Staff Profiles

Peter Ledochowitsch, Ph.D., Dipl.-Phys.

Senior Scientist

Peter Ledochowitsch is currently a Senior Scientist in the Department of Modeling, Analysis, and Theory (MAT), working with Michael Buice. Prior to that, Peter has been developing instrumentation as a Research Engineer III in the Department of Research Engineering under Peter Saggau. Peter originally joined the Allen Institute in 2014 as a Scientist I working with Timothy J. Blanche in the Department of Neural Coding.

Peter earned a Joint Ph.D. in bioengineering from the University of California, Berkeley and from the University of California, San Francisco, where he was co-advised by Dr. Michel M. Maharbiz and Dr. Jose M. Carmena.  Peter’s Ph.D. work focused on the development of electrocorticographic microelectrode arrays, and on their application to functional brain mapping and brain-machine interfaces. He also earned a Management of Technology certificate from Haas Business School, and co-founded the medical device start up Cortera Neurotechnologies, Inc.

Peter holds a Dipl.-Phys. in physics with a minor in chemistry from the Georg August University in Göttingen (Germany). His thesis research on organic field effect transistors, was completed externally under the supervision of Dr. Alan J. Heeger at the University of California, Santa Barbara.

View Publications on Google Scholar


Research Interests

I am interested in elucidating universal principles of cortical computation, which generalize across distinct functional areas, as well as in translational projects that address clinical needs. I am involved in several projects at the interface of modeling, technology development, basic neuroscience, and translational medicine. My main focus is currently Visual Coding; more specifically the analysis of electrophysiological and two-photon imaging data using modern machine learning techniques.


  • Extracellular electrophysiology
  • Optogenetics
  • Optics
  • Brain-machine interfaces
  • Electrocorticography
  • Neural probe development
  • Micro- and nanofabrication
  • Multimodal interrogation of neural activity
  • Machine Learning
  • Multi-photon fluorescence imaging
  • Animal behavior tracking


Research Programs

  • Neural Coding
  • Research Engineering
  • Cell Types
  • Mindscope


Selected Publications View Publications

Columnar Localization and Laminar Origin of Cortical Surface Electrical Potentials

Journal of Neuroscience
May 4, 2022

Baratham VL, Dougherty ME, Hermiz J, Ledochowitsch P, Maharbiz MM, Bouchard KE

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.

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

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

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

Two-photon frequency division multiplexing for functional in vivo imaging: a feasibility study

Optics Express
February 18, 2019

Tsyboulski D, Orlova N, Ledochowitsch P, Saggau P

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

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

Inferring cortical function in the mouse visual system through large-scale systems neuroscience

July 5, 2016

Hawrylycz M, Anastassiou C, Arkhipov A, Berg J, Buice M, et al.

A Large-Scale Interface for Optogenetic Stimulation and Recording in Nonhuman Primates

March 2, 2016

Yazdan-Shahmorad A, Diaz-Botia C, Hanson TL, Kharazia V, Ledochowitsch P, Maharbiz MM, Sabes PN

Demonstration of a setup for chronic optogenetic stimulation and recording across cortical areas in non-human primates

March 10, 2015

Yazdan-Shahmorad A, Diaz-Botia C, Hanson T, Ledochowitsch P, Maharabiz MM, Sabes PN

Strategies for optical control and simultaneous electrical readout of extended cortical circuits

Journal of Neuroscience Methods
December 30, 2015

Ledochowitsch P, Yazdan-Shahmorad A, Bouchard KE, Diaz-Botia C, Hanson TL, He JW, Seybold BA, Olivero E, Phillips EA, Blanche TJ, Schreiner CE, Hasenstaub A, Chang EF, Sabes PN, Maharbiz MM

A minimally invasive 64-channel wireless μECoG implant

IEEE Journal of Solid-State Circuits
January 2015

Muller R, Le H-P, Li W, Ledochowitsch P, Gambini S, Bjorninen T, Koralek A, Carmena JM, Maharbiz MM, Alon E, Rabaey JM