Academic Appointments

Honors & Awards

  • Award for Excellence in Graduate Teaching, Stanford University (2023)
  • McKnight Scholar, McKnight Foundation (2021)
  • Sloan Research Fellow, Sloan Foundation (2021)

Current Research and Scholarly Interests

Our research goal is to understand how dynamics in neuronal circuits relate and constrain the representation of information and computations upon it. We adopt three synergistic strategies: First, we analyze neural circuit population recordings to better understand the relation between neural dynamics and behavior, Second, we theoretically explore the types of dynamics that could be associated with particular network computations. Third, we analyze the structural properties of neural circuits.

2023-24 Courses

Stanford Advisees

Graduate and Fellowship Programs

All Publications

  • Transforming a head direction signal into a goal-oriented steering command. Nature Westeinde, E. A., Kellogg, E., Dawson, P. M., Lu, J., Hamburg, L., Midler, B., Druckmann, S., Wilson, R. I. 2024


    To navigate, we must continuously estimate the direction we are headed in, and we must correct deviations from our goal1. Direction estimation is accomplished by ring attractor networks in the head direction system2,3. However, we do not fully understand how the sense of direction is used to guide action. Drosophila connectome analyses4,5 reveal three cell populations (PFL3R, PFL3L and PFL2) that connect the head direction system to the locomotor system. Here we use imaging, electrophysiology and chemogenetic stimulation during navigation to show how these populations function. Each population receives a shifted copy of the head direction vector, such that their three reference frames are shifted approximately 120° relative to each other. Each cell type then compares its own head direction vector with a common goal vector; specifically, it evaluates the congruence of these vectors via a nonlinear transformation. The output of all three cell populations is then combined to generate locomotor commands. PFL3R cells are recruited when the fly is oriented to the left of its goal, and their activity drives rightward turning; the reverse is true for PFL3L. Meanwhile, PFL2 cells increase steering speed, and are recruited when the fly is oriented far from its goal. PFL2 cells adaptively increase the strength of steering as directional error increases, effectively managing the tradeoff between speed and accuracy. Together, our results show how a map of space in the brain can be combined with an internal goal to generate action commands, via a transformation from world-centric coordinates to body-centric coordinates.

    View details for DOI 10.1038/s41586-024-07039-2

    View details for PubMedID 38326621

    View details for PubMedCentralID 5613981

  • Brain-wide neural activity underlying memory-guided movement. Cell Chen, S., Liu, Y., Wang, Z. A., Colonell, J., Liu, L. D., Hou, H., Tien, N., Wang, T., Harris, T., Druckmann, S., Li, N., Svoboda, K. 2024; 187 (3): 676


    Behavior relies on activity in structured neural circuits that are distributed across the brain, but most experiments probe neurons in a single area at a time. Using multiple Neuropixels probes, we recorded from multi-regional loops connected to the anterior lateral motor cortex (ALM), a circuit node mediating memory-guided directional licking. Neurons encoding sensory stimuli, choices, and actions were distributed across the brain. However, choice coding was concentrated in the ALM and subcortical areas receiving input from the ALM in an ALM-dependent manner. Diverse orofacial movements were encoded in the hindbrain; midbrain; and, to a lesser extent, forebrain. Choice signals were first detected in the ALM and the midbrain, followed by the thalamus and other brain areas. At movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

    View details for DOI 10.1016/j.cell.2023.12.035

    View details for PubMedID 38306983

  • Temporal scaling of motor cortical dynamics reveals hierarchical control of vocal production. Nature neuroscience Banerjee, A., Chen, F., Druckmann, S., Long, M. A. 2024


    Neocortical activity is thought to mediate voluntary control over vocal production, but the underlying neural mechanisms remain unclear. In a highly vocal rodent, the male Alston's singing mouse, we investigate neural dynamics in the orofacial motor cortex (OMC), a structure critical for vocal behavior. We first describe neural activity that is modulated by component notes (~100 ms), probably representing sensory feedback. At longer timescales, however, OMC neurons exhibit diverse and often persistent premotor firing patterns that stretch or compress with song duration (~10 s). Using computational modeling, we demonstrate that such temporal scaling, acting through downstream motor production circuits, can enable vocal flexibility. These results provide a framework for studying hierarchical control circuits, a common design principle across many natural and artificial systems.

    View details for DOI 10.1038/s41593-023-01556-5

    View details for PubMedID 38291282

    View details for PubMedCentralID 6015850

  • Mapping the neural dynamics of locomotion across the Drosophila brain. Current biology : CB Brezovec, B. E., Berger, A. B., Hao, Y. A., Chen, F., Druckmann, S., Clandinin, T. R. 2024


    Locomotion engages widely distributed networks of neurons. However, our understanding of the spatial architecture and temporal dynamics of the networks that underpin walking remains incomplete. We use volumetric two-photon imaging to map neural activity associated with walking across the entire brain of Drosophila. We define spatially clustered neural signals selectively associated with changes in either forward or angular velocity, demonstrating that neurons with similar behavioral selectivity are clustered. These signals reveal distinct topographic maps in diverse brain regions involved in navigation, memory, sensory processing, and motor control, as well as regions not previously linked to locomotion. We identify temporal trajectories of neural activity that sweep across these maps, including signals that anticipate future movement, representing the sequential engagement of clusters with different behavioral specificities. Finally, we register these maps to a connectome and identify neural networks that we propose underlie the observed signals, setting a foundation for subsequent circuit dissection. Overall, our work suggests a spatiotemporal framework for the emergence and execution of complex walking maneuvers and links this brain-wide neural activity to single neurons and local circuits.

