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10 Janelia Publications

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    Chklovskii LabFlyEM
    08/06/15 | Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit.
    Bharioke A, Chklovskii DB
    PLoS Computational Biology. 2015 Aug 6;11(8):e1004315. doi: 10.1371/journal.pcbi.1004315
    Chklovskii Lab
    01/21/15 | A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans.
    Butler VJ, Branicky R, Yemini E, Liewald JF, Gottschalk A, Kerr RA, Chklovskii DB, Schafer WR
    Journal of the Royal Society Interface. 2015 Jan 6;12(102):20140963

    Although undulatory swimming is observed in many organisms, the neuromuscular basis for undulatory movement patterns is not well understood. To better understand the basis for the generation of these movement patterns, we studied muscle activity in the nematode Caenorhabditis elegans. Caenorhabditis elegans exhibits a range of locomotion patterns: in low viscosity fluids the undulation has a wavelength longer than the body and propagates rapidly, while in high viscosity fluids or on agar media the undulatory waves are shorter and slower. Theoretical treatment of observed behaviour has suggested a large change in force-posture relationships at different viscosities, but analysis of bend propagation suggests that short-range proprioceptive feedback is used to control and generate body bends. How muscles could be activated in a way consistent with both these results is unclear. We therefore combined automated worm tracking with calcium imaging to determine muscle activation strategy in a variety of external substrates. Remarkably, we observed that across locomotion patterns spanning a threefold change in wavelength, peak muscle activation occurs approximately 45° (1/8th of a cycle) ahead of peak midline curvature. Although the location of peak force is predicted to vary widely, the activation pattern is consistent with required force in a model incorporating putative length- and velocity-dependence of muscle strength. Furthermore, a linear combination of local curvature and velocity can match the pattern of activation. This suggests that proprioception can enable the worm to swim effectively while working within the limitations of muscle biomechanics and neural control.

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    Chklovskii Lab
    11/05/14 | A neuron as a signal processing device
    Tao Hu , Towfic Z, Pehlevan C, Genkin A, Chklovskii D
    2013 Asilomar Conference on Signals, Systems and Computers. 05/2014:. doi: 10.1109/ACSSC.2013.6810296

    A neuron is a basic physiological and computational unit of the brain. While much is known about the physiological properties of a neuron, its computational role is poorly understood. Here we propose to view a neuron as a signal processing device that represents the incoming streaming data matrix as a sparse vector of synaptic weights scaled by an outgoing sparse activity vector. Formally, a neuron minimizes a cost function comprising a cumulative squared representation error and regularization terms. We derive an online algorithm that minimizes such cost function by alternating between the minimization with respect to activity and with respect to synaptic weights. The steps of this algorithm reproduce well-known physiological properties of a neuron, such as weighted summation and leaky integration of synaptic inputs, as well as an Oja-like, but parameter-free, synaptic learning rule. Our theoretical framework makes several predictions, some of which can be verified by the existing data, others require further experiments. Such framework should allow modeling the function of neuronal circuits without necessarily measuring all the microscopic biophysical parameters, as well as facilitate the design of neuromorphic electronics.

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    Chklovskii Lab
    07/11/14 | Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis.
    Peng H, Tang J, Xiao H, Bria A, Zhou J, Butler V, Zhou Z, Gonzalez-Bellido PT, Oh SW, Chen J, Mitra A, Tsien RW, Zeng H, Ascoli GA, Iannello G, Hawrylycz M, Myers E, Long F
    Nature Communications. 2014 Jul 11;5:4342. doi: 10.1038/ncomms5342

    Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.

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    Chklovskii Lab
    06/01/12 | Betamax: towards optimal sampling strategies for high-throughput screens.
    Grover D, Nunez-Iglesias J
    Journal of Computational Biology: A Journal of Computational Molecular Cell Biology. 2012 Jun;19(6):776-84. doi: 10.1089/cmb.2012.0036

    Sample size is a critical component in the design of any high-throughput genetic screening approach. Sample size determination from assumptions or limited data at the planning stages, though standard practice, may at times be unreliable because of the difficulty of a priori modeling of effect sizes and variance. Methods to update the sample size estimate during the course of the study could improve statistical power. In this article, we introduce an approach to estimate the power and update it continuously during the screen. We use this estimate to decide where to sample next to achieve maximum overall statistical power. Finally, in simulations, we demonstrate significant gains in study recall over the naive strategy of equal sample sizes while maintaining the same total number of samples.

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    Chklovskii Lab
    09/23/10 | Ultrastructural analysis of hippocampal neuropil from the connectomics perspective.
    Mishchenko Y, Hu T, Spacek J, Mendenhall J, Harris KM, Chklovskii DB
    Neuron. 2010 Sep 23;67(6):1009-20. doi: 10.1371/journal.pcbi.1001066

    Complete reconstructions of vertebrate neuronal circuits on the synaptic level require new approaches. Here, serial section transmission electron microscopy was automated to densely reconstruct four volumes, totaling 670 μm(3), from the rat hippocampus as proving grounds to determine when axo-dendritic proximities predict synapses. First, in contrast with Peters’ rule, the density of axons within reach of dendritic spines did not predict synaptic density along dendrites because the fraction of axons making synapses was variable. Second, an axo-dendritic touch did not predict a synapse; nevertheless, the density of synapses along a hippocampal dendrite appeared to be a universal fraction, 0.2, of the density of touches. Finally, the largest touch between an axonal bouton and spine indicated the site of actual synapses with about 80% precision but would miss about half of all synapses. Thus, it will be difficult to predict synaptic connectivity using data sets missing ultrastructural details that distinguish between axo-dendritic touches and bona fide synapses.

