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

TL;DR

This paper presents a comprehensive protocol for cortex-wide, chronic imaging of specific neuronal populations in behaving mice using widefield calcium imaging, including setup, surgery, and data analysis methods.

Contribution

It introduces a cost-effective, high-throughput widefield imaging protocol with cloud-based analysis for long-term, cell-specific neural activity measurement during behavior.

Findings

Enables cortex-wide imaging in behaving mice

Provides a scalable, cloud-based data analysis pipeline

Facilitates long-term, cell-specific neural activity studies

Abstract

Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes like 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. Widefield 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 widefield setup, a surgical preparation to image through the intact skull, and imaging neural activity chronically in behaving, transgenic mice that express a calcium indicator in specific subpopulations of cortical neurons. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets labs that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging, and/or analyze cortex-wide neuronal recordings.