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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 – Open until October 24

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

Instruct course on flexibility analysis using Scipion. Madrid, April 07 – 11, 2025

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, April 07 – 11, 2025

Contact Us – I2PC – Instruct Image Processing Center

Overall Aims and Course Outline
Cryo-Electron Microscopy (CryoEM) has become a well-established technique for determining the three-dimensional structures of biological macromolecules. It currently achieves atomic resolution and enables the study of conformationally heterogeneous samples as well as macromolecular complexes. CryoEM complements other structural techniques such as X-ray crystallography and Nuclear Magnetic Resonance and is currently the fastest-growing technique in atomic structure depositions in public databases like the PDB.

The aim of this course is to introduce participants to the analysis of conformational flexibility/heterogeneity, a crucial step in CryoEM image processing to obtain dynamic information in the form of conformational landscapes. The I2PC has extensive experience in organizing courses on this topic, with previous editions being in high demand.

This course is intended for researchers at all levels.

Motivation for the I2PC Course on Conformational and Compositional Heterogeneity
The goal is to introduce researchers to flexibility/heterogeneity analysis, one of the most advanced areas in Single Particle Analysis (SPA). The course will cover the theory behind the most commonly used methods in the field and include hands-on practical sessions within the Scipion Flexibility Hub environment, facilitating the use of multiple tools within a single workflow.

Expected Impact for Young Researchers
Flexibility analysis in CryoEM is an emerging technique that enables the capture of different conformations of studied macromolecules. Gaining expertise in this area provides an added value for researchers with prior experience in CryoEM image processing, enhancing their analytical capabilities and understanding of the structural dynamics of biomolecules.

 

Contacts

Lead contact:
Carlos Oscar Sorzano
email: coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marcos Gragera(MG) – Single Particle Analysis specialist, BCU/I2PC
David Herreros (DH) – Flexibility Hub head developer, BCU
Carlos Oscar Sorzano (COS) – Group leader, BCU; Technical Director, I2PC.
Slavica Jonic (SK) – Research Director, CNRS

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)

Agenda

 Times are expressed in CET time Zone

DAY 1: 

09:30-10:00: Introduction to Scipion
10:00 – 10:30: Introduction to macromolecular flexibility, state of the art, and Flexibility Hub
10:30 – 11:00: Preparing the project, importing the data, and how to work with Scipion

11:00 – 11:30: Coffee break
11:30 – 12:15: HetSIREN (Theory)
12:15-13:00: HetSIREN (Practice – Hints on how to select parameters and customization for different datasets)

13:00-14:00: Lunch break
14:00-14:30: Dimensionality reduction of estimated landscapes
14:30 – 16:00: Landscape exploration: interactive tools

16:00 – 16:30: Coffee break
16:30 – 17:00: Useful tools to simplify data analysis (automatic filtering of “bad” particles, automatic clustering…)
17:00 – 17:30 :End of the day

DAY 2: 

9:30 – 10:00: Review from the previous day
10:00 – 10:30: Zernike3Deep (Theory)
10:30 – 11:00: Zernike3Deep (Practice – Hints on how to select parameters and customization for different datasets)

11:00 – 11:30: Coffee break
12:00 – 12:30: Exploring continuous landscapes and differences with heterogeneous reconstruction methods
12:30 – 13:00: Understanding protein motions: visualizing of deformation fields, strain/rotation analysis, focused landscapes on regions of interest

13:00 – 14:00: Lunch break
14:00 – 14:30: Beyond motion blur: ZART and flexible refinement (Theory)
14:30 – 15:15: ZART (Practice)
15:15 – 16:00: Flexible refinement (Practice)

16:00 – 16:30: Coffee break
16:30 – 17:00: How to use ZART on a specific conformation?

17:00 – 17:30: End of the day

DAY 3: 

9:30 – 10:00: Review from the previous day
10:00 – 10:30: CryoDRGN (Theory)
10:30 – 11:00: CryoDRGN (Practice)

11:00 – 11:30: Coffee break
11:30 – 12:00: 3DVA (Theory)
12:00 – 13:00: 3DVA (Practice)

13:00 – 14:00: Lunch break
14:00 – 14:30: 3DFlex (Theory)
14:30 – 15:30: 3DFlex (Practice)
15:30 – 16:00: Analyzing the stability of conformational landscapes with FlexConsensus (Theory)

16:00 – 16:30: Coffee break
16:00 – 17:00: FlexConsensus (Practice)
17:00 – 17:30: End of the day

DAY 4: 

