birdbrain: a library for viewing songbird (and bat) brain atlases

Posted on Fri 15 March 2019 in Birdsong

I wrote a small python library called birdbrain for viewing the songbird/bat brain atlas' made available from the Bio-Imaging Lab at the University of Antwerp. It is currently a work-in-progress, but it works with all of the atlases currently on their website.

Figure 1: An example navigation of the European starling dataset

It is available on pip, and can easily be installed as pip install birdbrain. There are a number of examples and demonstrations that can be accessed without having to install any software, or know any python. They can be accessed through Binder. I'm still working on some features - For example I would like to be able to

  • Estimate nuclei locations in one songbird brain based upon another
  • Easily add new structures to the atlases
  • Export high resolution plots of recording sites mapped onto the 2D and 3D images.

If you're interested in any of these, or have new ideas to add to package, let me know!

Figure 2: (left) Nuclei plotted in their respective brain regions (right) nuclei plotted over 2D MRI image