07 June 2021 - Research

A new Nature protocols paper by researchers from the Urban lab describes how to follow brain-wide activity in awake head-fixed mice using functional ultrasound imaging, a method that tracks cerebral blood volume dynamics. It details how to set up a functional ultrasound imaging system, and includes code and software for analysis.

The new Nature Protocols paper follows two other recent publicatons, one by Macé et al. on the identification of brain regions functionally involved in the sensorimotor integration of awake mice, and another by Sans-Dublanc, Chrzanowska et al. on the organization of functional networks governing innate behaviors of mice. Now, the team details their methods in a protocol paper to provide neuroscientists with a standard approach for capturing in an unbiased way the whole-brain activity elicited by a behavior or brain function in head-fixed mice.

Clément Brunner, co-first author: "In the new paper, we guide you step by step to set up your own functional ultrasound imaging system to investigate whole-brain functions/circuits of behaving mice. The software to image whole-brain functions is open source and thus available to everyone."

Protocol Paper Image Clement

"Once the chronic cranial window is implanted and your animal is trained, you are ready for data acquisition. Use the analysis software - which is also provided - to register and segment your whole-brain volume with the Allen Mouse Brain Common Coordinate Framework. You can extract both the spatial and temporal analysis of your signal and dive into the global brain processes you are interested in!"

The CAD files of dedicated tools and software for both data acquisition and analysis are available with the article and on Github. "Stay tuned," Brunner adds. "An updated version is coming soon!"

Alan Urban: "We believe that this protocol is essential to facilitate comparisons across laboratories, and for this method to be widely adopted in systems neuroscience."

Congrats to the entire team on the efforts to make the protocol available to new and future users of the functional ultrasound imaging technology.

Our protocol paper "Whole-brain functional ultrasound imaging in awake head-fixed mice" is now out in @NatureProtocols
A thread 🧵

— Clément Brunner (@Clembrunner) June 4, 2021
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