# Protocol for synthesizing, implanting, and using polydimethylsiloxane as skull replacement in mice for imaging, electrophysiology, and optogenetics

## TL;DR

This paper provides a detailed protocol for using PDMS as a skull replacement in mice to enable long-term brain imaging and optogenetics.

## Contribution

A novel protocol for PDMS skull replacement that supports chronic optical and electrophysiological studies in mice.

## Key findings

- PDMS windows allow chronic wide-field and two-photon calcium imaging in mice.
- The protocol includes steps for viral injections and silicon probe implantation for optogenetics.
- PDMS provides both optical and mechanical access to the brain for extended studies.

## Abstract

Many techniques to record and manipulate neuronal activity across large portions of the vertebrate brain are now available. However, few effective approaches enable both optical and mechanical access to the brain. Here, we present a protocol for synthesizing, implanting, and using polydimethylsiloxane (PDMS) windows as skull replacements for chronic wide-field and two-photon calcium imaging in mice. We also describe steps for performing viral injections and multi-site silicon probe implantation.

•Guidance on synthesis of PDMS windows for skull replacement•Instructions for implantation of PDMS windows as skull replacement•Steps for optogenetic viral injection and Neuropixels probe insertion•Assessment of cortical activity via wide-field and two-photon calcium imaging

Guidance on synthesis of PDMS windows for skull replacement

Instructions for implantation of PDMS windows as skull replacement

Steps for optogenetic viral injection and Neuropixels probe insertion

Assessment of cortical activity via wide-field and two-photon calcium imaging

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Many techniques to record and manipulate neuronal activity across large portions of the vertebrate brain are now available. However, few effective approaches enable both optical and mechanical access to the brain. Here, we present a protocol for synthesizing, implanting, and using polydimethylsiloxane (PDMS) windows as skull replacements for chronic wide-field and two-photon calcium imaging in mice. We also describe steps for performing viral injections and multi-site silicon probe implantation.