I2PC – Instruct course on Cryo-Electron Tomography Image Processing. Madrid, December 12 – 15, 2023


The course will take place in person at CNB-CSIC 
December 12 – 15, 2023 from 09:00 to 18:00 CET
You do not need to install any special software to connect. A modern browser should be enough.

Overall aims and course outline

Cryo-electron Tomography is a rapidly growing technique that can visualize cell organelles and biological macromolecules in their cellular context. Image processing algorithms allow the identification of the macromolecules of interest in the electron tomograms. Then, by extracting small subtomograms around those locations and identifying those similar particles, we may average them and recognize their different conformations. This latter process is called subtomogram averaging and has allowed solving a growing number of macromolecules with a resolution between 20-5A.

The course aims at providing a comprehensive overview of the whole image processing pipeline in Electron Tomography (ET) from the movie alignment of the tilt series, 3D reconstruction of the tomogram, particle identification, and subtomogram averaging, all inside Scipion integration framework.  

With the experience gained in the organization of virtual and in-person courses, we plan to organize this course in an in-person modality. 20 people will be able to physically attend.

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, Federico de Isidro,
David Herreros, Jorge Jiménez, Patricia Losana, Jose Luis Vilas, Borja Rodriguez,
CryoEM CNB-CSIC: Francisco Javier Chichón, Jose Javier Conesa.
Ramón y Cajal Researcher – Department of Information and Communication Engineering – University of Murcia: Antonio Martínez
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: 

From movies to tomograms

9:30 – Welcome(Jose Maria Carazo & Carlos Oscar Sorzano)
9:45 – Course introduction(Jose Luis Vilas)
10:00 – Tomography in Scipion(Jose Luis Vilas)
10:30 – Import Tilt Series, automatic alignment(Federico de Isidro)
11:30 – 10 minutes break
11:40 – CTF estimation and correction –  (Federico de Isidro)
13:00 – Lunch break
14:00 – Tomogram reconstruction(Federico de Isidro)
15:30 – 10 minutes break
15:40 – eTomo(Grigory Sharov)
17:00 – AreTomo, ctfFind4 and novaCTF (Grigory Sharov)
17:30 – End of session

DAY 2: 

From tomograms to subtomograms- Picking and segmentation

9:30 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez)
11:10 – 10 minutes break
11:20 – Non-directional picking with cryolo and SPA leap – (Borja Rodriguez)
12:45 – Lunch break
13:45 – Tomogram denoising and membrane segmentation(Antonio Martinez)
14:15 – Membrane picking with PySeg (Jorge Jiménez)
15:00 – Dynamo(Pablo Conesa)
16:00 – 10 minutes break
16:10 – Practice: Dynamo(Pablo Conesa)
17:30 – End of session

DAY 3: 

Processing subtomograms

9:30 –  Subtomogram averaging with RELION4 – (Patricia Losana)
11:30 – 10 minutes break
11:40 – Subtomogram Averaging with RELION4(Patricia Losana)
13:00 – Lunch Break
14:00 – Subtomogram Averaging with EMAN – (Jorge Jiménez)
15:00 – 10 minutes break 
15:10 – Subtomogram Averaging with EMAN(Jorge Jiménez)
17:30 – End of session

DAY 4:  morning session

Tomogram Interpretation

9:30 – Tomogram segmentation. Basic use of SuRVoS for cellular tomogram segmentation and basic analysis. 3D rendering using ChimeraUSFC with masked data(Francisco Javier Chichón)
12:00/12:30 – End of coruse. Wrap Up.


Registration Fee

Fill your registration (Online registration closed)


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