I2PC hands on course on image processing applied to the structural characterization of biological macromolecules. Madrid, June 29th - July 3rd, 2015


Spanish National Center for Biotechnology/Instruct Image Processing Center (I2PC)


We aim at providing an in-depth presentation of current image processing methods in cryo-Electron Microscopy, specially targeting the structural analysis of purified macromolecules, a field normally referred to as “Single Particle Analysis”. The course will be of a very practical nature. Most of the I2PC personnel will be assigned to the course during that period, so as to provide very close personal support.You are invited to bring your own data (or arrange with I2PC for your images or movies to be downloaded beforehand)

Outline course content

The course will make use of the new workflow-oriented integrative software platform developed at the I2PC, referred to as Scipion. Therefore, participants will be exposed to workflows from most of the best known software packages in the field, such as Xmipp, EMAN, Relion, Frealign, SPIDER, and Bsoft.


Technical and scientific Contact:
Carlos-Oscar Sanchez-Sorzano, PhD (coss@cnb.csic.es)
Administrative Contact:
Ms. Blanca Benitez (blanca@cnb.csic.es)


You can click in any session title to download its corresponding slideshow.

Download the programme (PDF)

Monday, June 29

14:00 - 15:00
Jose Maria Carazo: "3D reconstruction"
15:00 – 16:00
Carlos Oscar Sorzano: "Basic Background: Fourier transform, central section theorem, sampling"
16:30 - 18:00
Roberto Marabini: "Introduction to imaging processing: Sampling, number of projections, backprojection, CTF"

Download basic image processing data:

rsync -av curso01@asimov.cnb.csic.es:/services/scipionwiki/data/htdocs/files/scipion/data/tests/basic_image_processing ~/

Tuesday, June 30

09:00 - 10:30
Javier Vargas: "The Electron Microscope: contrast transfer function, aberration"
11:00 - 12:30
Jose Miguel de la Rosa: "Introduction to Single Particle workflow in Scipion."
12:30 - 13:30, 14:30 - 15:00
Javier Vargas: "CTF", "DDD"
Vahid Abrishami. Practical work: "DDD, Screening micrographs and CTF"
15:00 - 16:00, 16:30 - 17:00
Carlos Oscar Sorzano: "Particle picking"
Vahid Abrishami. Practical work: "Particle picking and screening"
17:00 - 18:00
Scipion installation (optional)


Mix & match tutorial

Wednesday, July 1

09:00 - 10:30
Jose Miguel de la Rosa & Tanvir Shaikh. Practical work: "2D Classification."
11:00 - 12:00
Jose Maria Carazo. Practical work: "Initial Volume"
12:00 - 13:30
Carlos Oscar Sorzano & Tanvir Shaikh. Practical work: "RCT"
14:30 - 15:30
Javier Vargas. "Map Validation"
15:30 - 16:00, 16:30 - 17:00
Roberto Marabini & Roberto Melero. Practical work: "3D alignment and Reconstruction"
17:00 – 18:00
Roberto Marabini & Roberto Melero. Practical work: "3D flexibility/classification analysis"

Thursday, July 2

9:00 - 10:30
Josue Gómez & Joan Segura. Practical work: "Chimera fitting video preparation"
10:30 – 13:30
Josue Gómez & Joan Segura. "Chain tracing of atomic coordinates from EM maps"
14:30 - 15:30.
Joan Segura: "Hybrid models"
15:30 - 18:00
Scipion practical session. Students to go independently over the whole SPA work flow (you may use your own data . Otherwise, a data set different to the one so far used in the course will be provided to attendees)

Friday, July 3

09:00 - 10:30
Slavica Joinic & Carlos Oscar Sorzano: "Normal Modes"
11:00 – 13:30
Jose Miguel de la Rosa & Jose Maria Carazo. Scipion: web server, web interface, Instruct projects. Course evaluation.



Registration is closed. You can still direct any inquiry to blanca@cnb.csic.es

The course fee is 150 euro

Additionally, 5 travel grants are available for attendees from Instruct countries, to cover accommodation. Accommodation include breakfast and dinner (but airplane ticket and course fee are not included).

If you want to apply for a travel grant, please send an e-mail to blanca@cnb.csic.es including:

I2PC staff will be glad to help you booking a suitable accommodation in Madrid

Payment information

Bank transfer to:
Centro Nacional de Biotecnología - CNB
Bank Name:
Santander Central Hispano
Julio Palacios, 23. 28029, Madrid. Spain
0049 5926 41 2816155571
ES91 0049 5926 4128 1615 5571

Please include your name in the wire concept

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