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).


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.


See User guide.

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.