Dissecting the intricate connections of these neural circuits has been a long-standing challenge for neuroscientists, largely due to technical limitations in identifying and targeting specific neuronal cell-types. Neural circuits consist of heterogeneous cell-types receiving distinct inputs from both local and long-range sources. However, we will introduce a few recently developed opsins in order to illustrate the diverse properties of optogenetics and its unique applications. In this review, we will primarily focus on the applications of commonly used opsins, rather than covering all the different variants. In contrast, inhibitory opsins, such as the chloride pump halorhodopsin (eNpHR) and the proton pump Archaerhodospin (Arch), mediate hyperpolarizing currents which impede action potentials upon yellow light illumination (∼580 nm) ( Zhang et al., 2007 Chow et al., 2010). The most commonly used excitatory opsin is channelrhodopsin (ChR2), a cation channel that opens in the presence of blue light (∼470 nm) to depolarize neurons ( Nagel et al., 2003). These microbial opsins can be divided into excitatory opsins and inhibitory opsins. Opsins used in optogenetics were first discovered in microbes ( Soliman and Trüper, 1982 Mukohata et al., 1988) and later cloned and introduced into neurons ( Boyden et al., 2005). Although most of the examples in this review come from studies of sensory and motor systems, their diverse experimental designs and underlying principles are potentially useful for advancing our understanding of the structure and function of other brain circuits. Finally, we will discuss some of the limitations and future directions of optogenetics. In this review, we will first highlight the use of optogenetics in the investigation of neural connectivity, both within and between brain regions, and then its applications in identifying the functional roles of specific neural circuit components in behavior and physiology. In addition, when it is combined with the Cre- Lox recombinase system, it provides a spatiotemporally precise method to reversibly turn on and off the activity of genetically defined or projection-specific groups of neurons. This state-of-the-art technique utilizes light-sensitive channels or pumps, known as opsins, to manipulate the activity of neurons. However, only a handful of them have influenced and advanced modern neuroscience as heavily as optogenetics. In the past decades, numerous newly developed techniques have greatly assisted in dissecting connectivity and function of the brain. In summary, this review serves as a primer to exemplify how optogenetics can be used in sophisticated modern circuit analyses at the levels of synapses, cells, network connectivity and behaviors. Finally, we will discuss the prospect of new optogenetic tools and how their application can further advance modern neuroscience. We will then discuss how these tools can be used to reveal the functional roles of these cell-type specific connections in governing sensory information processing, and learning and memory in the visual cortex, somatosensory cortex, and motor cortex. Here, in the first half of the review, we will present applications of optogenetics in identifying connectivity between different local neuronal cell types and of long-range projections with both in vitro and in vivo methods. These advances greatly expand the scope of tractable experimental investigations. The recent development of optogenetic tools, combined with transgenic mouse lines, has endowed us with unprecedented spatiotemporal precision in circuit analysis. The ability to precisely map neural circuits and to selectively manipulate neural activity is critical to understanding brain function and has, therefore been a long-standing goal for neuroscientists. The exquisite intricacies of neural circuits are fundamental to an animal’s diverse and complex repertoire of sensory and motor functions. 5Center for Neural Dynamics, University of Ottawa, Ottawa, ON, Canada.4Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada.3Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.2Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.1Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.Candice Lee 1, Andreanne Lavoie 2,3, Jiashu Liu 2,3, Simon X.

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