The NeuARt II plug-in (named after a predecessor application NeuARt) provides an interface modeled on neuroanatomical atlases. The aim of this project to provide an infrastructure for neuroscientists to use neuroanatomical atlases to refer to and map their data. This project has now been described in a paper (published online in BMC Bioinformatics). The project effort is also described in a recent ISI news article.
Within the functional application, users may navigate between atlas plates, pan, zoom, measure their position with stereotaxic rulers and draw volumetric delineations over the brain at any scale of resolution. These delineations also have the capability of embedding ‘error bars’ into the representation to provide some measure of the uncertainty of the position of a given delineation.
The purpose of NeuARt is to provide a viewer where mapped data may be compared easily. This is illustrated more fully in Figure 1. It is possible to use NeuARt to look for overlap between mapped data sets and to store large numbers of maps in a single database, functionality that is not easily available through the use of standard drawing packages.
Figure 1: Screenshot of the NeuARt application showing multiple injection sites of different data maps taken from Risold & Swanson, (1997) J. Comp. Neurol. 24:115-95
We have received permission from Elsevier to incorporate data from Larry Swanson’s 2nd and 3rd edition atlases, and the Paxinos atlas 5th edition under the condition that the user must own a licensed copy of the commercial CD.
Within NeuroScholar, we define two views: a ‘BrainVolume’ view (a 3-dimensional delineation of a region of brain tissue) and a ‘DataMap’ view (mapped neuroanatomical data as a series of drawings overlaid onto atlas plates). These views are used within the knowledge representation as supporting information for other knowledge, for example, the injection site of a tract-tracing experiment is a specialized BrainVolume view and the labeling produced by one of these experiments may be represented as a DataMap.
- Spatial indexing for regions in the brain
- analysis functions
- Mechanisms for web-based data sharing.
- The use of the application as a framework for neuroscience facts, harvested from the literature.
Demos, Downloads and Documentation
The NeuARt II demo can be accessed here.
A small movie featuring the use of NeuARt can be found here.