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A mesoscale connectome of the mouse brain
Open accessAbstract
Comprehensive knowledge of the brain’s wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease.
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TL;DR
The paper presents the Allen Mouse Brain Connectivity Atlas, a brain-wide cellular-level mesoscale connectome of the adult mouse generated with EGFP-expressing AAV tracing and serial two-photon tomography. It reports a quantitative inter-areal connectivity matrix and analyses of network properties, including lognormal connection strengths, bilateral projections, and cortico-thalamic parallel pathways.
Key findings
- Phase I includes 469 image sets covering 295 non-overlapping anatomical regions, with only 18 intended structures completely missed. Connectivity strengths span a greater than 10^5-fold range; ipsilateral projections are generally stronger than contralateral ones, with total normalized projection volumes at a 4.3:1 ratio. Strong connections are sparse: 63% ipsilateral and 51% contralateral targets exceed the minimal true-positive level of 10^-4, but only 21% ipsilateral and 9% contralateral targets exceed 10^-2.
- A computational model inferred mutual connections among 213 regions. Sparsity upper bounds were 36% for the entire brain and 52% for cortico-cortical connections; lower bounds were 13% for the entire brain and 32% for cortico-cortical connections. Connection strengths negatively correlated with distance and were best fit by a lognormal distribution by AIC, although log-transformed strengths failed Shapiro-Wilk normality (ipsilateral P = 0.039; contralateral P = 0.023), with a two-component Gaussian mixture providing the best fit.
- Network analyses found a mean clustering coefficient of 0.42 versus 0.12 expected by a random network with identical sparseness; random graphs matched for node degree distribution dropped to 0.16. Neither a small-world nor a scale-free model simultaneously fit both clustering and degree distributions. Across 12 duplicate injection sets, average correlation was 0.90.
- In the cortico-thalamic analysis, 80 isocortical injections clustered into 21 groups, and the wiring diagram divided the cortico-thalamic system into six functional pathways: visual, somatosensory, auditory, motor, limbic, and prefrontal, with cross-talk mediated by associational cortical areas and integrative thalamic nuclei.
Methods
- C57BL/6J male mice at P56 received unilateral stereotaxic iontophoretic injections of AAV serotype 1 expressing EGFP under the human synapsin I promoter. Phase I regional projection mapping used wild-type mice; Phase II Cre-dependent mapping is described but not reported here.
- Brains were imaged with serial two-photon tomography at 0.35 μm x–y resolution, 100-μm z-sampling, 140 coronal sections, about 18.5 h per brain, and ~750 GB per brain. Image stacks were registered to a 3D Allen Reference Atlas via an iterative average template from 1,231 brains, segmented, and voxelized into 100 × 100 × 100 μm^3 voxels.
- Projection strength was defined as total segmented target volume normalized by injection site volume. The raw connectivity matrix used 469 Phase I experiments across 295 structures; a computational model with regional homogeneity and projection additivity inferred inter-region connections among 213 regions, followed by graph-theoretic, clustering, and virtual tractography analyses.
Limitations
- Stated limitations: Phase I lacks extensive redundancy; the AAV tracer may not be completely unbiased in labelling all neuronal types; the matrix contains false positives from tissue/imaging artefacts and injection tract contamination; cytoplasmic EGFP does not distinguish passing fibres from terminal zones; projection volume may underestimate dense projections; alignment between the average template brain and the Nissl-based Reference Atlas is imperfect; postsynaptic neuron identities are unknown; microscale synaptic details and gap junctions are missing; and the map is static structural connectivity, not functional connectivity.
- Evident from the text: only the completed Phase I study is reported, so cell-type-specific Cre-driver connectivity mapping is not included in this dataset; the 100-μm z-sampling prevents real single-axon tractography, requiring virtual tractography instead.
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96 Own result · 27 Not checked yet · 25 Own interpretation · 18 Own method · 15 No basis given
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“Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways.”
§ A mesoscale connectome of the mouse brain > Abstract
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“Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse.”
- Also stated in: § Abstract · plain
“Here we present a mesoscale connectome of the adult mouse brain, The Allen Mouse Brain Connectivity Atlas.”
