Skip to content
A library for viewing songbird brain atlases (European starling, Canary, Zebra finch, Pigeon, Mustached bat)
Jupyter Notebook Python Other
Branch: master
Clone or download
MarvinT and timsainb python 2 compatibility (#6)
* py2 test

* Fix a few typos (#17)

* Fix a few typos.

* Add periods.

* Plot2d (#22)

* mv test_make_atlas

* test_plot_2d

* pass starling_atlas

* um to vox

* import numpy

* starling_atlas

* update_color_labels

* remove unused const

* import copy and pd

* another deepcopy

* more dependencies in old_update_color_labels

* py2 test

* agg backend on travis
Latest commit cf16bb0 May 10, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
assets gitignore and cleanup (#14) Feb 28, 2019
birdbrain
docs first commit Feb 20, 2019
models first commit Feb 20, 2019
notebooks gitignore and cleanup (#14) Feb 28, 2019
references first commit Feb 20, 2019
reports first commit Feb 20, 2019
testing python 2 compatibility (#6) May 10, 2019
.gitignore gitignore and cleanup (#14) Feb 28, 2019
.travis.yml python 2 compatibility (#6) May 10, 2019
Index.ipynb Merge master (#10) Feb 27, 2019
LICENSE first commit Feb 20, 2019
Makefile first commit Feb 20, 2019
README.md Fix a few typos (#17) Apr 12, 2019
apt.txt added unrar for binder, updated readme (#13) Feb 27, 2019
environment.yml Merge master (#10) Feb 27, 2019
postBuild Merge master (#10) Feb 27, 2019
requirements.txt Merge master (#10) Feb 27, 2019
setup.py Black formatting (#15) Feb 28, 2019
tox.ini first commit Feb 20, 2019

README.md

Build Status Binder

birdbrain

Tim Sainburg & Marvin Thielk

This is a small library for viewing the songbird/bat brain atlases (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 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

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...

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

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)
You can’t perform that action at this time.