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.
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.
Alternatively, the plugin can be installed into a Python environment with
pip install brainreg-segment.