3D Visualization-Assisted Analysis (Vaa3D) is an open source cross-platform (Mac, Linux, and Windows) tool based on ITK libraries for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Registration required.