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32 Janelia Publications

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    Ji LabJayaraman LabSvoboda Lab
    02/27/17 | Video-rate volumetric functional imaging of the brain at synaptic resolution.
    Lu R, Sun W, Liang Y, Kerlin A, Bierfeld J, Seelig JD, Wilson DE, Scholl B, Mohar B, Tanimoto M, Koyama M, Fitzpatrick D, Orger MB, Ji N
    Nature Neuroscience. 2017 Feb 27;20(4):620-8. doi: 10.1038/nn.4516

    Neurons and neural networks often extend hundreds of micrometers in three dimensions. Capturing the calcium transients associated with their activity requires volume imaging methods with subsecond temporal resolution. Such speed is a challenge for conventional two-photon laser-scanning microscopy, because it depends on serial focal scanning in 3D and indicators with limited brightness. Here we present an optical module that is easily integrated into standard two-photon laser-scanning microscopes to generate an axially elongated Bessel focus, which when scanned in 2D turns frame rate into volume rate. We demonstrated the power of this approach in enabling discoveries for neurobiology by imaging the calcium dynamics of volumes of neurons and synapses in fruit flies, zebrafish larvae, mice and ferrets in vivo. Calcium signals in objects as small as dendritic spines could be resolved at video rates, provided that the samples were sparsely labeled to limit overlap in their axially projected images.

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    Ji Lab
    11/02/16 | Opportunities for Technology and Tool Development.
    Neuron. 2016 Nov 2;92(3):564-566. doi: 10.1016/j.neuron.2016.10.042

    Major resources are now available to develop tools and technologies aimed at dissecting the circuitry and computations underlying behavior, unraveling the underpinnings of brain disorders, and understanding the neural substrates of cognition. Scientists from around the world shared their views around new tools and technologies to drive advances in neuroscience.

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    Ji LabFreeman Lab
    08/26/16 | Technologies for imaging neural activity in large volumes.
    Ji N, Freeman J, Smith SL
    Nature Neuroscience. 2016 Aug 26;19(9):1154-64. doi: 10.1038/nn.4358

    Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Conventional microscopy collects data from individual planes and cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point-spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for processing and analyzing volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics and helping elucidate how brain regions work in concert to support behavior.

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    06/10/16 | in vivo brain imaging with adaptive optical microscope.
    Wang K, Sun W, Ji N, Betzig E
    Conference on Lasers and Electro-Optics (CLEO): Applications and Technology. 2016 Jun :AM40.1. doi: 10.1364/CLEO_AT.2016.AM4O.1

    The diffraction limited resolution of two photon and confocal microscope can be recovered using adaptive optics to explore the detailed neuronal network in the brains of zebrafish and mouse in vivo.

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    Ji Lab
    02/01/16 | Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs.
    Sun W, Tan Z, Mensh BD, Ji N
    Nature Neuroscience. 2016 Feb;19(2):308-15. doi: 10.1038/nn.4196

    Understanding the functions of a brain region requires knowing the neural representations of its myriad inputs, local neurons and outputs. Primary visual cortex (V1) has long been thought to compute visual orientation from untuned thalamic inputs, but very few thalamic inputs have been measured in any mammal. We determined the response properties of ~28,000 thalamic boutons and ~4,000 cortical neurons in layers 1–5 of awake mouse V1. Using adaptive optics that allows accurate measurement of bouton activity deep in cortex, we found that around half of the boutons in the main thalamorecipient L4 carried orientation-tuned information and that their orientation and direction biases were also dominant in the L4 neuron population, suggesting that these neurons may inherit their selectivity from tuned thalamic inputs. Cortical neurons in all layers exhibited sharper tuning than thalamic boutons and a greater diversity of preferred orientations. Our results provide data-rich constraints for refining mechanistic models of cortical computation.

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    11/01/15 | Minimally invasive microendoscopy system for in vivo functional imaging of deep nuclei in the mouse brain.
    Bocarsly ME, Jiang W, Wang C, Dudman JT, Ji N, Aponte Y
    Biomedical Optics Express. 2015 Nov 1;6(11):4546-56. doi: 10.1364/BOE.6.004546

    The ability to image neurons anywhere in the mammalian brain is a major goal of optical microscopy. Here we describe a minimally invasive microendoscopy system for studying the morphology and function of neurons at depth. Utilizing a guide cannula with an ultrathin wall, we demonstrated in vivo two-photon fluorescence imaging of deeply buried nuclei such as the striatum (2.5 mm depth), substantia nigra (4.4 mm depth) and lateral hypothalamus (5.0 mm depth) in mouse brain. We reported, for the first time, the observation of neuronal activity with subcellular resolution in the lateral hypothalamus and substantia nigra of head-fixed awake mice.

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    Ji LabGENIE
    07/29/15 | Neuronal representation of ultraviolet visual stimuli in mouse primary visual cortex.
    Tan Z, Sun W, Chen T, Kim D, Ji N
    Scientific Reports. 2015 Jul 29;5:12597. doi: 10.1038/srep12597

    The mouse has become an important model for understanding the neural basis of visual perception. Although it has long been known that mouse lens transmits ultraviolet (UV) light and mouse opsins have absorption in the UV band, little is known about how UV visual information is processed in the mouse brain. Using a custom UV stimulation system and in vivo calcium imaging, we characterized the feature selectivity of layer 2/3 neurons in mouse primary visual cortex (V1). In adult mice, a comparable percentage of the neuronal population responds to UV and visible stimuli, with similar pattern selectivity and receptive field properties. In young mice, the orientation selectivity for UV stimuli increased steadily during development, but not direction selectivity. Our results suggest that, by expanding the spectral window through which the mouse can acquire visual information, UV sensitivity provides an important component for mouse vision.

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    06/15/15 | Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue.
    Wang K, Sun W, Richie CT, Harvey BK, Betzig E, Ji N
    Nature Communications. 2015-Jun-15;6:7276. doi: 10.1038/ncomms8276

    Adaptive optics by direct imaging of the wavefront distortions of a laser-induced guide star has long been used in astronomy, and more recently in microscopy to compensate for aberrations in transparent specimens. Here we extend this approach to tissues that strongly scatter visible light by exploiting the reduced scattering of near-infrared guide stars. The method enables in vivo two-photon morphological and functional imaging down to 700 μm inside the mouse brain.

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    Ji Lab
    04/27/15 | Label-free spectroscopic detection of membrane potential using stimulated Raman scattering.
    Liu B, Lee HJ, Zhang D, Liao C, Ji N, Xia Y, Cheng J
    Applied Physics Letters. 2015 Apr 27;106:173704. doi: 10.1063/1.4919104

    Hyperspectral stimulated Raman scattering microscopy is deployed to measure single-membrane vibrational spectrum as a function of membrane potential. Using erythrocyte ghost as a model, quantitative correlation between transmembrane potential and Raman spectral profile was found. Specifically, the ratio between the area under Raman band at ∼2930 cm−1 and that at ∼2850 cm−1 increased by ∼2.6 times when the potential across the erythrocyte ghost membrane varied from +10 mV to −10 mV. Our results show the feasibility of employing stimulated Raman scattering microscopy to probe the membrane potential without labeling.

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    Ji Lab
    09/17/14 | The practical and fundamental limits of optical imaging in mammalian brains.
    Ji N
    Neuron. 2014 Sep 17;83(6):1242-1245. doi: 10.1016/j.neuron.2014.08.009

    Advances in chemistry and physics have profound effects on neuroimaging. Current and future progress in these disciplines will continue to aid in efforts to visualize neural circuitry, particularly in deeper layers of the brain.

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