Scipion Cryo-EM

Integration, Reproducibility and Analysis


Scipion is an image processing framework to obtain 3D models

of macromolecular complexes using Electron Microscopy

Getting organised

Scipion will help you to get your processing organized by projects. Differently to Relion, there is no need to launch Scipion from the project folder. It can be launched anywhere and then you can select the project you want to work on. Let’s start by a new project by launching the following command from a terminal:




Recalculate CTF

Sometimes the CTF estimation algorithm may fail to find the rings even if they can be seen by eye. If this is the case, you may help the algorithm to find the rings by clicking on the image with the mouse right-button and choosing Recalculate CTF in the menu that appears.


A graphical interface will help you to correctly identify the CTF. You must provide the fi rst CTF zero and the search range, and then press OK. When you fi nish, press red Recalculate CTFs button.

Analyzing results

When analyzing the resulting class reconstructions, it is extremely useful to also look at them in slices, not only as a thresholded map in for example UCSF Chimera. In the slices view you will get a much better impression of unresolved heterogeneity, which will show up as fuzzy or streaked regions in the slices. Slices also give a good impression of the atness of the solvent region.


When looking at your rendered maps in 3D, e.g. using UCSF Chimera, it is often a good idea to t them all into the best one, as maps may rotate slightly during refi nement.

Cryo-EM Services

RELION Cryo-EM Stack

We install our RELION Cryo-EM Stack as well as SCIPION.

  • CUDA v7.5, v8.0, v9.1, v9.2, v 10.0, v 10.1
  • NVIDIA driver
  • Motioncorr v2.1
  • CTFFind + Gctf
  • RELION 3. RELION 3.1 (beta) NEW !!
  • Chimera
  • Resmap
  • SCIPION with tutorials and examples

Basic Support (1 Year)

We provide 1 year support of Scipion Installation on our Workstatiosn and Servers.

  • Installation of Scipion and related Cryo-EM software stack.
  • Rapid fix of issues related to possible Scipion bugs.
  • Consultation of data processing strategies within Scipion.

Advanced Support (1 Year)

We provide 1 year support of Scipion Installation on our Workstatiosn and Servers.

  • All features included in the Basic Support.
  • Advice for configuration of Scipion and EM software in HPC environments.
  • Consultation for configuration of automation and on-the-fly data processing.
  • More priority of requested features for quicker implementation.
  • Update of new versions of the EM software stack.

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