The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content

Abstract

The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays.

Fig. 1

Components of the atlas viewer: a 2d panel displaying a single slice with the parcellation overlaid on the selected imaging modalities, along with a list of structures in the current view or the full region hierarchy (as in Fig. 3); b 3d panel with convex hulls for each slice, and the detailed parcellation for every 10^th slice. The current slice is highlighted as a blue contour. By default, the brain is elongated to better show the inside. The 3d surface rendering overlay is a static image, generated by the 3dBAR service (Sec. 5.1), with adjustable transparency; The marker named ‘Cd’ is created by the AddMarker plugin; c Plugin panel. When a plugin gets activated, it responds to changes in selected region, slice and coordinate

Fig. 2

Effect of the 3d smoothing kernel that is applied to volumes obtained after Surface to Volume conversion in Caret (Van Essen 2011). The blurring kernel is applied separately in each dimension with coefficients [1, 3, 6, 3, 1]. It effectively despeckles the 3d volume

Fig. 3

Coordinate transformation invoked from the AddLandmark plugin, powered by the INCF Digital Atlasing infrastructure. Here, the interpeduncular nucleus landmark is transformed from the WHS12 to the ABA12 template. Table 1 explains template names

Fig. 4

Various ways to interact with brain region shapes, with PHT00-V2 as an example: a Using Matlab functions to download a template, extract a region mask and display it (scripts at http://scalablebrainatlas.incf.org/howto/analyze_templates_in_matlab.php); b Using the SBA thumbnail service; c Using the 3dBAR plugin from within SBA; d Using the 3dBAR custom reconstruction service (service.3dbar.org), showing both hemispheres, two areas (V1,V2) and a transparent whole brain

Fig. 5

Output of the NeuroLex (a) and SBA Lookup (b) plugins, both with Th (Thalamus) as the selected region

Fig. 6

Output of the CoCoMac plugin: a the axonal projections of region PHT00-25 are displayed as markers with a color intensity that represents connection strength. Note that this strength measure is not an official CoCoMac variable, it is provided to display capabilities of the SBA; b tabular output, in which each connection is represented by a character string. Each character is a separate ‘piece of evidence’, whereby X,0,1,2,3 mean unknown strength, absent, weak, medium and strong tracer labelling, respectively; c Interactive tabular display at the CoCoMac.g-node.org website allows traceback to the original publication

Fig. 7

Sixteen fiducial points, shown by the Landmarks plugin in the 3d panel of the WHS12 template, overlaid on the mid-saggital T1 slice. Semi-occluded markers are highlighted on mouse hover. Abbreviations: CM Cerebellum middle, KM Cortex middle, PM Pontine nucleus middle, HM Hippocampus middle, IP Interpeduncular nucleus middle, IPL/IPR Interpeduncular nucleus left/right, CCM Corpus Callosum middle, VM Ventricle middle, ACL/ACR Anterior Commissure left/right, FM Frontal middle, FL/FR Frontal left/right, AC Anterior Commissure