This plugin allows to use motioncor3 program within the Scipion framework.
Motioncor3 is a GPU-accelerated program for correction of electron beam-induced sample motion. It is developed by Shawn Zheng.
IMPORTANT!
- If you have imported movies with a gain file in DM4 format, you need to flip the gain reference upside-down in the motioncor protocol! (see details)
- When importing EER movies, you should specify dose per single EER frame during import step.
- When importing EER tilt-series movies, you should specify dose per tilt during import step. It is not relevant for motion-correction (no dose-weighting is done here), but will be used later on.
- 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 Motioncor 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:
- Stable version
scipion installp -p scipion-em-motioncorr
Developer's version
- download repository
git clone -b devel https://github.com/scipion-em/scipion-em-motioncorr.git
- install
scipion installp -p /path/to/scipion-em-motioncorr --devel
Important: Starting from plugin v3.15, the config variables have been renamed. See: scipion3 config -p motioncorr
- Motioncor binaries will be installed automatically with the plugin, but you can also link an existing installation.
- Default installation path assumed is
software/em/motioncor3-1.1.1
, if you want to change it, set MOTIONCOR_HOME inscipion.conf
file to the folder where the Motioncor3 is installed. - Depending on your CUDA version this plugin will guess the right default binary from
MotionCor3_1.1.1_CudaXY_05-27-2024
(X is for cuda major version, Y for the minor). You can always set a different one by explicitly setting MOTIONCOR_BIN variable. - If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add MOTIONCOR_CUDA_LIB variable to the config file. Various binaries can be downloaded from the official UCSF website.
For an automatically updated installation of motioncor binaries, do not define neither MOTIONCOR_HOME nor MOTIONCOR_BIN.
To check the installation, simply run the following Scipion tests:
scipion test motioncorr.tests.test_protocols_motioncor.TestMotioncorAlignMovies scipion test motioncorr.tests.test_protocols_tomo.TestMotioncorTiltSeriesAlignMovies
Motioncor3 is provided under BSD-3-Clause license
- motioncor3 1.0.1, 1.1.1
- motioncor2 1.6.4
- movie alignment
- align tilt-series movies
- 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).