§ A mesoscale connectome of the mouse brain > Abstract
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In the paper
“Whereas 63% ipsilateral and 51% contralateral targets have projection strength values above the minimal true positive level of 10−4 (which has a potential false positive rate of 27%, Extended Data Fig. 7), only 21% ipsilateral and 9% contralateral targets have projection strength values above the intermediate level of 10−2.”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
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In the paper
“Each pair was highly correlated across a range of projection strengths.”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
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“Connection strengths spanned ~105-fold range, and negatively correlated with the distance between connected regions (Supplementary Notes and Supplementary Table 4).”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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“Differences between any two points were on average only a half order of magnitude (within one standard deviation).”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
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In the paper
“For cortico-cortical connections, both intra-and inter-hemispheric distributions are well fit by lognormals (ipsilateral: P = 0.23; contralateral: P = 0.21) individually (Fig. 4b), but they are different enough that when combined the distribution is no longer lognormal (P = 0.0019).”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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In the paper
“The informatics-derived assignment of injection site structures had > 75% voxel-level concordance with manual expert annotation for almost all injection sites (Extended Data Fig. 2c).”
§ A mesoscale connectome of the mouse brain > Creating the Allen Mouse Brain Connectivity Atlas
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“Based on the Akaike information criterion (AIC), among hypothesized connection strength distributions (lognormal, normal, exponential, inverse Gaussian) the brain-wide data are best fit by a lognormal distribution (Fig. 4b, red lines).”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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“However, the log-transformed connection strengths failed to pass the Shapiro-Wilk test for normality (ipsilateral: P = 0.039; contralateral: P = 0.023), and among Gaussian mixture models, a two-component one provided the best fit (Fig. 4b, green lines).”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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In the paper
“Second, there are prevalent bilateral projections to corresponding ipsilateral and contralateral target sites, with ipsilateral projections generally stronger than contralateral ones (total normalized projection volumes from all experiments are 4.3:1 between ipsilateral and contralateral hemispheres).”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
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“We also confirmed that AAV was at least as efficient as, and more specific than, the classic anterograde tracer biotinylated dextran amine (BDA) (Extended Data Fig. 1), as described separately21.”
§ A mesoscale connectome of the mouse brain > Creating the Allen Mouse Brain Connectivity Atlas
What the sources say
- Not checked yetcites [21] Wang, Q. et al. Systematic comparison of adeno-associated virus and biotinylated dextran amine reveals equivalent sensitivity between tracers and novel projection targets in the mouse brain. J. Comp. Neurol. http://dx.doi.org/10.1002/cne.23567 (Feb 22, 2014) source
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In the paper
“Using confidence values for each non-zero connection, the lower bound on sparsity is 13% for the entire brain and 32% for cortico-cortical connections.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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In the paper
“Based on the bounded optimization, the number of non-zero entries provides an upper bound estimate for sparsity: 36% for the entire brain and 52% for cortico-cortical connections.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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In the paper
“Whereas 63% ipsilateral and 51% contralateral targets have projection strength values above the minimal true positive level of 10−4 (which has a potential false positive rate of 27%, Extended Data Fig. 7), only 21% ipsilateral and 9% contralateral targets have projection strength values above the intermediate level of 10−2.”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
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In the paper
“We only report here on the completed Phase I study, which includes 469 image sets with injection sites covering nearly the entire brain (Fig. 1c, Extended Data Fig. 3 and Supplementary Video 3).”
§ A mesoscale connectome of the mouse brain > Mapping axonal projections in the whole mouse brain
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“We found a high degree of concordance among individual brains, with median variation < 49 μm in each dimension between each brain and the average template brain, which is comparable to the median inter-rater variation of < 39 μm.”
§ A mesoscale connectome of the mouse brain > Creating the Allen Mouse Brain Connectivity Atlas
plainn = 30- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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
“Whereas 63% ipsilateral and 51% contralateral targets have projection strength values above the minimal true positive level of 10−4 (which has a potential false positive rate of 27%, Extended Data Fig. 7), only 21% ipsilateral and 9% contralateral targets have projection strength values above the intermediate level of 10−2.”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The average percentages of total projection signals into 12 major brain subdivisions showed disproportionately large projections within the isocortex, as well as distinct subcortical distributions.”
§ A mesoscale connectome of the mouse brain > Mapping axonal projections in the whole mouse brain
plaincorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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
“For cortico-cortical connections, both intra-and inter-hemispheric distributions are well fit by lognormals (ipsilateral: P = 0.23; contralateral: P = 0.21) individually (Fig. 4b), but they are different enough that when combined the distribution is no longer lognormal (P = 0.0019).”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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In the paper
“Posterior groups (RSP, VIS) bypass the striatum but retain a strict topography following the medial/lateral axis (Fig. 5f).”
