The development of multi-photon microscopic technique has made it possible to image submicron structures deep in biological tissues.This technique is widely used for imaging of cortical structures in developing and adult animals,and there have been detail descriptions of in vivo imaging of synaptic structures in normal animals through a thinned-skull or open-skull cranial window.However,several challenges should be considered carefully for high-resolution imaging of cortical structures under pathological conditions.Here we describe a protocol for in vivo imaging of dendritic structures following ischemic stroke through thinned skull.This protocol can also be applied for acute or chronic imaging of neuronal structural plasticity,glial activation,cerebral microcirculation,or synaptic functions in other pathological conditions.