Xmipp

Timeline

Short history

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. Xmipp accumulates more several citations from journal papers, has an active users community.

This package was introduced more than a decade ago [1], written in C and based on the X-Windows graphical interface.

In 2004 a big re-implementation (completely done in C++) of the package was done [2], improving the hierarchical structure of well-documented data structures and functions.

In 2008 a series of protocols were introduced using Python-Tkinter guiding the user in the reconstruction work-flow [3]. These protocols represented a major standardization of numerous existing scripts and recipes that circulated among the Xmipp user community, thereby representing years of experience by multiple researchers and providing beginner users with a suitable tool to quickly obtain useful results with minimum efforts in learning about the details of the package.

In new version Xmipp 3.0 the relationship between different Protocols is clearer and the concept of Project has been reinforced. The protocols GUI have been significantly improved allowing users to track all processing tasks done and also results obtained. Now Xmipp is format-independent and support for reading/writing several image formats, which can be mapped on disk and this allow to work with bigger images/volumes files.

A large effort has been dedicated to have flexible input/output files and tools to operate with them. Libraries bindings for popular programming languages like Java and Python have been added to expose Xmipp functions to those languages. Code has been optimized, so now each program is much faster.

Know bugs and release notes

Main references

  • [1] R. Marabini, I. M. Masegosa, M. C. San Martín, S. Marco, J. J. Fernández, L. G. de la Fraga, C. Vaquerizo & J. M. Carazo (1996)
    "Xmipp: An image processing package for electron microscopy"
    J. Structural Biology, 116, 237-240
  • [2] C.O.S. Sorzano, R. Marabini, J. Velazquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo & A. Pascual-Montano (2004)
    "XMIPP: a new generation of an open-source image processing package for Electron Microscopy"
    J. Struct. Biol. 148(2), 194-204
  • [3] S.H.W. Scheres, R. Nuñez-Ramirez, C.O.S. Sorzano, J.M. Carazo & R. Marabini (2008)
    "Image processing for electron microscopy single-particle analysis using Xmipp"
    Nat. Protoc., 3, 977-990