§ A mesoscale connectome of the mouse brain > The cortico-striatal-thalamic network
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In the paper
“The number of strong correlations is larger than expected by chance, suggesting a tendency of regions to organize into clusters to allow for strong indirect connectivity.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
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In the paper
“The mouse brain shows defining features of both small-world and scale-free networks, that is, it clusters and has hubs; but neither of these models in isolation can fully explain it.”
§ A mesoscale connectome of the mouse brain > Discussion
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“Here, a better fit is achieved with a scale-free network32; however, neither model simultaneously fits both distributions.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
What the sources say
- Not checked yetcites [32] Barabási, A. L. & Albert, R. Emergence of scaling in random networks. Science 286, 509–512 (1999) source
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In the paper
“A ‘small-world’ network model31 approximates the clustering coefficient distribution after being fit to its mean; however, its node degree distribution poorly matches the data.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
What the sources say
- Not checked yetcites [31] Watts, D. J. & Strogatz, S. H. Collective dynamics of ‘small-world’ networks. Nature 393, 440–442 (1998) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Distance matrices for both ipsilateral and contralateral cortical targets were highly correlated with the distance matrix of injection sites, as were ipsilateral striatal and thalamic distance matrices.”
§ A mesoscale connectome of the mouse brain > The cortico-striatal-thalamic network
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In the paper
“BDA was clearly uptaken by passing fibres in some injections but AAV was not.”
§ A mesoscale connectome of the mouse brain > Extended Data
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In the paper
“In summary, for all POIs in template space, the observed median variation in each direction are 28 μm for left-right, 35 μm for inferior-superior, and 49 μm for anterior-posterior.”
§ A mesoscale connectome of the mouse brain > Extended Data
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“although the isocortex accounts for only 30.2% of total brain volume.”
§ A mesoscale connectome of the mouse brain > Extended Data
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In the paper
“Injection sites ranged from 0.002 to 1.359 mm3 in volume, with an average size of 0.24 mm3 across all 469 data sets.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
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In the paper
“These settings resulted in infection areas of approximately 400–1,000 μm in diameter, depending on target region.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
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In the paper
“In most cases, results obtained from manual and informatics annotations are the same.”
§ A mesoscale connectome of the mouse brain > METHODS > Quality control, injection site annotation and polygon drawing
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“Reducing the current strength to 1 mA decreased the area of infected neurons”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
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“Notable exceptions are found in specific circuits that might have certain types of strong presynaptic inputs, such as the entorhinal cortex projection to hippocampal subregions dentate gyrus and CA1, where retrogradely infected input cells can be brightly labelled.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
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In the paper
“The presynaptic reporter virus predominantly shows a punctate pattern of labelling consistent with presynaptic protein expression patterns, and indicative of terminal zones.”
§ A mesoscale connectome of the mouse brain > Extended Data
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In the paper
“Many puncta were colocalized (yellow arrows show select examples in q’ and r’)”
§ A mesoscale connectome of the mouse brain > Extended Data
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“Note that in some cases (for example, PTLp) axon pathways appear to be labelled in only one of the pair.”
§ A mesoscale connectome of the mouse brain > Extended Data
hedgedSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“For example, within the striatum (light blue), the percentage of total signal is low from auditory, retrosplenial and visual areas (6.2%, 3.4% and 7.6%, respectively), but much greater from frontal, motor, cingulate and somatosensory areas (16.5%, 27.7%, 20.3% and 17.6%, respectively).”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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
“it peaked between log10 = −3.5 and log10 = −3.0”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
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 cytoplasmic viral tracer labels axons, revealing dense branching patterns in presumed terminal zones.”
§ A mesoscale connectome of the mouse brain > Extended Data
plaindirectSingle case- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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
“There are also cases in which a connection was described in the literature but is excluded here because we could not find solid evidence in our data set to support it.”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Owing to the two-photon imaging wavelength used (925 nm), the tagRFP (red) signal is weak to non-existent in these images.”
§ A mesoscale connectome of the mouse brain > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Voxels belonging to the medial cortical groups have been omitted to reveal a reconstructed corpus callosum showing parallel crossings with a conserved spatial configuration.”
