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Plugin to use cisTEM programs within the Scipion framework
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cisTEM plugin

ATTENTION: This plugin is still in development and will eventually replace grigoriefflab plugin.

This plugin provide wrappers around several programs of cisTEM software suite.

build status


You will need to use 2.0 version of Scipion to be able to run these protocols. To install the plugin, you have two options:

  1. Stable version
scipion installp -p scipion-em-cistem
  1. Developer's version

    • download repository
    git clone
    • install
    scipion installp -p path_to_scipion-em-cistem --devel

cisTEM binaries will be installed automatically with the plugin, but you can also link an existing installation.

  • Default installation path assumed is software/em/cistem-1.0.0-beta, if you want to change it, set CISTEM_HOME in scipion.conf file pointing to the folder where the cisTEM is installed.
  • It's possible to use CTFFIND4 installed separately from cisTEM by defining CTFFIND4_HOME variable in scipion.conf.

To check the installation, simply run one of the following Scipion tests:

scipion test cistem.tests.test_protocols_cistem_movies.TestUnblur
scipion test cistem.tests.test_protocols_cistem.TestCtffind4
scipion test cistem.tests.test_protocols_cistem.TestFindParticles
scipion test cistem.tests.test_protocols_cistem.TestRefine2D

A complete list of tests can also be seen by executing scipion test --show --grep cistem

Supported versions



  • ctffind4
  • unblur
  • find particles
  • classify 2D


  1. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.
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