brainglobe-segmentation

Segmentation of anatomical structures in a common coordinate space

Installation

PyPI

pip install brainglobe-segmentation

conda

conda install -c conda-forge brainglobe-segmentation

N.B. Your data will need to be registered to an anatomical atlas first.

Usage

See user guide.

If you have any questions, head over to the image.sc forum.

Contributing

Contributions are very welcome. Please see the developers guide.

Citing brainglobe-segmentation

If you find brainglobe-segmentation 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