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

Couto, Joao, Musall, Simon, Sun, Xiaonan R, Khanal, Anup, Gluf, Steven, Saxena, Shreya, Kinsella, Ian, Abe, Taiga, Cunningham, John P, Paninski, Liam, Churchland, Anne K (June 2021) Chronic, cortex-wide imaging of specific cell populations during behavior. Nature Protocols. ISSN 1754-2189

DOI: 10.1038/s41596-021-00527-z


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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > analysis and processing
bioinformatics > computational biology
Investigative techniques and equipment > imaging
Investigative techniques and equipment > optical devices > microscope techniques or equipment
CSHL Authors:
Communities: CSHL labs > Churchland lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 2 June 2021
Date Deposited: 16 Jun 2021 13:37
Last Modified: 27 Jan 2022 15:30
PMCID: PMC8788140
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