A mesoscale connectome of the mouse brain

Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways.

“Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways.”

The Allen Mouse Brain Connectivity Atlas is a mesoscale connectome of the adult mouse brain.

“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.”

The minimal true positive level of 10^-4 has a potential false positive rate of 27%.

“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.”

Each pair of duplicate injections was highly correlated across a range of projection strengths.

“Each pair was highly correlated across a range of projection strengths.”

Connection strengths negatively correlated with the distance between connected regions.

“Connection strengths spanned ~105-fold range, and negatively correlated with the distance between connected regions (Supplementary Notes and Supplementary Table 4).”

Differences between any two points in duplicate injections were on average only a half order of magnitude (within one standard deviation).

“Differences between any two points were on average only a half order of magnitude (within one standard deviation).”

When combined, cortico-cortical intra- and inter-hemispheric distributions are no longer lognormal (P=0.0019).

“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).”

Informatics-derived assignment of injection site structures had > 75% voxel-level concordance with manual expert annotation for almost all injection sites.

“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).”

Based on AIC, among hypothesized connection strength distributions (lognormal, normal, exponential, inverse Gaussian) the brain-wide data are best fit by a lognormal distribution.

“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).”

Log-transformed connection strengths failed to pass Shapiro-Wilk test for normality (ipsilateral P=0.039; contralateral P=0.023).

“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).”

Infected neurons in injection sites often span several brain areas.

“Infected neurons in injection sites often span several brain areas.”

The median difference is < 71 μm between each brain and the Reference Atlas.

“The median difference is < 71 μm between each brain and the Reference Atlas.”

The final average template brain, averaged from 1,231 brains, shows remarkably clear anatomical features and boundaries.

“The final average template brain, averaged from 1,231 brains, shows remarkably clear anatomical features and boundaries.”

There are prevalent bilateral projections to corresponding ipsilateral and contralateral target sites.

“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).”

Among Gaussian mixture models, a two-component one provided the best fit.

“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).”

Only 18 intended structures were completely missed due to redundancy or injection difficulty.

“Only 18 intended structures were completely missed due to redundancy or injection difficulty (Supplementary Table 1).”

Connectivity strengths span a greater than 10^5-fold range across the brain.

“First, connectivity strengths span a greater than 105-fold range across the brain (Extended Data Fig. 7), suggesting that quantitative descriptions of connectivity must be considered for understanding neural network properties24.”

• cites [24] Markov, N. T. et al. A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb. Cortex 24, 17–36 (2014) sourceNot checked yet

  Not checked in the free run.

The projection data sets were consistent in quality to allow qualitative and quantitative comparisons.

“We examined multiple projection data sets in detail and found that they were complete in capturing all known projection target sites throughout the brain, sensitive in detecting thin axon fibres, and consistent in quality to allow qualitative and quantitative comparisons.”

A brain-wide, inter-areal, weighted connectivity matrix was constructed using the entire Phase I experimental data set.

“We constructed a brain-wide, inter-areal, weighted connectivity matrix using the entire Phase I experimental data set (Fig. 3, see Supplementary Table 2 for the underlying values).”

The projection data sets were complete in capturing all known projection target sites throughout the brain.

“We examined multiple projection data sets in detail and found that they were complete in capturing all known projection target sites throughout the brain, sensitive in detecting thin axon fibres, and consistent in quality to allow qualitative and quantitative comparisons.”

The Connectivity Atlas has brain-wide coverage.

“This Connectivity Atlas has all the desired features summarized in a mesoscale connectome position essay18: brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource and an open-access public online database.”

• cites [18] Bohland, J. W. et al. A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput. Biol. 5, e1000334 (2009) sourceNot checked yet

  Not checked in the free run.

Connection strengths spanned ~10^5-fold range.

“Connection strengths spanned ~105-fold range, and negatively correlated with the distance between connected regions (Supplementary Notes and Supplementary Table 4).”

The mouse brain has a higher mean clustering coefficient, 0.42, than expected by a random network with identical sparseness, 0.12.

