Instruct course on Cryo-Electron Tomography Image Processing. Madrid, December 13 – 16, 2022


The course will take place in person at CNB-CSIC 
December 13 – 16, 2022 from 09.30-17.30 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.
Leiden University Medical Centre (LUMC): Abraham J. Koster
Ramón y Cajal Researcher – Department of Information and Communication Engineering – University of Murcia: Antonio Martínez
Contacts: Lead contact:  Carlos Oscar Sorzano
Administrative Contact: Blanca Benitez




 Times are expressed in CET time Zone
DAY 1: From movies to tomograms 9:30 Welcome
9:45 Course introduction
10:00 Tomography in Scipion
10:15 Import Tilt Series, automatic alignment
1:30 10 minutes break
11:40: CTF estimation and correction
13:00 lunch break
14:00: tomogram reconstruction
15:30 10 minutes break
15:40: Local Resolution and alternative workflows
17:30 End of session

DAY 2: From tomograms to subtomograms. Picking and segmentation


9:30: Theory: Directional – Non-directional picking
9:50: Practice: directional picking
11:30: 10 minutes break
11:40: Practice: Non-directional picking (Cryolo)
13:00: lunch break
14:00-15:00: Tomogram denoising and membrane segmentation
10 minutes break
14:00-15:00: Tomogram denoising and membrane segmentation
10 minutes break
15:10-17:00: Particle identification: directional picking with PySeg and different strategies, particle filtering
17:30 Alternatives
17:30 End of session
DAY 3: Processing subtomograms 9:30 Theory: Subtomogram averaging (I)
10:00 Practice: STA HIV tutorial (I)
11:30-11:40 10 minutes break
11:40 Practice: STA HIV tutorial (II)
13:00 lunch break
13:00 Theory: Subtomogram averaging (II)
14:00 Practice: STA Ribosome tutorial (I)
15:00-15:10 10 minutes break
15:45: Practice: STA Ribosome tutorial (II)
17:00 Alternatives
17:30 End of session

DAY 4:  Tomogram interpretation


09:30 – 12:00 Tomogram segmentation
Basic use of SuRVoS for cellular tomogram segmentation and basic analysis. 3D rendering using ChimeraUSFC with masked data (FJCh, JC). Tutorial
12:00 – 12:30 End of course. Wrap up


Registration Fee

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