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Plugin to use cisTEM programs within the Scipion framework

Project description

ATTENTION: This plugin replaces grigoriefflab plugin. You cannot use both of them simultaneously.

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

PyPI release License Supported Python versions SonarCloud quality gate Downloads


You will need to use 3.0+ 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. Setting this value will have the priority over Ctffind inside cisTEM.

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
  • tilt-series 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.

Project details

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Files for scipion-em-cistem, version 3.1.1
Filename, size File type Python version Upload date Hashes
Filename, size scipion_em_cistem-3.1.1-py3-none-any.whl (163.9 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size scipion-em-cistem-3.1.1.tar.gz (154.5 kB) File type Source Python version None Upload date Hashes View

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