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 its 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.

User guide#


If you find brainreg-segment useful and use it in your research, please let us know and also cite the paper:

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022). Accurate determination of marker location within whole-brain microscopy images. Scientific Reports, 12, 867

Lastly, if you can, please cite the BrainGlobe Atlas API that provided the atlas:

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668,

Don’t forget to cite the developers of the atlas that you used (e.g. the Allen Brain Atlas)!