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    Magee LabChklovskii Lab
    12/01/09 | Experience-dependent compartmentalized dendritic plasticity in rat hippocampal CA1 pyramidal neurons.
    Makara JK, Losonczy A, Wen Q, Magee JC
    Nature Neuroscience. 2009 Dec;12(12):1485-7. doi: 10.1038/nn.2428

    The excitability of individual dendritic branches is a plastic property of neurons. We found that experience in an enriched environment increased propagation of dendritic Na(+) spikes in a subset of individual dendritic branches in rat hippocampal CA1 pyramidal neurons and that this effect was mainly mediated by localized downregulation of A-type K(+) channel function. Thus, dendritic plasticity might be used to store recent experience in individual branches of the dendritic arbor.

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    Chklovskii Lab
    07/28/09 | Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors.
    Wen Q, Stepanyants A, Elston GN, Grosberg AY, Chklovskii DB
    Proceedings of the National Academy of Sciences of the United States of America. 2009 Jul 28;106(30):12536-41. doi: 10.1371/journal.pcbi.1001066

    The shapes of dendritic arbors are fascinating and important, yet the principles underlying these complex and diverse structures remain unclear. Here, we analyzed basal dendritic arbors of 2,171 pyramidal neurons sampled from mammalian brains and discovered 3 statistical properties: the dendritic arbor size scales with the total dendritic length, the spatial correlation of dendritic branches within an arbor has a universal functional form, and small parts of an arbor are self-similar. We proposed that these properties result from maximizing the repertoire of possible connectivity patterns between dendrites and surrounding axons while keeping the cost of dendrites low. We solved this optimization problem by drawing an analogy with maximization of the entropy for a given energy in statistical physics. The solution is consistent with the above observations and predicts scaling relations that can be tested experimentally. In addition, our theory explains why dendritic branches of pyramidal cells are distributed more sparsely than those of Purkinje cells. Our results represent a step toward a unifying view of the relationship between neuronal morphology and function.

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    Chklovskii Lab
    01/30/09 | Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs.
    Mishchenko Y
    Journal of Neuroscience Methods. 2009 Jan 30;176(2):276-89. doi: 10.1016/j.jneumeth.2008.09.006

    We describe an approach for automation of the process of reconstruction of neural tissue from serial section transmission electron micrographs. Such reconstructions require 3D segmentation of individual neuronal processes (axons and dendrites) performed in densely packed neuropil. We first detect neuronal cell profiles in each image in a stack of serial micrographs with multi-scale ridge detector. Short breaks in detected boundaries are interpolated using anisotropic contour completion formulated in fuzzy-logic framework. Detected profiles from adjacent sections are linked together based on cues such as shape similarity and image texture. Thus obtained 3D segmentation is validated by human operators in computer-guided proofreading process. Our approach makes possible reconstructions of neural tissue at final rate of about 5 microm3/manh, as determined primarily by the speed of proofreading. To date we have applied this approach to reconstruct few blocks of neural tissue from different regions of rat brain totaling over 1000microm3, and used these to evaluate reconstruction speed, quality, error rates, and presence of ambiguous locations in neuropil ssTEM imaging data.

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    Chklovskii Lab
    01/01/09 | Reconstruction of sparse circuits using multi-neuronal excitation (RESCUME).
    Hu T, Chklovskii DB
    Neural Information Processing Systems. 2009;22:790-8

    One of the central problems in neuroscience is reconstructing synaptic connectivity in neural circuits. Synapses onto a neuron can be probed by sequentially stimulating potentially pre-synaptic neurons while monitoring the membrane voltage of the post-synaptic neuron. Reconstructing a large neural circuit using such a "brute force" approach is rather time-consuming and inefficient because the connectivity in neural circuits is sparse. Instead, we propose to measure a post-synaptic neuron's voltage while stimulating sequentially random subsets of multiple potentially pre-synaptic neurons. To reconstruct these synaptic connections from the recorded voltage we apply a decoding algorithm recently developed for compressive sensing. Compared to the brute force approach, our method promises significant time savings that grow with the size of the circuit. We use computer simulations to find optimal stimulation parameters and explore the feasibility of our reconstruction method under realistic experimental conditions including noise and non-linear synaptic integration. Multineuronal stimulation allows reconstructing synaptic connectivity just from the spiking activity of post-synaptic neurons, even when sub-threshold voltage is unavailable. By using calcium indicators, voltage-sensitive dyes, or multi-electrode arrays one could monitor activity of multiple postsynaptic neurons simultaneously, thus mapping their synaptic inputs in parallel, potentially reconstructing a complete neural circuit.

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