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  1. Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration

    Publication
    Tracking body parts in behaving animals, extracting fluorescence signals from cells embedded in deforming tissue, and analyzing cell migration patterns during development all require tracking objects with partially …

  2. Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis

    Publication
    A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. Unfortunately, modern data analyses have a hidden dependence upon …

  3. Blind demixing methods for recovering dense neuronal morphology from barcode imaging data

    Publication
    Cellular barcoding methods offer the exciting possibility of 'infinite-pseudocolor' anatomical reconstruction-i.e., assigning each neuron its own random unique barcoded 'pseudocolor,' and then using these pseudocolors …

  4. Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

    Publication
    We assembled a semi-automated reconstruction of L2/3 mouse primary visual cortex from ∼250 × 140 × 90 μm3 of electron microscopic images, including pyramidal and non-pyramidal neurons …

  5. Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders

    Publication
    ecent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting …

  6. Nonlinear Decoding of Natural Images From Large-Scale Primate Retinal Ganglion Recordings

    Publication
    Decoding sensory stimuli from neural activity can provide insight into how the nervous system might interpret the physical environment, and facilitates the development of brain-machine interfaces. Nevertheless …

  7. Chronic, cortex-wide imaging of specific cell populations during behavior

    Publication

  8. High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo

    Publication
    The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising …

  9. BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

    Publication
    Modern spatial transcriptomics methods can target thousands of different types of RNA transcripts in a single slice of tissue. Many biological applications demand a high spatial density of …

  10. NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans

    Publication
    Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic …

  11. Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.

    Publication
    Widefield calcium imaging enables recording of large-scale neural activity across the mouse dorsal cortex. In order to examine the relationship of these neural signals to the resulting …

  12. Rapid mesoscale volumetric imaging of neural activity with synaptic resolution.

    Publication
    Imaging neurons and neural circuits over large volumes at high speed and subcellular resolution is a difficult task. Incorporating a Bessel focus module into a two-photon fluorescence …

  13. Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics.

    Publication
    … fluorescence (ΔF/F) and SNR of optically recorded post-synaptic potentials (PSPs) as a function of the amplitude of the post-synaptic potentials. The voltage sensitivity was …

  14. Complementary networks of cortical somatostatin interneurons enforce layer specific control.

    Publication
    The neocortex is functionally organized into layers. Layer four receives the densest bottom up sensory inputs, while layers 2/3 and 5 receive top down inputs that may …

  15. Reinforcement Learning Recruits Somata and Apical Dendrites across Layers of Primary Sensory Cortex.

    Publication
    The mammalian brain can form associations between behaviorally relevant stimuli in an animal's environment. While such learning is thought to primarily involve high-order association cortex, even …

  16. Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience.

    Publication
    Modern large-scale multineuronal recording methodologies, including multielectrode arrays, calcium imaging, and optogenetic techniques, produce single-neuron resolution data of a magnitude and precision that were the realm …

  17. Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience.

    Publication
    Modern large-scale multineuronal recording methodologies, including multielectrode arrays, calcium imaging, and optogenetic techniques, produce single-neuron resolution data of a magnitude and precision that were the realm …

  18. Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.

    Publication
    In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the …

  19. Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data.

    Publication
    In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to …

  20. The central amygdala controls learning in the lateral amygdala.

    Publication
    Experience-driven synaptic plasticity in the lateral amygdala is thought to underlie the formation of associations between sensory stimuli and an ensuing threat. However, how the central amygdala …

  21. Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays.

    Publication
    Simultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these measurements is challenging …

  22. The Spatiotemporal Organization of the Striatum Encodes Action Space.

    Publication
    Activity in striatal direct- and indirect-pathway spiny projection neurons (SPNs) is critical for proper movement. However, little is known about the spatiotemporal organization of this activity. We …

  23. Multi-scale approaches for high-speed imaging and analysis of large neural populations.

    Publication
    Progress in modern neuroscience critically depends on our ability to observe the activity of large neuronal populations with cellular spatial and high temporal resolution. However, two bottlenecks constrain …