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Spider plugin

This plugin provide wrappers around several programs of SPIDER software suite.

prod: prod devel: devel support: support


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
    • 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. Similarly you can modify SPIDER_MPI variable (default spider_linux_mpi_opt64).

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


In 2018 the plugin was updated to support the latest (at that moment) SPIDER version - 25.02. This required a lot of code refactoring and the support of old SPIDER version 21.03 had to be discontinued. The full changelog since Scipion-1.x is available here.



  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.


Plugin to use Spider programs within the Scipion framework





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