Plugin to use AreTomo program within the Scipion framework

scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3, 0, tomo
pip install scipion-em-aretomo==3.9.1


AreTomo plugin

This plugin provides a wrapper for AreTomo program.

PyPI release


Supported Python versions

SonarCloud quality gate



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-aretomo
  1. Developer's version

    • download repository
    git clone -b devel
    • install
    scipion installp -p /path/to/scipion-em-aretomo --devel
  • AreTomo binaries will be installed automatically with the plugin, but you can also link an existing installation.
  • Default installation path assumed is software/em/aretomo2-1.1.2, if you want to change it, set ARETOMO_HOME in scipion.conf file to the folder where the AreTomo is installed.
  • Depending on your CUDA version this plugin will guess the right default binary from AreTomo2_1.1.2_CudaXY (X is for cuda major version, Y for the minor). You can always set a different one by explicitly setting ARETOMO_BIN variable.
  • If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add ARETOMO_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official website.

To check the installation, simply run the following Scipion test:

scipion test aretomo.tests.test_protocols_aretomo.TestAreTomo


AreTomo2 binaries is available under BSD-3 license

Supported versions

aretomo2: 1.0.0, 1.1.2 aretomo: 1.3.4


  • tilt-series align and reconstruct

Detailed manual can be found in software/em/aretomo2-1.1.2/bin/AreTomo2_Manual_1.1.pdf


  • AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Shawn Zheng, Georg Wolff, Garrett Greenan, Zhen Chen, Frank G. A. Faas, Montserrat Bárcena, Abraham J. Koster, Yifan Cheng, David Agard. JSB vol. 6, 2022, 100068.