Brain function emerges from the coordinated activity, over time, of large neuronal populations placed in different brain regions. Understanding the relationships of these specific areas and disentangling the contributions of individual neurons to overall function remain central goals for neuroscience. In this scenario, fluorescence microscopy has been proved as the tool of choice for in vivo recording of brain activity. Optical advances combined with genetically encoded indicators allow a large

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... flexibility in terms of spatiotemporal resolution and field of view while keeping invasiveness in living animals to a minimum. Here we describe the latest advancements in the field of linear and nonlinear optical microscopy with special attention to the exploration of brain functionality of model animals. The present review aims to guide the reader through the main optical systems in the field toward future directions for in vivo microscopy applications.