BrainGlobe Atlas API (brainglobe-atlasapi)

Many excellent brain atlases exist for different species. Some of them have an API (application programming interface) to allow users to interact with the data programmatically (e.g. the excellent Allen Mouse Brain Atlas), but many do not, and there is no consistent way to process data from multiple sources.

The brainglobe atlas API deals with this problem by providing a common interface for programmers to download and process data from multiple sources.

Each atlas consists of data files in a common format:

• A “reference” image of a brain (.tiff)

• An “annotation” image, with each brain region defined by a unique pixel value (.tiff)

• Meshes defining the surface of each brain region (.obj)

• A mapping of brain region pixel value to region name, and structure hierarchy (.json)

• Metadata defining the shape, orientation etc. of the data, and other info such as animal species and authors (.json)

Atlases available

A number of atlases are in development, but those available currently are:

• Allen Mouse Brain Atlas at 10, 25, 50 and 100 micron resolutions

• Allen Human Brain Atlas at 100 micron resolution

• Max Planck Zebrafish Brain Atlas at 1 micron resolution

• Enhanced and Unified Mouse Brain Atlas at 10, 25, 50 and 100 micron resolutions

• Smoothed version of the Kim et al. mouse reference atlas at 10, 25, 50 and 100 micron resolutions

• Gubra’s LSFM mouse brain atlas at 20 micron resolution

• 3D version of the Allen mouse spinal cord atlas at 20 x 10 x 10 micron resolution

• AZBA: A 3D Adult Zebrafish Brain Atlas at 4 micron resolution

• Waxholm Space atlas of the Sprague Dawley rat brain at 39 micron resolution

• 3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases (E13, E15, E18, P4, P14, P28 & P56)

• Princeton Mouse Brain Atlas at 20 micron resolution

• Kim Lab Developmental CCF (P56) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)

Installation

BrainGlobe AtlasAPI works with Python >=3.9, and can be installed from PyPI with:

pip install brainglobe-atlasapi

Usage

• Atlas details
• Available atlases
  • Mouse
  • Rat
  • Zebrafish
  • Human
• Python API
  • Creating a BrainGlobeAtlas object
  • Using the atlas
  • Query the atlas
• Command line interface
• Using the files directly

More details

• Adding a new atlas

Citation

If you find the BrainGlobe Atlas API useful, please cite the paper in your work:

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668

Don’t forget to cite the developers of the atlas that you used!