Optogenetics is a unique technique that allows controlling the physiological condition within single cellor specific cell population, including controlling individual neuron activity. In the present work optogenetics has been applied to control the morphology and density of synaptic connections between striatal and cortical neurons in mixed cortico-striatal co-culture system. Different methods for visualization of medium spiny neurons dendritic spines have been compared. Studying synaptic dysfunction is necessary for understanding both normal physiology of brain and pathological mechanisms in different neurodegenerative diseases. The described approach could be utilized in a numerous biomedical applications.