    View details for DOI 10.1016/j.cub.2023.12.063

    View details for PubMedID 38242122

  • A high-performance speech neuroprosthesis NATURE Willett, F. R., Kunz, E. M., Fan, C., Avansino, D. T., Wilson, G. H., Choi, E., Kamdar, F., Glasser, M. F., Hochberg, L. R., Druckmann, S., Shenoy, K. V., Henderson, J. M. 2023
  • A high-performance speech neuroprosthesis. Nature Willett, F. R., Kunz, E. M., Fan, C., Avansino, D. T., Wilson, G. H., Choi, E. Y., Kamdar, F., Glasser, M. F., Hochberg, L. R., Druckmann, S., Shenoy, K. V., Henderson, J. M. 2023


    Speech brain-computer interfaces (BCIs) have the potential to restore rapid communication to people with paralysis by decoding neural activity evoked by attempted speech into text1,2 or sound3,4. Early demonstrations, although promising, have not yet achieved accuracies sufficiently high for communication of unconstrained sentences from a large vocabulary1-7. Here we demonstrate a speech-to-text BCI that records spiking activity from intracortical microelectrode arrays. Enabled by these high-resolution recordings, our study participant-who can no longer speak intelligibly owing to amyotrophic lateral sclerosis-achieved a 9.1% word error rate on a 50-word vocabulary (2.7 times fewer errors than the previous state-of-the-art speech BCI2) and a 23.8% word error rate on a 125,000-word vocabulary (the first successful demonstration, to our knowledge, of large-vocabulary decoding). Our participant's attempted speech was decoded  at 62 words per minute, which is 3.4 times as fast as the previous record8 and begins to approach the speed of natural conversation (160 words per minute9). Finally, we highlight two aspects of the neural code for speech that are encouraging for speech BCIs: spatially intermixed tuning to speech articulators that makes accurate decoding possible from only a small region of cortex, and a detailed articulatory representation of phonemes that persists years after paralysis. These results show a feasible path forward for restoring rapid communication to people with paralysis who can no longer speak.

    View details for DOI 10.1038/s41586-023-06377-x

    View details for PubMedID 37612500

    View details for PubMedCentralID 4464168

  • Hypothalamic neurons that mirror aggression. Cell Yang, T., Bayless, D. W., Wei, Y., Landayan, D., Marcelo, I. M., Wang, Y., DeNardo, L. A., Luo, L., Druckmann, S., Shah, N. M. 2023


    Social interactions require awareness and understanding of the behavior of others. Mirror neurons, cells representing an action by self and others, have been proposed to be integral to the cognitive substrates that enable such awareness and understanding. Mirror neurons of the primate neocortex represent skilled motor tasks, but it is unclear if they are critical for the actions they embody, enable social behaviors, or exist in non-cortical regions. We demonstrate that the activity of individual VMHvlPR neurons in the mouse hypothalamus represents aggression performed by self and others. We used a genetically encoded mirror-TRAP strategy to functionally interrogate these aggression-mirroring neurons. We find that their activity is essential for fighting and that forced activation of these cells triggers aggressive displays by mice, even toward their mirror image. Together, we have discovered a mirroring center in an evolutionarily ancient region that provides a subcortical cognitive substrate essential for a social behavior.

    View details for DOI 10.1016/j.cell.2023.01.022

    View details for PubMedID 36796363

  • Unraveling the Entangled Brain: How Do We Go About It? Journal of cognitive neuroscience Druckmann, S., Rust, N. C. 2022: 1-4


    An impactful understanding of the brain will require entirely new approaches and unprecedented collaborative efforts. The next steps will require brain researchers to develop theoretical frameworks that allow them to tease apart dependencies and causality in complex dynamical systems, as well as the ability to maintain awe while not getting lost in the effort. The outstanding question is: How do we go about it?

    View details for DOI 10.1162/jocn_a_01950

    View details for PubMedID 36473096

  • Regional cytoarchitecture of the adult and developing mouse enteric nervous system. Current biology : CB Hamnett, R., Dershowitz, L. B., Sampathkumar, V., Wang, Z., Gomez-Frittelli, J., De Andrade, V., Kasthuri, N., Druckmann, S., Kaltschmidt, J. A. 2022


    The organization and cellular composition of tissues are key determinants of their biological function. In the mammalian gastrointestinal (GI) tract, the enteric nervous system (ENS) intercalates between muscular and epithelial layers of the gut wall and can control GI function independent of central nervous system (CNS) input.1 As in the CNS, distinct regions of the GI tract are highly specialized and support diverse functions, yet the regional and spatial organization of the ENS remains poorly characterized.2 Cellular arrangements,3,4 circuit connectivity patterns,5,6 and diverse cell types7-9 are known to underpin ENS functional complexity and GI function, but enteric neurons are most typically described only as a uniform meshwork of interconnected ganglia. Here, we present a bird's eye view of the mouse ENS, describing its previously underappreciated cytoarchitecture and regional variation. We visually and computationally demonstrate that enteric neurons are organized in circumferential neuronal stripes. This organization emerges gradually during the perinatal period, with neuronal stripe formation in the small intestine (SI) preceding that in the colon. The width of neuronal stripes varies throughout the length of the GI tract, and distinct neuronal subtypes differentially populate specific regions of the GI tract, with stark contrasts between SI and colon as well as within subregions of each. This characterization provides a blueprint for future understanding of region-specific GI function and identifying ENS structural correlates of diverse GI disorders.

