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:

Atlas Name

Resolution

Ages

Reference Images

Allen Mouse Brain Atlas

10, 25, 50, and 100 micron

P56

STPT

Allen Human Brain Atlas

100 micron

Adult

MRI

Max Planck Zebrafish Brain Atlas

1 micron

6-dpf

FISH

Enhanced and Unified Mouse Brain Atlas

10, 25, 50, and 100 micron

P56

STPT

Smoothed version of the Kim et al. mouse reference atlas

10, 25, 50 and 100 micron

P56

STPT

Gubra’s LSFM mouse brain atlas

20 micron

8 to 10 weeks post natal

LSFM

3D version of the Allen mouse spinal cord atlas

20 x 10 x 10 micron

Adult

Nissl

AZBA: A 3D Adult Zebrafish Brain Atlas

4 micron

15-16 weeks post natal

LSFM

Waxholm Space atlas of the Sprague Dawley rat brain

39 micron

P80

MRI

3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases

16, 16.75, and 25 micron

E13, E15, E18, P4, P14, P28 & P56

Nissl

Princeton Mouse Brain Atlas

20 micron

>P56 (older animals included)

LSFM

Kim Lab Developmental CCF

10 micron

P56

STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)

Blind Mexican Cavefish Brain Atlas

2 micron

1 year

IHC

BlueBrain Barrel Cortex Atlas

10 and 25 micron

P56

STPT

UNAM Axolotl Brain Atlas

40 micron

~ 3 months post hatching

MRI

Installation#

BrainGlobe AtlasAPI works with Python >=3.10, and can be installed from PyPI with:

pip install brainglobe-atlasapi

Usage#

More details#

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!