Scalable Brain Atlas  

Scalable Brain Atlas

The Scalable Brain Atlas (SBA) is a fully web-based display engine for brain atlases, imaging data and ontologies.
It allows client websites to show brain region related data in a 3D interactive context and provides
services to look up regions, generate thumbnails or download nomenclature- and delineation data.

Macaque atlases

Macaque brain The Calabrese et al. (2015) MRI+DTI atlas with Paxinos regions.
The Paxinos Rhesus Monkey atlas (2000).
The NeuroMaps Macaque atlas (2009).
The Markov et al. (2014) 91 cortical regions atlas.
Various templates available through Caret, registered to F99 space:

Mouse atlases

Mouse brain The INCF Waxholm Space for the mouse (2012).
[archived: 2011 version, 2010 version, 2009 version]
The Allen Mouse Brain Common Coordinate Framework version 3 (ABA_v3).
[archived: 2012 version, 2007 version]
The Hippocampus atlas of Badhwar et al. (2013).

Rat atlases

Rat brain The Waxholm Space Sprague Dawley rat atlas of Papp et al. (2014).
The MR-histology atlas (age P80) of Calabrese et al. (2013) at age P80.
The in vivo MRI template of Valdés-Hernández et al. (2011).
The DTI Atlas (age P72) of Rumple et al. (2013).
The Population-averaged DTI atlas of Veraart et al. (2011).

Human atlases

Human brain
The Harvard Oxford cortical parcellation, as distributed with FSL.
The JuBrain cytoarchitectonic atlas by Amunts, Zilles et al. with maximum probability maps from Eickhoff et al. (2005).
The Neuromorphometrics Inc. manually segmented brain, with cortical and subcortical parcellation.
The Brainnetome Atlas of Fan, Jiang et al. (2016), with maximum probability maps, anatomical and functional connectivity.
The LPBA40 parcellation, registered to SRI24 space.
The BigBrain Nissl stained slices resampled at 400 µm.
The Brodmann areas, projected on Conte69 space.

Marmoset atlas

Marmoset brain
The Marmoset atlas in Stereotactic Coordinates

Opossum atlas

Opossum brain The Multimodal atlas of gray short-tailed opossum brain by Chlodzinska, Majka et. al.

Ferret atlas

Ferret brain The Population based MRI/DTI atlas of the adult ferret by Hutchinson et al. (2017).

A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage, following these instructions. See the site map for more applications.

The SBA runs in recent versions of these web browsers (ordered by SVG rendering speed): Google Chrome 8+, Safari, Opera 10+, FireFox 3.6+, Internet Explorer 9+ (beta-release has bugs in SVG rendering). Users of Internet Explorer 8- need this plugin.

Development & Support

INCF logo
The viewer is developed by Rembrandt Bakker under supervision of Rolf Kötter at the Donders Institute, Radboud UMC Nijmegen, The Netherlands. It uses exploratory work of Gleb Bezgin, creator of the CoCoMac-Paxinos3D tool. Hosting and financial support are provided by the INCF.
To suggest a feature or report a bug, mail us.

The SBA was first presented as a poster and demo session at the INCF booth of SFN 2009 in Chicago.

Scalable Brain Atlas SFN 2009 poster

NITRC Listed Registered with NIF

Other atlasing resources

What's new Last update: Thursday, 9 November 2017