Tomography in Scipion
Introduction to how Scipion integration and visualization capabilities can simplify your cryo electron tomography pipeline.
Guide: Tomography intro
Tomogram Reconstruction
The main goal of this tutorial is to illustrate the combination of different tomography software packages in the same Scipion project.
Guide: Tomogram Reconstruction
Manual Tomogram Reconstruction with etomo
This tutorial shows how Scipion incorporates etomo (scipion-em-imod) and how the tomograms can be manually reconstrutedthewith it, inside a Scipion project.
Tomogram reconstruction with SCIPION: from raw movies to a tomogram
This tutorial aims to familiarize you with initial steps of cryo-electron tomogra- phy (cryo-ET) analysis using Scipion framework. We assume you are familiar with Scipion GUI and have some experience with cryo-ET data processing. Here we will demonstrate the workflow starting from raw data up to the tomogram reconstruction, highlighting the features of our software framework. After that, you should be able to run Scipion with your own data.
Picking Tutorial
This page will present the different picking protocols and strategies available in Scipion for Tomography and the Plugins where the various programs can be found. The tutorial will cover from the picking step to the extraction of the coordinates selected in the tomogram, including some useful tools to complement the protocols involved in the picking workflows.
Guide: Picking tutorial
Subtomogram Averaging HIV
This tutorial shows the complete pipeline from movies to averages inside the ScipionTomo framework. Our objective is to reconstruct the capsid of the HIV virus. The subtomogram averaging will be carried out with Relion, however, the preprocessing from movies to tomogram will involve a combination of different software packages
Guide:
Subtomogram Averaging Ribosome with EMAN plugin for Scipion
This tutorial illustrates how to carry out a subtomogram averaging (STA) with a per-particle per-tilt (PPPT) approach using EMAN plugin for Scipion combined with others
Guide: :ref:`Subtomogram Averaging Ribosome with EMAN plugin for Scipion <emantomo-sta-workflow>
Tomography in streaming
In work. Coming soon!