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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Written from the paper’s full text.

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

0 of 60 cited sources checked · 0 supported · 0 flagged

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
In the paper
“For instance, Brodmann's areas 22 and 21 (roughly corresponding to von Economo's areas TA and TEd) were subdivided into rostral, intermediate, and caudal parts based on different staining intensity in PV‐stained sections (Ding et al., 2009).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Creation of a unified structural brain ontology
What the sources say
- Not checked yetcites Ding et al., 2009
Strength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“Our mapping indicates that APro is much larger in human (Fig. 12) than in macaque monkey (Ding et al., 2003).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Identification of novel brain subregions
What the sources say
- Not checked yetcites Ding et al., 2003
Strength:hedged· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
- Rests on an assumption: The exact location and extent of area prostriata in the human brain has not been reported in detail so far.
In the paper
“Combining these features with basic spatial topography, the MG and DLG in the MRI scans from other brains from the Allen Human Brain Atlas (Hawrylycz et al., 2012) are clearly discerned (Fig. 14C,D).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Identifying anatomical landmarks in MRI data
What the sources say
- Not checked yetcites Hawrylycz et al., 2012
Load-bearingStrength:boosted· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“In many cases this parcellation agrees with those generated using other techniques such as receptor autoradiography and Nissl‐based gray‐level indices (Zilles and Amunts, 2009; Amunts et al., 2010; Vogt et al., 2013).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Zilles and Amunts, 2009
- Not checked yetcites Amunts et al., 2010 source
- Not checked yetcites Vogt et al., 2013
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“while the linkage to the Allen Human Brain Atlas (Hawrylycz et al., 2012) allowed corroboration of these structures with other gene expression data”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Identification of novel brain subregions
What the sources say
- Not checked yetcites Hawrylycz et al., 2012
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“A freely accessible online atlas browser was created to allow easy visualization and navigation, and the resource is integrated with other human brain cellular resolution gene expression and transcriptomic atlases (Hawrylycz et al., 2012; Miller et al., 2014).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Hawrylycz et al., 2012
- Not checked yetcites Miller et al., 2014
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“It also provides enhanced interlinking capabilities among a broad range of datasets including adult (Hawrylycz et al., 2012) and developing (Miller et al., 2014) human brain transcriptional atlases included in the Allen Brain Atlas (www.brain-map.org).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > RESULTS > Creation of a unified structural brain ontology
What the sources say
- Not checked yetcites Hawrylycz et al., 2012
- Not checked yetcites Miller et al., 2014
Load-bearingStrength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“they lack the cytoarchitectural resolution of single‐brain histological reference atlases (Evans et al., 2012; Caspers et al., 2013a)”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Evans et al., 2012
- Not checked yetcites Caspers et al., 2013a
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
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
“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.
In the paper
“Currently available large‐scale histological reference atlases of the human brain vary substantially in their degree of brain coverage, information content, and structural annotation (Table 1)”
§ Comprehensive cellular‐resolution atlas of the adult human brain > Abstract
What the sources say
- Not checked yetcites Table 1
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“This antibody specifically stained the 1999Ca‐binding “spot” of PV (MW 12,000) from rat cerebellum on 2D immunoblot assays (Celio et al., 1988)”
§ Comprehensive cellular‐resolution atlas of the adult human brain > MATERIALS AND METHODS > Antibody characterization
What the sources say
- Not checked yetcites Celio et al., 1988
Strength:plain· not yet calibratedCausal:direct· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“This antibody labels subsets of nonpyramidal neurons in cerebral cortex of many species including human (Hof et al., 1999; Nimchinsky et al., 1997; Ding and Van Hoesen, 2010, 2015).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > MATERIALS AND METHODS > Antibody characterization
What the sources say
- Not checked yetcites Hof et al., 1999
- Not checked yetcites Nimchinsky et al., 1997
- Not checked yetcites Ding and Van Hoesen, 2010
Strength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passes
In the paper
“and the relationship between cortical geometry and architectonic identity is variable across the cortex (Fischl et al., 2008).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Fischl et al., 2008
Load-bearingStrength:plain· not yet calibratedCausal:correlational· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“It is not currently possible to analyze large numbers of whole brains histologically and thus build a probabilistic histological atlas, although strong efforts are under way to move in the direction of generating probabilistic histological reference atlases using standard histological (JuBrain; Caspers et al., 2013a) as well as novel imaging techniques (Magnain et al., 2014, 2015; Wang et al., 201”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Caspers et al., 2013a
- Not checked yetcites Magnain et al., 2014, 2015
- Not checked yetcites Wang et al., 2014
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
In the paper
“All currently available human brain reference atlases lack some of these features (see Table 1), mainly due to the large size and structural complexity of the human brain and the resource‐intensive and technology‐limiting nature of the endeavor (Amunts et al., 2013).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Amunts et al., 2013
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“Furthermore, human brains exhibit a remarkable amount of interindividual variability, particularly in the gyri and sulci of the cerebral cortex (Mazziotta et al., 2001; Uylings et al., 2005; Toga et al., 2006; Amunts et al., 2007; Ding and Van Hoesen, 2010; Zilles and Amunts, 2010, 2013).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Mazziotta et al., 2001
- Not checked yetcites Uylings et al., 2005
- Not checked yetcites Toga et al., 2006
Load-bearingStrength:plain· not yet calibrated
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
None of the sources cited for this claim have been checked yet.
In the paper
“As we demonstrate, this dataset may thus allow feature extraction that can be applied to other brains to identify fine anatomical structures not otherwise identifiable, especially when higher resolution imaging techniques such as 9.4‐Tesla MRI, optical coherence tomography, and polarized light microscopy become available (Fatterpekar et al., 2002; Magnain et al., 2015; Zilles et al., 2016).”
§ Comprehensive cellular‐resolution atlas of the adult human brain > DISCUSSION
What the sources say
- Not checked yetcites Fatterpekar et al., 2002
- Not checked yetcites Magnain et al., 2015
- Not checked yetcites Zilles et al., 2016
Load-bearingStrength:hedged· not yet calibratedCausal:conditional· not yet calibratedSingle case
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes

