Motioncorr plugin
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.
Installation
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-motioncorrDeveloper’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-motioncorr.gitinstall
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/motioncor3-1.2.4, if you want to change it, set MOTIONCOR_HOME in scipion.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_1.2.4_CudaXY_13-05-2026 (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.TestMotioncorTiltSeriesAlignMoviesLicensing
Motioncor3 is provided under BSD-3-Clause license
Supported versions
motioncor3 1.2.4
Protocols
movie alignment
align tilt-series movies
References
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).
2 maintainers
Metadata
2 maintainers
Release files for scipion-em-motioncorr 4.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_em_motioncorr-4.0.1.tar.gz | 48.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_motioncorr-4.0.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 109.8 kB
Release files / scipion_em_motioncorr-4.0.1.tar.gz
| Download URL | scipion_em_motioncorr-4.0.1.tar.gz |
|---|---|
| Size | 48.0 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
937bc798d573470e1fb65b3bd7ba7a73f3fc90443caf059cfc9655d19725e09d
|
|
BLAKE2b-256 checksum How to use checksums |
2527088b46b785be205b4ca13b6029854ed93a979fa665fdf1f51e864c4a591d
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
Release files / scipion_em_motioncorr-4.0.1-py3-none-any.whl
| Download URL | scipion_em_motioncorr-4.0.1-py3-none-any.whl |
|---|---|
| Size | 61.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
cc53b995b60bf7c14679cb1844aa524703ed7e82ad84a465d4b5117c5479422c
|
|
BLAKE2b-256 checksum How to use checksums |
5d861989f39d6ae44e3a6fb1f589201a023e7688d19bc19654fe931e8cf35625
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
|
