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The Whole Brain Catalog is a 3D virtual environment to facilitate solutions for currently intractable challenges in brain research. It is meant to enable the synthesis of data measured from brains at different scales into more coherent models of brain structure and function. The Whole Brain Catalog is a client-server platform that provides rich 3D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. A 3D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations.