Instruct course on Image Processing for Electron Microscopy in the cloud. Madrid, January 17 – 19, 2018


National Center for Biotechnology (CNB), Madrid, Spain
Madrid, January 17 – 19, 2018


Overall aims and course outline

Electron Microscopy (EM) is rapidly growing as a high-resolution technique for structural biology. However, the high price of the electron microscopes is causing the concentration of scientific equipment in a few labs whose access is granted through infrastructure projects, like Instruct. A typical session in one of these high-end microscopes can generate up to 2TB of data per day, which is analysed by the researcher in its home institution. A new data acquisition will be performed when another access slot is granted. In this way, data analysis is coming at bursts, with high computational demands when the data arrives and low activity between acquisitions. Not all laboratories can justify the cost of a computer cluster with the necessary computational capabilities (in terms of number of cores, RAM memory, disk, GPU, …) with this intermittent use. Computer clouds offer a solution to this problem. This computing power is paid only on demand, and when there is no need of a computer for the data analysis, the machine is simply switched off with no associated cost (maintenance, amortization, dedicated installations and personnel, …).

EM software can easily run in the cloud. In fact, Scipion Cloud has been developed as an Instruct Pilot Project, and it is now publically available in the Amazon Cloud. The proposed course will have two aims:

 – The first one will be to show how to create, setup, use, stop and terminate cloud machines, including the appropriate EM software, so that users can easily adapt the computer power to their needs.
 – The second aim of the course will be to work with the course participants over a typical image processing workflow for single particle image processing.

The course will make extensive use of the I2PC software integration framework Scipion, accessing the most widely used software suites in the field, such as EMAN, Relion, Frealign and XMIPP.

The course is open to investigators at all levels. We will work with examples data, but participants can bring their own data to look at if they wish.



Lead Contact:
Carlos Oscar Sorzano Sanchez  (
Administrative Contact:
Ms. Blanca Benitez (


Wednesday, January 17:
13:00 Lunch and registration
14:00 Introduction to the course (Jose Maria Carazo)
14:15 Lecture: Introduction to 3D EM (Jose Maria Carazo)
15:00 Lecture: Basic background: sampling, Fourier Transform, central section, sampling, CTF (Carlos Oscar Sorzano)
16:00 Coffee/tea
16:30 Lecture: Cloud basics (Laura del Caño)
17:30 Practical work: Creating your course machine instance in the cloud (Laura del Caño)
18:30 End of day work

Thursday, January 18:
09:00 Practical work: Introduction to Single Particle workflow in Scipion (Jose Maria Carazo)
10:00 Practical work: DDD, Screening micrographs and CTF (Carlos Oscar Sorzano)
11:00 Coffee/tea
11:30 Practical work: particle picking and screening (Carlos Oscar Sorzano)
12:15 Practical work: 2D classification (Carlos Oscar Sorzano)
13:00 Lunch
14:00 Practical work: Initial volume (Jose Maria Carazo)
14:30 Practical work: alignment, classification, and reconstruction (Roberto Marabini)
16:00 Coffee/tea
16:30 Practical work: validation and analysis (Carlos Oscar Sorzano)
18:30 End of day work

Friday, January 19:
09:00 Practical work: Advanced aspects of the cloud (Laura del Caño)
11:00 Coffee/tea
11:30 Practical work: Image Processing and Workflow Questions (Jose Maria Carazo, Carlos Oscar Sorzano)
12:30 Dissemination: Infrastructure access through Instruct and iNext (Roberto Melero, Jose Maria Carazo, Carlos Oscar Sorzano)
13:00 Lunch and course end



(Registration Close) Online registration will be open from 01 – 30 November, 2017

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 €

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 november 30 including:

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

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.

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