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Plugin to use cryoSPARC2 programs within the Scipion framework
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cryosparc2 * Change some string protocols parameters as enumerator parameters Jul 12, 2019
.gitignore Initial plugin version May 27, 2019
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README.rst Update README.rst Jul 12, 2019 * Change the plugin version Jul 12, 2019


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 2.0.0 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

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 will be installed.
    CRYOSPARC_DIR = <install_path>
    # full name of the initial admin account to be created
    CRYOSPARC_USER = <user_name>
    # path on the worker node to a writable directory residing on the local SSD
    CRYOSSD_DIR = <ssd_path>

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
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