Skip to main content

Optical Physiology Group

Measuring neural circuit functions using light-sensitive molecules.


Research instruments used by the Optical Physiology group at the Allen Institute for Neural DynamicsGoals and Approach

Optical physiology uses light-sensitive molecules to measure and control brain function. Optical methods can measure and manipulate specific molecules (such as neurotransmitters, neuromodulators, and second messengers) to tease apart the components of a neural circuitIndicators and effectors can be targeted to specific cell types or subcellular compartments within neurons. Optical physiology can also perform dense recordings from many thousands of cells or cellular compartments at once in a small area, and can easily target rare cell types or specific structures. The Optical Physiology group at the Allen Institute for Neural Dynamics is taking advantage of all of these capabilities to better study neural circuit function. They are especially interested in how different neurotransmitter and neuromodulator inputs contribute to computations in specific cell types during behavior. 


Individual neurons in the brain receive inputs from many different sources and can combine them in complex ways to perform computations.

This project is investigating how neurons integrate inputs from different presynaptic sources to determine their firing and plasticity. We are developing fluorescent neurotransmitter indicators that report on a given neuron’s synaptic inputs and new microscopes to record from thousands of synapses onto an individual neuron at a time. Combining these tools, we are investigating how inputs are combined to determine cortical neurons’ output, and how those functions change during learning.


Small groups of neuromodulatory neurons send out broad projections that have especially strong effects on how the brain functions. This project is investigating how multiple neuromodulatory systems interact to control activity and plasticity in different brain areas. We are developing genetically encoded indicators and optical measurement methods to record multiple neuromodulators at a time at a given site, and working to target those recordings to specific neuron populations and projections across the brain. We will use these tools to investigate the logic of how these important systems coordinate to control learning, emotions, and actions. 


Science Programs at Allen Institute