Protocol for in vivo imaging and analysis of brainstem neuronal activity in the dorsal raphe nucleus of freely behaving mice

Abstract

Summary: In vivo brainstem imaging with miniature microscopy has been challenging due to surgical difficulty, high motion, and correlated activity between neurons. Here, we present a protocol for brainstem imaging in freely moving mice using the dorsal raphe nucleus as an example. We describe surgical procedures to inject a virus encoding GCaMP6m and securely implant a GRIN lens in the brainstem. We then detail motion correction and cell segmentation from the data to parse single-cell activity from correlated networks.For complete details on the use and execution of this protocol, please refer to Paquelet et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Microscopy
• Model Organisms
• Neuroscience
• Behavior