Chronic, cortex-wide imaging of specific cell populations during behavior

Couto, Joao; Saxena, Shreya; Sun, Xiaonan R.; Gluf, Steven; Paninski, Liam; Churchland, 9and Anne K.; Abe, Taiga; Kinsella, Ian; Khanal, Anup; Cunningham, John P.; Musall, Simon

doi:10.1038/s41596-021-00527-z

Journal Article

FZJ-2021-02792

Chronic, cortex-wide imaging of specific cell populations during behavior

Couto, J. ; Musall, S.FZJ* ; Sun, X. R. ; Khanal, A. ; Gluf, S. ; Saxena, S. ; Kinsella, I. ; Abe, T. ; Cunningham, J. P. ; Paninski, L. ; Churchland, 9. A. K. (Corresponding author)

2021
Nature Publishing Group Basingstoke

Nature protocols 16, 3241–3263 (2021) [10.1038/s41596-021-00527-z]

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Please use a persistent id in citations: http://hdl.handle.net/2128/28073 doi:10.1038/s41596-021-00527-z

Abstract: Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes such as attention, decision-making and action selection. However, techniques that allow cellular resolution measurements are expensive and require a high degree of technical expertise, which limits their broad use. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective and flexible approach to measure activity of specific cell populations with high temporal resolution and a cortex-wide field of view. Here we outline our protocol for assembling a wide-field macroscope setup, performing surgery to prepare the intact skull and imaging neural activity chronically in behaving, transgenic mice. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets laboratories that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging and/or analyze cortex-wide neuronal recordings. The entire protocol, including steps for assembly and calibration of the macroscope, surgical preparation, imaging and data analysis, requires a total of 8 h. It is designed to be accessible to laboratories with limited expertise in imaging methods or interest in high-throughput imaging during behavior.

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