Package: birdbrain
birdbrainTim Sainburg & Marvin ThielkThis is a small library for viewing thesongbird/bat 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 brainsPlotting recording locations in 2d and 3d on imaging data.Creating visualizations / movies videos of nuclei of interestThere is anonline interactive demowhich 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!Usage InstructionsYou can either view the data directly from thebinder notebooksvia your internet browser (reccomeded at first), or you can install and run this package locally on your own computer.InstallationTo install the python package:pip install birdbrainAdditional requirementsTo be added...CitationsIf 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}
}ReferencesBrain atlasfor starling, canary, zebra finch, pigeon, tilapia, and mustached bat brain atlas'VTK pythonfor 3d graphicsK3D toolsfor 3d visualizationnibabelFor reading/manipulating neuroimaging data (.img files)cookiecutter data scienceproject template was usedTODO:update to use high resolution T2 images rather than same resolution as delineationsEmbed the javascript directly (e.g. save 3d to be embedded into website) (this won't allow for selecting regions though)