Manual segmentation of 3D brain structures in a common anatomical space
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 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
- 26 August 2021
- 26 August 2020
- 4 - Beta
- Stars: 10
- Forks: 4
- Issues + PRs: 12
Python versions supported:
- Microsoft :: Windows :: Windows 10
- POSIX :: Linux
- napari (>=0.4.5)
- napari-plugin-engine (>=0.1.4)
- imlib (>=0.0.26)
- dask (>=2.15.0)