9:30 – 10:00: Review from the previous day
10:00 – 10:15: Introduction to ContinuousFlex (review of methods used in the workshop and historical background)
10:15 – 10:30: Hybrid/integrative methods (principle of using simulated dynamics to analyze cryo-EM/ET data)
10:30 – 11:00: Methods for simulating dynamics (normal modes, MD simulation, NMMD)

11:00 – 11:30: Coffee break

11:30 – 12:15: MDSPACE (Theory)
12:15 – 13:00: MDSPACE (Practice – Hints on how to select parameters, dimensionality reduction of estimated landscapes, interactive tools for landscape exploration)

13:00 – 14:00: Lunch break

14:00 – 14:30: MDTOMO (Theory)
14:30 – 15:00: MDTOMO (Practice – Hints on how to select parameters, dimensionality reduction of estimated landscapes, interactive tools for landscape exploration)
15:00 – 16:00: HEMNMA/DeepHEMNMA and HEMNMA-3D (Theory and Practice)

16:00 – 16:30: Coffee break

16:30– 17:00: Other methods in ContinuousFlex (TomoFlow, data synthesis for testing methods for conformational landscape estimation, …)
17:00 – 17:30: End of the day

DAY 5:     

9:30 – 10:00: Review from the previous day
10:00 – 11:00: Hints on defining flexibility workflows on different scenarios: Hints and examples on real/challenging cases

11:00 – 11:30: Coffee break
11:30 – 13:00: Hands-on on real data examples/One-to-one meetings between interested participants and course tutors

13:00 – 14:00: Lunch break
14:00 – 16:00: Hands-on on real data examples/One-to-one meetings between interested participants and course tutors
16:00 – 16:30: Closing remarks and end of the course

Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 17 – 21, 2024

Venue

Madrid’s Institute for Material Sciences (ICMM-CSIC), Madrid, Spain
Madrid, June 17 – 21, 2024
How to find us: Contact | ICMM (csic.es)

Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Motivation for the I2PC course on conformational and compositional heterogeneity:
We want this course to help researchers to get introduced in the area of flexibility/heterogeneity analysis, one of the most advanced topics in SPA. For some of the most used methods in the field (some developed by us, some by others) we will
present the theory behind the method and perform a short practical. We will do so within the integrative Scipion Flexibility Hub environment, to help in the use of these multiple methods.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.

Contacts

Lead contact:
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marta Martinez (MM) – Modelling specialist @BCU/i2PC
Roberto Marabini (RM) – Professor @UAM, Collaborator @BCU/i2PC
Carlos P. Mata (CM) – Single Particle Analysis specialist @BCU/i2pc
Marcos Gragera(MG) – Single Particle Analysis specialist @BCU/i2pc
David Herreros (DH) – Flexibility Hub head developer @BCU
James Krieger (JK) – Flexibility Analysis specialist @ BCU/i2PC
Carlos-Oscar Sorzano (COS) – Group leader @ BCU, Technical Director @ i2PC

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€

You can fill your registration here (closed)

Agenda

 Times are expressed in CET time Zone

DAY 1: Modeling

09:00-09:15 Welcome
09:15 – 10:15: Introduction to the compute environment to be used in this course (aws/scipion)
10:15 – 11:00:General introduction to model building in cryo-EM
11:00 – 11:30: Coffee break
11:30 – 13:00: Introduction to the data used in the practical session in homology modeling (details here) and de novo modeling
13:00-13:30: Map preprocessing I
13:30-14:30: Lunch break
14:30-16:00: Getting a first estimate of the model “de novo” (AlphaFold & ModelAngelo) and by sequence homology. 
16:00-16:30: Coffee break
16:30-17:00: Continuation of first estimation
17:00-17:30: Structure analysis: Structure comparison
17:30-18:00: Rigid Fitting of Initial Models
18:00: End of the day

DAY 2: Modelling

09:00-09:30: Review yesterday’s work 
09:30-11:00: Flexible fitting (Coot) and Validation
11:00-11:30: Coffee break
11:30-13:30: Flexible fitting and Validation
13:30-14:30: Lunch break
14:30-15:00: Review Kahoot students, teacher
15:00-16:00: Coffee break
16:30-17:00 Building the model of the whole protein
Chain merge & symmetrization
17:00-17:30: Submission of structures to EMDB. Understanding the validation report. Haemoglobin PDB full validation report 
Comparison validation scores PDB structure
17:30: Structure analysis: chain contacts Structural search
18:30:End of the day

