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A library for viewing songbird brain atlases (European starling, Canary, Zebra finch, Pigeon, Mustached bat)

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[![Build Status](https://travis-ci.org/timsainb/birdbrain.svg?branch=master)](https://travis-ci.org/timsainb/birdbrain)
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb)

birdbrain
==============================

Tim Sainburg & Marvin Thielk

This is a small library for viewing the [songbird/bat brain atlases](https://www.uantwerpen.be/en/research-groups/bio-imaging-lab/research/mri-atlases/starling-brain-atlas/) (Poirier et al., 2008; De Groof et al., 2016; Vellema et al., 2011; Güntürkün et al., 2013; Washington et al., 2018). It currently has examples of European starling, Canary, Zebra finch, Mustached bat, and Pigeon brain atlases.

The package can do things like:

- Nuclei localization relative to a set stereotaxic reference point (e.g. y-sinus in starlings).
- 3D printing an STL of the brains.
- Plotting recording locations in 2d and 3d on imaging data. 
- Creating visualizations / movies videos of nuclei of interest.

There is an [online interactive demo](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb) which should take no Python experience to use (just running cells in a Jupyter notebook). The demo uses Binder, which allows you to run a Jupyter notebook in a Docker environment online. It can take a few minutes to load, but has the benefit of not requiring you to install anything. If you want to install this software locally, the package is pip installable however (see below).

### Online demo:
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb)

### Usage Instructions
You can either view the data directly from the [binder notebooks](https://mybinder.org/v2/gh/timsainb/birdbrain/master?filepath=Index.ipynb) via your internet browser (reccomeded at first), or you can install and run this package locally on your own computer.

### Installation
To install the python package:

`pip install birdbrain`

##### Additional requirements
To be added...

### Citations

If you use this data, please cite the respecitve atlas papers:

**Zebra finch**

```
@article{poirier2008three,
  title={A three-dimensional MRI atlas of the zebra finch brain in stereotaxic coordinates},
  author={Poirier, Colline and Vellema, Michiel and Verhoye, Marleen and Van Meir, Vincent and Wild, J Martin and Balthazart, Jacques and Van Der Linden, Annemie},
  journal={Neuroimage},
  volume={41},
  number={1},
  pages={1--6},
  year={2008},
  publisher={Elsevier}
}
```

**European starling**

```
@article{de2016three,
  title={A three-dimensional digital atlas of the starling brain},
  author={De Groof, Geert and George, Isabelle and Touj, Sara and Stacho, Martin and Jonckers, Elisabeth and Cousillas, Hugo and Hausberger, Martine and G{\"u}nt{\"u}rk{\"u}n, Onur and Van der Linden, Annemie},
  journal={Brain Structure and Function},
  volume={221},
  number={4},
  pages={1899--1909},
  year={2016},
  publisher={Springer}
}
```

**Canary**

```
@article{vellema2011customizable,
  title={A customizable 3-dimensional digital atlas of the canary brain in multiple modalities},
  author={Vellema, Michiel and Verschueren, Jacob and Van Meir, Vincent and Van der Linden, Annemie},
  journal={Neuroimage},
  volume={57},
  number={2},
  pages={352--361},
  year={2011},
  publisher={Elsevier}
}

```

**Pigeon**

```
@article{gunturkun20133,
  title={A 3-dimensional digital atlas of the ascending sensory and the descending motor systems in the pigeon brain},
  author={G{\"u}nt{\"u}rk{\"u}n, Onur and Verhoye, Marleen and De Groof, Geert and Van der Linden, Annemie},
  journal={Brain Structure and Function},
  volume={218},
  number={1},
  pages={269--281},
  year={2013},
  publisher={Springer}
}

```

**Mustached bat**

```
@article{washington2018three,
  title={A three-dimensional digital neurological atlas of the mustached bat (Pteronotus parnellii)},
  author={Washington, Stuart D and Hamaide, Julie and Jeurissen, Ben and Van Steenkiste, Gwendolyn and Huysmans, Toon and Sijbers, Jan and Deleye, Steven and Kanwal, Jagmeet S and De Groof, Geert and Liang, Sayuan and others},
  journal={NeuroImage},
  volume={183},
  pages={300--313},
  year={2018},
  publisher={Elsevier}
}

```

#### References
- [Brain atlas](https://www.uantwerpen.be/en/research-groups/bio-imaging-lab/research/mri-atlases/starling-brain-atlas/) for starling, canary, zebra finch, pigeon, tilapia, and mustached bat brain atlases
- [VTK python](https://pypi.org/project/vtk/) for 3d graphics 
- [K3D tools](https://github.com/K3D-tools/K3D-jupyter) for 3d visualization
- [nibabel](http://nipy.org/nibabel/) For reading/manipulating neuroimaging data (.img files)
- [cookiecutter data science](https://drivendata.github.io/cookiecutter-data-science/) project template was used

#### TODO:
  - update to use high resolution T2 images rather than same resolution as delineations
  - Embed the javascript directly (e.g. save 3d to be embedded into website) (this won't allow for selecting regions though)

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