“Network analyses (Fig. 4c, see also Supplementary Notes) reveal that the mouse brain has a higher mean clustering coefficient (which gives the ratio of existing over possible connections), 0.42, than expected by a random network29,30 with identical sparseness, 0.12.”

• cites [29] Erdős, P. & Rényi, A. On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci. 5, 17–61 (1960)Not checked yet

  Not checked in the free run.

• cites [30] Bollobás, B. Random Graphs (Cambridge Univ. Press, 2001) sourceNot checked yet

  Not checked in the free run.

The 469 experiments allowed computation of mutual connections among 213 regions.

“The 469 experiments allowed us to compute the mutual connections among 213 regions.”

The projection data sets were sensitive in detecting thin axon fibres.

“We examined multiple projection data sets in detail and found that they were complete in capturing all known projection target sites throughout the brain, sensitive in detecting thin axon fibres, and consistent in quality to allow qualitative and quantitative comparisons.”

The Connectivity Atlas is an open-access public online database.

“This Connectivity Atlas has all the desired features summarized in a mesoscale connectome position essay18: brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource and an open-access public online database.”

• cites [18] Bohland, J. W. et al. A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput. Biol. 5, e1000334 (2009) sourceNot checked yet

  Not checked in the free run.

Seven representative isocortical injections reveal distinct projection patterns in striatum, thalamus, zona incerta, midbrain, pons and medulla.

“As an example, 7 representative isocortical injections (Fig. 2) reveal distinct projection patterns in the striatum, thalamus, zona incerta, midbrain, pons and medulla.”

Outside major fibre tracts, there was high correspondence between synaptic EGFP and cytoplasmic EGFP signals in target regions.

“Outside of major fibre tracts, there was high correspondence between synaptic EGFP and cytoplasmic EGFP signals in target regions.”

The entire data set preserves the 3D spatial relationship of different domains, pathways and topography.

“Furthermore, the entire data set preserves the 3D spatial relationship of different domains, pathways and topography (Fig. 5).”

Cross-talk between these pathways was observed, mediated by specific associational cortical areas and integrative thalamic nuclei.

“We also observed cross-talk between these pathways, mediated by specific associational cortical areas and integrative thalamic nuclei.”

Connection strengths at both cortico-cortical and whole-brain levels show lognormal distributions.

“Interestingly, the connection strengths at both cortico-cortical and whole-brain levels show lognormal distributions, that is, long-tailed distributions with small numbers of strong connections and large numbers of weak connections.”

Projections from different cortical regions divide up striatum and thalamus into distinct domains.

“To effectively visualize different projection patterns in a common 3D space, voxel densities from 21 selected injections, one (centrally located) from each cluster, were overlaid to create ‘dotograms’ (Fig. 5b, c and Extended Data Fig. 8c), demonstrating that projections from different cortical regions divide up striatum and thalamus into distinct domains.”

The wiring diagram demonstrates specific point-to-point interconnections between corresponding clusters that divide the cortico-thalamic system into six functional pathways: visual, somatosensory, auditory, motor, limbic and prefrontal.

“This wiring diagram demonstrates specific point-to-point interconnections between corresponding clusters that divide the cortico-thalamic system into six functional pathways: visual, somatosensory, auditory, motor, limbic and prefrontal.”

For the thalamus, anterior groups pass through fibre tracts in the striatum, narrowing through the globus pallidus, before spreading throughout the thalamus.

“In particular for the thalamus, anterior groups pass through fibre tracts in the striatum, narrowing through the globus pallidus, before spreading throughout the thalamus (Extended Data Fig. 9f).”

Weaker correlations were observed in contralateral striatum and thalamus.

“Weaker correlations were observed in contralateral striatum and thalamus.”

The high-throughput whole-brain mapping approach is remarkably consistent across animals, with an average correlation of 0.90 across 12 duplicate sets of mice.

“The high-throughput whole-brain mapping approach is remarkably consistent across animals, with an average correlation of 0.90 across 12 duplicate sets of mice (Extended Data Fig. 5).”

In connections among isocortex, striatum and thalamus, clustering analysis and virtual tractography recapitulate anatomical parcellation and topography of functional domains and projection pathways.

