11 pages, 2 figures.-- PMID: 15477099 [PubMed].-- Printed version published on Nov 2004. X-windows based microscopy image processing package (Xmipp) is a specialized suit 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. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community. We acknowledge partial support from the "Comunidad Autónoma de Madrid" through Grant CAM-07B-0032-2002, the "Comisión Interministerial de Ciencia y Tecnología" of Spain through Grants BIO2001-1237, BIO2001-4253-E, BIO2001-4339-E, and BIO2002-10855-E, the European Union through Grants QLK2-2000-00634, QLRI-2000-31237, QLRT-2000-0136, and QLRI-2001-00015, and the NIH through Grant HL70472. Partial support from the "Universidad San Pablo-CEU" Grant 17/02 is also acknowledged. Peer reviewed