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Scipion - PySeg plugin

This plugin allows to use PySeg - De novo analysis for cryo-electron tomography - within the Scipion framework.

Setup

  • System pre-requisites:

    1. Cmake 2.6.3+. The intallation command in Ubuntu is:
    sudo apt-get install cmake
    
    1. GSL (GNU Scientific Library). In Ubuntu, the installation command is:
    sudo apt-get install libgsl-dev
    
    1. gcc/g++ 5 (for DisPerSE compilation). In Ubuntu, the installation command is:
    sudo apt -y install gcc-5 g++-5
    
  • Install this plugin in devel mode:

Using the command line:

scipion3 installp -p local/path/to/scipion-em-pyseg --devel

Installation can be checked out running some tests (Important: TestPosRec requires Scipion plugin for Dynamo to be installed:

scipion3 tests pyseg.tests.test_preseg_graphs_fils_picking.TestFromPresegToPicking
scipion3 tests pyseg.tests.test_pos_rec.TestPostRec
  • Contact information:

If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue.

We'll be pleased to help.

Scipion Team

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Plugin to use PySeg programs within the Scipion framework

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