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-aretomoDeveloper’s version
download repository
git clone https://github.com/scipion-em/scipion-em-aretomo.gitinstall
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-1.0.12, 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_1.0.12_Cuda101 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
Protocols
tilt-series align and reconstruct
Detailed manual can be found in software/em/aretomo-1.0.12/bin/AreTomoManual-01-27-2022.pdf
References
Shawn Zheng, unpublished.
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