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Motioncorr plugin

This plugin allows to use motioncor2 program within the Scipion framework.

Motioncor2 is a GPU-accelerated program for correction of electron beam-induced sample motion. It is developed by Shawn Zheng.

PyPI release License Supported Python versions SonarCloud quality gate Downloads
prod: prod devel: devel support: support


If you have imported movies with a gain file in DM4 format, you need to flip the gain reference upside-down in the motioncor2 protocol! (bug details)


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-motioncorr
  1. Developer's version

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

Motioncor2 binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/motioncor2-1.4.2, if you want to change it, set MOTIONCOR2_HOME in scipion.conf file to the folder where the Motioncor2 is installed. Depending on your CUDA version you might want to change the default binary from MotionCor2_1.4.2_Cuda101-02-15-2020 to a different one by explicitly setting MOTIONCOR2_BIN variable. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add MOTIONCOR2_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official UCSF website.

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

scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies

Supported versions

1.2.6, 1.3.0, 1.3.1, 1.3.2, 1.4.0, 1.4.2


  • movie alignment
  • align tilt-series movies


  1. Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng & David A Agard. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods volume 14, pages 331–332 (2017).


Plugin to use Motioncor2 program within the Scipion framework





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