Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Want to learn more? See the wiki.
Xmipp is a specialized suite of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. It is a comprehensive suite of image processing algorithms with a strong emphasis in the analysis of single particles although it is extending towards electron tomography and X-ray tomography.