I2PC – Instruct-RI Hubs hybrid course on Electron Tomography and Subtomogram Averaging. Madrid, December 10 – 13, 2024


Hybrid course.
December 10 – 13, 2024 from 16:00 to 21:30 CET.
You do not need to install any special software to connect. A modern browser should be enough.

Overall aims and course outline

By using image processing algorithms, it becomes possible to pinpoint the macromolecules of interest within the electron tomograms. Subsequently, researchers can extract small subtomograms from these locations and identify similar particles, facilitating their averaging and the recognition of diverse conformations. This process, referred to as subtomogram averaging, has played a pivotal role in elucidating an increasing number of macromolecular structures, achieving resolutions ranging from 20 to 3 A.

The course is designed to offer a comprehensive overview of the whole image processing workflow in Electron Tomography (ET). This includes tasks such as aligning the tilt series, reconstructing 3D tomograms, identifying particles, performing subtomogram averaging or even to perform a tomogram segmentation, all inside Scipion integration framework.  

With the experience gained in the organisation of virtual and in-person courses, we intend to organise this course in a hybrid format. We will be able to accommodate up to 20 individuals for in-person attendance. However, other 20 participants will attend remotely. In total, we can host 40 attendees. 

The course is aimed at researchers of all levels wanting to adopt electron microscopy as one of the tools at their disposal for elucidating biological structures

Expected impact for young researchers

CryoET is one of the most promising structural techniques, and it bridges the gap between structural and molecular biology and cell biology. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.


  • You will need to bring a laptop with a modern browser
  • We will provide machines with the required software through Amazon Web Services.
  • We will provide launch and coffee breaks

Tutors: I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, David Herreros, Jorge Jiménez, Patricia Losana, Jose Luis Vilas, Ana Cuervo.
CryoEM CNB-CSIC: Francisco Javier Chichón.
Contacts: Lead contact:  Carlos Oscar Sorzano
E-mail: coss@cnb.csic.es
Administrative Contact: Blanca Benitez
E-mail: blanca@cnb.csic.es


 Times are expressed in CET time Zone

DAY 1: 

Tomogram reconstruction

16:00 – Welcome(Jose Maria Carazo & Carlos Oscar Sorzano)
16:30 – Movie alignment and Tilt Series alignment: fiducidal and fiducialles approaches – (Jose Luis Vilas)
19:00- Break
20:00 – 3D Reconstruction, CTF estimation and correction(Jose Luis Vilas)
21:30 – End of session

DAY 2: 

Particle Picking methods

16:00 – Particle identification: different strategies, particle filtering according to their orientation in the tomogram– (David Herreros, Jorge Jiménez)
19:00- Break
20:00 – Particle identification: different strategies, particle filtering according to their orientation in the tomogram– (David Herreros, Jorge Jiménez)
21:30 – End of session

DAY 3: 

Subtomogram Averaging techniques

16:00 – Subtomogram averaging– (Ana Cuervo, Patricia Losada)
19:00- Break
20:00 – Particle filtering using strategies based on the subtomogram averaging and mapping back subtomograms(Ana Cuervo, Patricia Losada)
21:30 – End of session

DAY 4: 

Tomogram segmentation

16:00 – Tomogram data analysis and representation– (Javier Conesa, Javier Chichón, Jose Luis Vilas)
19:00 – End of course
16:00 – Discussion with the audience and short talks of the students work