Introduction

About the brainreg plugin for napari

brainreg is software for the registration of whole-brain microscopy datasets to a reference atlas. This allows the brain to be segmented into individual regions based on the atlas, and for all data to be warped to a common anatomical reference frame.

To simplify use, we have created a plugin for napari, so that brainreg can be installed and used without touching the command line.

This page is about the plugin specifically, for more details about brainreg more generally, see the main page.

Installation

First install napari. You can then install the plugin from within napari (Plugins -> Install/Uninstall Package(s), choosing brainreg-napari).

N.B. brainreg is only fully supported on Windows and Linux (i.e. not macOS)

Usage

Please see the User guide, and the Tutorial.