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I2PC – Instruct Course on Electron Tomography and Subtomogram Averaging. Madrid, December 09 – 12, 2025.

Venue

National Center for Biotechnology (CNB), Madrid, Spain.
Madrid, December 09 – 12, 2025

Contact Us – I2PC – Instruct Image Processing Center

Overall Aims and Course Outline

Cryo-electron tomography (cryoET) is a cutting-edge imaging technique that  enables to visualize the three-dimensional structures of biological macromolecules and cellular organelles at nanometer resolution. With this 3D data, scientists can accurately locate macromolecules of interest in the cell and study them in their native state. Subtomogram averaging (STA) is a crucial method in this field, facilitating the extraction of high-resolution structural information from the identified proteins within the tomogram (3D representation of the sample). This course offers participants the theoretical knowledge and the practical skill to undertake cryoET and STA projects. 

Expected Impact for Young Researchers

Participants will gain practical, hands-on experience with essential tasks such as tilt-series alignment, 3D tomogram reconstruction, particle identification, subtomogram averaging, and tomogram segmentation. 

Over the course of four days, attendees will be introduced to both theoretical concepts and practical applications, allowing them to develop a deep understanding of the workflow from the raw data  to detailed 3D visualization. 

Tutors

Jose Luis Vilas – Instruct Spain (I2PC). National Center for Biotechnology – CSIC

Daniel Castaño Díez –Numerical Methods of Cryo Electron Tomography Group. Instituto Biofisika – CSIC

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€
Registration is now closed

COURSE CONTENTS

Day 1: From movies to tomograms 

  • Course introduction and fundamentals of cryoET image processing
  • Movie alignment
  • Tilt Series alignment: fiducial and fiducialless approaches
  • 3D Reconstruction
  • CTF estimation and correction

Day 2: Particle Picking methods  

  • Particle identification: different strategies, particle filtering according to their orientation in the tomogram
  • Particle picking of non oriented particles in the tomogram

Day 3: Subtomogram Averaging techniques  

  • Initial model generation
  • Map refinement
  • Post-processing and quality Analysis

Day 4: Tomogram segmentation 

  • Tomogram data analysis and representation
  • Segmentation tools
  • Discussion with the audience and short talks of the students work

I2PC Course on Single Particle analysis and modelling by Cryo-EM. Madrid, June 16 – 20, 2025

Venue

Madrid´s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain
Madrid, June 16 – 20, 2025

How to find us: Contact | ICMM

Overall Aims and Course Outline

Cryo-Electron Microscopy (Cryo-EM) allows the determination of three-dimensional structures of biological macromolecules at atomic resolution. This course provides an overview of image processing in Single Particle Analysis (SPA) using Scipion. In the first part of the course, participants will learn the fundamentals of reconstructing biological structures from single particle images obtained through cryo-EM, employing state-of-the-art software in the field.

The second part of the course will focus on interpreting reconstructed maps through atomic modeling. We will use the Scipion platform, integrating tools such as Coot, Chimera, Refmac, and AlphaFold. This course is open to researchers of all levels.

The course will be held in-person and is designed for researchers at any stage of their career who are interested in incorporating Cryo-EM into their research.


Expected Impact for Young Researchers
This course will equip young researchers with the knowledge and skills necessary to apply Cryo-EM in the study of biological macromolecules. Through training in image processing and the interpretation of reconstructed maps, participants will be able to address the structural characterization of biomolecules. These approaches will enhance the understanding of molecular mechanisms and facilitate the use of Cryo-EM as a tool in biomedical and biotechnological research.

Tutors

Marcos Gragera(MG) – Single Particle Analysis specialist, BCU/I2PC
Marta Martinez (MM) – Modelling specialist, BCU/I2PC
Roberto Marabini (RM) – Professor, UAM, Collaborator BCU/I2PC
Deborah Cezar Mendonca – Biologie structurale intégrative (IGBMC)

Registration Fee

  • Academic Registration Fee Instruct countries: Predocs & Postdosc 50€
  • Academic Registration Fee Instruct countries: Others 100€
  • Academic Registration Fee Non Instruct countries: Predocs & Postdosc 100€
  • Academic Registration Fee Non Instruct countries: Others 150€
  • Industrial Registration Fee 300€

Acommodations

Additionally, on our campus, there is a student residence that might have rooms available for those dates. Here are the links:

Residencia UAM: https://resa.es/residencias/madrid/erasmo/

Registration Here (closed)

Closes on 23 May 2025 at 12:00 PM

Day 1

10:30 – 11:00

Badge Pick-up & Welcome

11:00 – 13:00

Movie alignment, screening micrographs and CTF

13:00 – 14:00

Lunch Break

14:00 – 16:00

Particle picking and screening

16:00 – 16:30

Coffee break

16:30 – 17:30

2D classification

17:30

End of day

Day 2

09:30 – 11:00        

Initial volume

11:00 – 11:30

Coffee break

11:30 – 13:00

3D classification

13:00 – 14:00

Lunch Break

14:00 – 16:00

3D classification advanced (masking, classification with alignment…)

16:00 – 16:30

Coffee break

16:30 – 17:30

3D reconstruction

17:30

End of day

Day 3

09:30 – 11:00                   

Sharpening, local resolution and validation metrics

11:00 – 11:30

Coffee break

11:30 – 13:00

Sharpening, local resolution and validation metrics

13:00 – 14:00

Lunch Break

14:00 – 14:45

General introduction to model building in cryo-EM

14:45 – 15:15

Introduction to the data used in the practical session in homology modeling and de novo modeling

15:15 – 16:00

Map preprocessing I & II

16:00 – 16:30

Coffee break

16:30 – 17:30

Getting a first estimate of the model “de novo” and by sequence homology

Day 4

09:30 – 10:15       

Structure analysis: Structure comparison

10:15 – 11:00

Rigid Fitting of Initial Models

11:00 – 11:30

Coffee break

11:30 – 13:00

Flexible fitting (Coot) and Validation

13:00 – 14:00

Lunch Break

14:00 – 16:00

Flexible fitting (Phenix & Refmac) and Validation & Review Kahoot

16:00 – 16:30

Coffee break

16:30 – 17:30

Model building of human Hgb beta subunit

Day 5

09:30 – 09:45                     

Presentation of course questionnaire

09:45 – 11:00

Building the model of the whole protein

11:00 – 11:30

Coffee break

11:30 – 12:00

Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report.

12:00 – 12:30

Structure analysis: chain contacts

12:30 – 13:00

Structural search

13:00

Lunch Break and end of the day

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 (http://www.corbel-project.eu/1st-open-call.html).

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.

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