Manual segmentation of 3D brain structures in a common anatomical space
The old README can be found below.
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 were developed by Adam Tyson and Charly Rousseau in the Margrie Lab, based on aMAP by Christian Niedworok. The work was generously supported by the Sainsbury Wellcome Centre.
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.
Contributions are very welcome. Please see the developers 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 doi.org/10.1038/s41598-021-04676-9
- 06 November 2023
- 26 August 2020
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