§ A mesoscale connectome of the mouse brain > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
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
“and sending strong projections to MD”
§ A mesoscale connectome of the mouse brain > Extended Data
boosteddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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
“with both MOp and MOs receiving strong inputs from VM”
§ A mesoscale connectome of the mouse brain > Extended Data
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
In the paper
“C. elegans is the only species for which an essentially complete wiring diagram of its 302 neurons has been obtained through electron microscopy4.”
§ A mesoscale connectome of the mouse brain > Abstract
What the sources say
- Not checked yetcites [4] White, J. G., Southgate, E., Thomson, J. N. & Brenner, S. The structure of the nervous system of the nematode Caenorhabditis elegans. Phil. Trans. R. Soc. Lond. B 314, 1–340 (1986) source
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“In primate cortex, single tracer injections were also found to reliably predict mean values obtained from repeated injections into the same source24.”
§ A mesoscale connectome of the mouse brain > Brain-wide connectivity matrix
What the sources say
- Not checked yetcites [24] Markov, N. T. et al. A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb. Cortex 24, 17–36 (2014) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Owing to its block-face imaging nature, STP tomography essentially eliminates tissue distortions that occur in conventional section-based histological methods and provides a series of highly conformed, inherently pre-aligned images amenable to precise 3D mapping.”
§ A mesoscale connectome of the mouse brain > Creating the Allen Mouse Brain Connectivity Atlas
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“These observations combined indicate that connections might be lognormally distributed within a region, yet vary systematically with statistics unique to the region.”
§ A mesoscale connectome of the mouse brain > An inter-region connectivity model
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Stringent quality control criteria were applied, discarding ~25% of all scanned brains due to insufficient quality in labelling or imaging.”
§ A mesoscale connectome of the mouse brain > Creating the Allen Mouse Brain Connectivity Atlas
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Also, we cannot exclude the possibility that the AAV tracer we chose to use (with the specific promoter and serotype) may not be completely unbiased in labelling all neuronal types.”
§ A mesoscale connectome of the mouse brain > Discussion
hedged- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“Although the striatum is a cellularly homogeneous structure that can be subdivided into distinct domains selectively targeted by cortical and other inputs36 (Fig. 5e), the thalamus is highly heterogeneous, composed of up to 50 discrete nuclei37, receiving and relaying diverse sensory, motor, behavioural state and cognitive information in parallel pathways to and from the isocortex.”
§ A mesoscale connectome of the mouse brain > The cortico-striatal-thalamic network
What the sources say
- Not checked yetcites [37] Jones, E. G. The Thalamus (Cambridge Univ. Press, 2007)
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
In the paper
“Although the striatum is a cellularly homogeneous structure that can be subdivided into distinct domains selectively targeted by cortical and other inputs36 (Fig. 5e), the thalamus is highly heterogeneous, composed of up to 50 discrete nuclei37, receiving and relaying diverse sensory, motor, behavioural state and cognitive information in parallel pathways to and from the isocortex.”
§ A mesoscale connectome of the mouse brain > The cortico-striatal-thalamic network
What the sources say
- Not checked yetcites [36] Gerfen, C. R. in The Rat Nervous System (ed. Paxinos, G. ) 455–508 (Elsevier Academic Press, 2004) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Severe artefacts such as missing tissue or sections, poor orientation, edge cutoff, tessellation and low signal strength lead to elimination of the entire image series.”
§ A mesoscale connectome of the mouse brain > METHODS > Quality control, injection site annotation and polygon drawing
plaindirect- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Finally, we observed that the alignment between the average template brain and our existing Reference Atlas model (which was drawn upon Nissl sections) is not perfect, which leads to a degree of registration imprecision that could affect the accuracy of the quantitative connectivity matrices.”
§ A mesoscale connectome of the mouse brain > Discussion
hedgeddirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“To avoid possible bias introduced by using a single specimen as template and to increase the convergence rate of the registration algorithm, a registration template was created by iteratively averaging 1,231 registered and resliced brain specimens.”
§ A mesoscale connectome of the mouse brain > METHODS > Image data processing
plaindirectn = 1,231- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“First, AAV mediates robust fluorescent labelling of the soma and processes of infected neurons, which can be coupled with direct imaging methods for high-throughput production without additional histochemical staining steps.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
What the sources say
- Not checked yetcites [19] Chamberlin, N. L., Du, B., de Lacalle, S. & Saper, C. B. Recombinant adeno-associated virus vector: use for transgene expression and anterograde tract tracing in the CNS. Brain Res. 793, 169–175 (1998) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“A rigorous manual quality control protocol was established which includes identification of the injection structure(s) according to the Allen Reference Atlas ontology, delineation of the injection site location and decisions on failing an experiment due to production issues affecting specimen and image quality.”
