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Updated: Apr 16, 2026
Building a Simple and Versatile Illumination System for Optogenetic Experiments
Published on: January 12, 2021
Principles of designing interpretable optogenetic behavior experiments
Brian D Allen1, Annabelle C Singer1, Edward S Boyden2
1Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Abstract:
Over the last decade, there has been much excitement about the use of optogenetic tools to test whether specific cells, regions, and projection pathways are necessary or sufficient for initiating, sustaining, or altering behavior. However, the use of such tools can result in side effects that can complicate experimental design or interpretation. The presence of optogenetic proteins in cells, the effects of heat and light, and the activity of specific ions conducted by optogenetic proteins can result in cellular side effects. At the network level, activation or silencing of defined neural populations can alter the physiology of local or distant circuits, sometimes in undesired ways. We discuss how, in order to design interpretable behavioral experiments using optogenetics, one can understand, and control for, these potential confounds.
Insights
Optogenetic tools offer exciting ways to study behavior, but researchers must carefully manage cellular and network side effects. Understanding and controlling these confounds is key for interpretable optogenetic experiments.
Area of Science:
- Neuroscience
- Optogenetics
- Behavioral Science
Background:
- Optogenetic tools are widely used to investigate neural circuits and their role in behavior.
- Potential cellular and network side effects can complicate the interpretation of optogenetic experiments.
Purpose of the Study:
- To discuss potential confounds associated with optogenetic tools.
- To provide strategies for designing interpretable optogenetic behavioral experiments.
Main Methods:
- Review of optogenetic tool mechanisms and potential side effects.
- Discussion of cellular-level confounds (protein expression, light/heat effects, ion conductance).
- Analysis of network-level confounds (altered circuit physiology).
Main Results:
- Optogenetic tools can induce cellular side effects, including those from protein presence, light/heat, and ion flux.
- Neural population manipulation can lead to unintended alterations in local and distant circuits.
- These confounds can obscure the specific role of targeted neural elements in behavior.
Conclusions:
- Careful consideration of optogenetic side effects is crucial for experimental validity.
- Strategies to understand and control for confounds are necessary for accurate behavioral research.
- Interpretable optogenetic studies require rigorous experimental design to mitigate unintended consequences.
