First I2PC-FEI “hands on” course on image processing applied to the structural characterization of biological macromolecules. Madrid, October 17 - 20, 2016

Alcalá de Henares


Parador Nacional de Alcala de Henares, Madrid, Spain [ directions ]

Alcalá de Henares was named a World Heritage Site by UNESCO in 1998 in recognition of the fact that Alcalá was the first planned University City in the world. Alcalá de Henares was also the birthplace and residence of Miguel de Cervantes, the most illustrious Spanish writer of all times, author of "Don Quijote" (one of the world literary masterpieces). Founded in B.C. by the Romans, who named it "Complutum", its name was changed, during the Muslim rule (second half of 8th century) to "Qual´at abd al-Salam", where the present name of Alcalá comes from.


Go to INSTRUCT Web Page Go to FEI Web Page Go to Westlife Web Page

The Instruct Image Processing Center at the CNB-CSIC and FEI Corporation organize a joint course, targeting both industrial and academic attendees, aiming to provide an in-depth presentation of current image processing methods in cryo-Electron Microscopy. The focus will be on the structural analysis of purified macromolecules, a field normally referred to as “Single Particle Analysis”. The course will be very practical and specially centered on the image processing steps leading to a cryo EM map; no prior knowledge on cryoEM image processing will be assumed. Most of the I2PC personnel, together with some of the most qualified FEI personnel in cryoEM image processing, will be assigned to the course during that period, so as to provide very close personal support. Attendees are encouraged to bring their own data (videos, images...).

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. Special attention will be provided to automated data adquisition using FEI software EPU.


Technical and scientific Contact:
Carlos-Oscar Sanchez-Sorzano, PhD (
Local contact
Federico Gago, PhD (
Administrative Contact:
Ms. Blanca Benitez (


Download the programme (PDF)

Monday, October 17

12:00 - 12:30
12:30 - 13:30
Welcome Reception
13:30 - 13:45
Introduction to the course (Jose Maria Carazo)
13:45 - 15:00
Cryo EM and 3D reconstruction" (Jose Maria Carazo)
15:00 - 16:00
Basic Background: Fourier transform, central section theorem, sampling" (Carlos Oscar Sorzano)
16:30 - 18:00
"The Electron Microscope: Direct Electron Detectors, image formation, aberrations, the contrast transfer function (CTF)" (Jose Maria Carazo).

Tuesday, October 18

09:00 - 10:30
"Single Particle workflow" (Jose Miguel de la Rosa)
11:00 - 13:30
"Cryo-TEM: From Evolution to Revolution – the Dawn of a New Scientific Age (past, present and future....)" (Marc Storms)
14:30 - 16:00
"The single particle cryoTEM workflow - Practical aspects from sample preparation to automated image acquisition" (Sonja Welsch)
16:30 - 18:00
Practical work: "Video frame alignment, Contrast Transfer Function estimation, micrograph screening, particle picking and extraction" (Jose Luis Vilas, Jose Maria Carazo)

Wednesday, October 19

09:00 - 10:30
Practical work: "2D Classification and Exploration" (Jose Maria Carazo & Pablo Conesa)
11:00 - 13:30
Practical work: Initial Volume(computational procedures and introduction to Randon Conical Tilt)" (Pablo Conesa, Carlos Oscar Sorzano)
14:30 - 16:00, 16:30 - 18:00
Practical work: "3D alignment and classification" (Josué Gómez & Roberto Melero)

Thursday, October 20

09:00 - 10:30
Practical work: "3D validation and quality measures" (Javier Vargas)
11:00 – 13:30
Practical work: "Introduction to model building" (Roberto Marabini)
Instruct students are invited to join to the “First iNEXT all Hands Meeting”


Registration closed on July 31st, 2016.

Industry registration

Students & Senior Research Registration

We will contact the accepted participants in the first week of September

  Registration Fee
Instruct countries Non Instruct countries
Students* 100€ 150€
Senior Research* 200€ 250€
Corporative rate** 1.250€ 1.500€

Instruct Students – Senior Research are invited by I2PC to participate in the "1st iNEXT users meeting" on October 20th, 2016.

*There are 10 accommodation grants for attendees from Instruct countries.
If you want to apply, please send an e-mail to including:

The accommodation for this event will be at Parador Nacional Alcala de Henares hotel. Both students and Senior research will be asked to share a room during their stay.

Please take some time and reach out to your roommate and provide that information during the registration. If you do not provide a name, we will make the assignment for you.

** Corporate rate includes 3 nights accommodation and meals at the Parador in a single room

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 in the wire concept: I2PC-FEI + Your name

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


The city of Alcalá de Henares belongs to the Autonomous Community of Madrid. It is located 30 km. from the capital on the Madrid-Barcelona motorway, and 15 km. from the International Airport of Barajas.

You can find more information about the culture and tourism in Alcalá de Henares on Turismo de Alcalá and LaCalleMayor.

How to get to Alcalá de Henares from Madrid Airport - Barajas:


Typical gastronomy of Alcalá de Henares includes traditional Castilian cuisine, like fried bread crumbs with spicy sausage and garlic soup.

The most typical sweets are the costrada, cooked with meringue, cream and puff pastry; the sugared almonds and the donuts covered with honeyed orange sugar.

One of the most interesting things to do in Alcalá de Henares is to try the huge variety of appetizers ("tapas") that many bars and restaurant offer together with drinks.