=================
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 <https://github.com/czimaginginstitute/MotionCor3>`_.
.. image:: https://img.shields.io/pypi/v/scipion-em-motioncorr.svg
:target: https://pypi.python.org/pypi/scipion-em-motioncorr
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.. image:: https://img.shields.io/pypi/l/scipion-em-motioncorr.svg
:target: https://pypi.python.org/pypi/scipion-em-motioncorr
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-motioncorr.svg
:target: https://pypi.python.org/pypi/scipion-em-motioncorr
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-motioncorr?server=https%3A%2F%2Fsonarcloud.io
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.. image:: https://img.shields.io/pypi/dm/scipion-em-motioncorr
:target: https://pypi.python.org/pypi/scipion-em-motioncorr
:alt: Downloads
**IMPORTANT!**
1. 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 <https://github.com/I2PC/xmippCore/issues/39>`_)
2. When importing EER movies, you should specify dose per single EER frame during import step.
3. 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.
4. 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:
a) Stable version
.. code-block::
scipion installp -p scipion-em-motioncorr
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-motioncorr.git
* install
.. code-block::
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/motioncor3-1.0.1``, 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_1.0.1_CudaXY_10-26-2023`` (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:
.. code-block::
scipion test motioncorr.tests.test_protocols_motioncor.TestMotioncorAlignMovies
scipion test motioncorr.tests.test_protocols_tomo.TestMotioncorTiltSeriesAlignMovies
Licensing
---------
Motioncor3 is provided under BSD-3-Clause license
Supported versions
------------------
motioncor3 1.0.1
motioncor2 1.6.4
Protocols
---------
* movie alignment
* align tilt-series movies
References
----------
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).
Raw data
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"description": "=================\nMotioncorr plugin\n=================\n\nThis plugin allows to use motioncor3 program within the Scipion framework.\n\nMotioncor3 is a GPU-accelerated program for correction of electron beam-induced sample motion. It is developed by `Shawn Zheng <https://github.com/czimaginginstitute/MotionCor3>`_.\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-motioncorr.svg\n :target: https://pypi.python.org/pypi/scipion-em-motioncorr\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-motioncorr.svg\n :target: https://pypi.python.org/pypi/scipion-em-motioncorr\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-motioncorr.svg\n :target: https://pypi.python.org/pypi/scipion-em-motioncorr\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-motioncorr?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-motioncorr\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-motioncorr\n :target: https://pypi.python.org/pypi/scipion-em-motioncorr\n :alt: Downloads\n\n**IMPORTANT!**\n\n 1. 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 <https://github.com/I2PC/xmippCore/issues/39>`_)\n 2. When importing EER movies, you should specify dose per single EER frame during import step.\n 3. 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.\n 4. 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.\n\nInstallation\n------------\n\nYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-motioncorr\n\nb) Developer's version\n\n * download repository \n\n .. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-motioncorr.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-motioncorr --devel\n\n**Important:** Starting from plugin v3.15, the config variables have been renamed. See: `scipion3 config -p motioncorr`\n\n- Motioncor binaries will be installed automatically with the plugin, but you can also link an existing installation.\n- Default installation path assumed is ``software/em/motioncor3-1.0.1``, if you want to change it, set *MOTIONCOR_HOME* in ``scipion.conf`` file to the folder where the Motioncor3 is installed.\n- Depending on your CUDA version this plugin will guess the right default binary from ``MotionCor3_1.0.1_CudaXY_10-26-2023`` (X is for cuda major version, Y for the minor). You can always set a different one by explicitly setting *MOTIONCOR_BIN* variable.\n- 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.\n\nFor an automatically updated installation of motioncor binaries, do not define neither *MOTIONCOR_HOME* nor *MOTIONCOR_BIN*.\n\nTo check the installation, simply run the following Scipion tests:\n\n.. code-block::\n\n scipion test motioncorr.tests.test_protocols_motioncor.TestMotioncorAlignMovies\n scipion test motioncorr.tests.test_protocols_tomo.TestMotioncorTiltSeriesAlignMovies\n\nLicensing\n---------\n\nMotioncor3 is provided under BSD-3-Clause license\n\nSupported versions\n------------------\n\nmotioncor3 1.0.1\nmotioncor2 1.6.4\n\nProtocols\n---------\n\n* movie alignment\n* align tilt-series movies\n\nReferences\n----------\n\n1. 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\u2013332 (2017).\n\n\n",
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