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

arXiv: https://arxiv.org/abs/2010.15191 · HTML: https://mlsanity.com/paper/2010.15191/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 28 Oct 2020.

## Built on by (most cited first, 1 of 1)

- [Cross-Subject Modeling for Widefield Calcium Imaging via Atlas-Aligned Spatiotemporal Tokenization](https://mlsanity.com/paper/2607.09754/) (2026)

## Abstract (arXiv)

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.