“In connections among isocortex, striatum and thalamus, clustering analysis and virtual tractography recapitulate anatomical parcellation and topography of functional domains and projection pathways (Fig. 5).”

Contralateral connection strengths are significantly weaker than ipsilateral ones.

“We found that projections within the ipsilateral hemisphere and to the corresponding locations in the contralateral hemisphere are remarkably similar across the brain (Figs 3 and 4; Pearson’s r = 0.595), with the contralateral connection strengths significantly weaker than ipsilateral ones.”

Projections within the ipsilateral hemisphere and to corresponding locations in the contralateral hemisphere are remarkably similar across the brain (Pearson's r = 0.595).

“We found that projections within the ipsilateral hemisphere and to the corresponding locations in the contralateral hemisphere are remarkably similar across the brain (Figs 3 and 4; Pearson’s r = 0.595), with the contralateral connection strengths significantly weaker than ipsilateral ones.”

Such grouping effectively divides the cortex into 21 predominantly non-overlapping spatial zones defined by similar output projections.

“Such grouping effectively divides the cortex into 21 predominantly non-overlapping spatial zones as shown in a flat-map cortex representation (Fig. 5a) defined by similar output projections.”

Random graphs with matched node degree distribution show a similar drop in clustering coefficient to 0.16.

“Random graphs with matched node degree distribution show a similar drop in clustering coefficient to 0.16.”

Hierarchical clustering of Spearman's rank correlation coefficients of segmented projection volumes between every pair of 80 isocortical injection experiments led to 21 distinct groups, each containing 1 to 10 injections.

“We used 80 isocortical injection experiments to examine this. Spearman’s rank correlation coefficient of segmented projection volumes of all voxels across the entire brain was computed between every pair of experiments, and hierarchical clustering led to 21 distinct groups, each containing 1 to 10 injections (Extended Data Fig. 8a, b).”

The 3D tractography paths retain the same spatial organization.

“The tractography shows that the paths themselves also retain the same spatial organization.”

The specific observations from our data are mostly consistent (with a few additions) with extensive previous studies in rats and fewer studies in mice as well as with studies in other mammalian species.

“The specific observations from our data are mostly consistent (with a few additions) with extensive previous studies in rats and the fewer number of studies in mice (Extended Data Fig. 10) as well as with studies in other mammalian species37–39, providing a comprehensive and unifying view of mouse cortico-thalamic connections for the first time.”

• cites [37] Jones, E. G. The Thalamus (Cambridge Univ. Press, 2007)Not checked yet

  Not checked in the free run.

• cites [38] Jones, E. G. Viewpoint: the core and matrix of thalamic organization. Neuroscience 85, 331–345 (1998) sourceNot checked yet

  Not checked in the free run.

• cites [39] Scannell, J. W., Burns, G. A., Hilgetag, C. C., O’Neil, M. A. & Young, M. P. The connectional organization of the cortico-thalamic system of the cat. Cereb. Cortex 9, 277–299 (1999) sourceNot checked yet

  Not checked in the free run.

The majority of these 295 regions have at least one injection targeted to that structure as either the primary or secondary injection site.

“The majority of these 295 regions have at least one injection targeted to that structure as either the primary or secondary injection site (white bars); only 18 structures are not covered at all (grey bars, for details see Supplementary Table 1).”

Only 18 structures are not covered at all.

“only 18 structures are not covered at all”

Long-range projections from all studied regions were found with both tracers.

“We found the long-range projections from all studied regions with both tracers.”

For most cases, the anatomical area(s) of tracer uptake are well matched.

“For most cases, the anatomical area(s) of tracer uptake are well matched.”

For most structures, a single injection was sufficient to infect the majority of neurons in that region.

“For most structures, a single injection was sufficient to infect the majority of neurons in that region.”

Iontophoretic delivery of AAV gives rise to the most consistent and confined viral infection volume.

“and that iontophoretic delivery of AAV gives rise to the most consistent and confined viral infection volume.”

There were more retrogradely labelled neurons with BDA than AAV.

