Software at the SCI Institute is developed in close collaboration with application users to satisfy real needs within their research communities. We use a robust, yet agile software process that is fully open-source to produce software environments that integrate leading-edge algorithms in image processing, scientific visualization, and scientific computing. Software products include the SCIRun scientific software problem solving environment for geometric modeling, simulation, and visualization; BioPSE for biomedical computing and visualization; Uintah, designed for combustion, computational fluid dynamics, and mechanical modeling which is implemented on large-scale and distributed with shared memory architectures, map3d, an application to display and edit complex, three-dimensional surface models and associated scalar, time-dependent data; and VisTrails, providing data and process management support for exploratory computational tasks. Recently, the SCI Institute has been developing powerful, stand-alone applications. These software applications include ImageVis3d (formerly BioImage), a high performance volume rendering tool for image and other scalar volume data, BioTensor, a program that processes and visualizes diffusion tensor images, Seg3d, for volume segmentation and image processing, BioMesh3D, for creating tetrahedral and hexahedral meshes; and FusionViewer, for visualizing 3D scalar and vector magnetic fusion data.