© 2018, Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature. Microscopic imaging of the brain continues to reveal details of its structure, connectivity, and function. To further improve our understanding of the emergent properties and functions of neural circuits, we need to directly visualize the relationship between brain structure, neuron activity, and neurochemistry. Advances in the chemical and optical properties of nanomaterials, and developments in deep-tissue microscopy, may help to overcome the current challenges of in-vivo brain imaging, particularly when imaging the brain through optically-dense brain tissue, skull, and scalp. Developments in nanomaterials may enable the implementation of tunable chemical functionality for neurochemical targeting and sensing, and fluorescence stability for long-term imaging. In this review, we summarize the current methods used for brain microscopy and describe the diverse classes of nanomaterials recently offered as contrast agents and functional probes for microscopic optical imaging of the brain.