Instruct course on Image Processing for Electron Microscopy and hybrid modelling. Madrid, July 8 – 11, 2019


National Center for Biotechnology (CNB), Madrid, Spain

Madrid, July 8 – 11, 2019

Overall aims and course outline

Software platforms as Scipion facilitate the integration of packages from many different laboratories, and promote the cross-checking of the results by alternative methods. Additionally, it keeps track of all the operations, parameters and steps undertaken from the raw data to the final maps and models, promoting, in this way, the reproducibility of the results. Scipion was originally designed to support image processing operations in Single Particle Analysis. However, due to the widespread need to related quasi atomic Coulomb potential maps and model building, with an ever growing potential of simultaneously combining features of both, Sicipion is currently being extended into the atomic modelling domain. In this way it integrates software like Coot, Chimera, Refmac, and Phenix, and the number of integrated packages and procedures is quickly growing. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.

The course is interesting for users to know the image processing and the atomic modelling capabilities of Scipion. This course will bring a timely introduction to these possibilities to investigators at all levels (Ph.D. students, postdocs and senior researchers).. (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: Blanca Benitez


Monday, July 8:

13:00 Lunch and registration
14:00 Introduction to the course (Jose Maria Carazo)
14:15 Introduction to 3D EM (Jose Maria Carazo)
15:00 Basic background: sampling, Fourier Transform, central section, sampling, CTF (Carlos Oscar Sorzano)
16:00 Coffee/tea
16:30 Movie alignment, quality estimation, CTF determination (Carlos Oscar Sorzano)
18:30 End of day

Tuesday, July 9:

09:00 Particle picking and particle screening (Carlos Oscar Sorzano)
11:00 Coffee/tea
11:30 2D Classification (Carlos Oscar Sorzano)
13:00 Lunch
14:00 Initial volume, 3D alignment and reconstruction (Carlos Oscar Sorzano)
16:00 Coffee/tea
16:30 3D Classification (Carlos Oscar Sorzano)
18:30 End of day

Wednesday, July 10:

09:00 Resolution and quality assessment (Carlos Oscar Sorzano)
11:00 Coffee/tea
11:30 Structure prediction by sequence homolohy (Marta Martínez and Roberto Marabini)
13:00 Lunch
14:00 Rigid fitting (Marta Martínez and Roberto Marabini)
16:00 Coffee/tea
16:30 Flexible fitting (Marta Martínez and Roberto Marabini)
18:30 End of day

Thursday, July 11

9:00 Structure validation and comparison (Marta Martínez and Roberto Marabini)
11:00 Coffee/tea
11:30 Building the unit cell and the whole macromolecule (Marta Martínez and Roberto Marabini)
13:00 End of course

Submission & Registration:

The application  period for this course will be open from 01 – 31 May, 2019.  We will contact you after June 1st if your application is accepted.

Fill  your application here: (Online Registration closed)

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 May 31 including:

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

Key dates:

01 – 31 May, 2019: Submission of the course application
01 – 31 May, 2019: Submission of the accommodation grants application
01 – 15 June, 2019: Communication of awarded applications (course and grants)
15  – 30 June, 2019: 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 €

Payment information

Bank transfer to Centro Nacional de Biotecnología – CNB
Bank Name: Santander Central Hispano

Address: Julio Palacios, 23. 28029, Madrid. Spain

Account: 0049 5926 41 2816155571

IBAN: ES91 0049 5926 4128 1615 5571


Please include your name in the wire concept

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.