Staff Profiles

Quanxin Wang, Ph.D.

Principal Scientist

Quanxin Wang joined the Allen Institute in 2010 as an expert neuroanatomist to help guide the creation of multiple reference atlases. Since joining the Allen Institute he has worked on the anatomical reference atlases for both the Allen Mouse Brain Atlas and the Allen Mouse Brain Connectivity Atlas – large-scale and high-throughput mapping efforts of the genes and neural connectivity in the mouse brain, respectively. His primary interest is to understand how visual information is processed in the mouse visual system. Prior to joining the Allen Institute, Wang studied the mouse visual cortex at Washington University in St. Louis. As a postdoctoral fellow at Osaka University, he used a tract tracing technique to study the postnatal development of intrinsic horizontal axons in the inferior temporal cortex and primary visual cortex of the macaque brain. Wang received a M.D. from Heilongjiang University of Traditional Chinese Medicine in China and a Ph.D. in anatomy from Toyama Medical and Pharmaceutical University in Japan.


Research Interests

Research Interests The mouse visual system has increasingly been used as model to study vision. The most important reason for shifting from primate and carnivore models to the mouse is that transgenetic mice can be routinely used in laboratories. Recently, ample evidence has shown that the mouse has a more complex visual system than previously thought, composed of at least ten visual areas. These visual areas are interconnected to form dorsal and ventral visual processing streams, which are similar to those in monkeys and cats. However, the most popular anatomical atlases such as the Allen Reference Atlas and the Mouse Brain in Stereotactic Coordinates only show six and four visual areas, respectively. Clearly, these atlases need to be updated with the most recent knowledge of mouse visual cortex in order to adequately use them to study mouse vision at different levels from cell types and neuronal coding to behavior and finally to computational model. My first interest is to build a three-dimensional common coordinate framework where the data collected from different modalities can be put into the same common space. My second interest is to map the cell numbers in mouse brain because this information is essential for building a computational model and comparing with aging and diseased brain and understand the revolutionary scaling law. My third interest is to understand the intrinsic connections of mouse primary visual cortex. The intrinsic connections derived from layer 2/3 pyramidal neurons in primates and cats may be linked to functional columns such as orientation columns. However, such orientation columns have not been observed in mouse primary visual cortex. The functional role of intrinsic connections in the mouse primary visual cortex remains mystery. Through leading studies such as those described above I aim to make a great contribution to the research programs at the Allen Institute.  


  • Neuroanatomy

Research Programs

  • Cell types
  • Neural coding
  • Atlasing

Selected Publications View Publications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

May 14, 2020

Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L

Hierarchical organization of cortical and thalamic connectivity

October 30, 2019

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Choi H, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feiner A, Feng D, Gaudreault N, Gerfen CR, Graddis N, Groblewski PA, Henry AM, Ho A, Howard R, Knox JE, Kuan L, Kuang X, Lecoq J, Lesnar P, Li Y, Luviano J, McConoughey S, Mortrud MT, Naeemi M, Ng L, Oh SW, Ouellette B, Shen E, Sorensen SA, Wakeman W2, Wang Q2, Wang Y, Williford A, Phillips JW, Jones AR, Koch C, Zeng H

The organization of intracortical connections by layer and cell class in the mouse brain

April 18, 2018

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Knox J, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feng D, Gaudreault N, Gerfen C, Graddis N, Groblewski PA, Henry A, Ho A, Howard R, Kuan L, Lecoq J, Luviano J, McConoughey S, Mortrud M, Naeemi M, Ng L, Oh SW, Ouellette B, Sorensen SA, Wakeman W, Wang Q, Williford A, Phillips J, Jones A, Koch C, Zeng H

Visual physiology of the Layer 4 cortical circuit in silico

PLoS Computational Biology
November 12, 2018

Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-LLavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C

Automatic navigation system for the mouse brain

Journal of Comparative Neurology
October 13, 2018

Tappan S, Eastwood BS, O'Connor N, Wang Q, Ng L, Feng D, Hooks B, Gerfen CR, Hof PR, Schmitz S, Glaser JR

Gateways of ventral and dorsal streams in mouse visual cortex

Journal of Neuroscience
February 2011

Wang Q, Gao E, Burkhalter A

Area map of mouse visual cortex

Journal of Comparative Neurology
May 2007

Wang Q & Burkhalter A

In vivo transcranial imaging of connections in mouse visual cortex

Journal of Neuroscience Methods
January 2007

Wang Q, Gao E, Burkhalter A