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4 Janelia Publications

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    11/30/18 | Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function.
    Vladimirov N, Wang C, Höckendorf B, Pujala A, Tanimoto M, Mu Y, Yang C, Wittenbach J, Freeman J, Preibisch S, Koyama M, Keller PJ, Ahrens MB
    Nature Methods. 2018 Nov 30;15(12):1117-1125. doi: 10.1038/s41592-018-0221-x

    Whole-brain imaging allows for comprehensive functional mapping of distributed neural pathways, but neuronal perturbation experiments are usually limited to targeting predefined regions or genetically identifiable cell types. To complement whole-brain measures of activity with brain-wide manipulations for testing causal interactions, we introduce a system that uses measuredactivity patterns to guide optical perturbations of any subset of neurons in the same fictively behaving larval zebrafish. First, a light-sheet microscope collects whole-brain data that are rapidly analyzed by a distributed computing system to generate functional brain maps. On the basis of these maps, the experimenter can then optically ablate neurons and image activity changes across the brain. We applied this method to characterize contributions of behaviorally tuned populations to the optomotor response. We extended the system to optogenetically stimulate arbitrary subsets of neurons during whole-brain imaging. These open-source methods enable delineating the contributions of neurons to brain-wide circuit dynamics and behavior in individual animals.

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    08/11/15 | Whole-central nervous system functional imaging in larval Drosophila.
    Lemon WC, Pulver SR, Höckendorf B, McDole K, Branson KM, Freeman J, Keller PJ
    Nature Communications. 2015 Aug 11;6:7924. doi: 10.1038/ncomms8924

    Understanding how the brain works in tight concert with the rest of the central nervous system (CNS) hinges upon knowledge of coordinated activity patterns across the whole CNS. We present a method for measuring activity in an entire, non-transparent CNS with high spatiotemporal resolution. We combine a light-sheet microscope capable of simultaneous multi-view imaging at volumetric speeds 25-fold faster than the state-of-the-art, a whole-CNS imaging assay for the isolated Drosophila larval CNS and a computational framework for analysing multi-view, whole-CNS calcium imaging data. We image both brain and ventral nerve cord, covering the entire CNS at 2 or 5 Hz with two- or one-photon excitation, respectively. By mapping network activity during fictive behaviours and quantitatively comparing high-resolution whole-CNS activity maps across individuals, we predict functional connections between CNS regions and reveal neurons in the brain that identify type and temporal state of motor programs executed in the ventral nerve cord.

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    12/30/14 | Light-sheet imaging for systems neuroscience.
    Keller PJ, Ahrens MB, Freeman J
    Nature Methods. 2014 Dec 30;12(1):27-9. doi: 10.1038/nmeth.3214

    Developments in electrical and optical recording technology are scaling up the size of neuronal populations that can be monitored simultaneously. Light-sheet imaging is rapidly gaining traction as a method for optically interrogating activity in large networks and presents both opportunities and challenges for understanding circuit function.

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    Ahrens LabLooger LabKeller LabFreeman Lab
    07/27/14 | Light-sheet functional imaging in fictively behaving zebrafish.
    Vladimirov N, Mu Y, Kawashima T, Bennett DV, Yang C, Looger LL, Keller PJ, Freeman J, Ahrens MB
    Nature Methods. 2014 Jul 27;11(9):883-4. doi: 10.1038/nmeth.3040

    The processing of sensory input and the generation of behavior involves large networks of neurons, which necessitates new technology for recording from many neurons in behaving animals. In the larval zebrafish, light-sheet microscopy can be used to record the activity of almost all neurons in the brain simultaneously at single-cell resolution. Existing implementations, however, cannot be combined with visually driven behavior because the light sheet scans over the eye, interfering with presentation of controlled visual stimuli. Here we describe a system that overcomes the confounding eye stimulation through the use of two light sheets and combines whole-brain light-sheet imaging with virtual reality for fictively behaving larval zebrafish.

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