“There were more retrogradely labelled neurons with BDA than AAV”

The largest projection signal from each cortical injection is found within isocortex (range of 45.4-69.8% of projection signals depending on source region, with an average of 59% for all cortical injections).

“The largest projection signal from each cortical injection is found within isocortex (range of 45.4–69.8% of projection signals depending on source region, with an average of 59% for all cortical injections)”

AAV serotype 1 produces the most robust and uniform neuronal tropism.

“We found that AAV serotype 1 produces the most robust and uniform neuronal tropism”

A few retrograde neurons were observed in all studied regions with both tracers.

“although a few retrograde neurons were observed in all studied regions with both tracers.”

Injection sites of AAV and BDA are mostly overlapping.

“Injection sites of AAV and BDA are mostly overlapping (yellow), with a blue DAPI counterstain.”

Their patterns were similar between the two tracers in mostly overlapped injection cases.

“Their patterns were similar between the two tracers in mostly overlapped injection cases.”

The cortical and subcortical projections from MOp injection are labelled similarly with the AAV tracer and conventional tracer BDA.

“The cortical and subcortical projections from MOp injection are labelled similarly with the AAV tracer (green) and conventional tracer BDA (red).”

In Nissl space, these observed median variations are 42, 71 and 60 μm, respectively.

“In Nissl space, these observed median variations are 42, 71 and 60 μm, respectively.”

In this study, retrogradely infected cells were seen only rarely.

“In this study, retrogradely infected cells were seen only rarely.”

False positives were almost exclusively due to small segmentation artefacts in areas without actual fluorescently labelled axon fibres.

“False positives were almost exclusively due to small segmentation artefacts in areas without actual fluorescently labelled axon fibres.”

Punctate or diffuse labelling was observed with the synaptic reporter virus in nearly all MOp target regions manually and computationally identified using the cytoplasmic reporter, including those with both large and small signals.

“Punctate or diffuse labelling was observed with the synaptic reporter virus in nearly all MOp target regions manually and computationally identified using the cytoplasmic reporter, including those with both large and small signals.”

Voxel densities of whole brains from two distant injections (ACAd and SSp-m) show little correlation (ρ = −0.03).

“whereas that of two distant injections (ACAd and SSp-m) shows little correlation (ρ = −0.03)”

At a threshold of log10 = −4, the false positive rate was 27%.

“at a threshold of log10 = −4, the false positive rate was 27%”

High-resolution images of terminal zones in the somatosensory cortex and thalamus identified using the cytoplasmic viral tracer show axon ramification and punctate structures consistent with bouton labelling, similar to the synaptic reporter in the corresponding regions.

“High-resolution images of terminal zones in the somatosensory cortex (m) and thalamus (o) identified using the cytoplasmic viral tracer show axon ramification and punctate structures consistent with bouton labelling, similar to the synaptic reporter in the corresponding regions (n, p).”

The entire range of normalized projection volumes in the matrix was between log10 = −14 and log10 = 1.5.

“The entire range of the normalized projection volumes in this matrix was between log10 = −14 and log10 = 1.5”

Confocal images at a single plane show punctate labelling indicative of presynaptic boutons for both sypGFP and synapsin or SV2.

“Confocal images at a single plane show punctate labelling indicative of presynaptic boutons for both sypGFP and synapsin or SV2.”

Scatter plots of all ipsilateral and contralateral target structure values above a minimum threshold in both members of the pair show significant correlations between each pair of injections across a four orders of magnitude range of projection strengths.

“Scatter plots of all ipsilateral and contralateral target structure values above a minimum threshold in both members of the pair (log10 = −3.5; non-blue values from a) show significant correlations between each pair of injections across a four orders of magnitude range of projection strengths.”

Maximal density projections of whole brain signals from each of the two spatially overlapping injection experiments per source region visibly demonstrate consistency of brain-wide connections.

“Maximal density projections of whole brain signals from each of the two spatially overlapping injection experiments per source region visibly demonstrate consistency of brain-wide connections.”

A top-down view of 3D tractography paths into the ipsilateral thalamus for all voxels excluding the RSP/VIS groups shows axonal projections passing through fibre tracts in the striatum, narrowing through the globus pallidus, before spreading throughout the thalamus.

