Metadata-Version: 2.1
Name: brainglobe-segmentation
Version: 1.2.3
Summary: Segmentation of anatomical structures in a common coordinate space
Author-email: "Adam Tyson, Horst Obenhaus" <code@adamltyson.com>
License: BSD-3-Clause
Project-URL: Homepage, https://brainglobe.info/
Project-URL: Source Code, https://github.com/brainglobe/brainglobe-segmentation
Project-URL: Bug Tracker, https://github.com/brainglobe/brainglobe-segmentation/issues
Project-URL: Documentation, https://brainglobe.info/documentation/brainglobe-segmentation/index.html
Project-URL: User Support, https://forum.image.sc/tag/brainglobe
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: brainglobe-atlasapi >=2.0.1
Requires-Dist: brainglobe-napari-io >=0.3.0
Requires-Dist: brainglobe-utils >=0.4.0
Requires-Dist: napari >=0.4.5
Requires-Dist: numpy
Requires-Dist: pandas[hdf5]
Requires-Dist: qtpy
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: tifffile
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: gitpython ; extra == 'dev'
Requires-Dist: pre-commit ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Requires-Dist: pytest-qt ; extra == 'dev'
Requires-Dist: napari-time-slicer ; extra == 'dev'

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# 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](https://brainglobe.info/documentation/brainglobe-segmentation/index.html).

If you have any questions, head over to the [image.sc forum](https://forum.image.sc/tag/brainglobe).

## Contributing

Contributions are very welcome. Please see the [developers guide](https://brainglobe.info/community/developers/index.html).

### 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., V&eacute;lez-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](https://doi.org/10.1038/s41598-021-04676-9)
