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

Fill your registration here

(Online registration closed)


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


CORBEL launches 1st Open Call for research projects

CORBEL – Coordinated Research Infrastructures Building Enduring Life-science services – is an EC Horizon2020 project uniting 11 Biological and Medical Science Research Infrastructures (RIs). In CORBEL, the participating RIs expand their cooperation in order to harmonise researchers’ access to their cutting-edge technologies and services by establishing a sustainable platform of aligned services that will enable faster admission to and a wider portfolio of technologies and services to boost research projects.

The CORBEL Open Call invites researchers to apply to access technologies and services from more than 15 facilities from eight different research infrastructures across Europe. Selected projects will be allocated to so-called Access Tracks and gain unprecedented opportunities to utilise a wide range of high-end technologies and services. These include state-of-the-art offers from the fields of advanced imaging, biobanking, curated databases, marine model organisms, mouse mutant phenotyping, screening and medicinal chemistry, structural biology as well as systems biology.

Projects will be supported at every stage, with CORBEL project managers on hand to help scientists navigate between different service providers and exploit the full potential of the offers available.

Learn more about the CORBEL Open Call by visiting our website (

Instruct Biennial Structural Biology Meeting #IBSBM2017

Brno, Czech Republic, 24th to 26th May 2017

Instruct Biennial Structural Biology Meeting will be held at the International Best Western Hotel, Brno, CzechRepublic. The meeting will showcase integrative structural biology and its impact on biological research. The program will include sessions that represent recent advances in structural biology towards cellular biology, emerging methods and technologies and results of biomedical importance. Young scientists who want to know what structural biology can offer for their research and what are the future trends, are especially encouraged to attend.

Register today

Instruct is a distributed European Research Infrastructure, which provides scientists with access to all major cutting edge technologies that enable biomacromolecular structure determination at atomic resolution. Access to all of these technologies has been available to European member researchers from February 2012

First iNEXT All Hands Meeting

First iNEXT All Hands Meeting. Madrid, 19 – 21 October, 2016.

AHM 2016 is the first annual meeting of iNEXT. It aims at gathering not only iNEXT Partners, but also iNEXT Users (or intended users) contacted directly by the different Facilities in the project. iNEXT Partners, together with the Scientific Advisory Board and the Industry Panel, will review the work performed in the project, including its different Joint Research Activities. iNEXT meeting web page

I2PC-CCISB hands on spring course

From 2D images to 3D structures: A practical course on Electron Microscopy Single Particle Analysis. Madrid, May 17 – 20, 2016

A joint computational course between the Instruct Image Processing Center (I2PC) and the Collaborative Computational Project for Electron cryo-Microscopy (CCP-EM, a member of CCISB). Tutors from Spain and the UK will address the complete image processing workflow typical for macromolecular structural determination, from processing the raw images taken on the electron microscope to the interpretation of the derived 3D volumetric structure.

Instruct call for proposals

Instruct has 16 Instruct Centres in Europe and Israel offering access to a full range of advanced technologies and expert support.

Access to the infrastructure at Instruct Centres is provided for all Instruct members and there are no charges (consumable costs, accommodation and travel are supported by Instruct funds, up to a maximum of €1100 per visit).

The deadline for this round of proposal submission is 5pm CET, Thursday 30th April 2015. Submit your proposal.