“A top-down view of 3D tractography paths into the ipsilateral thalamus for all voxels excluding the RSP/VIS groups showing axonal projections passing through fibre tracts in the striatum, narrowing through the globus pallidus, before spreading throughout the thalamus.”

At a threshold of log10 = −3.5, the false positive rate was 14.5%.

“dropping to 14.5% at log10 = −3.5”

Voxel densities of whole brains from two nearby anterior cingulate injections (ACAd and ACAv) show a strong correlation (Spearman's ρ = 0.82).

“Scatter plot of the voxel densities (excluding injection sites) of the whole brains from two nearby anterior cingulate injections (ACAd and ACAv) shows a strong correlation between the two (Spearman’s ρ = 0.82)”

True positive values predominantly fall within the range of log10 = −4 to 1.5.

“True positive values predominantly fall within the range of log10 = −4 to 1.5.”

LGv does not project back to cortex.

“LGv does not project back to cortex.”

Differences in the subcortical distribution of relative signal strength between cortical sources were also observed.

“Differences in the subcortical distribution of relative signal strength between cortical sources were also observed.”

LD receives strong projections from all visual cortical areas.

“receives strong projections from all visual cortical areas.”

Thalamic nuclei PO, VM, CM, RH and RE all send out widely distributed, albeit weak, projections to many cortical areas in different pathways.

“Finally, the thalamic nuclei PO, VM, CM, RH and RE all send out widely distributed, albeit weak, projections to many cortical areas in different pathways”

MOs projects widely into many medial, midline and intralaminar nuclei.

“and additionally with MOs projecting widely into many medial, midline and intralaminar nuclei.”

PTLp projects strongly to both LP and LD.

“projects strongly to both LP and LD.”

PTLp hardly receives any inputs from the thalamus.

“PTLp, while hardly receiving any inputs from the thalamus”

LD projects quite exclusively to the limbic cortical areas.

“LD, while projecting quite exclusively to the limbic cortical areas”

With recent advances in computing power and optical imaging techniques, it is now feasible to systematically map connectivity throughout the entire brain.

“With recent advances in both computing power and optical imaging techniques, it is now feasible to systematically map connectivity throughout the entire brain.”

• cites [7] Chiang, A. S. et al. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr. Biol. 21, 1–11 (2011) sourceNot checked yet

  Not checked in the free run.

• cites [8] Jenett, A. et al. A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2, 991–1001 (2012) sourceNot checked yet

  Not checked in the free run.

Our knowledge of whole-brain connectivity is fragmented, without a cohesive and comprehensive understanding in any single vertebrate animal species.

“Thus, our knowledge of whole-brain connectivity is fragmented, without a cohesive and comprehensive understanding in any single vertebrate animal species (see for example the BAMS database for the rat brain6).”

• cites [6] Bota, M., Dong, H. W. & Swanson, L. W. Combining collation and annotation efforts toward completion of the rat and mouse connectomes in BAMS. Front. Neuroinform. 6, 2 (2012) sourceNot checked yet

  Not checked in the free run.

The connectivity matrix contains passing fibre signals within grey matter.

“Nonetheless, it should be noted that the connectivity matrix contains passing fibre signals within grey matter, the nature of which should be manually examined in 2D section images.”

At the mesoscale, both long-range and local connections can be described using a sampling approach with various neuroanatomical tracers that enable whole-brain mapping in a reasonable time frame across many animals.

“At the mesoscale, both long-range and local connections can be described using a sampling approach with various neuroanatomical tracers that enable whole-brain mapping in a reasonable time frame across many animals.”

The remaining difference is mainly due to imperfect alignment between average template brain and Nissl-section-based Reference Atlas.

“The remaining difference is mainly due to the imperfect alignment between the average template brain and the Nissl-section-based Reference Atlas (Supplementary Video 2).”

This extends previously reported findings that cortico-cortical connections follow a lognormal distribution in primate and mouse cortex to the entire mouse brain.

“This extends previously reported findings that cortico-cortical connections follow a lognormal distribution in the primate24,25 and mouse cortex26 to the entire mouse brain.”

• cites [24] Markov, N. T. et al. A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb. Cortex 24, 17–36 (2014) sourceNot checked yet

  Not checked in the free run.

• cites [25] Ercsey-Ravasz, M. et al. A predictive network model of cerebral cortical connectivity based on a distance rule. Neuron 80, 184–197 (2013) sourceNot checked yet

  Not checked in the free run.

• cites [26] Wang, Q., Sporns, O. & Burkhalter, A. Network analysis of corticocortical connections reveals ventral and dorsal processing streams in mouse visual cortex. J. Neurosci. 32, 4386–4399 (2012) sourceNot checked yet

  Not checked in the free run.

These analyses confirmed relatively high fidelity of co-registration of raw image data with Allen Reference Atlas.

“These analyses confirmed the relatively high fidelity of co-registration of raw image data with the Allen Reference Atlas.”

The connectivity matrix has been shown to contain false positive signals, mainly due to tissue and imaging artefacts and injection tract contaminations.

“The connectivity matrix has been shown to contain false positive signals (Extended Data Fig. 7), mainly due to tissue and imaging artefacts and injection tract contaminations.”

The computed distance matrices show that the spatial relationship between injection sites is recapitulated in the projections to striatum and thalamus, with some transformation of scale and rotation.

“The computed distance matrices show that the spatial relationship between injection sites is recapitulated in the projections to striatum and thalamus, with some transformation of scale and rotation.”

The standardized projection data set and informatics framework provide a brain-wide, detailed and quantitative connectivity map that is the most comprehensive, to date, in any vertebrate species.

“The standardized projection data set and the informatics framework built around it provide a brain-wide, detailed and quantitative connectivity map that is the most comprehensive, to date, in any vertebrate species.”

Different cortical areas project to different domains of striatum and thalamus with some degree of topography.

“Different cortical areas project to different domains of striatum and thalamus with some degree of topography33–35.”

• cites [33] Groenewegen, H. J. & Berendse, H. W. The specificity of the ‘nonspecific’ midline and intralaminar thalamic nuclei. Trends Neurosci. 17, 52–57 (1994) sourceNot checked yet

  Not checked in the free run.

• cites [34] Joel, D. & Weiner, I. The organization of the basal ganglia-thalamocortical circuits: open interconnected rather than closed segregated. Neuroscience 63, 363–379 (1994) sourceNot checked yet

  Not checked in the free run.

• cites [35] Mailly, P., Aliane, V., Groenewegen, H. J., Haber, S. N. & Deniau, J. M. The rat prefrontostriatal system analyzed in 3D: evidence for multiple interacting functional units. J. Neurosci. 33, 5718–5727 (2013) sourceNot checked yet

  Not checked in the free run.

The true range of projection strengths may go beyond the 10^5-fold reported here.

“Thus, the true range of projection strengths may go beyond the 105-fold reported here.”

The connectivity matrix based on cytoplasmic EGFP labelling does not distinguish passing fibres from terminal zones.

“The connectivity matrix based on cytoplasmic EGFP labelling does not distinguish passing fibres from terminal zones, and examination of raw images is needed to help with such distinction, using features such as ramification of axon fibres, and boutons or enlargements in axons.”

The extensive reciprocal connections between isocortex and thalamus illustrate general principles of network segregation and integration.

“The extensive reciprocal connections between isocortex and thalamus (Fig. 6) further illustrate general principles of network segregation and integration.”

The use of projection volume will probably underestimate the strength of dense projections.

“However, the use of projection volume will probably underestimate the strength of dense projections.”

Compared to conventional tracers which often have mixed anterograde and retrograde transport, retrograde labelling with AAV (except for certain serotypes) is generally negligible.

“Second, compared to conventional tracers which often have mixed anterograde and retrograde transport, retrograde labelling with AAV (except for certain serotypes) is generally negligible.”

• cites [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) sourceNot checked yet

  Not checked in the free run.

Identities of the postsynaptic neurons at the receiving end of the mapped connections are not labelled and therefore unknown.

“Beyond the above technical issues, identities of the postsynaptic neurons at the receiving end of the mapped connections are not labelled and therefore unknown.”