    View details for DOI 10.1016/j.cub.2022.08.030

    View details for PubMedID 36070775

  • Towards a more general understanding of the algorithmic utility of recurrent connections. PLoS computational biology Larsen, B. W., Druckmann, S. 2022; 18 (6): e1010227


    Lateral and recurrent connections are ubiquitous in biological neural circuits. Yet while the strong computational abilities of feedforward networks have been extensively studied, our understanding of the role and advantages of recurrent computations that might explain their prevalence remains an important open challenge. Foundational studies by Minsky and Roelfsema argued that computations that require propagation of global information for local computation to take place would particularly benefit from the sequential, parallel nature of processing in recurrent networks. Such "tag propagation" algorithms perform repeated, local propagation of information and were originally introduced in the context of detecting connectedness, a task that is challenging for feedforward networks. Here, we advance the understanding of the utility of lateral and recurrent computation by first performing a large-scale empirical study of neural architectures for the computation of connectedness to explore feedforward solutions more fully and establish robustly the importance of recurrent architectures. In addition, we highlight a tradeoff between computation time and performance and construct hybrid feedforward/recurrent models that perform well even in the presence of varying computational time limitations. We then generalize tag propagation architectures to propagating multiple interacting tags and demonstrate that these are efficient computational substrates for more general computations of connectedness by introducing and solving an abstracted biologically inspired decision-making task. Our work thus clarifies and expands the set of computational tasks that can be solved efficiently by recurrent computation, yielding hypotheses for structure in population activity that may be present in such tasks.

    View details for DOI 10.1371/journal.pcbi.1010227

    View details for PubMedID 35727818

  • Transforming representations of movement from body- to world-centric space. Nature Lu, J., Behbahani, A. H., Hamburg, L., Westeinde, E. A., Dawson, P. M., Lyu, C., Maimon, G., Dickinson, M. H., Druckmann, S., Wilson, R. I. 1800


    When an animal moves through the world, its brain receives a stream of information about the body's translational velocity from motor commands and sensory feedback signals. These incoming signals are referenced to the body, but ultimately, they must be transformed into world-centric coordinates for navigation1,2. Here we show that this computation occurs in the fan-shaped body in the brain of Drosophila melanogaster. We identify two cell types, PFNd and PFNv3-5, that conjunctively encode translational velocity and heading as a fly walks. In these cells, velocity signals are acquired from locomotor brain regions6 and are multiplied with heading signals from the compass system. PFNd neurons prefer forward-ipsilateral movement, whereas PFNv neurons prefer backward-contralateral movement, and perturbing PFNd neurons disrupts idiothetic path integration in walking flies7. Downstream, PFNd and PFNv neurons converge onto hDeltaB neurons, with a connectivity pattern that pools together heading and translation direction combinations corresponding to the same movement in world-centric space. This network motif effectively performs a rotation of the brain's representation of body-centric translational velocity according to the current heading direction. Consistent with our predictions, we observe that hDeltaB neurons form a representation of translationalvelocity in world-centric coordinates. By integrating this representation over time, it should be possible for the brain to form a working memory of the path travelled through the environment8-10.

    View details for DOI 10.1038/s41586-021-04191-x

    View details for PubMedID 34912123

  • Modularity and robustness of frontal cortical networks. Cell Chen, G., Kang, B., Lindsey, J., Druckmann, S., Li, N. 2021


    Neural activity underlying short-term memory is maintained by interconnected networks of brain regions. It remains unknown how brain regions interact to maintain persistent activity while exhibiting robustness to corrupt information in parts of the network. We simultaneously measured activity in large neuronal populations across mouse frontal hemispheres to probe interactions between brain regions. Activity across hemispheres was coordinated to maintain coherent short-term memory. Across mice, we uncovered individual variability in the organization of frontal cortical networks. A modular organization was required for the robustness of persistent activity to perturbations: each hemisphere retained persistent activity during perturbations of the other hemisphere, thus preventing local perturbations from spreading. A dynamic gating mechanism allowed hemispheres to coordinate coherent information while gating out corrupt information. Our results show that robust short-term memory is mediated by redundant modular representations across brain regions. Redundant modular representations naturally emerge in neural network models that learned robust dynamics.

    View details for DOI 10.1016/j.cell.2021.05.026

    View details for PubMedID 34214471

  • Targeted photostimulation uncovers circuit motifs supporting short-term memory. Nature neuroscience Daie, K., Svoboda, K., Druckmann, S. 2021


    Short-term memory is associated with persistent neural activity that is maintained by positive feedback between neurons. To explore the neural circuit motifs that produce memory-related persistent activity, we measured coupling between functionally characterized motor cortex neurons in mice performing a memory-guided response task. Targeted two-photon photostimulation of small (<10) groups of neurons produced sparse calcium responses in coupled neurons over approximately 100mum. Neurons with similar task-related selectivity were preferentially coupled. Photostimulation of different groups of neurons modulated activity in different subpopulations of coupled neurons. Responses of stimulated and coupled neurons persisted for seconds, far outlasting the duration of the photostimuli. Photostimuli produced behavioral biases that were predictable based on the selectivity of the perturbed neuronal population, even though photostimulation preceded the behavioral response by seconds. Our results suggest that memory-related neural circuits contain intercalated, recurrently connected modules, which can independently maintain selective persistent activity.

