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3D imaging is the science of the methods of defining, visualizing, manipulating, and analyzing 3D object information captured in multidimensional images acquired from multiple modalities. This paper gives an overview of this science and identifies the major challenges currently faced in its medical applications. It describes the 3D imaging operations under four groups: preprocessing, visualization, manipulation, and analysis. Preprocessing operations go toward defining objects in given images. Visualization operations facilitate seeing and comprehending objects in their full dimensionality. Manipulation allows altering object structures and relationship among objects. Analysis deals with methods of quantifying object information. The paper describes the concepts underlying these operations. It draws two main conclusions. (1) There are two classes of approaches to 3D imaging-those based directly on image intensities and those based on object shape. (2) There are two main groups of challenges, related to object delineation and validation.