The entire atlas data generation was standardized with the use of AAV serotype 1 and iontophoresis for stereotaxic injections.

“Thus, the entire atlas data generation was standardized with the use of AAV serotype 1 and iontophoresis for stereotaxic injections20.”

• cites [20] Harris, J. A., Oh, S. W. & Zeng, H. Adeno-associated viral vectors for anterograde axonal tracing with fluorescent proteins in nontransgenic and Cre driver mice. Curr. Protoc. Neurosci. 59, 1.20.1–1.20. 18 http://dx.doi.org/10.1002/0471142301.ns0120s59 (2012) sourceNot checked yet

  Not checked in the free run.

Connections labelled in black are not previously described in the rodent literature to our knowledge.

“whereas those labelled in black are not previously described in the rodent literature to our knowledge.”

LP potentially modulates the function of all visual cortical areas.

“and LP potentially modulating the function of all visual cortical areas”

The visual pathway is composed of primary and associational visual cortical areas (VISp, VISam, VISal/l, and TEa) and thalamic nuclei LGd, LGv, and LP.

“The visual pathway is composed of primary and associational visual cortical areas (VISp, VISam, VISal/l, and TEa) and thalamic nuclei LGd, LGv, and LP100,103,109”

• cites [100] Sanderson, K. J., Dreher, B. & Gayer, N. Prosencephalic connections of striate and extrastriate areas of rat visual cortex. Exp. Brain Res. 85, 324–334 (1991) sourceNot checked yet

  Not checked in the free run.

• cites [103] Shi, C. J. & Cassell, M. D. Cortical, thalamic, and amygdaloid projections of rat temporal cortex. J. Comp. Neurol. 382, 153–175 (1997) sourceNot checked yet

  Not checked in the free run.

• cites [109] Simmons, P. A., Lemmon, V. & Pearlman, A. L. Afferent and efferent connections of the striate and extrastriate visual cortex of the normal and reeler mouse. J. Comp. Neurol. 211, 295–308 (1982) sourceNot checked yet

  Not checked in the free run.

All connections described in Extended Data Figure 10 were found in our data set.

“All the connections described here were found in our data set.”

Quantification of colocalization was not reliable due to the very high density of presynaptic labelling by anti-Synapsin and anti-SV2.

“although quantification was not reliable due to the very high density of presynaptic labelling by anti-Synapsin and anti-SV2.”

SSp and VPM/VPL play primary roles in processing incoming somatosensory information.

“with SSp and VPM/VPL playing primary roles in processing incoming somatosensory information”

The cortico-thalamic system can be divided into six functional pathways: visual, somatosensory, auditory, motor, limbic and prefrontal.

“Specifically, the cortico-thalamic system can be divided into six functional pathways: visual, somatosensory, auditory, motor, limbic and prefrontal.”

Peaks in the pseudo-F statistics (for example, at n = 3, 8 and 21 clusters) are indicators of greater cluster separation.

“Peaks in the pseudo-F statistics (for example, at n = 3, 8 and 21 clusters) are indicators of greater cluster separation.”

The somatosensory pathway is composed of primary and secondary somatosensory cortical areas (SSp and SSs) and thalamic nuclei VPM, VPL and PO.

“Similarly, the somatosensory pathway is composed of primary and secondary somatosensory cortical areas (SSp and SSs) and thalamic nuclei VPM, VPL and PO48,74”

• cites [48] Aronoff, R. et al. Long-range connectivity of mouse primary somatosensory barrel cortex. Eur. J. Neurosci. 31, 2221–2233 (2010) sourceNot checked yet

  Not checked in the free run.

• cites [74] Killackey, H. P. & Sherman, S. M. Corticothalamic projections from the rat primary somatosensory cortex. J. Neurosci. 23, 7381–7384 (2003) sourceNot checked yet

  Not checked in the free run.

The auditory pathway involves primary and secondary AUD areas and different MG nuclei.

