Josh Siegle
Scalable systems neuroscience
My work pushes the limits of large-scale neural recording, produces widely used open datasets and software, and has revealed fundamental links between brain anatomy and spiking dynamics.
Positions
-
Senior Scientist, Allen Institute for Neural Dynamics (2021-present)
Leader of the Electrophysiology Group -
Assistant Investigator, Allen Institute MindScope Program (2020-2021)
Collected and shared massive open datasets of spiking activity from the mouse visual system -
Scientist I & II, Allen Institute MindScope Program (2014-2020)
Early adopter of Neuropixels probes for in vivo electrophysiology
Education
- PhD, Neuroscience, Massachusetts Institute of Technology (2014)
- ScB, Neuroscience, Brown University (2007)
Publications
- Buccino AP, Sridhar A, Feng D, Svoboda K, Siegle JH (2026) “Efficient and reproducible pipelines for spike sorting large-scale electrophysiology data” eLife 15, RP110170.
- Lakunina A, Socha KZ, Ladd A, […] Siegle JH, Carandini M (2025) “Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics” bioRxiv.
- Newman JP, Zhang J, Cuevas-López A […] Siegle JH, Harnett MT, Wilson MA, Voigts J (2025) “ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior.” Nature Methods 22, 187-192.
- Ye Z, Shelton AM, Shaker JR, Boussard J […] Siegle JH, Koch C, Olsen SR, Harris TD, Steinmetz NA (2025) “Ultra-high-density Neuropixels probes improve detection and identification in neuronal recordings.” Neuron 113, 3966-3982.e12.
- Arora V, Lachi D, Knight IJ, Azabou M, Richards B, Hurwitz CL, Siegle JH, Dyer EL (2025) “Know thyself by knowing others: Learning neuron identity from population context.” arXiv.
- Bennett C, Gale S, Heller G, Ramirez T, Belski H […] Siegle JH […] Koch C, Olsen SR (2025) “Map of spiking activity underlying change detection in the mouse visual system.” bioRxiv.
- Arkhipov A, da Costa N, de Vries S, Bakken T […] Siegle JH […] Koch C, Zeng H (2025) “Integrating multimodal data to understand cortical circuit architecture.” Nature Neuroscience 28, 717-730.
- Roszko DA, Chen FD, Straguzzi J, Wahn H […] Siegle JH, Poon JKS, Sacher WD (2025) “Foundry-fabricated dual-color nanophotonic neural probes for photostimulation and electrophysiological recording.” Neurophotonics 12, 025002.
- Akella S, Ledochowitsch P, Siegle JH et al. “Deciphering neuronal variability across states reveals dynamic sensory encoding.” Nature Communications 16, 1768.
- Bennett C, Ouellette B, Ramirez TK […] Siegle JH, Farrell C, Groblewski PA, Olsen SR (2024) “SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain.” Neuron 112, 2869-2885.e8.
- Buccino AP, Winter O, Bryant D, Feng D, Svoboda K, Siegle JH (2023) “Compression strategies for large-scale electrophysiology data.” Journal of Neural Engineering 20, 056009.
- De Vries SEJ, Siegle JH, Koch C (2023) “Sharing neurophysiology data from the Allen Brain Observatory.” eLife 12, e85550.
- Birman D, Yang KJ […] Siegle JH, Steinmetz NA (2023) “Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment.” bioRxiv.
- Rimehaug AE, Stasik AJ, Hagen E, Billeh YN, Siegle JH et al. (2023) “Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex.” eLife 12, e87169.
- Wei Y, Nandi A, Jia X, Siegle JH et al. (2023) “Associations between in vitro, in vivo, and in silico classes in mouse primary visual cortex.” Nature Communications 14, 2344.
- Durand S, Heller GR, Ramirez TK […] Siegle JH, Olsen SR (2023) “Acute head-fixed recordings in awake mice with multiple Neuropixels probes.” Nature Protocols 18, 424-457.
- Koch C, Svoboda K, Bernard A, Basso MA […] Siegle JH, Zador A (2022) “Next-generation brain observatories.” Neuron 110, 3661-3666.
- Jia X, Siegle JH, Durand S, Heller G, Ramirez TK, Koch S, Olsen SR (2022) “Multi-regional module-based signal transmission in mouse visual cortex.” Neuron 110, 1585-1598.
- Petersen PC, Siegle JH, Steinmetz NA, Mahallati S, Buzsáki G (2021) “CellExplorer: A framework for visualizing and characterizing single neurons.” Neuron 109, 3594-3608.
- Lecoq J, Oliver M, Siegle JH, Orlova N, Ledochowitsch P, Koch C (2021) “Removing independent noise in systems neuroscience data using DeepInterpolation.” Nature Methods 18, 3594-3608.
- Siegle JH, Ledochowitsch P, Jia X, Millman DJ et al. (2021) “Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology.” eLife 10, e69068.
- Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H et al. (2021) “Survey of spiking in the mouse visual system reveals functional hierarchy.” Nature 592, 86-92.
