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Introduction
Manually segment 1/2/3D structures for volumetric analysis
brainreg-segment is a companion to brainreg allowing manual segmentation of regions/objects within the brain (e.g. injection sites, probes etc.) allowing for automated analysis of brain region distribution, and visualisation (e.g. in brainrender).

Installation

brainreg-segment comes bundled with brainreg, so see the brainreg installation instructions. brainreg-segment can be installed on it's own (see below), but you will need to register your data with brainreg first.

Usage

Standalone installation

If you don't want to install brainreg, brainreg-segment can be installed on its own. brainreg-segment is distributed as a plugin for napari, so first follow the napari installation instructions. You can then install brainreg-segment from the napari plugin menu.
Installing from the napari plugin menu
Alternatively, the plugin can be installed into a Python environment with pip install brainreg-segment.
Last modified 8mo ago