§ A mesoscale connectome of the mouse brain > METHODS > Quality control, injection site annotation and polygon drawing
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. 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
“Moreover, our mesoscale connectome provides a static, structural connectivity map, which is necessary but insufficient for understanding function.”
§ A mesoscale connectome of the mouse brain > Discussion
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
In the paper
“Finally, perhaps the greatest advantage of using AAV over conventional tracers is the flexible molecular strategies that can be used to introduce various transgenes and to label specific neuronal populations by combining cell-type-selective Cre driver mice with AAV vectors harbouring a Cre-dependent expression cassette.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
What the sources say
- Not checked yetcites [19] Chamberlin, N. L., Du, B., de Lacalle, S. & Saper, C. B. Recombinant adeno-associated virus vector: use for transgene expression and anterograde tract tracing in the CNS. Brain Res. 793, 169–175 (1998) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Microscale, synaptic-level details are missing, and electrical connections through gap junctions are not revealed.”
§ A mesoscale connectome of the mouse brain > Discussion
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“It should be noted that passing fibres and terminals are not distinguished.”
§ A mesoscale connectome of the mouse brain > METHODS > Image data processing
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“with LGd and VISp playing primary roles in processing incoming visual sensory information”
§ A mesoscale connectome of the mouse brain > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“visual associational areas involved in higher-order information processing”
§ A mesoscale connectome of the mouse brain > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
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
“(thus similar to the pulvinar in primates)”
§ A mesoscale connectome of the mouse brain > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“SSs in higher-order information processing”
§ A mesoscale connectome of the mouse brain > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
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
“This could be due to random differences in the proportion of corticospinal projecting neurons labelled in a particular injection within the same source area.”
§ A mesoscale connectome of the mouse brain > Extended Data
hedgedconditionalSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Connections labelled in red are previously known”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Eighty injections were used in the analysis for which the injection site is strictly within the isocortex and injection volume >0.07 mm3.”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“A manual analysis of true positive and true negative signals from 20 randomly chosen injection experiments, representing the range of injection sizes, was used to estimate the false positive rate at different threshold levels”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“although our current data do not have sufficient resolution to resolve fine details.”
§ A mesoscale connectome of the mouse brain > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The quote only partly states this claim.
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
“The reticular nucleus (RT) is unique in that it is a relay nucleus for all these pathways, receiving collaterals from both cortico-thalamic and thalamo-cortical projections although itself only projecting within the thalamus.”
§ A mesoscale connectome of the mouse brain > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
In the paper
“The prefrontal pathway, which is considered to play major roles in cognitive and executive functions, is composed of the medial, orbital and lateral prefrontal cortical areas (including PL, ILA, ORB and AI) and many of the medial, midline, and intralaminar nuclei of the thalamus (including MD, VM, AM, PVT, CM, RH, RE and PF)111.”
§ A mesoscale connectome of the mouse brain > Extended Data
What the sources say
- Not checked yetcites [111] Van der Werf, Y. D., Witter, M. P. & Groenewegen, H. J. The intralaminar and midline nuclei of the thalamus. Anatomical and functional evidence for participation in processes of arousal and awareness. Brain Res. Brain Res. Rev. 39, 107–140 (2002) source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The authors state this as an assumption.
Regional homogeneity: projections between source X and target Y regions are homogeneously distributed, so that infection of a subarea of the region is representative of the entire region.
“The first, regional homogeneity, assumes that projections between source X and target Y regions are homogeneously distributed, so that infection of a subarea of the region is representative of the entire region.”
The authors state this as an assumption.
Projection additivity: the projection density of multiple source regions sum linearly to produce projection density in a target region.
“The second assumption, projection additivity, assumes that the projection density of multiple source regions sum linearly to produce projection density in a target region.”
The paper relies on this without support.
Much of the histological tract tracing data are qualitative, incomplete, variable, scattered and difficult to retrieve.
“However, much of these data are qualitative, incomplete, variable, scattered and difficult to retrieve.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“For mammals, tracer injection studies have mapped the axonal projections between brain regions of mouse74,75 and macaque76.”
