das et al., 2016
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Additional efforts have used ultra‐high‐resolution MRI of ex vivo brains to build intrinsically 3D models of cytoarchitectural boundaries, and quantify the predictive power of macroscopic features for localizing microscopically defined boundaries”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Augustinack et al., 2005
- Not checked yetcites Fischl et al., 2008
- Not checked yetcites Iglesias et al., 2015
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“The antibody against NFP (BioLegend, Cat.# SMI‐32, RRID: AB_2314904) is a mouse monoclonal IgG1 recognizing a double band at MW 200,000 and 180,000, which merge into a single neurofilament H line on 2D blots (Sternberger and Sternberger, 1983)”
§ Comprehensive cellular‐resolution atlas of the adult human brain > MATERIALS AND METHODS > Antibody characterization
What the sources say
- Not checked yetcites Sternberger and Sternberger, 1983
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“a 3‐dimensional (3D) model of an adult human brain based on whole‐brain serial sectioning, silver staining, and MRI (Amunts et al., 2013) was recently created”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Amunts et al., 2013
Strength:plain· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“There is therefore a strong need to bridge these levels of resolution to understand structure–function relationships in the human brain (Caspers et al., 2013a; Pascual et al., 2015).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Caspers et al., 2013a
- Not checked yetcites Pascual et al., 2015
Load-bearingStrength:boosted· not yet calibrated
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may be too vague to check against evidence.
None of the sources cited for this claim have been checked yet.
In the paper
“The most commonly used cytoarchitecture‐based human brain atlas is Brodmann's cortical map (Brodmann, 1909; Talairach and Tournoux, 1988; Simić and Hof, 2015)”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Brodmann, 1909
- Not checked yetcites Talairach and Tournoux, 1988
- Not checked yetcites Simić and Hof, 2015
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“and a probabilistic cytoarchitectural atlas (JuBrain; see Caspers et al., 2013a) is also being generated.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Caspers et al., 2013a
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“In human and monkey cerebral cortex, the antibody stains a subpopulation of large pyramidal neurons with the labeling largely restricted to dendritic processes and soma (Campbell and Morrison, 1989; Hof et al., 1995a, 1995b; Nimchinsky et al., 1997; Ding et al., 2003, 2009).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > MATERIALS AND METHODS > Antibody characterization
What the sources say
- Not checked yetcites Campbell and Morrison, 1989
- Not checked yetcites Hof et al., 1995a
- Not checked yetcites Ding et al., 2009
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The immunostaining of sections through human temporal cortex produced a pattern of NFP labeling that was identical to previous descriptions (Ding et al., 2009).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > MATERIALS AND METHODS > Antibody characterization
What the sources say
- Not checked yetcites Ding et al., 2009
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In this 7 T MRI dataset, like the “or” and “ar,” the “sr” is observed to stand out from surrounding white matter and thus deserves an independent term (i.e., somatosensory radiation) as do optic and auditory radiations.”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Whole‐brain histology‐based atlas with corresponding MRI and DWI
Load-bearingStrength:plain· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.
- Rests on an assumption: The somatosensory radiation is normally treated as part of the superior radiation in the literature and mainly originates from the ventroposterior lateral nucleus of the thalamus and targets the primary somatosensory cortex.
None of the sources cited for this claim have been checked yet.
In the paper
“Brain reference atlases are essential resources for neuroscience research, serving to identify and annotate the complex anatomical architecture of the brain and allow communication across laboratories and various research disciplines attempting to link structure to function (Fischl et al., 1999; Toga et al., 2006; Amunts et al., 2007; Evans et al., 2012).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Fischl et al., 1999
- Not checked yetcites Toga et al., 2006
- Not checked yetcites Amunts et al., 2007
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passes
Probably not a substantial claim. It may be too vague to check against evidence. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“It has been described in detail in macaque monkey (Morecraft et al., 2000; Ding et al., 2003) and is important for fast procession of peripheral vision (Yu et al., 2012).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Identification of novel brain subregions
What the sources say
- Not checked yetcites Morecraft et al., 2000
- Not checked yetcites Ding et al., 2003
- Not checked yetcites Yu et al., 2012
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passes
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“For instance, one brain may have area 35 located in the medial bank of a deep collateral sulcus (CoS), while another may have its area 35 in the lateral bank of a shallow CoS, or even the crown of the anterior fusiform gyrus (Ding and Van Hoesen, 2010).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Ding and Van Hoesen, 2010
Load-bearingStrength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
It may state two separate claims as one.