    View details for DOI 10.1038/s41593-020-00776-3

    View details for PubMedID 33495637

  • Decoding spoken English from intracortical electrode arrays in dorsal precentral gyrus. Journal of neural engineering Wilson, G. H., Stavisky, S. D., Willett, F. R., Avansino, D. T., Kelemen, J. N., Hochberg, L. R., Henderson, J. M., Druckmann, S., Shenoy, K. V. 2020; 17 (6): 066007


    OBJECTIVE: To evaluate the potential of intracortical electrode array signals for brain-computer interfaces (BCIs) to restore lost speech, we measured the performance of decoders trained to discriminate a comprehensive basis set of 39 English phonemes and to synthesize speech sounds via a neural pattern matching method. We decoded neural correlates of spoken-out-loud words in the 'hand knob' area of precentral gyrus, a step toward the eventual goal of decoding attempted speech from ventral speech areas in patients who are unable to speak.APPROACH: Neural and audio data were recorded while two BrainGate2 pilot clinical trial participants, each with two chronically-implanted 96-electrode arrays, spoke 420 different words that broadly sampled English phonemes. Phoneme onsets were identified from audio recordings, and their identities were then classified from neural features consisting of each electrode's binned action potential counts or high-frequency local field potential power. Speech synthesis was performed using the 'Brain-to-Speech' pattern matching method. We also examined two potential confounds specific to decoding overt speech: acoustic contamination of neural signals and systematic differences in labeling different phonemes' onset times.MAIN RESULTS: A linear decoder achieved up to 29.3% classification accuracy (chance = 6%) across 39 phonemes, while an RNN classifier achieved 33.9% accuracy. Parameter sweeps indicated that performance did not saturate when adding more electrodes or more training data, and that accuracy improved when utilizing time-varying structure in the data. Microphonic contamination and phoneme onset differences modestly increased decoding accuracy, but could be mitigated by acoustic artifact subtraction and using a neural speech onset marker, respectively. Speech synthesis achieved r = 0.523 correlation between true and reconstructed audio.SIGNIFICANCE: The ability to decode speech using intracortical electrode array signals from a nontraditional speech area suggests that placing electrode arrays in ventral speech areas is a promising direction for speech BCIs.

    View details for DOI 10.1088/1741-2552/abbfef

    View details for PubMedID 33236720

  • Approaches to inferring multi-regional interactions from simultaneous population recordings: Inferring multi-regional interactions from simultaneous population recordings. Current opinion in neurobiology Kang, B., Druckmann, S. 2020; 65: 108–19


    Most past studies of neural representations and dynamics have focused on recordings from single brain areas. However, growing evidence of brain-wide, parallel representations of cognitive variables suggests that analyzing neural representations and dynamics in individual brain areas can benefit from understanding the context of multi-regional interactions that support them. Moreover, perturbation experiments revealed that the manner in which these parallel representations interact with each other can differ dramatically across different pairs of brain areas. Recent advances in recording technology offer a potentially powerful substrate to study how multi-regional interactions coordinate neural representations in individual brain areas and dictate behavior on a single-trial basis through simultaneous recordings of multiple brain areas. We review pragmatic approaches to studying multi-regional interactions and illustrate them in the concrete context of a rodent delayed response task paradigm.

    View details for DOI 10.1016/j.conb.2020.10.004

    View details for PubMedID 33227602

  • A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology. PLoS computational biology Wei, Z. n., Lin, B. J., Chen, T. W., Daie, K. n., Svoboda, K. n., Druckmann, S. n. 2020; 16 (9): e1008198


    Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and low-pass filtering, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, including changes in single-neuron selectivity and population decoding. These were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

    View details for DOI 10.1371/journal.pcbi.1008198

    View details for PubMedID 32931495

  • Neural ensemble dynamics in dorsal motor cortex during speech in people with paralysis. eLife Stavisky, S. D., Willett, F. R., Wilson, G. H., Murphy, B. A., Rezaii, P., Avansino, D. T., Memberg, W. D., Miller, J. P., Kirsch, R. F., Hochberg, L. R., Ajiboye, A. B., Druckmann, S., Shenoy, K. V., Henderson, J. M. 2019; 8


    Speaking is a sensorimotor behavior whose neural basis is difficult to study with single neuron resolution due to the scarcity of human intracortical measurements. We used electrode arrays to record from the motor cortex 'hand knob' in two people with tetraplegia, an area not previously implicated in speech. Neurons modulated during speaking and during non-speaking movements of the tongue, lips, and jaw. This challenges whether the conventional model of a 'motor homunculus' division by major body regions extends to the single-neuron scale. Spoken words and syllables could be decoded from single trials, demonstrating the potential of intracortical recordings for brain-computer interfaces to restore speech. Two neural population dynamics features previously reported for arm movements were also present during speaking: a component that was mostly invariant across initiating different words, followed by rotatory dynamics during speaking. This suggests that common neural dynamical motifs may underlie movement of arm and speech articulators.

