Source-linked AI summary
The Scalable Brain Atlas: instant web-based access to public brain atlases and related content
Rembrandt Bakker, Paul Tiesinga, Rolf Kötter
TL;DR
Public neuroscience data tied to brain coordinates require spatial navigation and stereotactic display beyond ontology-based database queries. The SBA addresses this gap with a lightweight, plugin-enabled web atlas integrating multiple species, atlas templates, and external resources; it currently provides a first step toward cross-template and cross-species data integration, while copyright transfers exclude some popular print atlases.
Problem
Spatially registered neuroscience data need region or coordinate navigation and stereotactic display, which ontology-based queries do not adequately provide.
Method
The SBA integrates atlas templates into an SVG-based browser viewer with plugins and services that query external resources, transform coordinates, and display region information.
Results
The SBA contains twenty atlas templates across six species and has taken a first step toward integrating data across templates and species.
Takeaways & Limitations
The SBA provides a maintained web toolkit for atlas comparisons, searches, coordinate transformations, interactive displays, and linked brain-region resources.
Takeaways & Limitations
Copyright transfers to publishers prevent the SBA from parsing several popular print atlases.
Abstract
from arXiv · showhide
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.
1. Introduction
The SBA evolved from a Macaque- and CoCoMac-specific visualization tool into a generalized, lightweight web atlas supporting multiple species, atlases, and interactive plugins. Its viewer combines 2D slice navigation, quasi-3D display, stereotaxic coordinates, region selection, and web queries.
- Introduction: The framework addresses the need to navigate spatially registered brain data, select regions or coordinates, and display query results in stereotactic space.Existing ontology-based queries were described as impractical for accessing spatially registered content.
- Web-based interactive brain atlas: The SBA uses stacked 2D drawings to create a quasi-3D browser experience and selected SVG for its open standard and broad cross-browser support.This design simplified 3D requirements while avoiding the bandwidth and browser-support constraints described for full 3D rendering.
- Web-based interactive brain atlas: The SBA generalized CP3D from a Macaque-specific application into a multi-species, multi-atlas web toolkit with plugins and twenty imported atlases.Its scalability derives from supporting multiple species and atlases, bidirectional plugin interaction, and SVG-based rendering.
- Web-based interactive brain atlas: The viewer presents a selected slice with delineated regions, imaging modalities, stereotaxic coordinates, region hierarchies, and markers.The 3D panel stacks slices and shows the full extent of selected regions.
- Web-based interactive brain atlas: Selecting a region highlights corresponding structures across the 2D panel, 3D panel, and hierarchical region list, while notifying the active plugin.Plugins respond to changes in selected regions, slices, and coordinates.
- Web-based interactive brain atlas: The SBA also provides services for bitmap conversion, label-volume export, hierarchical region lists, region centers, distance matrices, and downloadable atlas files.These services extend atlas-derived data access beyond the interactive viewer.
2. Methods
The methods convert heterogeneous atlas sources into browser-ready representations and implement client-side interaction with extensible plugins and web services. Atlas data are delivered through SVG, JSON, JavaScript, PHP, and server-mediated requests to external resources.
- Creating atlas templates: Atlas templates are built from vector drawings, labelled volumes, and cortical surface parcellations converted into closed curves or label volumes.The pipeline addresses open vector boundaries, misplaced labels, contour tracing, and surface-to-volume conversion.
- Creating atlas templates: Surface-derived label volumes are smoothed after conversion by decomposing regions, filtering them individually, and regenerating the volume.The smoothing step addresses ragged region boundaries produced by discretization.
- Creating interactive SVG-based webpages: The browser downloads atlas JSON files, stores them in JavaScript memory, and generates HTML and SVG through the Document Object Model.The SBA core keeps interactivity client-side after the page loads.
- Bilateral client-server communication: PHP generates pages containing JavaScript, atlas JSON, HTML markup, and styling, while plugins initiate client-server requests using query parameters.The service framework exposes parameter names and admissible values when requests are incomplete.