55 of 55

The paper relies on this without support.
A single adult female brain without neurological disease is representative of the adult human brain for the purpose of a reference atlas.
“The brain used for this reference atlas was from a 34‐year‐old female donor with no history of neurological diseases or remarkable brain abnormality”
The paper relies on this without support.
Anatomical delineations and annotations based on this one brain can be transferred to MRI data from other brains.
“Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains.”
The paper relies on this without support.
The homologs of MDam and BMm in other species have not been reported.
“The homologs of MDam and BMm in other species have not been reported.”
The paper relies on this without support.
The exact location and extent of area prostriata in the human brain has not been reported in detail so far.
“Although its existence in the human brain was briefly described, its exact location and extent has not been reported in detail so far.”
The paper relies on this without support.
The somatosensory radiation is normally treated as part of the superior radiation in the literature and mainly originates from the ventroposterior lateral nucleus of the thalamus and targets the primary somatosensory cortex.
“The “sr” is normally treated as part of the superior radiation in the literature and mainly originates from the ventroposterior lateral nucleus of the thalamus and targets the primary somatosensory cortex.”

5 of 5

Claims other papers make about this one

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Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

Anti-NFP antibody dilution differs between methods and Table 2
Minor
The methods give the SMI-32 dilution as 1:3,000, while Table 2 lists 1:5,000 for the same antibody.
Reported section dimensions cannot fit on the stated slides
Minor
A section described as approximately 3.2 × 4.3 metres cannot be mounted on a 3 × 5 inch slide. The dimension or its unit is inconsistent with the stated slide size.
Figure 2 cortical-map labels are reversed
Minor
The Figure 2 caption assigns modified Brodmann areas to I1 and the gyral map to I2, but the results text assigns them the other way around.
Figure 6 references swap the nerve-root and commissure panels
Minor
The results cite panel G for motor roots and panel F for the inferior-colliculus commissure. The Figure 6 caption identifies F as a nerve-root panel and G as the commissure panel.
Figure 17 repeats section 05_047 at levels 44 and 65
Minor
The same section identifier appears at two widely separated anterior-to-posterior levels. Level 65 also falls among entries identified as slab 06 rather than slab 05.

5 of 5

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Research works printed but not linked: 5