    View details for DOI 10.7554/eLife.46015

    View details for PubMedID 31820736

  • Kilohertz frame-rate two-photon tomography. Nature methods Kazemipour, A., Novak, O., Flickinger, D., Marvin, J. S., Abdelfattah, A. S., King, J., Borden, P. M., Kim, J. J., Al-Abdullatif, S. H., Deal, P. E., Miller, E. W., Schreiter, E. R., Druckmann, S., Svoboda, K., Looger, L. L., Podgorski, K. 2019; 16 (8): 778–86


    Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits its speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and computationally recovers high-resolution images, attaining voxel rates of over 1 billion Hz in structured samples. Using a static image as a prior for recording neural activity, we imaged visually evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250m and frame rates over 1kHz. Dendritic glutamate transients in anesthetized mice are synchronized within spatially contiguous domains spanning tens of micrometers at frequencies ranging from 1-100Hz. We demonstrate millisecond-resolved recordings of acetylcholine and voltage indicators, three-dimensional single-particle tracking and imaging in densely labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.

    View details for DOI 10.1038/s41592-019-0493-9

    View details for PubMedID 31363222

  • An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability. Nature communications Wei, Z., Inagaki, H., Li, N., Svoboda, K., Druckmann, S. 2019; 10 (1): 216


    Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

    View details for PubMedID 30644387

  • Single-Cell Reconstruction of Emerging Population Activity in an Entire Developing Circuit. Cell Wan, Y. n., Wei, Z. n., Looger, L. L., Koyama, M. n., Druckmann, S. n., Keller, P. J. 2019


    Animal survival requires a functioning nervous system to develop during embryogenesis. Newborn neurons must assemble into circuits producing activity patterns capable of instructing behaviors. Elucidating how this process is coordinated requires new methods that follow maturation and activity of all cells across a developing circuit. We present an imaging method for comprehensively tracking neuron lineages, movements, molecular identities, and activity in the entire developing zebrafish spinal cord, from neurogenesis until the emergence of patterned activity instructing the earliest spontaneous motor behavior. We found that motoneurons are active first and form local patterned ensembles with neighboring neurons. These ensembles merge, synchronize globally after reaching a threshold size, and finally recruit commissural interneurons to orchestrate the left-right alternating patterns important for locomotion in vertebrates. Individual neurons undergo functional maturation stereotypically based on their birth time and anatomical origin. Our study provides a general strategy for reconstructing how functioning circuits emerge during embryogenesis. VIDEO ABSTRACT.

    View details for DOI 10.1016/j.cell.2019.08.039

    View details for PubMedID 31564455

  • Active dendritic integration and mixed neocortical network representations during an adaptive sensing behavior. Nature neuroscience Ranganathan, G. N., Apostolides, P. F., Harnett, M. T., Xu, N., Druckmann, S., Magee, J. C. 2018


    Animals strategically scan the environment to form an accurate perception of their surroundings. Here we investigated the neuronal representations that mediate this behavior. Ca2+ imaging and selective optogenetic manipulation during an active sensing task reveals that layer 5 pyramidal neurons in the vibrissae cortex produce a diverse and distributed representation that is required for mice to adapt their whisking motor strategy to changing sensory cues. The optogenetic perturbation degraded single-neuron selectivity and network population encoding through a selective inhibition of active dendritic integration. Together the data indicate that active dendritic integration in pyramidal neurons produces a nonlinearly mixed network representation of joint sensorimotor parameters that is used to transform sensory information into motor commands during adaptive behavior. The prevalence of the layer 5 cortical circuit motif suggests that this is a general circuit computation.

    View details for PubMedID 30349100

  • Schaffer Collateral Inputs to CA1 Excitatory and Inhibitory Neurons Follow Different Connectivity Rules JOURNAL OF NEUROSCIENCE Kwon, O., Feng, L., Druckmann, S., Kim, J. 2018; 38 (22): 5140–52


    Neural circuits, governed by a complex interplay between excitatory and inhibitory neurons, are the substrate for information processing, and the organization of synaptic connectivity in neural network is an important determinant of circuit function. Here, we analyzed the fine structure of connectivity in hippocampal CA1 excitatory and inhibitory neurons innervated by Schaffer collaterals (SCs) using mGRASP in male mice. Our previous study revealed spatially structured synaptic connectivity between CA3 and CA1 pyramidal cells (PCs). Surprisingly, parvalbumin-positive interneurons (PVs) showed a significantly more random pattern spatial structure. Notably, application of Peters' rule for synapse prediction by random overlap between axons and dendrites enhanced structured connectivity in PCs, but, by contrast, made the connectivity pattern in PVs more random. In addition, PCs in a deep sublayer of striatum pyramidale appeared more highly structured than PCs in superficial layers, and little or no sublayer specificity was found in PVs. Our results show that CA1 excitatory PCs and inhibitory PVs innervated by the same SC inputs follow different connectivity rules. The different organizations of fine scale structured connectivity in hippocampal excitatory and inhibitory neurons provide important insights into the development and functions of neural networks.SIGNIFICANCE STATEMENT Understanding how neural circuits generate behavior is one of the central goals of neuroscience. An important component of this endeavor is the mapping of fine-scale connection patterns that underlie, and help us infer, signal processing in the brain. Here, using our recently developed synapse detection technology (mGRASP and neuTube), we provide detailed profiles of synaptic connectivity in excitatory (CA1 pyramidal) and inhibitory (CA1 parvalbumin-positive) neurons innervated by the same presynaptic inputs (CA3 Schaffer collaterals). Our results reveal that these two types of CA1 neurons follow different connectivity patterns. Our new evidence for differently structured connectivity at a fine scale in hippocampal excitatory and inhibitory neurons provides a better understanding of hippocampal networks and will guide theoretical and experimental studies.

