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braincoordinator

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Open-source stereotaxic coordinator

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# Brain Coordinator [![License: MIT](https://img.shields.io/badge/license-MIT-green)](https://www.gnu.org/licenses/gpl-3.0) [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/simonarvin/braincoordinator/issues) ![version](https://img.shields.io/badge/version-0.11--beta-brightgreen) ![beta](https://img.shields.io/badge/-beta-orange)

Brain Coordinator is a Python 3-based stereotaxic coordinator compatible with any stereotaxic atlas. This software is actively maintained: Users are encouraged to contribute to its development.

## Features ##
- [x] **Easily coordinate your stereotaxic procedures**, with an angle or not.
- [x] Compatible with **any stereotaxic atlas**.
- [x] **Avoid** sensitive structures.
- [x] Vary your path of entry to **reduce confounders**.
- [x] **Actively maintained**.

## Overview ##
- [Getting started](#getting-started)
- [Authors](#authors)

## Getting started ##

### Installation ###

Download Brain Coordinator by cloning the repository:
```
git clone https://github.com/simonarvin/braincoordinator.git
```

You may want to use a Conda or Python virtual environment when installing `braincoordinator`, to avoid mixing up with your system dependencies.

Using pip and a virtual environment:

```python -m venv venv```

```source venv/bin/activate```

```(venv) pip install .```

> Remember to ```cd [path]``` to your braincoordinator directory.

Then, initiate ```braincoordinator``` by running

```braincoordinator```

> Write ```braincoordinator --help``` for instructions.

### Add an atlas ###

To see a list of all available atlases, run

```braincoordinator --get list```

To download and install an atlas, run

```braincoordinator --get [atlas_id]```

> e.g., ```braincoordinator --get mouse_allen``` to add the mouse brain atlas from Allen Institute.

Finally, to test your new atlas, run

```braincoordinator --animal [atlas_id]```

### Controls ###
Hold <kbd>CTRL</kbd> and press:
- <kbd>A</kbd>/<kbd>S</kbd>: previous/next coronal slice.
- <kbd>Z</kbd>/<kbd>X</kbd>: previous/next sagittal slice.
- <kbd>D</kbd>: place marker at mouse location.
- <kbd>F</kbd>: remove most recent marker.

Click and drag to move markers.

## Known issues ##
None yet.

## License ##
This project is licensed under the MIT License. Note that the software is provided "as is", without warranty of any kind, express or implied.

## Authors ##

**Lead Developer:**
Simon Arvin, sarv@dandrite.au.dk

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