Intrinsic optical signal imaging and targeted injections through a chronic cranial window of a head-fixed mouse

Intrinsic optical signal imaging (ISI) is a hemodynamic response-based technique to map the functional architecture of the cortex. ISI is often used as an auxiliary method to localize cortical areas for targeted electrophysiology, pharmacology, or imaging experiments. Here, we provide a protocol for ISI through a cranial window with an access port to identify the area of the primary visual cortex (V1) in a head-fixed mouse, followed by targeted viral vector injection, which enables subsequent two-photon imaging of V1 layer 6 corticothalamic neurons. For complete details on the use and execution of this protocol, please refer to our paper Augustinaite and Kuhn (2020b).