This plugin provides wrappers for 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
Developer's version
- download repository
git clone -b devel https://github.com/scipion-em/scipion-em-spider.git
- 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
26.06
- Align AP SR
- Align pairwise
- CA PCA
- Classification protocols: Diday, K-means, Ward
- Custom 2D mask
- Filter particles
- Reconstruct Fourier
- Refinement
- J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.