brainglobe-segmentation
Segmentation of anatomical structures in a common coordinate space
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.
Seeking help or contributing
We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.
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
Version:
- 1.3.3
Last updated:
- 2025-05-30
First released:
- 2023-11-06
License:
- BSD-3-Clause
Python versions supported:
Operating system:
- Information not submitted
Requirements:
- brainglobe-atlasapi>=2.0.1
- brainglobe-napari-io>=0.3.0
- brainglobe-utils>=0.5.0
- napari!=0.6.0,>=0.5
- numpy
- pandas[hdf5]
- qtpy
- scikit-image
- scipy
- tifffile
- qt-niu
- black; extra == "dev"
- gitpython; extra == "dev"
- pre-commit; extra == "dev"
- pytest; extra == "dev"
- coverage; extra == "dev"
- pytest-cov; extra == "dev"
- pytest-qt; extra == "dev"
- napari-time-slicer; extra == "dev"