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.”

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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.

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A global optimisation method for robust affine registration of brain images
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Genome-wide atlas of gene expression in the adult mouse brain
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., et al. (2007) · Nature · doi:10.1038/nature05453 · Cited by 5,572
Self-citation
A multi-modal parcellation of human cerebral cortex
Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell, J., Yacoub, E., Ugurbil, K., Andersson, J., Beckmann, C. F., Jenkinson, M., et al. (2016) · Nature · doi:10.1038/nature18933 · Cited by 5,111
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An anatomically comprehensive atlas of the adult human brain transcriptome
Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., van de Lagemaat, L. N., Smith, K. A., Ebbert, A., Riley, Z. L., et al. (2012) · Nature · doi:10.1038/nature11405 · Cited by 3,083
Self-citation
The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture
Fan, L., Li, H., Zhuo, J., Zhang, Y., Wang, J., Chen, L., Yang, Z., Chu, C., Xie, S., Laird, A. R., et al. (2016) · Cerebral Cortex · doi:10.1093/cercor/bhw157 · Cited by 3,083
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Self-citation
A probabilistic atlas and reference system for the human brain: International Consortium for Brain Mapping (ICBM)
Mazziotta, J. C., Toga, A. W., Evans, A. C., Fox, P. T., Lancaster, J. L., Zilles, K., Woods, R. P., Paus, T., Simpson, G. V., Pike, G. B., et al. (2001) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2001.0915 · Cited by 2,417

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1 of the 91 references couldn’t be matched to a known paper.

Research works printed but not linked: 5

Brodmann K, 1909, Localisation in the cerebral cortex
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Mai JK, 2008, Atlas of the human brain
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Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI
Schaefer, A., Kong, R., Gordon, E. M., Laumann, T. O., Zuo, X.-N., Holmes, A. J., Eickhoff, S. B., & Yeo, B. T. T. (2018) · Cerebral Cortex · doi:10.1093/cercor/bhx179 · Cited by 3,657
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Self-citation
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
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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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