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Graphical interface manuals

The following guides show you how to perform certain actions using the GUI:


Introduction to Scipion


This tutorial provides a quick introduction to 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.

Initial model estimation


This tutorial uses different methods to obtain an initial 3D map. Methods covered are RCT, Ransac, Eman and Reconstruct Significant.

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 Beta-galactosidase data.

Guide: scipion_tutorial_betagal.pdf

You may download a fully solved project of this tutorial from here.

Full processing video tutorial

4 video tutorials in a list to go from movies to a 3D volume using betagalactosidase data.

Take a look at our tutorial videos in the Scipion youtube channel.

Know more about the theory and practice behind Image Processing in EM.

Mouse apoferritin image processing in Scipion 2.0.0


This tutorial presents a complete workflow of Cryo-EM single particles inside Scipion. It demonstrates the combination of different EM-packages with high focus on Xmipp higres.



Model Building


The recent development of single-particle electron cryo-microscopy (cryo-EM) allows structures to be solved at almost atomic resolutions. Providing a basic introduction to model building, this tutorial shows a workflow aimed at obtaining high-quality atomic models from cryo-EM data by using scipion software framework..

Guide: scipion_tutorial_modelBuilding.pdf

Workflow: download

Initial volume validation by SAXS


This tutorial provides a guide to the validation of the initial volume estimations using SAXS curves in Scipion.

Guide: scipion_tutorial_SAXS.pdf

Localized reconstruction in Scipion


In this tutorial, we provide a step-by-step guide for handling symmetry mismatches in single-particle analysis using a new plugin called LocalRec (Ilca et al. 2015) in Scipion (Abrishami et al. 2020).

Guide: scipion_tutorial_localrec.pdf

Processing How To’s

Importing Data

Importing Data: Importing data is the first step for any Scipion project. Find out how to import movies, micrographs, CTFs, and particles and which are the formats currently supported.

Creating subsets

Creating subsets: Find out how to create subsets from micrographs, particles, volumes or from 2D/3D classifications. This tool is valid for results from any package.

How to create 2D masks

How to create 2D masks: Guide to creating 2D masks, either interactively or through protocols.


FAQ: Frequently Asked Questions

Relion in Scipion

Relion in Scipion: Check how to use Relion inside Scipion. Some of the original Relion FAQ are addressed.