Instruct – I2PC- Thermo Fisher Scientific: Facility-based Image Processing for Electron Microscopy. Madrid, June 27 – 29, 2018


National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 27 – 29, 2018

Overall aims and course outline

I2PC is organising its first Cryo-EM Scipion course for Facilities, which is the second one in the series “I2PC-Thermo Fisher Scientific Course“. Scipion team and collaborators have been working in the last years in what we call streaming processing. We understand the importance of having feedback during acquisition and this is precisely what will be covered in this course. From basic processing like movie alignment and ctf estimation on the fly to automatic picking an extraction. Scipion is equipped with several consensus protocols that might help in your automated pipeline to screen and select the best micrograph, CTFs or particles. 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. Additionally, scipion API allows the integration with your LIMS system. Currently released Scipion 1.2 goes in streaming all the way to particle extraction, and during the course we will present current work in 2D classification and initial volume, in collaboration with Xmipp team.

The topic of general pipelines for Single Particle Analysis with Scipion will also be covered, as it will be Scipion usage on the cloud (Note: all practical work will be performed on Amazon cloud, and attendees are required to bring their own personal computer to access the cloud via a web browser)


Lead contact: Carlos Oscar Sorzano Sánchez
Administrative Contact:


Wednesday, June 27:

12:00- 13:30 Buffet lunch at CNB (buffer time for everybody to arrive. We are 20’ from airport)
13:30-13:35: Introduction to the course (Jose Maria Carazo)
13:35-14:00: General introduction to Single Particle cryoEM workflow in Scipion (Jose Maria Carazo)
14:00-14:30: The importante of streaming/life data processing (Erik Franken – Thermo Fisher Scientific)
14:30-16:30: Facility set up in depth: The CNB case (Roberto Marabini):

Setup, data flow, infrastructure
Scipion installation
“Scipion demo”

16:30-17:00: Coffee break
17:00:18:00: Scipion set up at other Facilities (coordinator: Pablo Conesa)

Thursday, June 28:

9:00-13:00 Practical work (coordinator Pablo Conesa): 

Streaming protocol options in Scipion, from videos to 2D classes, including multiple filters and consensus options.
(11:00-11:30: Coffee break)
Create your dream workflow.
HTML Monitor and status alarms

13:00-14:00: Lunch
14:00-15:00: Scipion as part of the general Facility pipeline, including LIMS connection  (coordinator Pablo Conesa)
15:00-16:00: After data collection, how to keep processing in Scipion in a cluster and in the cloud (including “Scipion project structure”) (coordinator Pablo Conesa)
16:00-16:30: Coffee break
16:30-17:30: Scipion workflow submission, HTML workflow viewer and results reproducibility (coordinator Pablo Conesa)

Friday, June 29:

9:00-12:45: Practical work: Options for SPA complete workflow in Scipion (Carlos Oscar Sorzano)
(11:00-11:30: Coffee break)
12:45-14:00: Lunch

Submission & Registration:

The application  period for this course will be open from 01 – 30 April, 2018.  We will contact you after May 1st if your application is accepted.

(Registration Close)  Fill  your application here.

Additionally, there are 10 accommodation grants for attendees from Instruct countries

If you want to apply for an accommodation  grant, please send an e-mail to before April 30 including:

  • short CV
  • brief explanation of the impact of this course in your work

Key dates:

01 – 30 April, 2018: Submission of the course application
01 – 30 April, 2018: Submission of the accommodation grants application
01 – 15 May, 2018: Communication of awarded applications (course and grants)
May 15  – June 15: Payment due

Registration Fee:

Academic Registration Fee Instruct countries
Predocs 100 €
Postdocs and Others 150 €
Academic Registration Fee Non Instruct countries
Predoc 150 €
Postdocs and Others 200 €
Industrial Registration Fee 500 €

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and West-life UE grant

ScipionCloud has been funded by EGI – Mobrain & West-life UE grants