Plugin to use AreTomo program within the Scipion framework

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for azazello from gravatar.com azazello Avatar for scipion from gravatar.com scipion

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v3 (GPLv3)
  • Author: Grigory Sharov
  • Tags scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3.0
Classifiers

Project description

This plugin provides a wrapper for AreTomo program.

PyPI release License Supported Python versions SonarCloud quality gate Downloads

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:

  1. Stable version

scipion installp -p scipion-em-aretomo

  1. 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/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.

  • Depending on your CUDA version this plugin will guess the right default binary from AreTomo2_1.1.3_CudaXY (X is for cuda major version, Y for the minor). You can always set 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 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.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page