DAY 3: Flexibility

9:30 – 10:00: Introduction to macromolecular flexibility and Flexibility Hub
10:00 – 10:15: Presentation of the dataset and workflows of the day (Zernike3D – HetSIREN)
10:15 – 11:00: Zernike3Deep (Theory)
11:00 – 11:30: Coffee break
11:30 – 12:30: Zernike3Deep (Practice)
12:30 – 13:00: HetSIREN (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: HetSIREN (Practice)
15:00 – 15:30: Dimensionality reduction of estimated landscapes
15:30 – 16:00: Landscape exploration: interactive tools
16:00 – 16:30: Coffee break
16:00 – 17:00: Landscape exploration: interactive tools
17:00 – 17:30: End of the day

DAY 4: Flexibility

9:30 – 10:00: Review from the previous day
10:00 – 10:15: Presentation of the workflows of the day (FlexConsensus – ZART – CryoDRGN)
10:15 – 11:00: Should we trust our conformational landscapes? FlexConsensus (Theory)
11:00 – 11:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
11:30 – 12:00: Coffee break
12:00 – 12:30: Should we trust our conformational landscapes? FlexConsensus (Practice)
12:30 – 13:00: Beyond motion blurr: ZART and flexible refinement (Theory)
13:00 – 14:00: Lunch break
14:00 – 15:00: Beyond motion blurr: ZART and flexible refinement (Practice)
15:00 – 15:30: CryoDRGN (Theory)
15:30 – 16:00: CryoDRGN (Practice)
16:00 – 16:30: Coffee break
16:30 – 17:00: CryoDRGN (Practice)
17:00 – 17:30: Landscape exploration: interactive tools
17:30 – 18:00: End of the day

DAY 5: Flexibility

9:30 – 9:45: Review from the previous day
9:45 – 10:00: Presentation of the workflows of the day (ContinuousFlex – 3DVA – 3DFlex – Prody)
10:00 – 11:00: ContinuousFlex
11:00 – 11:30: Coffee break
11:30 – 12:00: 3DVA (Theory)
12:00 – 13:00: 3DVA (Practice)
13:00 – 14:00: Lunch break
14:00 – 14:30: 3DFlex (Theory)
14:30 – 15:30: 3DFlex (Practice)
15:30 – 16:00: Prody
16:00 – 16:30: Coffee break
16:00 – 17:00: Prody
17:00 – 17:30: End of the day (closing remarks)

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

VENUE

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.

Prerequisites

  • 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

Agenda

 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.

 

Instruct course on flexibility analysis and integrative modelling using Scipion. Madrid, June 19 – 23, 2023

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 19 – 23, 2023
How to find us: https://i2pc.es/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established itself as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and is capable of accessing the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like the PDB.
The aim of the course is to introduce attendees to two techniques that are normally needed at the end of the Cryo-Electron Microscopy image processing pipeline: 1) understanding the possible continuous heterogeneity/flexibility of the sample, helping to obtain dynamical information in the form of conformational landscapes, and 2) interpreting the reconstructed map by means of an atomic model. The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.
We will use our software platform Scipion to present these two topics. Scipion is an integrative platform that allows interoperability among different software packages. In the domain of flexibility analysis, we include our own developments in Xmipp as well as tools coming from CryoDrgn, ProDy and HEMNMA. For the atomic modelling part, we include software like Coot, Chimera, Refmac, Phenix, and AlphaFold. In addition to simplifying the access to all these software packages in an integrated manner, Scipion adds a traceability and reproducibility layer so that any other researcher can understand the modelling workflow followed to reach a particular model.
This course is addressed to investigators at all levels.

Expected impact for young researchers

Atomic modelling of the CryoEM map is currently at the moment the natural next step once the map is reconstructed. Flexibility analysis is currently not so common, but the advantage of CryoEM is that it can capture the different conformations of the macromolecules under study. Both techniques are valuable assets in young researchers already with a background on image processing in CryoEM.

Contacts

Lead contact:
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

I2PC staff: David Herreros (DH), James Krieger (JK), Marcos Gragera (MG), Marta Martínez (MM), Roberto Marabini (RM), Daniel del Hoyo (DDH)
CNRS IMPMC-CNRS UMR 7590. Sorbonne Université: Remi Vuillemot (RV)

You can fill your registration here (Online registration closed)

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€
Program
Day 1: June 19, 2023

09:30: Introduction to Scipion and AWS
10:15: Introduction to macromolecular flexibility and Flexibility Hub
10:30: Flexibility approaches (theory): 
– Deformation field-based approach
– Density-based approach
11:00: Coffee break
11:30: Presentation of the dataset to be used during the practical session
11:45: Estimation of conformational landscapes
12:45: Flexibility consensus (theory)
13:30: Lunch
14:30: Flexibility consensus (practice)
15:15: Dimensionality reduction of estimated landscapes
16:00: Coffee break
16:30: Conformational landscape analysis tools
– Interactive landscape clustering and real-time inspection of conformations
– Best number of clusters analysis
18:00 – 18:30: End of the day
Day 2 June 20, 2023

