Abstract
BackgroundAnatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomical atlases provide a spatial framework for these studies. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework not only captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system.ResultsWe have developed an atlas-viewing application ('NeuARt II') in the Java language with unique functional properties. These include the ability to use copyrighted atlases as templates within which users may view, save and retrieve data-maps and annotate them with volumetric delineations. NeuARt II also permits users to view multiple levels on multiple atlases at once. Each data-map in this system is simply a stack of vector images with one image per atlas level, so any set of accurate drawings made onto a supported atlas (in vector graphics format) could be uploaded into NeuARt II. Presently the database is populated with a corpus of high-quality neuroanatomical data from the laboratory of Dr Larry Swanson (consisting 64 highly-detailed maps of PHAL tract-tracing experiments, made up of 1039 separate drawings that were published in 27 primary research publications over 17 years). Herein we take selective examples from these data to demonstrate the features of NeuArt II. Our informatics tool permits users to browse, query and compare these maps. The NeuARt II tool operates within a bioinformatics knowledge management platform (called 'NeuroScholar') either as a standalone or a plug-in application.ConclusionAnatomical localization is fundamental to neuroscientific work and atlases provide an easily-understood framework that is widely used by neuroanatomists and non-neuroanatomists alike. NeuARt II, the neuroinformatics tool presented here, provides an accurate and powerful way of representing neuroanatomical data in the context of commonly-used brain atlases for visualization, comparison and analysis. Furthermore, it provides a framework that supports the delivery and manipulation of mapped data either as a standalone system or as a component in a larger knowledge management system.
Highlights
Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community
NeuARt II provides an intuitive framework for browsing, comparing, interpreting and summarizing neuroanatomical data. This system capitalizes on the fact that virtually all neuroscience researchers use brain atlases to identify brain structures and that the electronic versions of the atlas plates can serve as templates to map anatomical data
We present 'NeuARt II', an informatics system that acts as a visual interface for experimental neuroanatomical work that is based on existing practices within the field
Summary
Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. We have built an informatics framework based on these atlases for the representation of neuroanatomical knowledge. This framework captures current methods of anatomical data acquisition and analysis, it allows these studies to be collated, compared and synthesized within a single system. Previous attempts to construct atlas-based neuroanatomical databases have met with limited success due mainly to issues related to data registration across experiments. These issues are addressed implicitly by neuroanatomists when comparing nuclei and landmarks illustrated in a standard atlas to experimental data or published figures to one another
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