birdbrain 0.1.2

Tools for using the songbird brain atlas

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/

Online demo!

Usage Instructions

You can either view the data directly from the binder notebooks 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 for starling, canary, zebra finch, pigeon, tilapia, and mustached bat brain atlas'
• VTK python for 3d graphics
• K3D tools for 3d visualization
• nibabel For reading/manipulating neuroimaging data (.img files)
• 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