    View details for PubMedID 29728449

  • Nonlinear Dimensionality Reduction Via Polynomial Principal Component Analysis Kazemipour, A., Druckmann, S., IEEE IEEE. 2018: 1336–40
  • central brain. Science (New York, N.Y.) Kim, S. S., Rouault, H., Druckmann, S., Jayaraman, V. 2017; 356 (6340): 849-853


    Ring attractors are a class of recurrent networks hypothesized to underlie the representation of heading direction. Such network structures, schematized as a ring of neurons whose connectivity depends on their heading preferences, can sustain a bump-like activity pattern whose location can be updated by continuous shifts along either turn direction. We recently reported that a population of fly neurons represents the animal's heading via bump-like activity dynamics. We combined two-photon calcium imaging in head-fixed flying flies with optogenetics to overwrite the existing population representation with an artificial one, which was then maintained by the circuit with naturalistic dynamics. A network with local excitation and global inhibition enforces this unique and persistent heading representation. Ring attractor networks have long been invoked in theoretical work; our study provides physiological evidence of their existence and functional architecture.

    View details for DOI 10.1126/science.aal4835

    View details for PubMedID 28473639

  • Angular velocity integration in a fly heading circuit ELIFE Turner-Evans, D., Wegener, S., Rouault, H., Franconville, R., Wolff, T., Seelig, J. D., Druckmann, S., Jayaraman, V. 2017; 6


    Many animals maintain an internal representation of their heading as they move through their surroundings. Such a compass representation was recently discovered in a neural population in theDrosophila melanogastercentral complex, a brain region implicated in spatial navigation. Here, we use two-photon calcium imaging and electrophysiology in head-fixed walking flies to identify a different neural population that conjunctively encodes heading and angular velocity, and is excited selectively by turns in either the clockwise or counterclockwise direction. We show how these mirror-symmetric turn responses combine with the neurons' connectivity to the compass neurons to create an elegant mechanism for updating the fly's heading representation when the animal turns in darkness. This mechanism, which employs recurrent loops with an angular shift, bears a resemblance to those proposed in theoretical models for rodent head direction cells. Our results provide a striking example of structure matching function for a broadly relevant computation.

    View details for DOI 10.7554/eLife.23496

    View details for Web of Science ID 000401797600001

    View details for PubMedID 28530551

  • Maintenance of persistent activity in a frontal thalamocortical loop NATURE Guo, Z. V., Inagaki, H. K., Daie, K., Druckmann, S., Gerfen, C. R., Svoboda, K. 2017; 545 (7653): 181-?


    Persistent neural activity maintains information that connects past and future events. Models of persistent activity often invoke reverberations within local cortical circuits, but long-range circuits could also contribute. Neurons in the mouse anterior lateral motor cortex (ALM) have been shown to have selective persistent activity that instructs future actions. The ALM is connected bidirectionally with parts of the thalamus, including the ventral medial and ventral anterior-lateral nuclei. We recorded spikes from the ALM and thalamus during tactile discrimination with a delayed directional response. Here we show that, similar to ALM neurons, thalamic neurons exhibited selective persistent delay activity that predicted movement direction. Unilateral photoinhibition of delay activity in the ALM or thalamus produced contralesional neglect. Photoinhibition of the thalamus caused a short-latency and near-complete collapse of ALM activity. Similarly, photoinhibition of the ALM diminished thalamic activity. Our results show that the thalamus is a circuit hub in motor preparation and suggest that persistent activity requires reciprocal excitation across multiple brain areas.

    View details for DOI 10.1038/nature22324

    View details for Web of Science ID 000400963800026

    View details for PubMedID 28467817

  • Multiplicative Updates for Optimization Problems with Dynamics Kazemipour, A., Babadi, B., Wu, M., Podgorski, K., Druckmann, S., Matthews, M. B. IEEE COMPUTER SOC. 2017: 2025–29
  • Robust neuronal dynamics in premotor cortex during motor planning NATURE Li, N., Daie, K., Svoboda, K., Druckmann, S. 2016; 532 (7600): 459-?


    Neural activity maintains representations that bridge past and future events, often over many seconds. Network models can produce persistent and ramping activity, but the positive feedback that is critical for these slow dynamics can cause sensitivity to perturbations. Here we use electrophysiology and optogenetic perturbations in the mouse premotor cortex to probe the robustness of persistent neural representations during motor planning. We show that preparatory activity is remarkably robust to large-scale unilateral silencing: detailed neural dynamics that drive specific future movements were quickly and selectively restored by the network. Selectivity did not recover after bilateral silencing of the premotor cortex. Perturbations to one hemisphere are thus corrected by information from the other hemisphere. Corpus callosum bisections demonstrated that premotor cortex hemispheres can maintain preparatory activity independently. Redundancy across selectively coupled modules, as we observed in the premotor cortex, is a hallmark of robust control systems. Network models incorporating these principles show robustness that is consistent with data.

