Plugin to use AreTomo program within the Scipion framework
Project description
This plugin provides a wrapper for AreTomo program.
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-aretomo
Developer’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-aretomo.git
install
scipion installp -p /path/to/scipion-em-aretomo --devel
AreTomo binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/aretomo-1.2.5, if you want to change it, set ARETOMO_HOME in scipion.conf file to the folder where the AreTomo is installed. Depending on your CUDA version you might want to change the default binary from AreTomo_1.2.5_Cuda101_08-01-2022 to a different one by explicitly setting ARETOMO_BIN variable. If you need to use CUDA different from the one used during Scipion installation (defined by CUDA_LIB), you can add ARETOMO_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 aretomo.tests.test_protocols_aretomo.TestAreTomo
Licensing
AreTomo is free for academic use only. For commercial use, please contact David Agard or Yifan Cheng for licensing:
Supported versions
1.0.6, 1.0.8, 1.0.10, 1.0.12, 1.1.0, 1.1.1, 1.2.0, 1.2.5
Protocols
tilt-series align and reconstruct
Detailed manual can be found in software/em/aretomo-1.2.5/bin/AreTomoManual-08-01-2022.pdf
References
AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Shawn Zheng, Georg Wolff, Garrett Greenan, Zhen Chen, Frank G. A. Faas, Montserrat Bárcena, Abraham J. Koster, Yifan Cheng, David Agard. bioRxiv 2022.02.15.480593; doi: https://doi.org/10.1101/2022.02.15.480593
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