Optogenetics Resources, Guides, and Protocols

We would like to share some of the many resources our customers and the broader research community have found useful for planning optogenetics projects. This page is intended as a practical starting point for researchers exploring experimental design, neural circuit mapping, switch selection, transgenic models, and in vitro or in vivo system setup.

Understanding in vivo and in vitro optogenetics

Optogenetics experiments are typically performed in two main contexts, each serving different
research goals:

• In vivo optogenetics allows researchers to study neural circuits and behavior in living organisms in real time.
• In vitro optogenetics is used in controlled environments such as brain slices or cell cultures to investigate cellular mechanisms with precision.

Many workflows use both approaches—starting with controlled in vitro studies and extending findings to in vivo systems.

Starting from scratch

For neuroscientists, Karl Deisseroth’s Optogenetics resources are one of the best starting points
when planning an experiment. The Deisseroth Lab provides optogenetics resource pages, sequence and expression information, hardware setup references, material request information, and training workshops.

Mapping neural circuits

Karl Deisseroth’s 2016 Cell paper on targeting neural circuits serves as both a primer on neural circuit interrogation and a review of optogenetic approaches used for this kind of work.

Finding the best switch

If you are looking for the right optogenetic tool for your project, OptoBase is a valuable resource.
It provides curated databases, publication indexing, tagging, and search tools that can help narrow
down relevant applications and methods.

Preventing phototoxicity during in vitro experiments

Phototoxicity can introduce artifacts or cell death in both in vitro and in vivo experiments,
particularly at shorter wavelengths. A useful open-access paper discusses strategies to reduce
light-induced damage in vitro and improve cell survival.

Non-neuronal optogenetics

For researchers interested in non-neuronal or broader biological applications of optogenetics,
EMBL provides a self-paced introductory course covering concepts, applications, and practical guidance.

Transgenic Models – Ready to Go

The Jackson Laboratory maintains an optogenetics resource with mouse lines expressing commonly used optogenetic proteins, including channelrhodopsin, halorhodopsin, and archaerhodopsin.

Turnkey In Vitro and Wireless In Vivo Optogenetics Systems

In addition to external educational resources, Amuza offers tools for both in vivo and in vitro
optogenetics workflows.