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.


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.