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

Grace E Paquelet; Kassandra Carrion; Clay O Lacefield; Pengcheng Zhou; Rene Hen; Bradley R Miller

doi:10.1016/j.xpro.2023.102074

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

STAR Protoc. 2023 Mar 17;4(1):102074. doi: 10.1016/j.xpro.2023.102074. Epub 2023 Jan 28.

Authors

Grace E Paquelet¹, Kassandra Carrion², Clay O Lacefield³, Pengcheng Zhou⁴, Rene Hen⁵, Bradley R Miller⁶

Affiliations

¹ Department of Neuroscience, Columbia University, New York, NY 10032, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA. Electronic address: gp2512@cumc.columbia.edu.
² Division of Systems Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA.
³ Division of Systems Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA.
⁴ Department of Neuroscience, Columbia University, New York, NY 10032, USA; Department of Statistics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
⁵ Department of Neuroscience, Columbia University, New York, NY 10032, USA; Division of Systems Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA.
⁶ Division of Systems Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA. Electronic address: bradley.miller@nyspi.columbia.edu.

Abstract

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.

Keywords: Behavior; Bioinformatics; Microscopy; Model Organisms; Neuroscience.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brain Stem* / diagnostic imaging
Dorsal Raphe Nucleus*
Mice
Microscopy
Neurons / physiology

Abstract

Publication types

MeSH terms

Grants and funding