2nd Scipion Facilities Course. Madrid, 2020.


National Center for Biotechnology (CNB), Madrid, Spain
Madrid, 2020
Dates: Postponed until the second half of the year. The final dates will be announced.


The aim of this meeting is to show what scipion offers to a Cryo-em facility. The course will have a strong “practical component”, since workflows will be running live on the Amazon cloud.

I2PC is organising a Cryo-EM Scipion course specifically for Facilities. Scipion team and collaborators have been working in the last years in what we call streaming processing. We understand the importance of monitoring the acquisition in real time to take early decisions to improve the acquisition performance. In addition, Scipion incorporates new techniques to automate the real time image processing pipeline until 2D classification and even an initial estimation of 3D heterogeneity. Moreover, Scipion is equipped with several consensus protocols to get combined results from different EM-packages to screen and select the best micrographs, CTFs, particles or 2D-classes. All with the benefit of Scipion flexibility and ”mix and match” capabilities. Scipion is also able to gather all the processing information and present it in a HTML report that could be served over the web and automatically refreshed. It also offers automatic tools for direct submission to databases, like EMPIAR, when appropriate.

No programming skills are required.

Target Audience:

Cryo em facility operators wanting to do or already doing on the fly processing. The course will address both Single Particle Analysis (SPA) and Tomography, although the stress will be in SPA.


Attendees should bring their own laptop with a modern browser.
No programming skills are required.
AWS machines will be provided by us.


Intro – welcome
CNB setup (talk + visit) -> Roberto
Scipion intro:
 – Basic architecture ( 1 project 1 folder, 1 protocol 1 folder ….)
 – Basic usage
 – Demo scipion

Streaming protocols: 
 – Consensus

Breaking the stream
Kicking off scipion:
 – Creating templates

Monitoring acquisition
Practical session: create your own workflow template.
What do you miss in the Scipion pipeline?
Comparison with other software?

Key dates:

01 – 30 April, 2020: Submission of the course application

01 – 15 May, 2020: Communication of awarded applications

Fill  your application here. (Registration will be open soon)