Matching Spatial with Ontological Brain Regions using Java Tools for Visualization, Database Access, and Integrated Data Analysis

Abstract

Brain atlases are widely used in experimental neuroscience as tools for locating and targeting specific brain structures. Delineated structures in a given atlas, however, are often difficult to interpret and to interface with database systems that supply additional information using hierarchically organized vocabularies (ontologies). Here we discuss the concept of volume-to-ontology mapping in the context of macroscopical brain structures. We present Java tools with which we have implemented this concept for retrieval of mapping and connectivity data on the macaque brain from the CoCoMac database in connection with an electronic version of “The Rhesus Monkey Brain in Stereotaxic Coordinates” authored by George Paxinos and colleagues. The software, including our manually drawn monkey brain template, can be downloaded freely under the GNU General Public License. It adds value to the printed atlas and has a wider (neuro-)informatics application since it can read appropriately annotated data from delineated sections of other species and organs, and turn them into 3D registered stacks. The tools provide additional features, including visualization and analysis of connectivity data, volume and centre-of-mass estimates, and graphical manipulation of entire structures, which are potentially useful for a range of research and teaching applications.

Appendix

Abbreviations used in this paper

10:

area 10 of cortex

10D:

area 10 of cortex, dorsal part

10M:

area 10 of cortex, medial part

10V:

area 10 of cortex, ventral part

23:

area 23 of cortex (posterior cingulate cortex)

8A:

area 8A (frontal eye field)

PG:

parietal area PG (caudal inferior parietal lobule)

PGa:

area PG associated region in the superior temporal sulcus

TPO:

temporal parietooccipital associated area in the superior temporal sulcus

V1:

area V1 (primary visual cortex)

V2:

area V2 (secondary visual cortex)

V3A:

visual area V3A

V4:

visual area 4

V4D:

visual area 4, dorsal part

V4V:

visual area 4, ventral part

X:

an existing connection with unknown density ranking

Code organization

Aiming to describe each of the software modules presented in the Software architecture section in more detail, we will start from the ones having been developed formerly for representing the rat brain structures.

Java3d Handler module introduces widgets for the rendering of three-dimensional structures, in addition to those presented in Java3d API itself. It consists of the following classes:

• Java3DBehavior.java handles various structure manipulation options, such as rotating, scaling, shifting, and mouse behaviour.

• Java3DColours.java consists of static methods representing various colors options; all those methods return objects of type Color3f except for one, which generates a Material instance (see Java3D API javadoc, http://java.sun.com/products/java-media/3D/forDevelopers/J3D_1_2_API/j3dapi/javax/media/j3d/Material.html)

• Java3DDebug.java—debugger widgets.

• Java3DHandler.java, the main module class which implements basic rendering, parameter setting, and event handling.

• Java3DModel.java is a supplementary class for the previous one, providing additional necessary capabilities and setting default options.

• Java3DPanel.java integrates the features into the graphical user interface (GUI).

• Java3DPopupMenu.java does the obvious.

• Java3DSurface.java presents several options for surface rendering.

• Java3DToolbar.java is a supplementary class for Java3DPanel.java.

The MorphML handler package contains classes necessary for rendering particular brain structures. It also contains parsers for Neurolucida (http://www.mbfbioscience.com/neurolucida/) and Accustage (http://www.accustage.com/) file formats, not used by our tools, which do not deal with microscopic structures and therefore for practical reasons exploit SVGs for graphical representations instead. Therefore, we would make an outlook at those classes being used for our particular tool. Here are the descriptions of these classes:

• Feature.java and ComplexFeature.java. They introduce the entities representing the brain structures. The former class displays entities as they are depicted in the original atlas, whereas the latter one describes those brain structures consisting of sub-features, according to the CoCoMac nomenclature.

• MorphMLHandler.java class instances are called by reference when the features have to be loaded into the atlas. The class implements the creation of new entities, which represent brain structures.

• MorphMLJava3DPanel.java extends Java3DPanel.java class (see description above), adapting it to deal with concrete brain structures. In addition to capabilities for rendering geometrical primitives (e.g., cubes, spheres, cylinders), provided in the parent class, here those for rendering specific brain features are presented.

• MorphMLRenderer.java introduces various options for brain structures rendering—representing them as a wireframe mesh, or as solid structures of particular thickness. For our tool, we used only the latter representation.

• MorphMLTree.java organizes the structures list hierarchically. In the Fig. 9, it is shown as a separate module (Structures tree) for clarity.

• MorphMLUtil.java provides additional rendering widgets, and necessary geometrical algorithms.

• Morphology.java class represents the entity containing all Feature.java and ComplexFeature.java instances, and methods for rendering the entire set of brain structures loaded into the electronic atlas.

The remaining modules were created specifically for the present tool.

The file parsers shown as SVG parser and Structure names file handler modules contain two following classes:

• SVGHandler.java. This class provides an appropriate handling for instructions given in SVG scripts for displaying the atlas graphics files. Among other instructions, there are also cubic Bezier curves present, to allow a smoother polygon representation. The following parametric form represents the mathematical basis of this instruction:

  $$B\left( t \right) = \left( {1 - t} \right)^3 P_0 + 3t\left( {1 - t} \right)^2 P_1 + 3t^2 \left( {1 - t} \right)P_2 + t^3 P_3 ,\,\,t \in \left[ {0,1} \right]$$

  (4)

using starting point P ₀, end point P ₃ and two control points, P ₁ and P ₂.

• PaxinosHandler.java. This class uses JXL API (http://docjar.com/docs/api/jxl/) developed for working with Excel files in Java. It reads the data file containing area names, acronyms, RGB patterns and descriptions of hierarchical organization for complex features.

• CoCoMac query module is represented by the classes CoCoMacHandler.java and CoCoMacQueryMaker.java. The former class enables the display of information related to connectivity, mapping, literature and brain sites in a system default internet browser, whereas the latter class connects to the database directly via a JDBC-ODBC interface bridge, and handles appropriate SQL statements necessary for displaying connectivity data graphically.

The rest of the modules are parts of uk.ac.ed.paxinos3d package, which contains appropriate widgets necessary exclusively for the current project. Here are the descriptions of the classes included:

• DataVisualisation.java and Query.java handle the graphical display of connectivity data specific for the current atlas.

• View.java creates a GUI specific for the current project. It integrates the features introduced by two classes in MorphML handler API, namely MorphMLJava3DPanel.java and MorphMLTree.java, providing a native look and feel.

• Model.java handles all the events occurring in the above class.

• Controller.java class initializes all the event handlers for the previous class.

The last three classes are integrated by the class Main.java which launches the software.

Finally, there are some supplementary classes—e.g., the one allowing to display a URL in a browser, regardless of the operating system used (Previewer.java), and a class providing native look and feel (WindowUtilities.java); constants related to this particular atlas (Paxinos et al. 2000) are handled in a separate class Constants.java.