Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases.

Ilya Zaslavsky,Richard A Baldock,Jyl Boline

doi:10.3389/fninf.2014.00074

Abstract

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today's data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems (SRSs) and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project.

Highlights

Asked questions in neuroscience are “where” in the brain something is happening, “what” is happening “here,” and “what” is this structure
We focus on the formal definition of coordinate systems and coordinate transformations for rodent brain, a service interface for Digital Atlasing Infrastructure (DAI) services, and a standards-based XML schema for encoding atlas information, called Waxholm2 Markup Language (WaxML)
Tools like Google Maps are appealing because they serve as gateways to enormous amounts of spatially-registered information

Summary

INTRODUCTION

Asked questions in neuroscience are “where” in the brain something is happening, “what” is happening “here,” and “what” is this structure. The GetStructureNamesByPOI method supports structure lookup for a canonical set of segmentations defined for an atlas, returning WaxML descriptions of structures found in the vicinity of a POI, along with geometric properties of each structure if available While at this stage DAI is primarily concerned with coordinate information exchange and spatial requests (e.g., POI-based requests), atlas hubs may include queries that don’t involve brain location, e.g., queries by structure name, gene name, or similar. A Python API accessing atlas web services has been developed (http:// software.incf.org/software/incfdai?searchterm=python+DAI) With these applications, users can compare anatomic feature descriptions, gene expression and other types of data available in different atlases and at different locations of interest. Tools to more implement an atlas hub, at least for certain data types

CONCLUSIONS AND FUTURE WORK

Conference Abstract