- Bilateral client-server communication: Plugins are triggered by selected regions, slices, or coordinates and can modify their own frames or the viewer’s 2D and 3D panels.Approved plugins can be hosted externally, but external plugin URLs must be white-listed.
- Bilateral client-server communication: Because browser same-origin restrictions limit external requests, SBA PHP proxy scripts relay queries for plugins such as CoCoMac, NeuroLex, Wikipedia, and DAI.JSONP is also described as a way to bypass the same-origin policy.
3. Imported atlas templates
The SBA imports atlas templates using explicit inclusion criteria and provides unified access to twenty templates spanning six species. Waxholm Space and other reference spaces support interoperability by making mappings between atlases explicit or computable.
- Imported atlas templates: Templates qualify for inclusion when at least four criteria are met, including peer-reviewed description, parcellation with underlying modality, neuroscience value, reference-space status, and parseable format.The criteria include NIfTI-1 or CAF availability for parsing.
- Imported atlas templates: Twenty atlas templates covering six species are included, with Macaque overrepresented because SBA originated as a CoCoMac connectivity viewer.Atlases whose copyrights were transferred to publishers are underrepresented.
- Citation policy: SBA users must cite the defining publications of atlas creators even when templates are transformed or combined.This citation policy is intended to protect the scientific careers of atlas creators.
- Waxholm Space: Waxholm Space templates WHS12 and PLCJB14 are promoted by INCF as standard reference spaces, enabling data transfer and joint display through mappings to a common space.WHS12 is based on 21.5 μm isotropic MR imaging data.
- Waxholm Space: Rat resources include the PLCJB14 Waxholm reference atlas, CBWJ13 MR-histology data, RMJetal13 age-specific DTI data, and population-averaged DTI and in-vivo MRI templates.The listed resources span postnatal day 72 and 80 datasets and include T2*, DTI, DWI, and fractional anisotropy.
- Waxholm Space: Some atlas entries are derived from cortical surfaces converted to volumes using an assumed constant cortical thickness of 1.8 mm.One footnote identifies these data as obtained from SumsDB and processed with Caret; another defines F99 resolution and MRI abbreviations.
4. Services
SBA services expose atlas data through URL queries and return images, JSON, or web pages to plugins, clients, and other websites. They support template discovery, region lookup, coordinate-to-region mapping, slice rendering, and region thumbnails.
- URL queries invoke SBA operations and return formatted images, JSON data, or web pages to plugins, clients, or other websites.
- Atlas viewer: The atlas viewer loads a specified template and accepts parameters for highlighting regions, activating plugins, and selecting image modalities.
- Template and region services provide available atlas metadata, region names, parent acronyms, and visibility-related shape codes.
- Coordinate to region: Coordinate lookup maps a stereotactic x,y,z triplet to a region name using the corresponding coronal slice pixel and rgb2acr.json color mapping.
- Atlas rendering: Slice rendering generates color-coded SVG or raster images, while Matlab scripts support downloading complete atlases and visualizing individual regions.
- Region thumbnails: Thumbnail generation produces selectable layouts and image sizes showing a region’s appearance and location, including combined 2d and 3d views.
5. Plugins
SBA plugins extend the viewer with web-based interactions and external atlas resources. The 3dBAR plugin supports three-dimensional region reconstruction and exchange of atlas templates between SBA and 3dBAR.
- Eight general-purpose Javascript plugins provide viewer extensions, while some atlas templates offer additional plugins for high-resolution original datasets.
- Three-dimensional Brain Atlas Reconstructor (3dBAR): The 3dBAR plugin displays three-dimensional reconstructions of selected brain regions and links to 3dBAR for constructing complex scenes.
- Three-dimensional Brain Atlas Reconstructor (3dBAR): SBA and 3dBAR exchange atlas templates through SBA import of CAF files and direct 3dBAR import of SBA templates.
- Three-dimensional Brain Atlas Reconstructor (3dBAR): For selected regions, the plugin shows precomputed thumbnails before linking to the external reconstruction service.