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Comparison of the connectivity of the posterior intralaminar thalamic nucleus and peripeduncular nucleus in rats and mice
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Structural brain preservation: a potential bridge to future medical technologies
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Establishing sample-preparation protocols for X-ray phase-contrast CT of rodent spinal cords: Aldehyde fixations and osmium impregnation
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LayNii: A software suite for layer-fMRIPreprint
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Ependymal cells surface of human third brain ventricle by scanning electron microscopy
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Afferent Projections to Area Prostriata of the Mouse
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Fetal development of the human amygdala
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Lamination, Borders, and Thalamic Projections of the Primary Visual Cortex in Human, Non-Human Primate, and Rodent Brains
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Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder
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The prefrontal cortex of the bottlenose dolphin (Tursiops truncatus Montagu, 1821): a tractography study and comparison with the human
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Diurnal variation of brain activity in the human suprachiasmatic nucleus
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Towards Differential Connectomics with NeuroVIISAS
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Sustaining wakefulness: Brainstem connectivity in human consciousnessPreprint
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Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments
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Reduced synaptic vesicle protein 2A in extracellular vesicles and brains of Alzheimer’s disease: associations with Aβ, tau, synaptic proteins and APOE ε4
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Multiscale imaging of the rat brain using an integrated diceCT and histology workflow
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Chemoarchitecture of area prostriata in adult and developing mice: Comparison with presubiculum and parasubiculum
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A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain
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Pre-Brodmann pioneers of cortical cytoarchitectonics II: Carl Hammarberg, Alfred Walter Campbell and Grafton Elliot Smith
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Cytoarchitectonic Maps of the Human Metathalamus in 3D Space
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Population-Averaged Atlas of the Macroscale Human Structural Connectome and Its Network TopologyPreprint
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Sub-millimeter fMRI reveals multiple topographical digit representations that form action maps in human motor cortexPreprint
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Mapping the human subcortical auditory system using histology, post mortem MRI and in vivo MRI at 7TPreprint
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Pitfalls in Recording Bold Signal Responses to Light in Small Hypothalamic Nuclei Using Ultra-High-Field 7 Tesla MRIPreprint
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The prosubiculum in the human hippocampus: A rostrocaudal, feature‐driven, and systematic approach
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Neuroanatomical evidence and a mouse calcitonin gene–related peptide model in line with human functional magnetic resonance imaging data support the involvement of peptidergic Edinger–Westphal nucleus in migraine
Al-Omari, A., Gaszner, B., Zelena, D., Gecse, K., Berta, G., Biró-Sütő, T., Szocsics, P., Maglóczky, Z., Gombás, P., Pintér, E., et al. (2024) · Pain · doi:10.1097/j.pain.0000000000003294 · Cited by 8
Effects of KCNQ potassium channel modulation on ventral tegmental area activity and connectivity in individuals with depression and anhedonia
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A biomechanical-based approach to scale blast-induced molecular changes in the brain
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Pitfalls in recording BOLD signal responses to light in small hypothalamic nuclei using Ultra-High-Field 7 Tesla MRI
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Sulci of the canine brain: a review of terminologyPreprint
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Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivityPreprint
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High-resolution atlasing and segmentation of the subcortex: Review and perspective on challenges and opportunities created by machine learning
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Intracranial electrophysiological biomarkers of compulsivity in obsessive–compulsive disorder
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Mapping human brain pathways: challenges and opportunities in the integration of scales
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High angular resolution susceptibility imaging and estimation of fiber orientation distribution functions in primate brain
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Blunted Ventral Striatal Reactivity to Social Reward Is Associated with More Severe Motivation and Pleasure Deficits in Psychosis
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Current and Future Challenges of Functional MRI and Diffusion Tractography in the Surgical Setting: From Eloquent Brain Mapping to Neural Plasticity
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Advances in Neuroanatomy through Brain Atlasing
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Homotopic Commissural Projections of Area Prostriata in Rat and Mouse: Comparison With Presubiculum and Parasubiculum
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Cellular and Molecular Probing of Intact Transparent Human OrgansPreprint
Zhao, S., Todorov, M. I., Cai, R., Steinke, H., Kemter, E., Wolf, E., Lipfert, J., Bechmann, I., & Ertürk, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/643908 · Cited by 7
Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference AtlasPreprint
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Spatial Single-cell Analysis Decodes Cortical Layer and Area SpecificationPreprint
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A cross-species spatial transcriptomic atlas of the human and non-human primate basal gangliaPreprint
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Human subcortical pathways automatically detect collision trajectory without attention and awareness
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DHARANI: A 3D Developing Human‐Brain Atlas Resource to Advance Neuroscience Internationally Integrated Multimodal Imaging and High‐Resolution Histology of the Second Trimester
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Wide field block face imaging using deep ultraviolet induced autofluorescence of the human brain
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Synaptic development of layer V pyramidal neurons in the prenatal human prefrontal neocortex: a Neurolucida-aided Golgi study
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Real-time spatial registration for 3D human atlas
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Unfolding the hippocampus: an intrinsic coordinate system for subfield segmentations and quantitative mappingPreprint
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Interaction of Hippocampal Ripples and Cortical Slow Waves Leads to Coordinated Large-Scale Sleep RhythmPreprint
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Evolution is in the details: Regulatory differences in modern human and NeanderthalPreprint
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Overlooked tertiary sulci serve as a meso-scale link between microstructural and functional properties of human lateral prefrontal cortexPreprint
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Whole Human-Brain Mapping of Single Cortical Neurons for Profiling Morphological Diversity and StereotypyPreprint
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A Contrast‐Agnostic Method for Ultra‐High Resolution Claustrum Segmentation
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Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans
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Post-Mortem Analysis of Neuropathological Changes in Human Tinnitus
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A novel subdivision of the bed nucleus of stria terminalis in monkey, rat, and mouse brains
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A brain flatmap data visualization tool for mouse, rat, and human
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Parvalbumin interneurons in human ventromedial prefrontal cortex: a comprehensive post-mortem study of myelination and perineuronal nets in neurotypical individuals and depressed suicides with and without a history of child abuse
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The Allen Brain Atlas
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Model-Based Refinement of Nonlinear Registrations in 3D Histology Reconstruction
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Genome-scale transcriptional regulatory network models of psychiatric and neurodegenerative disordersPreprint
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Quantitative modeling links in vivo microstructural and macrofunctional organization of human and macaque insular cortex, and predicts cognitive control abilitiesPreprint
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Human-specific enrichment of schizophrenia risk-genes in callosal neurons of the developing neocortexPreprint
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A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortexPreprint
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Spatially-resolved molecular sex differences at single cell resolution in the adult human ventromedial and arcuate hypothalamus
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Targeting Kinin B1R Attenuates Hypertension Through AT1R-Dependent Mechanisms
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A comprehensive and reliable protocol for manual segmentation of the human claustrum using high-resolution MRI
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Volume alterations of the hippocampus and amygdala in patients with schizophrenia and persistent auditory hallucinations
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Prior‐guided individualized thalamic parcellation based on local diffusion characteristics
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Beta Oscillations in the Sensory Thalamus During Severe Facial Neuropathic Pain Using Novel Sensing Deep Brain Stimulation
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Elevated tau in the piriform cortex in Alzheimer's but not Parkinson's disease using PET‐MR
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White Matter Tracts Visualized by Parvalbumin in Nonhuman Primates
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Interpreting Deep Neural Networks for Medical Imaging Using Concept Graphs
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Abstracting Deep Neural Networks into Concept Graphs for Concept Level Interpretability
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Specific pattern of melanin-concentrating hormone (MCH) neuron degeneration in Alzheimer’s disease and possible clinical implicationsPreprint
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The need for validation in layer-specific fMRIPreprint
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A general strategy for generating expert-guided, simplified views of ontologiesPreprint
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BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial TranscriptomicsPreprint
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Stereological analysis of cholinergic neurons within bilateral pedunculopontine nuclei in health and when affected by Parkinson's disease
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Morphological heterogeneity of neurons in the human central amygdaloid nucleus
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The involvement of the piriform cortex in non-lesional temporal lobe epilepsy: an uncommon component of the epileptogenic network
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eLemur: A cellular-resolution 3D atlas of the mouse lemur brain
Jeon, H., Kim, J., Kim, J., Choi, Y. K., Ho, C. L. A., Pifferi, F., Huber, D., Feng, L., & Kim, J. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2413687121 · Cited by 5

