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Plugin to use cisTEM programs within the Scipion framework

Project description

This plugin provides wrappers for 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 -b devel
    • install

    scipion installp -p /path/to/scipion-em-cistem --devel

Important: Starting from plugin v3.9, the config variables have been renamed. See: scipion3 config -p cistem

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 CTFFIND installed separately from cisTEM by defining CTFFIND_HOME variable in scipion.conf. Setting this value will have the priority over Ctffind inside cisTEM.

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

Supported versions

  • 1.0.0-beta (cistem)

  • 4.1.13, 4.1.14 (ctffind4)

  • 5.0 (ctffind5)



  • ctffind

  • import tomo CTFs

  • tilt-series ctffind

  • unblur

  • find particles

  • classify 2D


  1. Johannes Elferich, Lingli Kong, Ximena Zottig, Nikolaus Grigorieff. (2024) CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples. bioRxiv 2024.02.26.582023; doi:

  2. 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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