scipion-em-warp

Plugin to use Warp within the Scipion framework


Keywords
scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3, 0, spa, tomo
License
GPL-3.0
Install
pip install scipion-em-warp==3.4.2

Documentation

Warp plugin

This plugin provides a wrapper for some of the programs of the Warp software.

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-warp
  1. Developer's version

    • download repository
    git clone -b devel https://github.com/scipion-em/scipion-em-warp.git
    
    • install
    scipion installp -p /path/to/scipion-em-warp --devel
    

Verifying

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

  • scipion3 tests warp.tests.protocols_tomo_tests.TestWarpEstimateCTFTomoReconstruction
  • scipion3 tests warp.tests.protocols_tomo_tests.TestDeconvolveTomo
  • scipion3 tests warp.tests.test_protocols.TestWarpMotionCorrection
  • scipion3 tests warp.tests.test_protocols.TestDeconvolveMics

Protocols

  • deconvolve micrographs
  • deconvolve tomograms
  • deconvolve tilt-series
  • tomo reconstruction
  • motion correction (for SPA)
  • tilt-series motion and ctf estimation (includes ctf estimation and defocus handedness)

References

  1. Dimitry Tegunov and Patrick Cramer. Real-time cryo-electron microscopy data preprocessing with Warp. Nature Methods 16(11), 2019, p. 1146-1152.