Authors: Ding, S., 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., Riley, Z. L., Sandman, D., Shen, E., van der Kouwe, A., Varjabedian, A., Write, M., Zollei, L., Dang, C., Knowles, J. A., Koch, C., Phillips, J. W., Sestan, N., Wohnoutka, P., Zielke, H. R., Hohmann, J. G., Jones, A. R., Bernard, A., Hawrylycz, M. J., Hof, P. R., Fischl, B., & Lein, E. S.
Affiliations: Allen Institute for Brain Science (US)
Harvard University (US)
Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown Massachusetts 02129
University of Southern California (US)
Allen Institute for Brain Science Seattle Washington 98109
Department of Neurobiology and Kavli Institute for Neuroscience Yale University School of Medicine New Haven Connecticut 06510
University of Maryland, Baltimore (US)
Icahn School of Medicine at Mount Sinai (US)
Corresponding author: Ding, Song‐Lin
Lein, Ed S.
ORCID: Ding, Song‐Lin
Sunkin, Susan M.
Ng, Lydia
Lesnar, Phil
Szafer, Aaron
Dolbeare, Tim A.
Stevens, Allison
Tirrell, Lee
Caldejon, Shiella
Dalley, Rachel A.
Dee, Nick
Nyhus, Julie
Reding, Melissa
Knowles, James A.
Phillips, John W.
Wohnoutka, Paul
Hohmann, John G.
Jones, Allan R.
Bernard, Amy
Hawrylycz, Michael J.
Hof, Patrick R.
Fischl, Bruce
Lein, Ed S.
Venue: Journal of Comparative Neurology
Publisher: Wiley
Published: 2016-09-15
Volume: 524
Issue: 16
Pages: 3127-3481
ISSN: 0021-9967 (ISSN-L)
1096-9861
DOI: 10.1002/cne.24080
PMC: PMC5054943
OpenAlex: W2504912000
Cited by: 447
References: 91
Citations by year: 2026: 39 · 2025: 59 · 2024: 52 · 2023: 55 · 2022: 46 · 2021: 49 · 2020: 50 · 2019: 42 · 2018: 35 · 2017: 18 · 2016: 2
FWCI: 28.05
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-nd
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
Locations: The Journal of Comparative Neurology (publishedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
Funders: National Institutes of Health (RC2 MH089921)
NIH Blueprint for Neuroscience Research (5U01‐MH093765)
National Institute on Aging (5R01AG008122 & R01AG016495)
Topics: Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
Physical Sciences › Engineering › Biomedical Engineering › Anatomy and Medical Technology
Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
Keywords: digital brain atlas, white matter tracts, cytoarchitecture, chemoarchitecture, Nissl staining, immunohistochemistry, diffusion-weighted imaging, MRI-histology correlation, Brodmann areas, female brain
MeSH terms: Adult, Anatomy, Artistic, Brain, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Parvalbumins, Neurofilament Proteins, Diffusion Magnetic Resonance Imaging

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Comprehensive cellular‐resolution atlas of the adult human brain

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