SUMMARY We present a modular approach for analyzing calcium imaging recordings of large neuronal ensembles. Our goal is to simultaneously identify the locations of the neurons, demix spatially overlapping components, and denoise and deconvolve the spiking activity from the slow dynamics of the calcium indicator. Our approach relies on a constrained nonnegative matrix factorization that expresses the spatiotemporal fluorescence activity as the product of a spatial matrix that encodes the spatial footprint of each neuron in the optical field and a temporal matrix that characterizes the calcium concentration of each neuron over time. This framework is combined with a novel constrained deconvolution approach that extracts estimates of neural activity from fluorescence traces, to create a spatiotemporal processing algorithm that requires minimal parameter tuning. We demonstrate the general applicability of our method by applying it to in vitro and in vivo multineuronal imaging data, whole-brain light-sheet imaging data, and dendritic imaging data.

Neuronal ensembles are coactive groups of neurons that may represent emergent building blocks of neural circuits. They could be formed by Hebbian plasticity, whereby synapses between coactive neurons are strengthened. Here we report that repetitive activation with two-photon optogenetics of neuronal populations in visual cortex of awake mice generates artificially induced ensembles which recur spontaneously after being imprinted and do not disrupt preexistent ones. Moreover, imprinted ensembles can be recalled by single cell stimulation and remain coactive on consecutive days. Our results demonstrate the persistent reconfiguration of cortical circuits by two-photon optogenetics into neuronal ensembles that can perform pattern completion.

SUMMARY Neurons in cortical circuits are often coactivated as ensembles, yet it is unclear whether ensembles play a functional role in behavior. Some ensemble neurons have pattern completion properties, triggering the entire ensemble when activated. Using two-photon holographic optogenetics in mouse primary visual cortex, we tested whether recalling ensembles by activating pattern completion neurons alters behavioral performance in a visual task. Disruption of behaviorally relevant ensembles by activation of non-selective neurons decreased performance, whereas activation of only two pattern completion neurons from behaviorally relevant ensembles improved performance, by reliably recalling the whole ensemble. Also, inappropriate behavioral choices were evoked by the mistaken activation of behaviorally relevant ensembles. Finally, in absence of visual stimuli, optogenetic activation of two pattern completion neurons could trigger behaviorally relevant ensembles and correct behavioral responses. Our results demonstrate a causal role of neuronal ensembles in a visually guided behavior and suggest that ensembles implement internal representations of perceptual states.

Summary Recording the activity of large populations of neurons is an important step towards understanding the emergent function of neural circuits. Here we present a simple holographic method to simultaneously perform two-photon calcium imaging of neuronal populations across multiple areas and layers of mouse cortex in vivo. We use prior knowledge of neuronal locations, activity sparsity and a constrained nonnegative matrix factorization algorithm to extract signals from neurons imaged simultaneously and located in different focal planes or fields of view. Our laser multiplexing approach is simple and fast and could be used as a general method to image the activity of neural circuits in three dimensions across multiple areas in the brain.

Integrated optoelectronics has seen its rapid development in the past decade. From its original primary application in long-haul optical communications and access network, integrated optoelectronics has expanded itself to data center, consumer electronics, energy harness, environmental sensing, biological and medical imaging, industry manufacture control etc. This revolutionary progress benefits from the advancement in light generation, manipulation, detection and its interaction with other systems. Device innovation is the key in this advancement. Together they build up the component library for integrated optoelectronics, which facilities the system integration.High contrast grating (HCG) is an emerging element in integrated optoelectronics. Compared to the other elements, HCG has very rich properties and design flexibility. Some of them are fascinating and extraordinary, such as broadband high reflectivity, and high quality factor resonance -all it needs is a single thin-layer of HCG. Furthermore, it can be a microelectromechanical structure. These rich properties are readily to be harnessed and turned into novel devices.This dissertation is devoted to investigate the physical origins of the extraordinary features of HCG, and explore its applications in novel devices for integrated optoelectronics. An intuitive picture will be presented to explain the HCG physics. The essence of HCG lies in its superb manipulation of light, which can be coupled to applications in light generation and detection. Various device innovations, such as lowloss hollow-core waveguide, fast optical phased array, tunable VCSEL and detector are demonstrated with the HCG as a key element. This breadth of functionality of HCG suggests that HCG has reached beyond a single element in integrated optoelectronics; it has enabled a new platform for integrated optoelectronics.