Scalable Brain Atlas

The Scalable Brain Atlas (SBA) is a fully web-based display engine for brain atlases, imaging data and topologies.
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
	The Paxinos Rhesus Monkey atlas (2000)
	Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991) Lewis and Van Essen (2000) Regional Map from Kötter and Wanke (2005) Paxinos Rhesus Monkey (2000)
	The NeuroMaps Macaque atlas (2008)
Mouse atlases
	The INCF Waxholm Space for the mouse (2011) [archived: 2010 version, 2009 version]
	The Allen Mouse Brain volumetric atlas (ABA07)
Human atlases
	The LPBA40 parcellation, registered to SRI24 space

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

The viewer is developed by Rembrandt Bakker and Gleb Bezgin under supervision of Rolf Kötter at the NeuroPI group of the Donders Institute, Radboud UMC Nijmegen, The Netherlands. Hosting and financial support are provided by the INCF.
To suggest a feature or report a bug, mail to Rembrandt Bakker, r.bakker at donders.ru.nl.

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

What's new

2011-09: An updated version of the Waxholm mouse atlas has been imported: WHS11, it has a hierarchical region tree and supports the NeuroLex plugin
2011-09: Landmarks updated for WHS10 template
2011-09: Distance matrix service added
2011-08: Fixed 60 acronym mismatches (mostly capitalization) between CoCoMac and SBA to prevent empty results in cocomac plugin
2011-08: Created landmark plugin for WHS10 with Andreas Hess and Marina Sergejeva.
2011-08: Fixed 60 acronym mismatches (mostly capitalization) between CoCoMac and SBA to prevent empty results in cocomac plugin.
2011-08: Status of Allen Brain Mouse atlas upgraded from "As Is" to "supported". Including Nissl!
2011-08: 3D view now fits better in its frame.
2011-08: WHS09 and WHS10 templates show additional overlay 'rgb'. It can be used to check the accuracy of the polygon extraction procedure (bitmap to curves). Other templates will follow.
2011-07: PHT00 and DB08 atlas pages show small 3d renderings (powered by 3dbar!) of whole brain in top-right corner.
2011-07: Export region hierarchy tree in NeuroVIISAS format, plus XSL app to view XML as table.
2011-05: Add Marker enhanced: you can get a marker coordinate by clicking anywhere in the 2d slice.
2011-03: Bug-fix to make SBA work in FireFox 4.
2011-03: New exciting plugin: 3D Brain Atlas Reconstructor. Will later be available for all templates, now only for WHS10.
2011-02: Automatically generated sitemap and navigation bar on top of every page
2011-02: Most services now show user friendly dialog when called without proper arguments
2011-02: First self-explanatory service: rgbslice.php
2011-01: Experimental CoCoMac plugin available for preview
2011-01: Added support for Internet Explorer 9 beta, and solved several issues with Opera and Chrome
2011-01: The Scalable Brain Atlas is NITRC listed
2011-01: You can open a plugin directly from the URL by adding &plugin=PluginName
2011-01: The spacing between slices in the 3D view can now be selected: by default the brain is stretched in the posterior/anterior dimension to get a better view. The new control includes a fiducial mode, to see what the brain looks like without deformations.
2011-01: The new Error Console replaces disturbing javascript alerts.
2010-12: Added INCF-DAI coordinate transformations to the WHS09 template (AddMarker plugin)
2010-12: Created CIVM Image Viewer plugin for WHS09 template, it shows the WHS images in original resolution. Could not find a way to directly link to individual coronal slices.
2010-11: Added human LPBA40 parcellation in SRI24 space.
2010-11: First version of CoCoMac plugin: only avaible on development server.
2010-11: Properties plugin shows volume and centerpoint for selected region.
2010-11: Existing services reimplemented as plugins: NeuroLex (for template PHT00), Brain Region Hierarchy.
2010-11: The new FreeBase plugin automatically looks up brain site names in Wikipedia.
2010-11: Created ipad-style Plugin window to provide intuitive access to features and services.
2010-10: Volume and centerpoints are computed for each template.
2010-10: Stereotaxic coordinates are shown for most templates, and also work with MRI overlays.
2010-10: Finished templates obtained through Caret by adding full names and MRI overlays, and switching hemisphere from R to L.
2010-10: First attempt to include three templates that are available through David van Essen's Caret software. Needed a lot of work to get the png-to-svg conversion right.
2010-10: Improved handling of regions that are part of the original atlas, but not of the imported atlas template
2010-10: Automatically generated guide to SBA services
2010-09: View the region hierarchy of each template separately: e.g. hierarchy.php?template=PHT00
2010-09: Improved sorting of region lookup: suggestions starting with the typed characters appear first
2010-09: First attempt to include the Human - Talairach template
2010-09: In progress: Follow up on Doug Bowdens comments to clean up the region list and hierarchy. Done: Show only viewable regions
2010-09: Made a crippled, thumbnail-based version of the SBA for SVG-incapable browsers (including the Google robot)
2010-09: Installed Google Analytics tracker
2010-08: DB08 and WHS09 template now show MRI overlays
2010-08: DB08 template now shows WikiPedia definitions, obtained from freebase.com
2010-08: Loading of templates nearly 3 times faster using gzip compression
2010-08: Fixed bug (work-around) in Corel Trace, leading to spurious horizontal lines in SVG output
2010-08: Dubach and Bowden 2008 Macaque template added, including NeuroNames hierarchy
2010-07: Automated pipeline for template import from png sources
2010-07: Get templates/regions as tab-separated data using listregions.php
2010-06: Single php/html source for all templates, new features are automatically shared
2010-06: Comparison of potrace vs. Corel trace to convert raster images to SVG: Corel makes better partitions, but potrace is much easier to automate
2010-05: Matlab interface to view 3d renderings of regions
2010-05: Lookup region name by stereotaxic coordinate implemented for PHT00
2010-04: Stereotaxic coordinates of mouse-cursor displayed in 2d view
2010-03: New atlas template: PHT00_on_F99
2010-03: Thumbnail service extended with 3d view and indexed-color png files
2010-03: Opera is now a supported browser
2010-03: Doubled speed of auto-complete function

Last update: Tuesday, 10 January 2012

Macaque atlases

Mouse atlases

Human atlases