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Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.


GNU/GPL v2 licence + citation request: If you have used Xmipp in your work, please cite our papers as given in the List Of References.


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of xmipp and load default version of xmipp as

module avail xmipp/ # list available modules
module load xmipp   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail xmipp

and choose explicit version you want to use. This makes available the path to program binaries as well as aliases for the most used ones:

alias xa='xmipp_apropos'
alias xb='xmipp_browser'
alias xic='xmipp_image_convert'
alias xih='xmipp_image_header'
alias xio='xmipp_image_operate'
alias xis='xmipp_image_statistics'
alias xmipp='xmipp_protocols'
alias xmipp_show='xmipp_showj'
alias xmp='xmipp_metadata_plot'
alias xmu='xmipp_metadata_utilities'
alias xp='xmipp_protocols'
alias xrf='xmipp_resolution_fsc'
alias xrs='xmipp_resolution_ssnr'
alias xs='xmipp_showj'
alias xsj='xmipp_showj'
alias xtf='xmipp_transform_filter'
alias xtg='xmipp_transform_geometry'
alias xtn='xmipp_transform_normalize'

Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.


User documentation is available in http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Documentation.