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AIR
A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.
BrainSuite

BrainSuite is a collection of software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain.

MultiTracer
MultiTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.
ShapeTools
The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines.
ShapeViewer

The ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java, it can run on a wide variety of computers.

SHIVA

The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets.