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scipion-em-tomo

Base Scipion plugin for Cryo-Tomography and Subtomogram averaging.

Current development setup

This plugin is currently under initial development and it is not ready for production yet.

In the meantime, it can be used for development, base on Scipion v2.x with plugins.

This tomography plugin can be enabled by cloning this repository and execute the command:

.. code-block::

git clone https://github.com/scipion-em/scipion-em-tomo.git
scipion installp -p ~/scipion-em-tomo --devel

or by adding the path to the $PYTHONPATH environment variable.

.. code-block::

# Enable the tomography plugin
export PYTHONPATH=$PYTHONPATH:$DEVEL_HOME/scipion-em-tomo

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

.. code-block::

   scipion test tomo.tests.test_tomo_base.TestTomoPreprocessing
   scipion test tomo.tests.test_tomo_base.TestTomoImportTs
   scipion test tomo.tests.test_tomo_base.TestTomoImportTomograms
   scipion test tomo.tests.test_tomo_base.TestTomoImportSubTomograms
   scipion test tomo.tests.test_tomo_base.TestTomoImportSetOfCoordinates3D
   scipion test tomo.tests.test_tomo_base.TestTomoBaseProtocols
   scipion test tomo.tests.test_tomo_base.TestTomoBase

A complete list of tests can also be seen by executing scipion test tomo.tests.test_tomo_base

Pre-requisites

  • Use scipion v3.0.0
  • Use scipion-em-tomo from branch 'tomo' (see previous section for a possible setup)
  • TestTomoPreprocessing test requires gctf and imod plugins to work properly. If these plugins cannot be found the test will not be executed. For this test to succeed one available GPU is needed, more GPUs can be defined defining the var SCIPION_TEST_GPULIST (e.g export SCIPION_TEST_GPULIST='0 1' )

This test will launch automatically the pre-processing following pipeline:

  • import tilt-series (only one)
  • run motioncor2
  • run gctf
  • run imod_auto3d (script ported from J.chichón)

Protocols

  • Import Titl Series
  • Import Titl Series Movies
  • Import Tomograms
  • Import Subtomograms
  • Import Coordinates 3D
  • Tilt Series Averaging

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Base tomography Scipion plugin with data model definition

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