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Plugin to use Spider programs within the Scipion framework

Project description

This plugin provides wrappers for several programs of SPIDER software suite.

PyPI release License Supported Python versions SonarCloud quality gate Downloads


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-spider
  1. Developer’s version

    • download repository

    git clone -b devel
    • install

    scipion installp -p /path/to/scipion-em-spider --devel

SPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/spider-26.06, if you want to change it, set SPIDER_HOME in scipion.conf file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate page. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :( Depending on you CPU type you might want to change the default binary from spider_linux_mp_intel64 to a different one by explicitly setting SPIDER variable.

To check the installation, simply run one of the following Scipion tests:

scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct
scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert
scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinement

A complete list of tests can also be seen by executing scipion test --show --grep spider

Supported versions




  1. J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.

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