
Jérôme Lecoq, Ph.D.
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
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
Selected Publications
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.
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.
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
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
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
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
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
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