Staff Profiles

Jun Zhuang, Ph.D.

Scientist III

Jun Zhuang joined Allen Institute for Brain Science as Scientist in 2013. Before he came to Allen Institute, Zhuang spend 6 years studying the effects of different brain states on the function of visual cortex in awake animals as a Ph.D. student in Dr. Harvey Swadlow’s lab. Zhuang have also studied the mechanisms of neurodegenerative diseases from human patients and animal models as a Master student in Dr. Jiang-Ning Zhou’s lab back in China. Zhuang got his Bachelor degree in Biology (2004), Master degree in Neurobiology (2007) from University of Science and Technology of China and Ph.D. in Psychology (2013) from University of Connecticut.


Research Interests

Zhuang is interested in understanding the basic brain functions at microcircuit level, e.g. what kind of cortical network could give rise to the functionality of mammalian visual system, such as adaptation and feature selection/integration. At Allen Institute, by taking advantage of various genetically engineered mouse lines, Zhuang focuses on studying functional cortical circuits on behaving animals by imaging activities of different cell types across different brain areas.


  • Electrophysiology
  • Vision physiology
  • Optical physiology

Research Programs

  • Neural Coding

Contact Infomation

  • junz<at>alleninstitute<dot>org

Selected Publications View Publications

Structure and function of axo-axonic inhibition

December 1, 2021

Schneider-Mizell CM, Bodor AL, Collman F, Brittain D, Bleckert A, Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Zhuang J, Nandi A, Hu B, Buchanan J, Takeno MM, Torres R, Mahalingam G, Bumbarger DJ, Li Y, Chartrand T, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Popovych S, Wong W, Castro M, Jordan CS, Froudarakis E, Becker L, Suckow S, Reimer J, Tolias AS, Anastassiou CA, Seung HS, Reid RC, da Costa NM

Laminar distribution and arbor density of two functional classes of thalamic inputs to primary visual cortex

Cell Reports
October 12, 2021

Zhuang J, Wang Y, Ouellette ND, Turschak EE, Larsen RS, Takasaki KT, Daigle TL, Tasic B, Waters J, Zeng H, Reid RC

Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

PLoS One
May 1, 2019

Waters J, Lee E, Gaudreault N, Griffin F, Lecoq J, Slaughterbeck C, Sullivan D, Farrell C, Perkins J, Reid D, Feng D, Graddis N, Garrett M, Li Y, Long F, Mochizuki C, Roll K, Zhuang J, Thompson C

Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging

Journal of Neurophysiology
November 20, 2019

Valley MT, Moore MG, Zhuang J, Mesa N, Castelli D, Sullivan D, Reimers M, Waters J

Activation of neuromodulatory axon projections in primary visual cortex during periods of locomotion and pupil dilation

December 19, 2018

Larsen RS, Turschak E, Daigle T, Zeng H, Zhuang J, Waters J

Directional selective neurons in the awake LGN: Response properties and modulation by brain state

Journal of Neurophysiology
July 2014

Hei X, Stoelzel CR, Zhuang J, Bereshpolova YI, Huff J, Alonso JM, Swadlow HA.

Brain state effects on layer 4 of the awake visual cortex.

Journal of Neuroscience
March 12, 2014

Zhuang J, Bereshpolova YI, Stoelzel CR, Huff J, Hei X, Alonso JM, Swadlow HA.

Layer 4 in primary visual cortex of the awake rabbit: contrasting properties of simple cells and putative feed-forward inhibitory interneurons

Journal of Neuroscience
July 2013

Zhuang J, Stoelzel CR, Bereshpolova YI, Huff J, Hei X, Alonso JM, Swadlow HA

Getting drowsy? Alert/nonalert transitions and visual thalamocortical network dynamics

Journal of Neuroscience
November 2011

Bereshpolova YI, Stoelzel CR, Zhuang J, Amitai Y, Alonso JM, Swadlow HA

Cultured rat cortical astrocytes synthesize melatonin: absence of a diurnal rhythm

Journal of Pineal Research
October 2007

Liu YJ, Zhuang J, Zhu HY, Shen YX, Tan ZL, Zhou JN