Article

Network anatomy and in vivo physiology of visual cortical neurons

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Abstract

In the cerebral cortex, local circuits consist of tens of thousands of neurons, each of which makes thousands of synaptic connections. Perhaps the biggest impediment to understanding these networks is that we have no wiring diagrams of their interconnections. Even if we had a partial or complete wiring diagram, however, understanding the network would also require information about each neuron's function. Here we show that the relationship between structure and function can be studied in the cortex with a combination of in vivo physiology and network anatomy. We used two-photon calcium imaging to characterize a functional property—the preferred stimulus orientation—of a group of neurons in the mouse primary visual cortex. Large-scale electron microscopy of serial thin sections was then used to trace a portion of these neurons’ local network. Consistent with a prediction from recent physiological experiments, inhibitory interneurons received convergent anatomical input from nearby excitatory neurons with a broad range of preferred orientations, although weak biases could not be rejected.

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Acknowledgements

We thank E. Raviola for discussions and technical advice on all aspects of EM; J. Stiles for support and advice concerning the alignment and stitching effort at The Pittsburgh Supercomputing Center; J. Lichtman for discussions and, along with K. Blum and J. Sanes, support from the Center for Brain Science; A. Cardona for help with TrakeEM2, and many modifications of it; and H. Pfister and S. Warfield for discussions and help with computational issues. We also thank S. Butterfield for programming, and L. Benecchi and Harvard Medical School EM Core Facility for technical support. For technical help with EM and its interpretation, we thank K. Harris, M. Bickford, M. Ellisman, K. Martin and T. Reese. We thank J. Assad, R. Born, J. Maunsell, J. Stiles, E. Raviola, and members of the Reid laboratory for critical reading of the manuscript. This work was supported by the Center for Brain Science at Harvard University, Microsoft Research, and the NIH though the NEI to R.C.R. (EY10115 and EY18742) and through resources provided by the NRBSC (P41 RR06009), which is part of The Pittsburgh Supercomputing Center; and by fellowships from Harvard Center of Neurodegeneration and Repair to D.D.B. and the NEI to W.-C.A.L. (EY18532).

Author information

Affiliations

  1. Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Davi D. Bock
    • , Wei-Chung Allen Lee
    • , Aaron M. Kerlin
    • , Mark L. Andermann
    • , Sergey Yurgenson
    • , Hyon Suk Kim
    •  & R. Clay Reid
  2. The Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA

    • Davi D. Bock
    • , Wei-Chung Allen Lee
    • , Edward R. Soucy
    • , Hyon Suk Kim
    •  & R. Clay Reid
  3. National Resource for Biomedical Supercomputing, Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA

    • Greg Hood
    •  & Arthur W. Wetzel

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Contributions

D.D.B., E.R.S., S.Y. and R.C.R. designed and built the TEMCA system, and D.D.B. programmed it. A.M.K. and M.L.A. performed the in vivo imaging and A.M.K. analysed it. D.D.B. processed the tissue, and D.D.B. and W.-C.A.L. aligned the block with the in vivo imaging. W.-C.A.L. sectioned the series, and D.D.B., W.-C.A.L. and H.S.K. imaged it on the TEMCA. G.H. and A.W.W. stitched and aligned the images into a volume. D.D.B., W.-C.A.L. and H.S.K. did most of the segmentation. D.D.B., W.-C.A.L. and S.Y. performed quantitative analysis on the tracing. D.D.B., W.-C.A.L. and R.C.R. designed the experiment and wrote the paper, with considerable help from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to R. Clay Reid.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures

    The file contains Supplementary Figures 1-8 with legends.

Videos

  1. 1.

    Supplementary Movie 1

    The movie shows section-by-section fly-through of the aligned EM series. Please see Methods for directions to the publicly accessible high-resolution aligned dataset.

  2. 2.

    Supplementary Movie 2

    The movie shows section-by-section fly-through of a cropped (8.2 x 8.2 µm) region traversing a sixth of the aligned EM sections at the level of the functionally imaged plane. With global 3-D alignment of the EM data set, many of the finest processes in the neuropil (e.g. dendritic spines and fine axons) can be unambiguously followed for tens to hundreds of micrometres.

  3. 3.

    Supplementary Movie 3

    The movie shows fifty serial sections in the aligned EM series rotating as a false-colour volumetric rendering.

  4. 4.

    Supplementary Movie 4

    The movie shows zoomed-in view of a region through fifty serial sections rotating as a false-colour volumetric rendering.

  5. 5.

    Supplementary Movie 5

    The movie shows rotating 3-D renderings of the skeletonized arbors and cell bodies of the functionally characterized cells, their postsynaptic targets, and their convergence targets.

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