J.M. de la Rosa-Trevín, A. Quintana, L. del Cano, A. Zaldívar-Peraza, I. Foche, J. Gutiérrez, J. Gómez-Blanco, J. Burguet-Castells, J. Cuenca-Alba, V. Abrishami, J. Vargas, J. Otón, G. Sharov, J.L. Vilas, J. Navas, P. Conesa, M. Kazemi, R. Marabini, C.O.S. Sorzano, J.M. Carazo. Scipion: a software framework toward integration, reproducibility, and validation in 3D Electron Microscopy. J. Structural Biology, 195: 93-99 (2016)
In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.