Team

Staff Profiles

Principal Scientist

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.

Expertise

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

Research Programs

Cortical Activity Map

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

eNeuro
February 9, 2022

Mayner WGP, Marshall W, Billeh YN, Gandhi SR, Caldejon S, Cho A, Griffin F, Hancock N, Lambert S, Lee EK, Luviano JA, Mace K, Nayan C, Nguyen TV, North K, Seid S, Williford A, Cirelli C, Groblewski PA, Lecoq J, Tononi G, Koch C, Arkhipov A.

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

eLife
July 16, 2021

Siegle JH, Ledochowitsch P, Jia X, Millman DJ, Ocker GK, Caldejon S, Casal L, Cho A, Denman DJ, Durand S, Groblewski PA, Heller G, Kato I, Kivikas S, Lecoq J, Nayan C, Ngo K, Nicovich PR, North K, Ramirez TK, Swapp J, Waughman X, Williford A, Olsen SR, Koch C, Buice MA, de Vries SE.

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

eLife
March 8, 2021

Huang L, Ledochowitsch P, Knoblich U, Lecoq J, Murphy GJ, Reid RC, de Vries SEJ, Koch C, Zeng H, Buice MA, Waters J, Li L

Survey of spiking in the mouse visual system reveals functional hierarchy

Nature
January 20, 2021

Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries S., Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo D, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C

Removing independent noise in systems neuroscience data using DeepInterpolation

Nature Methods
November 18, 2021

Lecoq J, Oliver M, Siegle JH, Orlova N, Ledochowitsch P, Koch C

A standardized head-fixation system for performing large-scale, in vivo physiological recordings in mice

Journal of Neuroscience Methods
September 15, 2020

Groblewski PA, Sullivan D, Lecoq J, de Vries SEJ, Caldejon S, L'Heureux Q, Keenan T, Roll K, Slaughterback C, Williford A, Farrell C

Fundamental bounds on the fidelity of sensory cortical coding

Nature
April 2020

Rumyantsev OI, Lecoq JA, Hernandez O, Zhang Y, Savall J, Chrapkiewicz R, Li J, Zeng H, Ganguli S, Schnitzer MJ

VIP interneurons in mouse primary visual cortex selectively enhance responses to weak but specific stimuli

eLife
October 27, 2020

Millman DJ, Ocker GK, Caldejon S, Kato I, Larkin JD, Lee EK, Luviano J, Nayan C, Nguyen TV, North K, Seid S, White C, Lecoq J, Reid C, Buice MA, de Vries SE

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

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

Nature Neuroscience
December 16, 2019

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

Hierarchical organization of cortical and thalamic connectivity

Nature
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

Wide. Fast. Deep. Recent Advances in Multi-Photon Microscopy of in vivo Neuronal Activity

Journal of Neuroscience
October 2, 2019

Lecoq J, Orlova N, Grewe BF

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

Cell
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

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

bioRxiv
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

Nature
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