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Simplify and update readme #151

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Simplify and update readme
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[![PyPI](https://img.shields.io/pypi/v/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation)
[![Wheel](https://img.shields.io/pypi/wheel/brainglobe-segmentation.svg)](https://pypi.org/project/brainglobe-segmentation)
[![Development Status](https://img.shields.io/pypi/status/brainglobe-segmentation.svg)](https://github.com/brainglobe/brainglobe-segmentation)
[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)](
https://github.com/brainglobe/brainglobe-segmentation/actions)
[![codecov](https://codecov.io/gh/brainglobe/brainglobe-segmentation/branch/master/graph/badge.svg?token=WP9KTPZE5R)](https://codecov.io/gh/brainglobe/brainglobe-segmentation)[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
[![Tests](https://img.shields.io/github/workflow/status/brainglobe/brainglobe-segmentation/tests)](https://github.com/brainglobe/brainglobe-segmentation/actions)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
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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).

### Citing brainglobe-segmentation

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