Staff Profiles

Soumya Chatterjee, Ph.D.

Senior Scientist

Soumya Chatterjee joined the Neural Coding group at the Allen Institute in 2013 to investigate the functional properties of cortical microcircuits, working at the interface of neural ensembles and single-neuron computation. Prior to joining the Institute, his main area of research was the cortical representation of color in trichromatic primates. As a graduate student with Ed Callaway at the Salk Institute, he used electrophysiological and neuroanatomical methods to show the parallel organization of early color pathways and their cortical targets. As a postdoctoral fellow with Clay Reid at Harvard Medical School, he followed these chromatic inputs into the circuitry of primary visual cortex, identifying a fine-scale architecture of color by bringing the technique of in vivo two-photon imaging to the primate visual system. He holds an A.B. in Physics from Harvard and a Ph.D. in Neurosciences from the University of California, San Diego.


Research Interests

The early visual system takes input, given to it in a language of photon catches and wavelength, and paraphrases it in a very different language of spike patterns that represent low-level properties of the visual scene. This information is combined and processed and recombined into progressively more complicated representations in a hierarchical system that ultimately provides the animal with what it needs to interact with the world. We know much about the response properties of individual neurons in visual cortex, about simple cells and complex cells and direction-selective cells and many others in a menagerie of richly varied circuit elements. But each of these cells is driven by a network of hundreds or thousands of other cells directly connected to it (a monosynaptic circuit), which provides it with all the information it will ever get about the outside world. We don’t know the functional properties of these circuits, the geometry and logic of their connectivity, or how single neurons take the spatiotemporal patterns of inputs bombarding their dendritic trees and transform them into outputs that feed into the next stage of processing. These are the basic questions of microcircuitry and single-neuron computation that inform my research, and by combining new circuit tracing methods with optical physiology in behaving animals, it may be possible to finally glimpse how these circuits are wired and function in vivo.


  • Functional neuroanatomy
  • Cortical microcircuits
  • Parallel pathways

Selected Publications

RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations

Nature Methods
March 23, 2020

Yao S, Yuan P, Ouellette B, Zhou T, Mortrud M, Balaram P, Chatterjee S, Wang Y, Daigle TL, Tasic B, Kuang X, Gong H, Luo Q, Zeng S, Curtright A, Dhaka A, Kahan A, Gradinaru V, Chrapkiewicz R, Schnitzer M, Zeng H, Cetin A

Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons

Nature Neuroscience
March 5, 2018

Chatterjee S, Sullivan H, MacLennan BJ, Xu R, Hou Y, Lavin TK, Lea N, Michalski J, Babcock K, Dietrich S, Matthews GA, Beyeler A, Calhoon GG, Glober G, Whitesell J, Yao S, Cetin A, Harris J, Zeng H, Tye K, Reid RC, Wickersham IR