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Virtual Rat Brain Project

The RatBrain project has developed tools for integrating 3D reconstructions of neurons and populations in the rat brain. The initial data comes from systems including Neurolucida and Accustage, and all data are "warped" to a common coordinate system, or reference brain.

The project homepage is at : below we list some of the components.

RatBrain Project is available for redistribution under these terms of the Lesser General Public License, LGPL.

The E-brain Builder

The E-brain Builder Tool will convert Neurolucida and MDPlot/Accustage data files to an XML based format, MorphML. The tool visualizes the neuroanatomical data with both perspective and orthogonal viewing systems. It permits real-time translation, moving, scaling, rotation and zooming. This can be used to generate enhanced views of 3D data, including annotations.

MorphML Viewer

The MorphML Viewer Tool allows the user to browse the contents of the Neuro-anatomical database at Rutgers University.

The Iso-density Surface Mapper Tool
The Iso-density Surface Mapper Tool visually represent the cell population distributions. If a voxel, a 3D space contain more than a certain threshold of cell bodies the voxel is rendered.
The Overlapping Analysis Tool
The Overlapping Analysis Tool compares the density and overlap between two or more cell populations.
The Java3D Handler

The Java3D Handler library is a collection of widgets used for rendering 3D data.

MorphML Handler

The MorphML Handler library can read and write MorphML files to and from the file system.


The RatBrain Framework is available for Unix, Linux x86, Windows NT4.0/2000/XP platforms.

[NOTE: Mac OS X can be supported if required.]

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