09:30: Review from the previous day
09:45: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (2D-based tools)
11:00: Coffee break
11:30: Conformational landscape analysis tools (continuation)
– Interactive landscape annotation and real-time inspection of conformations (3D-based and hybrid tools)
13:30: Lunch
14:30: Extracting conformational states from landscape selections:
Application of deformation fields to maps and structural models + strain/rotation analysis + motion statistics
15:00: Interactive local analysis of motions
15:30: Heterogeneity correction with ZART (theory)
16:00: Coffee break
16:30: Heterogeneity correction with ZART (practice)
17:15: Heterogeneity correction of different landscapes states with ZART
18:00 – 18:30: End of the day
Day 3 June 21, 2023

09:00: Review from the previous day
9:45: Introduction to atomic structure ensemble analysis, normal mode analysis, and ProDy
10:15: Ensemble analysis with ProDy ensemble construction, PCA and landscape projection, and motion analysis with NMWiz
11:00: Coffee break
11:30: Conformational landscapes from normal modes and molecular dynamics using ContinuousFlex (theory and practice)
13:30: Lunch
14:30: Introduction to model building in cryo-EM
  – How to get a first estimation of the model (homology, alphafold, modelangelo)
15:15: Presentation of the data used in the practical session
– Kahoot
15:45 min: Map preprocessing – I
  16:00: coffee break
16:30: Map preprocessing – II
17:00 : Getting a first estimate of the model
18:00-30: End of the day
Day 4 June 22, 2023

09:30 Structure analysis: Structure comparison
10:15: Rigid fitting of initial models
11:00: Coffee Break
11:30: Flexible fitting (coot) and validation (phenix)
13:30: lunch
14:30: Flexible fitting (coot) and validation (phenix) (cont)
15:30: kahoot
16:00: coffee break
16:30: Model building of the Beta sub-unit
18:00-30: end of the day
Day 5 June 23, 2023

09:30: Presentation of the course questionnaire
09:45: Building the model of the protein complex
10:30: kahoot.
11:00: Coffee Break
11:30: Submission of structures to EMDB. Understanding the validation report.
12:00: Structure analysis: Chain contacts
13:00: INSTRUCT short message and farewell
13:30: lunch and end of the day

Fill your registration here (Online registration closed)

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

iNEXT Discovery – I2PC Course on Single Particle Analysis by CryoEM. Madrid, 27 – 29 March, 2023

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, March 27 – 29, 2023
How to find us: https://i2pc.es/contact-us/

Overall aims and course outline

Cryo-Electron Microscopy has established as a mature technique to determine the three-dimensional structure of biological macromolecules. It is currently reaching atomic resolution and it is capable of accessing to the structure of conformationally heterogeneous samples, as well as macromolecular complexes. It is complementary to other structural techniques like X-ray crystallography and Nuclear Magnetic Resonance and at the moment it is the most rapidly growing technique in atomic structure depositions at public databases like PDB.

The aim of the course is to give an overall overview of the image processing in single particle analysis (SPA). The I2PC has a long tradition of organizing courses of image processing and atomic modelling, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to be able to attend its demand.

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

CryoEM is the most rapidly growing structural technique. PhD students as well as young post-docs will certainly benefit from approaching this technique. Knowing it will open new doors to new positions worldwide.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Carlos Oscar Sorzano Sánchez (COSS), José-María Carazo (JMC), Marcos Gragera (MG), Carlos Perez Mata (CPM)

Program

Day 1: Data processing
9:30 Morning session:
– Movie alignment, Screening micrographs and CTF
– Particle picking and screening
13:00 Lunch Break
14:00 Afternoon session:
– Particle picking and screening
– 2D classification
17:00 End of day

Day 2:
9:30 Morning session
– Initial volume
– 3D classification
13:00 Lunch Break
14:00 Afternoon session
– 3D classification advanced (masking, classification with no alignment…)
– 3D reconstruction
17:00 End of day

Day 3:
9:30 Morning session
– Sharpening, local resolution and validation
13:00 Lunch Break
14:00 Afternoon session
– One-to-one troubleshooting meeting. NEW
17:00 End of day

REGISTRATION

Registration will be free for all attendees.
Fill  your application here.  (Registration is closed)

This course is organized by iNEXT Discovery (UE Proposal:  871037) and I2PC in collaboration with  Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project


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

VENUE

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.

