Fiber Photometry

Platform

Fiber photometry (or “FP”) is a widely used technique in neuroscience to optically measure neural activity in live animals, in combination with genetically encoded fluorescent indicators. This method is particularly valuable for studying brain function and behavior because it allows researchers to monitor specific populations of neurons in real time. We are using this platform to understand how multiple neuromodulators guide flexible decision-making, such as foraging for reward in a dynamic environment. Overall, fiber photometry is a powerful tool for understanding neural circuits' function and dynamics in behaving animals, providing insights into how specific brain regions, cell-types, neuromodulators/transmitters contribute to complex cognitive behaviors.

Low-cost scalable FP system

Top-down view of a low-cost scalable photometry system with black knobs and black and red cords on a platform.
Diagram of the low-cost scalable photometry system, using color-coded lines to represent different processes within the machine.

We need scalable photometry setups that, in combination with behavioral training rigs, can be used to chronically record optical signals from behaving mice during daily training. To address this, we modified an existing design (Frame-projected Independent Photometry; Kim et al., 2016), relying only on inexpensive commercially available off-the-shelf components. To complement the hardware, we have developed data acquisition software in Bonsai, an open source software platform. Both the hardware and software are modular, and thus, excitation light sources and optical filter settings can be quickly changed, and the system can be combined with virtually any behavioral apparatus and with other recording devices. Our hardware designs and software are freely available through protocols.io.

In AIND, we use this system in combination with multiple behavioral paradigms, in particular, to measure neuromodulator dynamics in mice engaging the dynamic foraging task (cross-link here). Furthermore, by integrating this system into the large-scale ephys platform (cross-link here) we perform simultaneous optical and electrophysiological recordings in the same brain areas.

In vivo indicator benchmarking

To allow the large community of users to better design and interpret optical measurements in behavioral experiments, we will perform rigorous and systematic in vivo benchmarking of indicators, in particular, genetically encoded neuromodulator indicators. We will develop and assess benchmarking protocols and standards using optogenetic stimulation calibrated to behavior-associated signals. For each indicator class, we will select appropriate cell types, brain regions, behavioral calibrations, and stimulation patterns to enable fair comparisons between indicator variants. Resultant data will be rapidly shared as a growing online database.

Our projects

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OpenScope

OpenScope provides access to cutting-edge neurophysiological methods to scientists across the world. Similar to astronomical observatories, scientists propose experiments that are then executed at the Allen Institute.

Brain-Wide Neuromodulation

We are studying the molecular and anatomical subclasses of neuromodulator neurons and exploring how networks use neuromodulators to drive learning and decision making.

Dynamic Routing

We are studying task-switching behaviors in mice to determine how the brain controls the flow of its own activity and how neuronal circuits are reconfigured to dynamically route information for different tasks.

Data platforms accelerate our work

Surgery

The Surgery team offers a variety of aseptic rodent surgical procedures ranging from stereotaxic injections to headpost implantation and cranial windowing.

Neuropixels Electrophysiology

The Neuropixels platform uses pioneering technology for highly reproducible, targeted, brain-wide, cell-type-specific electrophysiology to record neural activity from defined neuron types across the brain.

Brain-Wide Anatomy At Cellular Resolution

The Molecular Anatomy platform combines innovative histology, imaging, and analysis techniques to map the morphology and molecular identity of neuron types across the whole brain.

Fiber Photometry

The Fiber Photometry platform enables optical measurement of neural activity in live animals to study neural circuits' function and dynamics in behaving animals.

Behavior

The Behavior platform uses advanced technology to implement a standardized, modular, multi-task virtual reality gymnasium for mice, with the goal to study brain function across different behaviors at scale.