This plugin provide wrappers around several programs of SPIDER software suite.
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-spider
- download repository
git clone https://github.com/scipion-em/scipion-em-spider.git
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
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
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.
- Align AP SR
- Align pairwise
- CA PCA
- Classification protocols: Diday, K-means, Ward
- Custom 2D mask
- Filter particles
- Reconstruct Fourier
- J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.