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birdbrain-0.1.3
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مشاهده بیشترتوضیحات
Tools for using the songbird brain atlas
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | birdbrain-0.1.3 |
| نام | birdbrain |
| نسخه کتابخانه | 0.1.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Tim Sainburg |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | https://github.com/timsainb/birdbrain |
| آدرس اینترنتی | https://pypi.org/project/birdbrain/ |
| مجوز | BSD-3 |
[](https://travis-ci.org/timsainb/birdbrain)
[](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 atlas'](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; Gunturken et al., 2013; Washington et al., 2018). It currently has examples of European starling, Canary, Zebra finch, Mustached bat, and Pigeon brain atlas'.
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 is a allows you to run a Jupyter notebook in a Docker environment online. It can take a bit 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.
### Online demo!
[](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 atlas'
- [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)
نیازمندی
| مقدار | نام |
|---|---|
| >=7.0.1 | ipywidgets |
| - | ipydatawidgets |
| - | traittypes |
| - | traitlets |
| >=1.11.0 | numpy |
| - | k3d |
| - | nibabel |
| - | nipy |
| - | scipy |
| - | matplotlib |
| - | vtk |
| - | pandas |
| - | scikit-image |
| - | tqdm |
| - | patool |
نحوه نصب
نصب پکیج whl birdbrain-0.1.3:
pip install birdbrain-0.1.3.whl
نصب پکیج tar.gz birdbrain-0.1.3:
pip install birdbrain-0.1.3.tar.gz