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Anatomy and function of an excitatory network in the visual cortex

Nature volume 532, pages 370–374 (2016)Cite this article

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Abstract

Circuits in the cerebral cortex consist of thousands of neurons connected by millions of synapses. A precise understanding of these local networks requires relating circuit activity with the underlying network structure. For pyramidal cells in superficial mouse visual cortex (V1), a consensus is emerging that neurons with similar visual response properties excite each other1,2,3,4,5, but the anatomical basis of this recurrent synaptic network is unknown. Here we combined physiological imaging and large-scale electron microscopy to study an excitatory network in V1. We found that layer 2/3 neurons organized into subnetworks defined by anatomical connectivity, with more connections within than between groups. More specifically, we found that pyramidal neurons with similar orientation selectivity preferentially formed synapses with each other, despite the fact that axons and dendrites of all orientation selectivities pass near (<5 μm) each other with roughly equal probability. Therefore, we predict that mechanisms of functionally specific connectivity take place at the length scale of spines. Neurons with similar orientation tuning formed larger synapses, potentially enhancing the net effect of synaptic specificity. With the ability to study thousands of connections in a single circuit, functional connectomics is proving a powerful method to uncover the organizational logic of cortical networks.

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Figure 1: Functional organization of cortical excitatory network connectivity.
Figure 2: Synaptic connectivity between pyramidal cells predicted by function, over and above proximity.
Figure 3: Multiple synapses between neurons are found above chance levels; clustered synapses are frequently observed, but are not specifically enriched.
Figure 4: Sensory physiology predicts synaptic size.

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Acknowledgements

We thank R. Arora, E. Ashbolt, L. Bailey, L. Beaton, P. Chopra, A. Coda, M. Driesbach, R. Fang, M. Fisher, A. Giuliano, H. Godtfredsen, A. Henry, E. Holtzman, P. Hughes, K. Joines, J. Larson, S. Maillet, K. Moody, E. Nguyen, A. Orban, V. Osuiji, K. Robertson, D. Sandman, S. Schwartz, E. Sczerzenie, N. Thatra, L. Thomas, B. Titus, R. Torres for tracing and reconstruction; E. Raviola for discussions and advice; H. Kim for technical support at the beginning of the study; A. Wetzel for help with alignment and stitching; A. Cardona and S. Saalfeld for the CATMAID project being openly available; and N. da Costa for launching the EM annotation program at the Allen Institute for Brain Science, with help and support from B. Youngstrom, R. Young, C. Dang and J. Phillips. We also thank D. Brittain, W. Gray Roncal, L. Thomas, S. Yurgenson, H. Elliot, and the HMS Image and Data Analysis Core for programming; E. Benecchi and the HMS EM Core Facility for technical support; P.J. Manavalan, K. Lillaney, and R. Burns, for helping make the data freely available; and S. Druckmann, Y. Park, C. Priebe, and J. Vogelstein for discussions on statistical analyses. We are indebted to M. Andermann, S. Chatterjee, N. da Costa, L. Glickfeld, C. Harwell, D. Hildebrand, M. Histed, S. Mihalas, L. Ostroff, E. Raviola, and J. T. Vogelstein for critical reading of various versions of the manuscript. This work was supported by NIH grants to RCR (R01 EY10115 and R01 NS075436); through resources provided by the NRBSC (P41 RR06009) and MMBioS (P41 GM103712); the HMS Vision Core Grant (P30 EY12196); and the AIBS. We thank the Allen Institute founders, P. G. Allen and J. Allen, for their vision, encouragement, and support. WCL was also supported by the Bertarelli Program in Translational Neuroscience and Neuroengineering, Edward R. and Anne G. Lefler Center, and Stanley and Theodora Feldberg Fund, and the NIH (R21 NS085320). VB was also supported by Neuro-Electronics Research Flanders. The project described was partially supported by the NIH by the above named awards. Its content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Author information

Authors and Affiliations

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

    Wei-Chung Allen Lee, Vincent Bonin, Michael Reed, Brett J. Graham & R. Clay Reid

  2. Neuro-Electronics Research Flanders, a research initiative by imec, Vlaams Instituut voor Biotechnologie (VIB) and Katholieke Universiteit (KU), Leuven, Leuven, 3001, Belgium

    Vincent Bonin

  3. Biomedical Applications Group, Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Greg Hood

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

    Katie Glattfelder & R. Clay Reid

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Contributions

W.-C.A.L. and V.B. performed the in vivo calcium imaging and analysed it. W.-C.A.L. processed the tissue for EM, sectioned the series, and aligned the block with the in vivo imaging. W.-C.A.L. and M.R. imaged it on the TEMCA. G.H. and W.-C.A.L. aligned the EM images into a volume. W.-C.A.L., M.R., K.G. annotated the EM dataset and W.-C.A.L. and K.G. supervised segmentation efforts. B.J.G. and W.-C.A.L. generated software for visualization and analysis. W.-C.A.L. performed quantitative analysis on the tracing. W.-C.A.L., V.B., and R.C.R. designed the experiment and wrote the paper.

