Abstract

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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Acknowledgements

We wish to thank the Allen Mouse Brain Connectivity Atlas Advisory Council members, D. Anderson, E. M. Callaway, K. Svoboda, J. L. R. Rubenstein, C. B. Saper and M. P. Stryker for their insightful advice. We thank T. Ragan for providing invaluable support and advice in the development and customization of the TissueCyte 1000 systems. We are grateful for the technical support of the many staff members in the Allen Institute who are not part of the authorship of this paper. This work was funded by the Allen Institute for Brain Science. The authors wish to thank the Allen Institute founders, P. G. Allen and J. Allen, for their vision, encouragement and support.

Author information

Author notes

    • Seung Wook Oh
    • , Julie A. Harris
    •  & Lydia Ng

    These authors contributed equally to this work.

Affiliations

  1. Allen Institute for Brain Science, Seattle, Washington 98103, USA

    • Seung Wook Oh
    • , Julie A. Harris
    • , Lydia Ng
    • , Brent Winslow
    • , Nicholas Cain
    • , Stefan Mihalas
    • , Quanxin Wang
    • , Chris Lau
    • , Leonard Kuan
    • , Alex M. Henry
    • , Marty T. Mortrud
    • , Benjamin Ouellette
    • , Thuc Nghi Nguyen
    • , Staci A. Sorensen
    • , Clifford R. Slaughterbeck
    • , Wayne Wakeman
    • , Yang Li
    • , David Feng
    • , Anh Ho
    • , Eric Nicholas
    • , Karla E. Hirokawa
    • , Phillip Bohn
    • , Kevin M. Joines
    • , Hanchuan Peng
    • , Michael J. Hawrylycz
    • , John W. Phillips
    • , John G. Hohmann
    • , Paul Wohnoutka
    • , Christof Koch
    • , Amy Bernard
    • , Chinh Dang
    • , Allan R. Jones
    •  & Hongkui Zeng
  2. Laboratory of Systems Neuroscience, National Institute of Mental Health, Bethesda, Maryland 20892, USA

    • Charles R. Gerfen

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Contributions

H.Z., S.W.O., J.A.H. and L.N. contributed significantly to overall project design. S.W.O. and H.Z. did initial proof-of-principle studies. J.A.H., M.T.M., B.O., P.B., T.N.N., K.E.H. and S.A.S. conducted tracer injections and histological processing. B.W., C.R.S., E.N., A.H., P.W. and A.B. carried out imaging system establishment, maintenance, and imaging activities. L.N., C.L., L.K., W.W., Y.L., D.F. and H.P. conducted informatics data processing and online database development. A.M.H., K.M.J. and Q.W. conducted image quality control and data annotation. N.C., S.M. and C.K. performed computational modelling. H.Z., S.W.O., A.R.J., C.D., C.K., A.B., J.G.H., J.W.P. and M.J.H. performed managerial roles. H.Z., J.A.H., L.N., S.M., N.C., Q.W., S.W.O., C.R.G. and C.K. were main contributors to data analysis and manuscript writing, with input from other co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hongkui Zeng.

The Allen Mouse Brain Connectivity Atlas is accessible at (http://connectivity.brain-map.org). All AAV viral tracers are available at Penn Vector Core, and AAV viral vector DNA constructs have been deposited at the plasmid repository Addgene.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains a detailed description of the construction of the computational connectivity model and the network analyses based on this model, Supplementary Figures 1-5, Supplementary Tables 5-8 and Supplementary references.

Excel files

  1. 1.

    Supplementary Table 1

    The 295 non-overlapping, mid-level anatomical regions selected from the Allen Reference Atlas ontology that have tiling coverage of the entire brain space. These regions were used for both targeted stereotaxic injections and for connectivity data analysis. The first tab shows all 1204 non-fiber tract brain regions and fiber tracts delineated in the Allen Reference Atlas, in ontological order. The final selected 295 brain regions are marked as “1”. The second tab lists only the 295 selected regions, ordered by volumes (voxel counts). A histogram of the voxel counts for all 295 regions is also shown. The 18 regions that were not covered in the Phase I dataset are marked in the “Structure Hit with rAAV” column. The next two columns indicate whether a structure was infected as the primary site or secondary site of any injection experiment. The last column shows the structures that were included in the linear model matrix (figure 4a).

  2. 2.

    Supplementary Table 2

    Normalized projection strength values underlying the Connectivity Matrix in figure 3. Values from all 469 injections (in rows) and the 295 anatomical target regions on both ipsilateral and contralateral hemispheres (in columns) are shown here. Each value is the normalized projection volume (sum of segmented pixels across all voxels in one target region / sum of segmented pixels across voxels in injection volume). Also shown are the manually annotated primary and secondary anatomical structures contained within each injection site, as well as the volume of each injection site.

  3. 3.

    Supplementary Table 3

    Quantitative projection strength values underlying the linear model based Connectivity Matrix in figure 4a. The 213 anatomical regions as both source regions (in rows) and target regions on both ipsilateral and contralateral hemispheres (in columns) are shown here. See Supplementary Table 1 for the corresponding full name and acronym of each region.

  4. 4.

    Supplementary Table 4

    Cartesian distances between the centers of mass of all the interconnected source and target region pairs for the 213 anatomical regions used in the linear model based Connectivity Matrix in figure 4a. Names of source regions (in rows) are shown in Column A, and names for target regions on both ipsilateral and contralateral hemispheres (in columns) are shown in Row 1. See Supplementary Table 1 for the corresponding full name and acronym of each region.

Videos

  1. 1.

    Exemplar TissueCyte STP tomography image sets showing axonal projections throughout the brain

    The image sets are from 5 anatomically distinct injection sites representing several major brain subdivisions: primary motor area (MOp), centromedial nucleus of the thalamus (CM), medial preoptic area of the hypothalamus (MPO), pontine central gray (PCG), and intermediate reticular nucleus of the medulla (IRN).

  2. 2.

    Average template brain and its alignment with Allen Reference Atlas

    Coronal image series of the average template brain at 10 µm X-Y and 25 µm Z sampling rate is shown first. Coronal image series of the alignment of the Allen Reference Atlas structures (at 27% opacity) onto the average template brain at the same sampling rate is shown next.

  3. 3.

    Locations of all injection sites

    Physical locations of all 469 injection sites are superimposed onto the coronal image series of the average template brain, to show the overall anatomical coverage of the Phase I experiments. Each injection site is shown as a group of 100 x 100 x 100 µm3 voxels contained within its injection site polygon, and in the ontology color of the primary anatomical structure it occupies. In some cases, viral infections along the injection tracts can be seen.

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DOI

https://doi.org/10.1038/nature13186

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