Staff Profiles

Josh Siegle, Ph.D.

Senior Scientist

Josh Siegle joined the Allen Institute in 2014 as part of the Neural Coding research program. He received his PhD in Neuroscience from MIT, where he studied hippocampal circuits with Dr. Matthew Wilson and cortical and thalamic circuits with Dr. Christopher Moore. In both labs, he combined optogenetics and extracellular electrophysiology in order to investigate the impact of neural oscillations on behavior. In addition to his scientific work, Josh has been heavily involved in the design and distribution of open-source tools for electrophysiology. He co-founded Open Ephys in order to centralize some of the development efforts occurring across the community. Josh has also carried out research at the Max Planck Institute for Biological Cybernetics and Brown University, where he earned an Sc.B. in Neuroscience.


Research Interests

The effortless way in which we see the world around us belies the complexity of the neural circuits that make our perceptions possible. All of our experience requires the precise coordination of distributed networks of cells, which fluidly converge and diverge in response to novel external challenges and shifting internal goals. I'm interested in studying how neural activity on the timescale of milliseconds underlies the brain's tremendous versatility. At the Allen Institute, I will apply new techniques for multichannel electrophysiology and optogenetics in order to observe and perturb the visual system in real time.


  • Large-scale electrophysiology
  • Optogenetics
  • Open-source tool development

Research Programs

  • Neural Coding

Selected Publications View Publications

Multi-regional module-based signal transmission in mouse visual cortex

May 4, 2022

Jia X, Siegle JH, Durand S, Heller G, Ramirez TK, Koch C, Olsen SR

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

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.

Survey of spiking in the mouse visual system reveals functional hierarchy

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

Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex

March 5, 2020

Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A

High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification

Journal of Neurophysiology
March 6, 2019

Jia X, Siegle JH, Bennett C, Gale SD, Denman DJ, Koch C, Olsen SR

Fully integrated silicon probes for high-density recording of neural activity

November 8, 2017

Jun JJ, Steinmetz NA, Siegle JH, Denman DJ, Bauza M, Barbarits B, Lee AK, Anastassiou CA, Andrei A, Aydın Ç, Barbic M, Blanche TJ, Bonin V, Couto J, Dutta B, Gratiy SL, Gutnisky DA, Häusser M, Karsh B, Ledochowitsch P, Lopez CM, Mitelut C, Musa S, Okun M, Pachitariu M, Putzeys J, Rich PD, Rossant C, Sun WL, Svoboda K, Carandini M, Harris KD, Koch C5 O'Keefe J, Harris TD

Gamma-range synchronization of fast-spiking interneurons can enhance detection of tactile stimuli

Nature Neuroscience
August 24, 2014

Siegle JH, Pritchett DL, Moore CI

Selective optical drive of thalamic reticular nucleus generates thalamic bursts and cortical spindles

Nature Neuroscience
July 2011

Halassa MM, Siegle JH, Ritt J, Ting JT, Feng G, & CI Moore