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16 Publications

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    06/05/18 | CalmAn: An open source tool for scalable Calcium Imaging data Analysis
    Giovannucci A, Friedrich J, Gunn P, Kalfon J, Koay SA, Taxidis J, Najafi F, Gauthier JL, Zhou P, Tank DW, Chklovskii D, Pnevmatikakis EA
    bioRxiv. 06/2018:. doi: 10.1101/339564

    Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

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    10/03/17 | Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex
    Homann J, Koay SA, Glidden AM, Tank DW, Berry MJ
    bioRxiv. 10/2017:. doi: 10.1101/197608

    To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (\~2%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

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    03/20/17 | Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)
    Song A, Charles AS, Koay SA, Gauthier JL, Thiberge SY, Pillow JW, Tank DW
    Nature Methods. 03/2017;14(4):420 - 426. doi: 10.1038/nmeth.4226

    Two-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large-scale recording of neural activity in vivo. Here, we introduce volumetric two-photon imaging of neurons using stereoscopy (vTwINS), a volumetric calcium imaging method that uses an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced 'image pairs' in the resulting 2D image, and the separation distance between projections is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a modified orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrated vTwINS by imaging neural population activity in the mouse primary visual cortex and hippocampus. Our results demonstrated that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame rate.

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    03/05/17 | Stochastic filtering of two-photon imaging using reweighted ℓ<inf>1</inf>
    Charles AS, Song A, Koay SA, Tank DW, Pillow JW
    2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). 03/2017:. doi: 10.1109/ICASSP.2017.7952314

    Two-photon (TP) calcium imaging is an important imaging modality in neuroscience, allowing for large-scale recording of neural activity in awake, behaving animals at behavior-relevant timescales. Interpretation of TP data requires the accurate extraction of temporal neural activity traces, which can be accomplished via manual or automated methods. In this work we seek to improve the accuracy of both manual and automated TP microscopy demixing methods by introducing a denoising algorithm based on a statistical model of TP data which includes spatial contiguity, sparse activity and Poisson observations. Our method leverages recent developments in stochastic filtering of structured signals based on Laplacian-scale mixture models (LSMs) to model the neural activity in TP data as a set of spatially correlated sparse variables. We apply our method on TP images taken from the visual cortex of an awake, behaving mouse, and demonstrate improved neural activity demixing over current pre-processing techniques.

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    01/10/12 | Simplified models for LHC new physics searches
    Alves D, Arkani-Hamed N, Arora S, Bai Y, Baumgart M, Berger J, Buckley M, Butler B, Chang S, Cheng H, Cheung C, Chivukula RS, Cho WS, Cotta R, D’Alfonso M, Hedri SE, Essig R, Evans JA, Fitzpatrick L, Fox P, Franceschini R, Freitas A, Gainer JS, Gershtein Y, Gray R, Gregoire T, Gripaios B, Gunion J, Han T, Haas A, Hansson P, Hewett J, Hits D, Hubisz J, Izaguirre E, Kaplan J, Katz E, Kilic C, Kim H, Kitano R, Koay SA, Ko P, Krohn D, Kuflik E, Lewis I, Lisanti M, Liu T, Liu Z, Lu R, Luty M, Meade P, Morrissey D, Mrenna S, Nojiri M, Okui T, Padhi S, Papucci M, Park M, Park M, Perelstein M, Peskin M, Phalen D, Rehermann K, Rentala V, Roy T, Ruderman JT, Sanz V, Schmaltz M, Schnetzer S, Schuster P, Schwaller P, Schwartz MD, Schwartzman A, Shao J, Shelton J, Shih D, Shu J, Silverstein D, Simmons E, Somalwar S, Spannowsky M, Spethmann C, Strassler M, Su S, Tait T, Thomas B, Thomas S, Toro N, Volansky T, Wacker J, Waltenberger W, Yavin I, Yu F, Zhao Y, Zurek K, LHC New Physics Working Group
    Journal of Physics G: Nuclear and Particle Physics. Jan-10-2012;39(10):105005. doi: 10.1088/0954-3899/39/10/105005

    This document proposes a collection of simplified models relevant to the design of new-physics searches at the Large Hadron Collider (LHC) and the characterization of their results. Both ATLAS and CMS have already presented some results in terms of simplified models, and we encourage them to continue and expand this effort, which supplements both signature-based results and benchmark model interpretations. A simplified model is defined by an effective Lagrangian describing the interactions of a small number of new particles. Simplified models can equally well be described by a small number of masses and cross-sections. These parameters are directly related to collider physics observables, making simplified models a particularly effective framework for evaluating searches and a useful starting point for characterizing positive signals of new physics. This document serves as an official summary of the results from the 'Topologies for Early LHC Searches' workshop, held at SLAC in September of 2010, the purpose of which was to develop a set of representative models that can be used to cover all relevant phase space in experimental searches. Particular emphasis is placed on searches relevant for the first ~50–500 pb−1 of data and those motivated by supersymmetric models. This note largely summarizes material posted at, which includes simplified model definitions, Monte Carlo material, and supporting contacts within the theory community. We also comment on future developments that may be useful as more data is gathered and analyzed by the experiments.

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    04/11/07 | Observability of Higgs produced with top quarks and decaying to bottom quarks
    Benedetti D, Cucciarelli S, Hill C, Incandela J, Koay SA, Riccardi C, Santocchia A, Schmidt A, Torre P, Weiser C
    Journal of Physics G: Nuclear and Particle Physics. 04/20027;34(5):N221 - N250. doi: 10.1088/0954-3899/34/5/N03

    The decay, , is dominant for a Standard Model Higgs boson in the mass range just above the exclusion limit of 114.4 GeV/c2 reported by the LEP experiments. Unfortunately, an overwhelming abundance of  events arising from more mundane sources, together with the lack of precision inherent in the reconstruction of the Higgs mass, renders this decay mode a priori undetectable in the case of direct Higgs production at the LHC. It is therefore of no small interest to investigate whether  can be observed in those cases where the Higgs is produced in association with other massive particles. In this note, the results of a study of Higgs bosons produced in association with top quarks and decaying via  are presented. The study was performed as realistically as possible by employing a full and detailed Monte Carlo simulation of the CMS detector followed by the application of trigger and reconstruction algorithms that were developed for use with real data. Important systematic effects resulting from such sources as the uncertainties in the jet energy scale and the estimated rates for correctly tagging b jets or mistagging non-b jets have been taken into account. The impact of large theoretical uncertainties in the cross sections for  plus N jets processes due to an absence of next-to-leading order calculations is also considered.

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