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 -b devel 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/aretomo2-1.1.3, if you want to change it, set ARETOMO_HOME in scipion.conf file to the folder where the AreTomo is installed.
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 website.
To check the installation, simply run the following Scipion test:
scipion test aretomo.tests.test_protocols_aretomo
Licensing
AreTomo2 binaries are available under BSD-3 license
Supported versions
aretomo2: 1.1.3
Protocols
tilt-series align and reconstruct
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. JSB vol. 6, 2022, 100068.
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-aretomo 4.0.0
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_aretomo-4.0.0.tar.gz | 47.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_aretomo-4.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 97.1 kB
Release files / scipion_em_aretomo-4.0.0.tar.gz
| Download URL | scipion_em_aretomo-4.0.0.tar.gz |
|---|---|
| Size | 47.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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Release files / scipion_em_aretomo-4.0.0-py3-none-any.whl
| Download URL | scipion_em_aretomo-4.0.0-py3-none-any.whl |
|---|---|
| Size | 49.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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