AreTomo plugin
This plugin provide a wrapper around 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-1.0.8, 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_1.0.8_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
Protocols
tilt-series align and reconstruct
Detailed manual can be found in software/em/aretomo-1.0.8/bin/AreTomoManual-06-24-2021.pdf
References
Shawn Zheng, unpublished.
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-aretomo 3.0.0
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| File | Size | Uploaded | Provenance | Actions |
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| scipion-em-aretomo-3.0.0.tar.gz | 25.9 kB | Without provenance | Details for scipion-em-aretomo-3.0.0.tar.gz |
Release files / scipion-em-aretomo-3.0.0.tar.gz
| Download URL | scipion-em-aretomo-3.0.0.tar.gz |
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| Size | 25.9 kB |
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twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.8.11
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