User Documentation
Table of Contents:
Introduction to Scipion: 
This tutorial provides a quick introduction into processing with Scipion. It is designed to take a short time while illustrating the main concepts. The tutorial uses 3 micrographs from the Grigorieff BPV dataset. A final virus 3D map is obtained.
Guide: scipion_tutorial_intro.pdf
Initial model estimation 
This tutorial uses different methods to obtain a initial 3D map. Methods covered are: RCT, Ransac, Eman.
Guide: scipion_tutorial_initialvolume.pdf
Mix-and-match in Scipion: 
This tutorial presents a more complete workflow of Cryo-EM single particles inside Scipion. It is focused on demonstrate the combination of different EM-packages. This tutorial follows the processing pipeline described for Relion 1.3 tutorial with Betagalactose data.
Guide: scipion_tutorial_betagal_20150520.pdf
- Scipion GUI: Get familiar with Scipion GUI.
- ShowJ: is the default viewer for Scipion objects. It can display data in gallery and table modes and navigate through different blocks of data. Single images are opened using Image Window.
- Particle Picker: The Xmipp Particles Picker allows the user to iterate over the micrographs to pick particles either manually or automatically, or visualize them. It is the default viewer for Scipion coordinates.
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Importing Data: Importing data is the first step for any Scipion project. Find how to import movies, micrographs, ctf and particles and which are the formats currently supported.
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Creating subsets: Check how to create subsets from Micrographs, Particles, Volumes or from 2D/3D classfications. This tools are valid for results from any package.
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How to create 2D mask: Guide of how to create 2D masks, either interactive or through some protocols.
- 2015 - 05: Presentation at IGBMC, Strasbourg.
- 2015 - 04: Scipion_20150428_Cambridge.pdf Scipion presentation at MRC-LMB, Cambridge.
- 2014 - 09: Scipion_20140915_Scripps.pdf Scipion overview presented at Scripps.