Numerous digital atlases of the brain have been developed for different species through the efforts of researchers around the world. For a comprehensive picture of brain morphology and function, it is important to discover and bring together various images, segmentations and markup, generated within different projects, and juxtapose them within a single federated atlas interface. This paper describes strategies and tools for integrating distributed sources of brain data spatially. We focus on the organization of web-enabled spatial data sources which include ArcIMS feature and image services and distributed grid sources, and on the Smart Atlas, a GIS-based atlas environment enabling users to discover, access, visualize and query heterogeneous images and image markup. We demonstrate construction of spatial databases from unorganized vector and raster brain data based on ontological relationships between anatomical features from the Unified Medical Language System, spatial registration mechanisms, and tools and user interfaces for federated brain data visualization and analysis.