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	Name in API
Allen Mouse Brain Atlas	10, 25, 50, and 100 micron	P56	STPT	allen_mouse_10um, allen_mouse_25um, allen_mouse_100um
Allen Human Brain Atlas	500 micron	Adult	MRI	allen_human_500um
Max Planck Zebrafish Brain Atlas	1 micron	6-dpf	FISH	mpin_zfish_1um
Enhanced and Unified Mouse Brain Atlas	10, 25, 50, and 100 micron	P56	STPT	kim_mouse_10um, kim_mouse_25um, kim_mouse_50um, kim_mouse_100um
Smoothed version of the Kim et al. mouse reference atlas	10, 25, 50 and 100 micron	P56	STPT	osten_mouse_10um, osten_mouse_25um, osten_mouse_50um, osten_mouse_100um
Gubra’s LSFM mouse brain atlas	20 micron	8 to 10 weeks post natal	LSFM	perens_lsfm_mouse_20um
3D version of the Allen mouse spinal cord atlas	20 x 10 x 10 micron	Adult	Nissl	allen_cord_20um
AZBA: A 3D Adult Zebrafish Brain Atlas	4 micron	15-16 weeks post natal	LSFM	azba_zfish_4um
Waxholm Space atlas of the Sprague Dawley rat brain	39 micron	P80	MRI	whs_sd_rat_39um
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	admba_3d_e11_5_mouse_16um, admba_3d_e13_5_mouse_16um, admba_3d_e15_5_mouse_16um, admba_3d_e18_5_mouse_16um, admba_3d_p14_mouse_16.752um, admba_3d_p28_mouse_16.752um, admba_3d_p4_mouse_16.752um, admba_3d_p56_mouse_25um
Princeton Mouse Brain Atlas	20 micron	>P56 (older animals included)	LSFM	princeton_mouse_20um
Kim Lab Developmental CCF	10 micron	P56	STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)	kim_dev_mouse_stp_10um, kim_dev_mouse_idisco_10um, kim_dev_mouse_mri_a0_10um, kim_dev_mouse_mri_adc_10um, kim_dev_mouse_mri_dwi_10um, kim_dev_mouse_mri_fa_10um, kim_dev_mouse_mri_mtr_10um, kim_dev_mouse_mri_t2_10um
Blind Mexican Cavefish Brain Atlas	2 micron	6 days post fertilisation	IHC	sju_cavefish_2um
BlueBrain Barrel Cortex Atlas	10 and 25 micron	P56	STPT	allen_mouse_bluebrain_barrels_10um, allen_mouse_bluebrain_barrels_25um
UNAM Axolotl Brain Atlas	40 micron	~ 3 months post hatching	MRI	unam_axolotl_40um
Prairie Vole Brain Atlas	25 micron	Unknown	LSFM	prairie_vole_25um

Installation

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

pip install brainglobe-atlasapi

Usage

• Atlas details
• Available atlases
  • Mouse
  • Rat
  • Other rodent
  • Fish
  • Amphibian
  • 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!