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

Abstract

Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes like attention, decisionmaking, 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.

Pyramidal cell types drive functionally distinct cortical activity patterns during decision-making

“…To better capture such differences in cortexwide activity, we performed semi-nonnegative matrix factorization (sNMF). This analysis captures the majority (at least 99%) of the variance by reducing the imaging data to a small number of spatial-and temporal components 23,33 . Here, two factors could point to PyN-specific differences in cortex-wide activity: the number of required components, capturing the overall complexity of cortical dynamics in each PyN type, and the pattern of the recovered spatial components, capturing the correlation structure between cortical areas.…”

“…An ideal method to address this question is widefield calcium imaging, which allows measuring neural activity across the dorsal cortex with cell-type specificity [22][23][24] . Indeed, interneuronspecific widefield imaging has already revealed clear differences in the spatiotemporal dynamics of different inhibitory cell types during an odor detection task 25 .…”

Wide-field calcium imaging of cortex-wide activity in awake, head-fixed mice

“…Therefore, this protocol has a broad application to study different macroscopic properties of brain functions. The readers are encouraged to reference a recent protocol paper of similar experiments ( Couto et al., 2021 ). It should be noted that this protocol, together with any modifications, should be approved by the Institutional Animal Care and Use Committee (IACUC) before implementation.…”

“… Alternatives: There are a number of vendors that produce wide-field microscopes. Wide-field microscopes can also be custom-built ( Couto et al., 2021 ). Scientific cameras with a large field of view, high quantum efficiency, and fast frame rates are suitable for this protocol.…”

Go with the FLOW: visualizing spatiotemporal dynamics in optical widefield calcium imaging

“…Widefield optical imaging of calcium activity provides a unique opportunity to study coordinated spatiotemporal neural activity among brain areas, because this experimental approach achieves large fields of view with high temporal and spatial resolution [17,18]. In general, widefield imaging experiments involve fluorescence imaging of the entire brain surface of animals that express optical indicator proteins in known populations of neurons [19][20][21][22][23][24]. Many experiments choose to use genetically encoded calcium indicators from the GCaMP family to image neural calcium dynamics, which is a proxy for electrical neuronal activity [25][26][27][28]; more generally, the visualization methods we discuss here can be applied to any widefield optical imaging experiment, such as imaging with voltage-sensitive dyes [29,30].…”