From Neuronal wiring diagram of an adult brain (2024) · cites this paper as [75]
In the citing paper
“Collaborative and consortium-level efforts have made substantial progress by mapping transcriptomic, epigenomic and proteomic landscapes in the brain8–10.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [9]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“Reducing the current strength to 1 mA decreased the area of infected neurons, and was used when 3 μA currents produced infection areas larger than ~700 μm.”
§ A mesoscale connectome of the mouse brain > METHODS > Stereotaxic injections of AAV using iontophoresis
Reported 1 · recomputed 333.333333
Citations
Cites
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White, J. G., Southgate, E., Thomson, J. N., & Brenner, S. (1986) · Philosophical Transactions of the Royal Society of London. B, Biological Sciences · doi:10.1098/rstb.1986.0056 · Cited by 5,589
Paxinos, G. (1985) · Cited by 3,715
Research works printed but not linked: 2
- Sporns, O. Networks of the Brain 412 (The MIT Press, 2011)
- Jones, E. G. The Thalamus (Cambridge Univ. Press, 2007)
Cited by
Sorted by citations
Items 301–400 of 1,012
aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data
Niedworok, C. J., Brown, A. P. Y., Cardoso, M. J., Osten, P., Sebastien Ourselin, A., Marc Modat, A., & Margrie, T. W. (2016) · Nature Communications · doi:10.1038/ncomms11879 · Cited by 124
The functional organization of cortical feedback inputs to primary visual cortex
Marques, T., Nguyen, J. K., Fioreze, G. T., & Petreanu, L. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0135-z · Cited by 122
Wide. Fast. Deep: Recent Advances in Multiphoton Microscopy ofIn VivoNeuronal Activity
Lecoq, J. A., Orlova, N., & Grewe, B. F. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.1527-18.2019 · Cited by 122
Whole-brain comparison of rodent and human brains using spatial transcriptomics
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Metadata
- Authors
- Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., Wang, Q., Lau, C., Kuan, L., Henry, A. M., Mortrud, M. T., Ouellette, B., Nguyen, T. N., Sorensen, S. A., Slaughterbeck, C. R., Wakeman, W., Li, Y., Feng, D., Ho, A., Nicholas, E., Hirokawa, K. E., Bohn, P., Joines, K. M., Peng, H., Hawrylycz, M. J., Phillips, J. W., Hohmann, J. G., Wohnoutka, P., Gerfen, C. R., Koch, C., Bernard, A., Dang, C., Jones, A. R., & Zeng, H.
- Affiliations
- Allen Institute for Brain Science (US)
- National Institutes of Health (US)
- Corresponding author
- Zeng, Hongkui
- ORCID
- Oh, Seung Wook
- Harris, Julie A.
- Ng, Lydia
- Winslow, Brent
- Cain, Nicholas
- Wang, Quanxin
- Henry, Alex M.
- Nguyen, Thuc Nghi
- Sorensen, Staci A.
- Wakeman, Wayne
- Feng, David
- Ho, Anh
- Hirokawa, Karla E.
- Bohn, Phillip
- Joines, Kevin M.
- Hawrylycz, Michael J.
- Phillips, John W.
- Hohmann, John G.
- Wohnoutka, Paul
- Gerfen, Charles R.
- Bernard, Amy
- Jones, Allan R.
- Zeng, Hongkui
- Venue
- Nature
- Published
- 2014-04
- Volume
- 508
- Issue
- 7495
- Pages
- 207-214
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5102064
- OpenAlex
- W1975389666
- Semantic Scholar
- aa0af55eb8dabf91ad8aafc77f5b5566cdef4ae0
- Cited by
- 2,612
- References
- 130
- Citations by year
- 2026: 176 · 2025: 233 · 2024: 274 · 2023: 254 · 2022: 238 · 2021: 247 · 2020: 250 · 2019: 229 · 2018: 187 · 2017: 153 · 2016: 176 · 2015: 132 · 2014: 61
- FWCI
- 97.03
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institutes of Health
- National Institute of Mental Health (ZIAMH002497)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Keywords
- whole-brain connectivity, axonal projections, Allen Mouse Brain Connectivity Atlas, brain network topology, human brain development, transcriptional atlas, BRAIN Initiative, neural circuits, neuroanatomy
- MeSH terms
- Animals, Atlases as Topic, Axons, Brain, Cerebral Cortex, Corpus Striatum, Male, Mice, Inbred C57BL, Models, Neurological, Thalamus, Mice, Neuroanatomical Tract-Tracing Techniques, Connectome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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