    View details for DOI 10.1038/nature17643

    View details for Web of Science ID 000374815900038

    View details for PubMedID 27074502

  • Dynamical feature extraction at the sensory periphery guides chemotaxis ELIFE Schulze, A., Gomez-Marin, A., Rajendran, V. G., Lott, G., Musy, M., Ahammad, P., Deogade, A., Sharpe, J., Riedl, J., Jarriault, D., Trautman, E. T., Werner, C., Venkadesan, M., Druckmann, S., Jayaraman, V., Louis, M. 2015; 4


    Behavioral strategies employed for chemotaxis have been described across phyla, but the sensorimotor basis of this phenomenon has seldom been studied in naturalistic contexts. Here, we examine how signals experienced during free olfactory behaviors are processed by first-order olfactory sensory neurons (OSNs) of the Drosophila larva. We find that OSNs can act as differentiators that transiently normalize stimulus intensity-a property potentially derived from a combination of integral feedback and feed-forward regulation of olfactory transduction. In olfactory virtual reality experiments, we report that high activity levels of the OSN suppress turning, whereas low activity levels facilitate turning. Using a generalized linear model, we explain how peripheral encoding of olfactory stimuli modulates the probability of switching from a run to a turn. Our work clarifies the link between computations carried out at the sensory periphery and action selection underlying navigation in odor gradients.

    View details for DOI 10.7554/eLife.06694

    View details for Web of Science ID 000356231400001

    View details for PubMedID 26077825

  • From a meso- to micro-scale connectome: array tomography and mGRASP FRONTIERS IN NEUROANATOMY Rah, J., Feng, L., Druckmann, S., Lee, H., Kim, J. 2015; 9


    Mapping mammalian synaptic connectivity has long been an important goal of neuroscience because knowing how neurons and brain areas are connected underpins an understanding of brain function. Meeting this goal requires advanced techniques with single synapse resolution and large-scale capacity, especially at multiple scales tethering the meso- and micro-scale connectome. Among several advanced LM-based connectome technologies, Array Tomography (AT) and mammalian GFP-Reconstitution Across Synaptic Partners (mGRASP) can provide relatively high-throughput mapping synaptic connectivity at multiple scales. AT- and mGRASP-assisted circuit mapping (ATing and mGRASPing), combined with techniques such as retrograde virus, brain clearing techniques, and activity indicators will help unlock the secrets of complex neural circuits. Here, we discuss these useful new tools to enable mapping of brain circuits at multiple scales, some functional implications of spatial synaptic distribution, and future challenges and directions of these endeavors.

    View details for DOI 10.3389/fnana.2015.00078

    View details for Web of Science ID 000356831800001

    View details for PubMedID 26089781

  • Structured Synaptic Connectivity between Hippocampal Regions NEURON Druckmann, S., Feng, L., Lee, B., Yook, C., Zhao, T., Magee, J. C., Kim, J. 2014; 81 (3): 629-640


    The organization of synaptic connectivity within a neuronal circuit is a prime determinant of circuit function. We performed a comprehensive fine-scale circuit mapping of hippocampal regions (CA3-CA1) using the newly developed synapse labeling method, mGRASP. This mapping revealed spatially nonuniform and clustered synaptic connectivity patterns. Furthermore, synaptic clustering was enhanced between groups of neurons that shared a similar developmental/migration time window, suggesting a mechanism for establishing the spatial structure of synaptic connectivity. Such connectivity patterns are thought to effectively engage active dendritic processing and storage mechanisms, thereby potentially enhancing neuronal feature selectivity.

    View details for DOI 10.1016/j.neuron.2013.11.026

    View details for Web of Science ID 000330965500016

    View details for PubMedID 24412418

  • Mapping mammalian synaptic connectivity CELLULAR AND MOLECULAR LIFE SCIENCES Yook, C., Druckmann, S., Kim, J. 2013; 70 (24): 4747-4757


    Mapping mammalian synaptic connectivity has long been an important goal of neuroscientists since it is considered crucial for explaining human perception and behavior. Yet, despite enormous efforts, the overwhelming complexity of the neural circuitry and the lack of appropriate techniques to unravel it have limited the success of efforts to map connectivity. However, recent technological advances designed to overcome the limitations of conventional methods for connectivity mapping may bring about a turning point. Here, we address the promises and pitfalls of these new mapping technologies.

    View details for DOI 10.1007/s00018-013-1417-y

    View details for Web of Science ID 000327095100008

    View details for PubMedID 23864031

  • A Hierarchical Structure of Cortical Interneuron Electrical Diversity Revealed by Automated Statistical Analysis CEREBRAL CORTEX Druckmann, S., Hill, S., Schuermann, F., Markram, H., Segev, I. 2013; 23 (12): 2994-3006


    Although the diversity of cortical interneuron electrical properties is well recognized, the number of distinct electrical types (e-types) is still a matter of debate. Recently, descriptions of interneuron variability were standardized by multiple laboratories on the basis of a subjective classification scheme as set out by the Petilla convention (Petilla Interneuron Nomenclature Group, PING). Here, we present a quantitative, statistical analysis of a database of nearly five hundred neurons manually annotated according to the PING nomenclature. For each cell, 38 features were extracted from responses to suprathreshold current stimuli and statistically analyzed to examine whether cortical interneurons subdivide into e-types. We showed that the partitioning into different e-types is indeed the major component of data variability. The analysis suggests refining the PING e-type classification to be hierarchical, whereby most variability is first captured within a coarse subpartition, and then subsequently divided into finer subpartitions. The coarse partition matches the well-known partitioning of interneurons into fast spiking and adapting cells. Finer subpartitions match the burst, continuous, and delayed subtypes. Additionally, our analysis enabled the ranking of features according to their ability to differentiate among e-types. We showed that our quantitative e-type assignment is more than 90% accurate and manages to catch several human errors.

