Metadata-Version: 2.1
Name: birdbrain
Version: 0.1.2
Summary: Tools for using the songbird brain atlas
Home-page: https://github.com/timsainb/birdbrain
Author: Tim Sainburg
License: BSD-3
Description: [![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
        
        Work in progress.
        
        This is a small library for viewing the songbird brain atlas' at https://www.uantwerpen.be/en/research-groups/bio-imaging-lab/research/mri-atlases/starling-brain-atlas/
        
        ![screenshot](assets/img/3d_screenshot.png)
        
        ![field_l](assets/img/field_l.png)
        
        ### 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...
        
        
        #### 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
        
        ### 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}
        }
        
        ```
        
        
        #### TODO:
          - update to use high resolution T2 images rather than same resolution as delineations
          - view other imaging structures in 3d view (skull, etc)
          - Take a 3d video (circle the structure - take screenshots every frame, tie them together)
          - Embed the javascript directly (this won't allow for selecting regions though)
          - option to add 3d imaging volumes to 3d plot
          
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Framework :: IPython
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Education
Classifier: Topic :: Multimedia :: Graphics
Classifier: Topic :: Scientific/Engineering :: Visualization
Description-Content-Type: text/markdown