- Buccino AP, Hurtwitz CL, Garcia S, Magland J, Siegle JH, Hurwitz R, Hennig Matthias H (2020) “SpikeInterface, a unified framework for spike sorting.” eLife 9, e61834.
- Billeh YN, Cai B, Gratiy S, Dai K, Iyer R, Gouwen NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A (2020) “Systematic integration of structural and functional data into multi-scale models of mouse primary visual cortex.” Neuron 106, 388-403.e18.
- Putzeys J, Raducanu BC, Carton A, De Ceulaer JD, Karsh B, Siegle JH et al. (2019) “Neuropixels data-acquisition system: a scalable platform for parallel recording of 10,000+ electrophysiological signals.” IEEE Transactions on Biomedical Circuits and Systems 13, 1635-1644.
- Jia X, Siegle JH, Bennett C, Gale S, Denman DJ, Koch C, Olsen S (2019) “High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification.” Journal of Neurophysiology 121, 1831-1847.
- Jun JJ, Steinmetz NA, Siegle JH, Denman DJ, Bauza M, Barbarits B, Lee AK, et al. (2017) “Fully integrated silicon probes for high-density recording of neural activity.” Nature 551, 232-236.
- Siegle JH, Cuevas López A, Patel Y, Abramov K, Ohayon S, Voigts J (2017) “Open Ephys: An open-source, plugin-based platform for multichannel electrophysiology.” Journal of Neural Engineering 14, 045003.
- Denman DJ, Siegle JH, Koch C, Reid RC, Blanche TJ (2017) “Spatial organization of chromatic pathways in the mouse dorsal lateral geniculate nucleus.” Journal of Neuroscience 37, 1102-1116.
- Teeters JL, Godfrey K, Young R, Dang C [...] Siegle JH et al. (2015) “Neurodata Without Borders: Creating a common data format for neurophysiology.” Neuron 88, P629-634.
- Pak N, Siegle JH, Kinney JP, Denman DJ, Blanche TJ, Boyden ES (2015) “Closed-loop, ultraprecise, automated craniotomies.” Journal of Neurophysiology 113, 3943-3953.
- Siegle JH, Hale GJ, Newman JP, Voigts J (2015) “Neural ensemble communities: Open-source approaches to hardware for large-scale electrophysiology.” Current Opinion in Neurobiology 32, 53-59.
- Pritchett DL, Siegle JH, Deister CA, Moore CI (2015) “For things needing your attention: the role of neocortical gamma in sensory perception.” Current Opinion in Neurobiology 31, 254-263.
- Siegle JH, Pritchett DL, Moore CI (2014) “Gamma-range synchronization of fast-spiking interneurons can enhance detection of tactile stimuli.” Nature Neuroscience 17, 1371-1379.
- Siegle JH, Wilson MA (2014) “Enhancement of encoding and retrieval functions through theta phase-specific manipulation of hippocampus.” eLife 3, e03061.
- Voigts J, Siegle JH, Pritchett DL, Moore CI (2013) “The flexDrive: an ultra-light implant for optical control and highly parallel chronic recording of neuronal ensembles in freely moving mice.” Frontiers in Systems Neuroscience 7.
- Carlen C, Meletis K, Siegle JH et al. (2012) “A critical role for NMDA receptors in parvalbumin interneurons for gamma rhythm induction and behavior.” Molecular Psychiatry 17, 537-548.
- Halassa MM, Siegle JH, Ritt JT, Ting JT, Feng G, Moore CI (2011) “Selective optical drive of thalamic reticular nucleus generates thalamic bursts and cortical spindles.” Nature Neuroscience 14, 1118-1120.
- Knoblich U, Siegle JH, Pritchett DL, Moore CI (2010) “What do we gain from gamma? Local dynamic gain modulation drives enhanced efficacy and efficiency of signal transmission.” Frontiers in Human Neuroscience 4.
- Siegle JH, Warren WH (2010) “Distal attribution and distance perception in sensory substitution.” Perception 39, 208-223.
Awards & Fellowships
- NRSA Fellowship (2012-2014)
- National Defense Science and Engineering Graduate Fellowship (2009-2012)
- Angus MacDonald Award for Excellence in Undergraduate Teaching (2011)
- Brown University Neuroscience Prize (2007)
- Sigma Xi (2007)
- Phi Beta Kappa (2006)
Teaching Experience
- Neuropixels and OpenScope Workshop, Organizer (2019-2025)
- MPFI Advanced Neurotechniques Course, Lecturer (2025)
- UCL Neuropixels Workshop, Lecturer (2023-2024)
- Paris Neuro Course, Lecturer (2022-2024)
- Summer Workshop on the Dynamic Brain, Instructor (2023)
- Karolinska Institute Brain Circuits Course, Instructor (2012, 2013, 2015)
- Transylvanian Experimental Neuroscience Summer School, Teaching Assistant (2014, 2016)
- MIT Independent Activities Period “Building Your Own Neuroscience Lab” Course, Organizer (2012)
- MIT Systems Neuroscience Laboratory, Teaching Assistant (2010-2011)
- Woods Hole Neural Systems and Behavior Summer Course, Teaching Assistant (2009)