Staff Profiles

Jérôme Lecoq, Ph.D.

Senior Manager, Optical Physiology

Jérôme Lecoq joined the Allen Institute in 2015 to lead efforts in mapping cortical computation using in vivo two-photon microscopy in behaving animals. He brings 10 years of experience in in vivo microscopy working with rodents. Prior to joining the Allen Institute, Lecoq was a postdoctoral scholar in Mark Schnitzer’s group at Stanford University, where he developed novel imaging methodologies to monitor large neuronal populations in the visual cortex of behaving mice.  Lecoq received a Ph.D. in Neuroscience from the Pierre and Marie Curie University in Paris and an M.S. in Physics from ESPCI ParisTech, a French multidisciplinary engineering school.


Research Interests

Understanding how the cortex works will require building complex models that capture the essence of its computational principles. To test each of these models, we need datasets that appropriately capture the dimensionality of all the phenomena we want to understand. I seek to generate the datasets that will allow us to test decades-old ideas on cortical function. What are the roles of the different cortical layers? How do multiple brain areas collaborate to bring about cortical computation? Using a combination of high-throughput neuronal population recordings via optical imaging and careful experimental design, I hope to alleviate a generic problem in neuroscience: overfitting. 


  • Neurophysiology
  • In vivo brain imaging
  • Two-photon microscopy
  • Optical development
  • Computational analysis
  • Brain metabolism

Research Programs

  • Cortical Activity Map

Selected Publications

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

September 12, 2018

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

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

July 12, 2018

Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ2, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

June 29, 2018

de Vries S, Lecoq J, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng F, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon S, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin J, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten D, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, R Reid C, Koch C

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

Neural ensemble dynamics underlying a long-term associative memory

March 30, 2017

Grewe BF, Gründemann J, Kitch LJ, Lecoq JA, Parker JG, Marshall JD, Larkin MC, Jercog PE, Grenier F, Li JZ, Lüthi A, Schnitzer MJ

Long-Term Optical Access to an Estimated One Million Neurons in the Live Mouse Cortex

Cell Reports
December 20, 2016

Kim TH, Zhang Y, Lecoq J, Jung JC, Li J, Zeng H, Niell CM, Schnitzer MJ

Visualizing mammalian brain area interactions by dual-axis two-photon calcium imaging

Nature Neuroscience
December 2014

Lecoq J, Savall J, Vučinić D, Grewe BF, Kim H, Li JZ, Kitch LJ, Schnitzer MJ

An infrared fluorescent protein for deeper imaging

Nature Biotechnology
August 2011

Lecoq J, Schnitzer MJ

Simultaneous two-photon imaging of oxygen and blood flow in deep cerebral vessels

Nature Medicine
June 5, 2011

Lecoq J, Parpaleix A, Roussakis E, Ducros M, Goulam Houssen Y, Vinogradov SA, Charpak S

Peripheral adaptation codes for high odor concentration in glomeruli

Journal of Neuroscience
March 11, 2009

Lecoq J, Tiret P, Charpak S

Odor-evoked oxygen consumption by action potential and synaptic transmission in the olfactory bulb

Journal of Neuroscience
February 4, 2009

Lecoq J, Tiret P, Najac M, Shepherd GM, Greer CA, Charpak S