I think the best way for you to acquire knowledge and skill to understand optogenetics studies and to plan yours is to read recently published papers. First, you may need to focus your study on a specific function or dysfunction of the nervous system, and where in the brain you would like to see the effects of your experiments.

Then you can narrow down the papers that would help you to implement the right protocol for your stimulation and recordings.

Try the following to get a clue:

A pioneering paper on optogenetics by Prof. Deisseroth:

https://www.nature.com/articles/nmeth.f.324.pdf?origin=ppub

another one:

Article Optogenetics in Neural Systems

Development and application of optogenetics by Prof. Deisseroth team:

Article The Development and Application of Optogenetics

https://www.nature.com/subjects/optogenetics

https://www.mpg.de/18011/Optogenetics

https://www.jax.org/research-and-faculty/resources/optogenetics-resource

There are also occasional webinars related to optogenetics on the web.

Search for possible online courses too.

Bahman Sadeghi Thanks a lot :)

Hi Andrzej,

If you want an accessible starting point to in vivo optogenetics, I'm writing an optogenetics guide: https://nicneuro.net/optogenetics-guide/ It has some background and the basics for planning and executing an in vivo optogenetics study.