Corresponding authors

Correspondence to Wei-Chung Allen Lee or R. Clay Reid.

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Competing interests

The authors declare no competing financial interests.

Additional information

The aligned EM dataset will be publicly accessible at http://neurodata.io/lee16.

Extended data figures and tables

Extended Data Figure 1 Sensory physiology is maintained over days.

a, Visually evoked calcium responses are maintained across days. Three example neurons (rows) on the first, ninth, and twelfth day (columns) of in vivo two-photon calcium imaging. Three individual trial responses (black lines) of 8 directions, 3 spatial and 2 temporal frequencies (left column, day 1); or 16 directions, 2 spatial and 2 temporal frequencies (middle and right rows, days 9 and 12). Scale bars, 100% ΔF/F and 4 s. Standard deviation of preferred direction across days for each neuron is to the upper right of activity matrices. b, Neurons direction selectivity is stable over days. Cumulative distribution of standard deviation of peak preferred direction (4.1° ± 1.7°, median ± s.e.m.) across days for 25 neurons measured over multiple days.

Extended Data Figure 2 Deep layer apical responses are likely suprathreshold reflecting activity at the soma.

Example ΔF/F time courses from a deep layer apical dendrite optically sectioned in vivo across 6–8 planes. Note, activity is correlated across depth and relatively stable over days (Extended Data Fig. 1).

Extended Data Figure 3 Distribution of orientation and direction tuned cells.

a, b, Histograms of functionally characterized cells with measured peak orientation (a) and direction preference (b).

Extended Data Figure 4 In vivo to EM correspondence of neuronal targets.

Top row, volumetric projections of the aligned in vivo and EM imaged volumes. Physiology planes were acquired horizontally and EM sections cut frontally (coronally) from the brain. Interdigitated physiology planes are from 2 representative volumetrically scanned experiments stacked atop one another in space (Fig. 1c) so as to span from the border of L1 and L2 through the depth of L2/3. Scale bar, 100 μm. middle and bottom rows, re-sliced planes through the in vivo volume corresponding to EM sections. Arrowheads indicate matching cell bodies, and arrows deep layer (putative L5) apical dendrites. Small black dots mark the centres of cell bodies corresponding principally to nuclei where calcium indicator fluorescence is typically excluded. Scale bar, 50 μm.

Extended Data Figure 5 En face synapse example.

Serial sections from an obliquely cut synapse (Fig. 1d, top right, same scale). Colour overlays correspond to peak orientation preference (colour key, same as Fig. 1a, bottom).

Extended Data Figure 6 Network reconstruction.

3D rendering of dendrites and axons, cell bodies (large spheres), and synapses (small spheres) of, a, 50 functionally characterized neurons reconstructed in the EM volume. Cell bodies, dendrites, axons, and synapses colour coded by peak preferred stimulus orientation (colour key, bottom right). Axons are the thinnest processes, dendrites of L2/3 neurons are thicker, and deep layer apical dendrites are rendered with the largest calibre. Dendritic spines were traced only if they participated in connections between reconstructed neurons. b, Approximately 1,800 additional neuronal targets reconstructed in the EM volume (transparent grey). Input and output synapses are coloured cyan and red respectively when orientation selectivity was not known. Bounding box matches region in Fig. 1f. Scale bar, 150 μm.

Extended Data Figure 7 Network modularity is significantly non-random.

