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Co-authored-by: Will Graham <[email protected]>

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Co-authored-by: Will Graham <[email protected]>
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# brainglobe-segmentation

Segmentation of 1/2/3D brain structures in a common anatomical space

`brainglobe-segmentation` is a companion to [`brainreg`](https://github.com/brainglobe/brainreg) allowing 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](https://github.com/brainglobe/brainrender)).
`brainglobe-segmentation` is the successor to [`brainreg-segment`](https://github.com/brainglobe/brainreg-segmentation).

`brainglobe-segmentation` and `brainreg` were developed by [Adam Tyson](https://github.com/adamltyson) and [Charly Rousseau](https://github.com/crousseau) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), based on [aMAP](https://doi.org/10.1038/ncomms11879) by [Christian Niedworok](https://github.com/cniedwor). The work was generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).
Segmentation of anatomical structures in a common coordinate space

## Installation
**PyPI**
```
pip install brainglobe-segmentation
```

brainglobe-segmentation comes bundled with [`brainreg`](https://github.com/brainglobe/brainreg), so see the [brainreg installation instructions](https://brainglobe.info/documentation/brainreg/index.html).

brainglobe-segmentation can be installed on it's own (`pip install brainglobe-segmentation`), but you will need to register your data with brainreg first.
**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).
Expand All @@ -32,7 +31,7 @@ If you have any questions, head over to the [image.sc forum](https://forum.image

## Contributing

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

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