Plugin to use cryoSPARC2 programs within the Scipion framework

scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3, 0, cryosparc, spa
pip install scipion-em-cryosparc2==3.3.16


cryoSPARC2 plugin

This plugin allows to use cryoSPARC2 programs within the Scipion framework

CryoSPARC is a backend and frontend software system that provides data processing and image analysis capabilities for single particle cryo-EM, along with a browser based user interface and command line tools.

You will need to use 3.0.0 version of Scipion to run these protocols.

  • 2D Classification: Classify particles into multiple 2D classes to facilitate stack cleaning and removal of junk particles. Also useful as a sanity check to investigate particle quality.
  • 3D Ab-Initio Reconstruction: Reconstruct a single (homogeneous) or multiple (heterogeneous) 3-D maps from a set of particles, without any initial models or starting structures required.
  • 3D Homogeneous Refinement: Rapidly refine a single homogeneous structure to high-resolution and validate using the gold-standard FSC.
  • 3D Non uniform Refinement: Apply non-uniform refinement to acheive higher resolution and map quality
  • Particle Subtraction: Subtract projections of a masked volume from particles.
  • 3D Local Refinement Naive local refinement.
  • Heterogeneous Refinement: Heterogeneous Refinement simultaneously classifies particles and refines structures from n initial structures, usually obtained following an Ab-Initio Reconstruction
  • Local CTF Refinement (per-particle defocus): Local CTF Refinement performs per-particle defocus estimation for each particle in a dataset, against a given 3D reference structure.
  • Global CTF Refinement (per-group beam tilt, trefoil, spherical aberration, tetrafoil): Global CTF Refinement performs per-exposure-group CTF parameter refinement of higher-order aberrations, against a given 3D reference.
  • Sharppening: Sharpen a volume following refinement.
  • Helical 3D Refinement: Reconstruct and refine a homogeneous helical assembly, with or without imposition and refinement of symmetry parameters.
  • 3D Homogeneous Refinement(new): Rapidly refine a single homogeneous structure to high-resolution and validate using the gold-standard FSC. Using new faster GPU code, and support for higher-order aberration (beam tilt, spherical aberration, trefoil, tetrafoil) correction and per-particle defocus refinement on the fly.
  • 3D Non uniform Refinement(new): Apply non-uniform refinement to achieve higher resolution and map quality. Specially designed for small proteins and membrane proteins.
  • 3D Local Refinement(new) Refine a masked region within a consensus structure by allowing particle alignments to vary only slightly.
  • Symmetry Expansion: Duplicate particles around a point-group symmetry.
  • Homogeneous Reconstruction: Reconstruct half-maps from input particles with alignments
  • 3D Classification: Classify particles into multiple 3D classes and optimize 3D class densities (currently, without re-aligning particle pose or shift).

Latest plugin versions


  • new * : Compatibility with cryoSPARC v4.1.0 and 4.1.1


  • new : Compatibility with cryoSPARC v4.0.0


  • new : Allow to import .cs particles files


  • fixed : Allow 31 or more classes in the 3D classification protocol


  • fixed : Fixed an error related with the slow loading protocols
  • fixed : Fixed an error in the 3D classification protocol


  • new : Compatibility with cryoSPARC v3.3.2
  • new : Added the option to use the plugin in a CS installation in a cluster
  • new : Added a wizard to select the lane where the protocols will be launched
  • new : Added the varaiable CRYOSPARC_DEFAULT_LANE to define the name of the cryoSPARC default lane
  • new : Added the variable CRYOSPARC_STANDALONE_INSTALLATION to specify whether the CS installation is standalone or not

Installing the plugin

In order to install the plugin follow these instructions:

  1. Install the plugin
scipion installp -p scipion-em-cryosparc2

or through the plugin manager by launching Scipion and following Configuration >> Plugins

  1. Install CryoSPARC software

CryoSPARC v2 software will NOT be installed automatically with the plugin. The independent installation of CryoSPARC software suite by the user is required before running the programs.

To install CryoSPARC v2 software review the detailed system requirements and install instructions available here. These cover workstation and cluster installs, file configuration and how to update cryoSPARC v2 when new versions become available.

  1. Add the following variables bellow the PACKAGES section at ~/.config/scipion/scipion.conf file:

    # The root directory where cryoSPARC code and dependencies is installed.
    CRYOSPARC_HOME = <install_path>   (CRYOSPARC_DIR will work for legacy reasons)
    # full name of the initial admin account to be created
    CRYOSPARC_USER = <user_name>
    # Optional variables
    #Folder (available to all workers) where scipion will create cryosparc projects
    CRYO_PROJECTS_DIR = <path> (default to <CRYOSPARC_HOME>/scipion_projects)
    # Specifies whether the CS installation is standalone or not. If False,
    # it is assumed that CS is installed in a cluster. If the variable is not
    # defined, by default assume that the installation is standalone and its
    # value would be True
    # Name of the default lane where the protocols will be launched
    CRYOSPARC_DEFAULT_LANE = <lane name>

To install in development mode

  • Clone or download the plugin repository
git clone
  • Install the plugin in developer mode.
scipion installp -p local/path/to/scipion-em-cryosparc2 --devel

Buildbot status

Status devel version:

Status production version: