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Plugin to use motioncorr programs within the Scipion framework

Project description

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


  1. 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! (see details)

  2. When importing EER movies, you should specify dose per single EER frame during import step.

  3. If you are processing EER movies and providing *.gain reference file camera defects will be automatically extracted from the gain file header and converted to Motioncor2 format. This step is omitted if you provide a defects file yourself.


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 -b devel
    • 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/motioncor2-1.5.0, 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 this plugin will guess the right default binary from MotionCor2_1.5.0_CudaXY_05-31-2022 (X is for cuda major version, Y for the minor). You can always set 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.

For an automatically updated installation of motioncor2 binaries, do not define neither MOTIONCOR2_HOME nor MOTIONCOR2_BIN.

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

scipion test motioncorr.tests.test_protocols_motioncor2.TestMotioncor2AlignMovies


Motioncor2 is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:

Supported versions

1.4.0, 1.4.2, 1.4.4, 1.4.5, 1.4.7, 1.5.0


  • 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).

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