5.3 BrainInfo and NeuroNames
BrainInfo and SBA plugins connect selected atlas regions with external anatomical resources and connectivity displays. Their outputs combine region-linked information, projection markers, tabular evidence, and publication traceability.
- BrainInfo and NeuroNames: BrainInfo provides detailed information on NeuroNames brain sites across synonyms, structure, cell types, genes, hierarchy, connections, and models.
- BrainInfo and NeuroNames: The BrainInfo plugin checks for a page matching the selected region and displays a link because BrainInfo lacks a structured-data service.
- Region lookup: The NeuroLex and SBA Lookup plugins display external information and cross-template matches for the selected Thalamus region.
- Connectivity: The CoCoMac plugin displays axonal projections as markers, tabular connection evidence, and links for tracing each projection to its source publication.
5.4 Wikipedia
The Wikipedia plugin dynamically retrieves content matching the full name of the selected brain region. Unlike NeuroLex, Wikipedia lacks neuroscience-specific attributes, so non-neuroscience ambiguities may occur.
- The plugin dynamically displays Wikipedia content matching the full name of the currently selected brain region.
- Wikipedia lacks attributes restricting results to neuroscience terms, allowing ambiguities with non-neuroscience meanings.
- The stereotactic marker plugin can transform locations between mouse atlas templates, illustrated by mapping the WHS12 Interpeduncular nucleus to ABA12.
5.6 Macaque connectivity (CoCoMac)
The CoCoMac plugin retrieves macaque structural connectivity for a selected region and presents outgoing projections across the SBA interface and linked publications. SBA Lookup complements this by finding corresponding regions across atlas templates.
- The plugin downloads macaque structural connectivity data from CoCoMac for the selected region.
- Outgoing projections appear as markers in the 3d panel and as a table in the plugin panel.
- Each projection links to CoCoMac.g-node.org, where its supporting publications can be tracked.
- SBA Lookup searches templates for matching acronyms, full names, or aliases and links to corresponding SBA pages.
5.8 Fiducial points (Landmarks)
The Landmarks plugin provides 16 validated fiducial points in the WHS12 template and displays them over a mid-sagittal T1 slice. These landmarks support recognition and future registration of whole-brain volumes.
- The WHS12-only Landmarks plugin presents 16 fiducial points validated as clearly recognizable in structural MR scans.
- Figure 7 overlays the landmarks on the WHS12 mid-sagittal T1 slice in the viewer’s 3d panel.
6. Discussion and Conclusion
SBA has expanded into a maintained, community-oriented web toolkit for integrating brain-atlas resources across templates and species. Planned developments target richer visualization, automated atlas import, nonlinear registration, higher resolution, and broader coverage, while publisher copyrights remain a limitation.
- SBA has grown from a CoCoMac visualization application into a web toolkit supporting multiple species, atlases, plugins, and self-search.
- The SBA Lookup plugin represents a first step toward integrating data across templates and species.
- Planned developments include sagittal and axial slice display, a fully automated atlas-template import pipeline, and nonlinear image registration.
- Nonlinear registration is intended to display user volumetric data with warped SBA parcellations and support the inverse transformation.
- A deep zoom plugin is planned to support responsive display of high-resolution atlas content and primary hosting of new atlases.
- Several popular printed atlases are omitted because transferred copyrights prevent SBA from parsing their content.
- The authors invite atlas owners to contribute and envision SBA as a community-driven resource with continued CoCoMac development.
Appendix B: example plugin code
Appendix B presents a minimal JavaScript plugin example and identifies the viewer state and lifecycle hooks available for extending SBA.
- The example plugin prints “Hello World” and the SBA state variables available for initiating queries.
- Plugins are stored in the plugins directory using the pattern pluginname_plugin.js.
- Plugins load after the global sbaViewer object has been initialized.
- The constructor derives from sbaPlugin_class and stores the atlas template name from sbaViewer.
- The activate hook runs when the plugin is first shown and can access the viewer state.
- The applyStateChange hook responds when SBA state changes, while the default implementation calls activate.