Prerequisites

  • 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
email. coss@cnb.csic.es
Administrative Contact: Blanca Benitez
email: blanca@cnb.csic.es

 

 

Agenda

 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.

 

I2PC – INSTRUCT COURSE: INTRODUCTION TO MODEL BUILDING

Venue

Remote course
June 22th to June 24th (2022) (3 days):
*3 Mornings: Presentations and training.
*2 Afternoons: Personal work.

Aim of the course:

Hands-On Training Course that introduces the  fundamentals and main tools needed to build an atomic model in the context of cryo-EM, starting from a 3D map and the aminoacid sequence of each protein chain. The  tools will be used inside the Scipion framework (de la Rosa-Trevin et al. 2016) and examples will focus on the modeling by homology scenario, including AlphaFold2 prediction models.

Expected impact for young researchers

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. In this course, we introduce the basic tools needed to perform this task. Ph.D. students, as well as post-docs, will undoubtedly benefit from approaching this technique since atomic models guide our mechanistic interpretation of cryo-EM structures.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Marta Martínez (MM), Roberto Marabini (RM)

Schedule and contents:

*June 22th:

  • 9:30: Welcome and presentation of the course, dynamics and mentors.
  • 10:00: Introduction to model building in the context of cryo-EM and Scipion
  • 10:30: Introduction to Scipion (import data)and AWS
  • 11:30: Map preprocessing
  • 12:00: Break
  • 12:15: Introduction to AlphaFold2 (Searching for prediction models)
  • 13:00: Searching models by homology
  • 13:30: Afternoon task proposal

*June 23th:

  • 9:30: Review of contents and follow up of the afternoon task proposal.
  • 10:00: Kahoot
  • 10:15: Rigid fitting of initial models
  • 11:00: Flexible fitting
  • 12:00: Break
  • 12:15: Flexible fitting (continuation)
  •  14:00: Afternoon task proposal

*June 24th:

  • 9:30: Review of contents and follow up of the afternoon task proposal.
  • 9:45: Presentation of the course questionnaire
  • 10:00: Kahoot
  • 10:15: Assessment and validation of models
  • 11: 00: Building the model of the protein complex
  • 11:15: Break
  • 11:30: Structure analysis: Chain contacts
  • 12:00: Structure analysis: Structure comparison
  • 12:30: Submission of structures
  • 13:00: Summary
  • 13:30: INSTRUCT short message and farewell

REGISTRATIONRegistration Fee: 50€ 
Registration online closed.

This course is organized by I2PC in collaboration with Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe and CRIOMECORR Project

Instruct virtual course on Electron Tomography by CryoEM. Madrid, December 13 – 16, 2021

Venue

Remote course
December 13 – 16, 2021 from 09.30-17.30 CET

Overall aims 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. The I2PC has a long tradition of organizing courses of image processing, with Instruct courses that have been heavily oversubscribed and had to be repeated twice in the same year to attend its demand. The length of the course is three days and a half.

Preventing possible traveling restrictions and seeing the previous virtual course’s successes, the whole course will be given online. An additional benefit of this circumstance is that the course can be recorded and stay as a permanent course in Instruct. Although the course is online, we will keep a close interaction with attendees. For this reason, we will limit the maximum number of attendees to 40.

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 researches

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.

Contacts

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

Ana Cuervo (AC), Federico de Isidro (FI), Estrella Fernández (EF), David Herreros (DH), Jorge Jiménez (JJ), Javier Conesa (JC), Roberto Melero (RM), Carlos Oscar Sorzano Sánchez (COSS), Jose-María Carazo (JMC), Patricia Losana (PL), Jose Luis Vilas (JLV)

Program

Day 1: From movies to tomograms

9:15   Course introduction. 
9:30   Movie alignment and Tilt Series alignment: fiducial and fiducialless approaches. 
12:30    Lunch Break
13:30 3D Reconstruction, CTF estimation and correction. 
17:30    End of day

Day 2: From tomograms to subtomograms

09:30    Tomogram denoising and segmentation. 
12:20    Lunch Break
13:30 Particle identification: different strategies, particle filtering according to their orientation in the tomogram. 
17:30    End of day

Day 3: Processing subtomograms

09:30    Subtomogram averaging. 
12:20    Lunch Break
13:30 Particle filtering using strategies based on the subtomogram averaging and mapping back subtomograms. 
17:30    End of day

Day 4: Tomogram interpretation

09:30    Tomogram segmentation.
12:20    End of course

Registration 

Registration online closed.

 

Registration Fee

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

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