a, Connectivity matrix of 201 excitatory neuronal targets in our network reconstruction with multiple synaptic partners (that is, degree ≥ 2, no leaf nodes, same as Fig. 1e). Colour represents the number of synapses (colour key, c, right) between pre- and post-synaptic neurons (same neuron order on both ordinate and abscissa). Subnetworks of interconnected neurons (white boxes) detected using a consensus method of Louvain clustering17,31. b, Modularity (Q) of the reconstructed network is significantly greater than null models with degree, weight, and strength preserved. Histograms of the modularity values for the reconstructed network (dark grey, Qmean = 0.55 ± 0.003, mean ± s.d., computed 1,000 times) is significantly greater than for the Qmean of shuffled null models (light grey, Qmean = 0.50 ± 0.009, mean ± s.d., P ≈ 0, permutation test, kshuffles = 1,000). c, Example of the shuffled connectivity matrix with a Q closest to the mean of the shuffled distribution with clustering (white boxes) computed as in a. d, Null models are well-shuffled, while approximating connection input and output strengths. Histograms of correlation coefficients between the reconstructed network and the null models’ in (blue: 0.92 ± 0.02, mean ± s.d.) and out (red: 96 ± 0.01, mean ± s.d.) strength and connectivity matrix (grey: 9.1 × 10−4 ± 0.01, mean ± s.d.). e, Occurrences of three neuron connectivity motifs found in the reconstructed network between excitatory neuronal targets.

Extended Data Figure 8 Cell bodies are functionally intermingled.

a, b, Differences in peak orientation (a) and direction preference (b) between neuron pairs plotted against the distance between their cell bodies. Uniform distributions of functional versus spatial distance suggest a salt and pepper intermingling of neuronal cell bodies across functional properties.

Extended Data Figure 9 Axons and dendrites are functionally intermingled at shorter length scales.

Uniform functional diversity and prediction of connectivity at finer length scales suggest a salt-and-pepper intermingling of axons and dendrites. a–d, Same as Fig. 2c–f for s = 1 μm. Significance tests: a, P ≈ 0, permutation test, nconnected pairs = 29, nunconnected pairs = 1,951; b, Between connected (red line) and unconnected pairs (blue line, P < 0.05, permutation test, nconnected pairs = 29, nunconnected pairs = 1,951) or a model distribution based on potential synapse length (black line, P < 0.01, permutation test, nconnected pairs = 29, nunconnected pairs = 1,951). Shaded regions, a, b, and error bars, d, represent bootstrapped standard error.

Extended Data Figure 10 Connectivity is not predicted by residual signal correlation after removal of orientation preference.

a–b, Example activity (ΔF/F individual trial time courses) for connected neurons from experiments varying direction, spatial and temporal frequencies of grating stimuli. a, Presynaptic cell (top row) and two of its postsynaptic partners’ (middle and bottom rows) for 3 spatial and 2 temporal frequencies and one orientation (orientation tuning was virtually identical). b, Presynaptic cell (top) and a postsynaptic deep layer apical dendrite’s (bottom) responses to 2 spatial and 2 temporal frequencies, and 2 directions, (again, orientation tuning was virtually identical). Grey window delineates time of stimulus presentation. Scale bars, 100% ΔF/F and 4 s. c, Cumulative distribution of signal correlations from simultaneously measured cells was significantly greater between connected than unconnected pairs (P < 0.01, permutation test, nconnected pairs = 10, nunconnected pairs = 426) or a model distribution based on potential synaptic connectivity (P < 0.05, permutation test). d, After averaging over orientations, the cumulative distribution of signal correlations was similar between connected and unconnected pairs (P > 0.14, permutation test, nconnected pairs = 10, nunconnected pairs = 426) and a model distribution based on potential synaptic connectivity (P > 0.25, permutation test, nconnected pairs = 10, nunconnected pairs = 426). Shaded regions, c, d, represent bootstrapped standard error.

Supplementary information

Supplementary Data

This file contains Supplementary Data 1-3. (PDF 926 kb)

In vivo fluorescence to EM correspondence

Fluorescence in vivo two-photon microscopy data 3-D aligned with the EM volume. To visualize three imaging datasets (in vivo anatomy: fluorescence volume, in vivo physiology: fluorescence planes; and EM) first, the volume is flown-through, oriented with the EM sections (coronally, relative to the brain). Then the volume is rotated so that the perspective is above the surface and horizontal relative to the brain. Next, descending into the brain, note the correspondence of GCaMP3 (green) and functionally colored cell bodies with the nuclei in EM, the blood vessels (red) with clear vasculature in EM, and track apical dendrites in vivo (green radially oriented processes) in EM (large caliber cylindrical dendrites with spines). (MOV 20389 kb)

EM volume overview

The video shows a fly-through of the aligned EM series. Please see Author Information for directions to the publicly accessible high-resolution aligned dataset. (MOV 18428 kb)

Higher resolution EM core

The video shows fly-through of a cropped (16.4 x 16.4 µm) region traversing 400 of the aligned EM sections in the functionally imaged volume. (MOV 27726 kb)

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Lee, WC., Bonin, V., Reed, M. et al. Anatomy and function of an excitatory network in the visual cortex. Nature 532, 370–374 (2016). https://doi.org/10.1038/nature17192

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