“and the auditory pathway (involving primary and secondary AUD areas and different MG nuclei)82,98”

• cites [82] Llano, D. A. & Sherman, S. M. Evidence for nonreciprocal organization of the mouse auditory thalamocortical-corticothalamic projection systems. J. Comp. Neurol. 507, 1209–1227 (2008) sourceNot checked yet

  Not checked in the free run.

• cites [98] Roger, M. & Arnault, P. Anatomical study of the connections of the primary auditory area in the rat. J. Comp. Neurol. 287, 339–356 (1989) sourceNot checked yet

  Not checked in the free run.

There is extensive cross-talk between the motor pathway and the prefrontal pathway.

“There is also extensive cross-talk between the motor pathway and the prefrontal pathway”

Between these pathways, we have observed cross-talks, mediated by specific associational cortical areas and thalamic nuclei that may be considered to play integrative functions.

“Between these pathways, we have observed cross-talks, mediated by specific associational cortical areas and thalamic nuclei that may be considered to play integrative functions.”

The gustatory/visceral and auditory pathways have similar organizations to the visual and somatosensory pathways.

“also have similar organizations”

Thalamic nuclei PO, VM, CM, RH and RE are potentially capable of modulating activities in large cortical fields.

“thus potentially capable of modulating activities in large cortical fields.”

The anterior cingulate cortex (ACA) appears to bridge the prefrontal and the limbic pathways, interconnecting extensively with both.

“For example, the anterior cingulate cortex (ACA) appears to bridge the prefrontal and the limbic pathways, interconnecting extensively with both.”

The posterior parietal cortex (PTLp) and the LD nucleus may relay information between the visual and the limbic pathways.

“The posterior parietal cortex (PTLp) and the LD nucleus may relay information between the visual and the limbic pathways.”

The gustatory and visceral pathway involves GU/VISC cortical areas and VPMpc/VPLpc nuclei.

“The gustatory and visceral pathway (involving GU/VISC cortical areas and VPMpc/VPLpc nuclei)55,108”

• cites [55] Cechetto, D. F. & Saper, C. B. Evidence for a viscerotopic sensory representation in the cortex and thalamus in the rat. J. Comp. Neurol. 262, 27–45 (1987) sourceNot checked yet

  Not checked in the free run.

• cites [108] Shipley, M. T. & Geinisman, Y. Anatomical evidence for convergence of olfactory, gustatory, and visceral afferent pathways in mouse cerebral cortex. Brain Res. Bull. 12, 221–226 (1984) sourceNot checked yet

  Not checked in the free run.

The limbic pathway is composed of the retrosplenial (RSP) and anterior cingulate (ACA) cortical areas and thalamic nuclei AV, AD and LD.

“The limbic pathway (which is closely integrated with the hippocampal formation system not discussed here) is composed of the retrosplenial (RSP) and anterior cingulate (ACA) cortical areas and thalamic nuclei AV, AD and LD107,114.”

• cites [107] Shibata, H. & Naito, J. Organization of anterior cingulate and frontal cortical projections to the anterior and laterodorsal thalamic nuclei in the rat. Brain Res. 1059, 93–103 (2005) sourceNot checked yet

  Not checked in the free run.

• cites [114] Van Groen, T. & Wyss, J. M. Projections from the anterodorsal and anteroventral nucleus of the thalamus to the limbic cortex in the rat. J. Comp. Neurol. 358, 584–604 (1995) sourceNot checked yet

  Not checked in the free run.

The motor pathway is composed of primary and secondary motor cortical areas (MOp and MOs) and the VAL nucleus.

“The motor pathway is composed of primary and secondary motor cortical areas (MOp and MOs) and the VAL nucleus92,94.”

• cites [92] Porter, L. L. & White, E. L. Afferent and efferent pathways of the vibrissal region of primary motor cortex in the mouse. J. Comp. Neurol. 214, 279–289 (1983) sourceNot checked yet

  Not checked in the free run.

• cites [94] Reep, R. L. & Corwin, J. V. Topographic organization of the striatal and thalamic connections of rat medial agranular cortex. Brain Res. 841, 43–52 (1999) sourceNot checked yet

  Not checked in the free run.

PO modulates the function of all somatosensory cortical areas.

“and PO modulating the function of all somatosensory cortical areas”