Yes you put in a "probe" (fiber optic), just like when you stimulate with an electrode. The difference is electricity stimulates everything, while the light can be targeted, not by what it illuminates but what responds* because...

Ahead of time, you either use viral tools or other genetic modifications to make specific cell types express the photorecrptor.

*there is an effect of light/heat that all cells are subject to, and good experiments try to control for this as best they can