    View details for DOI 10.1093/cercor/bhs290

    View details for Web of Science ID 000327431400020

    View details for PubMedID 22989582

  • Neuronal Circuits Underlying Persistent Representations Despite Time Varying Activity CURRENT BIOLOGY Druckmann, S., Chklovskii, D. B. 2012; 22 (22): 2095-2103


    Our brains are capable of remarkably stable stimulus representations despite time-varying neural activity. For instance, during delay periods in working memory tasks, while stimuli are represented in working memory, neurons in the prefrontal cortex, thought to support the memory representation, exhibit time-varying neuronal activity. Since neuronal activity encodes the stimulus, its time-varying dynamics appears to be paradoxical and incompatible with stable network stimulus representations. Indeed, this finding raises a fundamental question: can stable representations only be encoded with stable neural activity, or, its corollary, is every change in activity a sign of change in stimulus representation?Here we explain how different time-varying representations offered by individual neurons can be woven together to form a coherent, time-invariant, representation. Motivated by two ubiquitous features of the neocortex-redundancy of neural representation and sparse intracortical connections-we derive a network architecture that resolves the apparent contradiction between representation stability and changing neural activity. Unexpectedly, this network architecture exhibits many structural properties that have been measured in cortical sensory areas. In particular, we can account for few-neuron motifs, synapse weight distribution, and the relations between neuronal functional properties and connection probability.We show that the intuition regarding network stimulus representation, typically derived from considering single neurons, may be misleading and that time-varying activity of distributed representation in cortical circuits does not necessarily imply that the network explicitly encodes time-varying properties.

    View details for DOI 10.1016/j.cub.2012.08.058

    View details for Web of Science ID 000311523800017

    View details for PubMedID 23084992

  • Effective Stimuli for Constructing Reliable Neuron Models PLOS COMPUTATIONAL BIOLOGY Druckmann, S., Berger, T. K., Schuermann, F., Hill, S., Markram, H., Segev, I. 2011; 7 (8)


    The rich dynamical nature of neurons poses major conceptual and technical challenges for unraveling their nonlinear membrane properties. Traditionally, various current waveforms have been injected at the soma to probe neuron dynamics, but the rationale for selecting specific stimuli has never been rigorously justified. The present experimental and theoretical study proposes a novel framework, inspired by learning theory, for objectively selecting the stimuli that best unravel the neuron's dynamics. The efficacy of stimuli is assessed in terms of their ability to constrain the parameter space of biophysically detailed conductance-based models that faithfully replicate the neuron's dynamics as attested by their ability to generalize well to the neuron's response to novel experimental stimuli. We used this framework to evaluate a variety of stimuli in different types of cortical neurons, ages and animals. Despite their simplicity, a set of stimuli consisting of step and ramp current pulses outperforms synaptic-like noisy stimuli in revealing the dynamics of these neurons. The general framework that we propose paves a new way for defining, evaluating and standardizing effective electrical probing of neurons and will thus lay the foundation for a much deeper understanding of the electrical nature of these highly sophisticated and non-linear devices and of the neuronal networks that they compose.

    View details for DOI 10.1371/journal.pcbi.1002133

    View details for Web of Science ID 000294299700014

    View details for PubMedID 21876663

  • Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data BIOLOGICAL CYBERNETICS Druckmann, S., Berger, T. K., Hill, S., Schuermann, F., Markram, H., Segev, I. 2008; 99 (4-5): 371-379


    Neuron models, in particular conductance-based compartmental models, often have numerous parameters that cannot be directly determined experimentally and must be constrained by an optimization procedure. A common practice in evaluating the utility of such procedures is using a previously developed model to generate surrogate data (e.g., traces of spikes following step current pulses) and then challenging the algorithm to recover the original parameters (e.g., the value of maximal ion channel conductances) that were used to generate the data. In this fashion, the success or failure of the model fitting procedure to find the original parameters can be easily determined. Here we show that some model fitting procedures that provide an excellent fit in the case of such model-to-model comparisons provide ill-balanced results when applied to experimental data. The main reason is that surrogate and experimental data test different aspects of the algorithm's function. When considering model-generated surrogate data, the algorithm is required to locate a perfect solution that is known to exist. In contrast, when considering experimental target data, there is no guarantee that a perfect solution is part of the search space. In this case, the optimization procedure must rank all imperfect approximations and ultimately select the best approximation. This aspect is not tested at all when considering surrogate data since at least one perfect solution is known to exist (the original parameters) making all approximations unnecessary. Furthermore, we demonstrate that distance functions based on extracting a set of features from the target data (such as time-to-first-spike, spike width, spike frequency, etc.)--rather than using the original data (e.g., the whole spike trace) as the target for fitting-are capable of finding imperfect solutions that are good approximations of the experimental data.

    View details for DOI 10.1007/s00422-008-0269-2

    View details for Web of Science ID 000260938100011

    View details for PubMedID 19011925