Segmentation of 1/2/3D brain structures in a common anatomical space
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 (pip install brainreg-segment
), but you will need to register your data with brainreg first.
See user guide.
If you have any questions, head over to the image.sc forum.
If you find brainreg-segment useful, and use it in your research, please let us know and also cite the preprint:
Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W. (2021) “Tools for accurate post hoc determination of marker location within whole-brain microscopy images’ bioRxiv, doi.org/10.1101/2021.05.21.445133