Manual segmentation of 3D brain structures in a common anatomical space
Project description
brainreg-segment
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).
Installation
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.
Usage
See user guide.
If you have any questions, head over to the image.sc forum.
Citing brainreg-segment
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
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