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2025

Scipion for facilities Workshop. October 30 – 31, 2025

Dates: October 30-31, 2025 

Venue: hybrid

National Center for Biotechnology (CNB), Madrid, Spain.
Madrid, October 30 – 31, 2025

Contact Us – I2PC – Instruct Image Processing Center

Aim:

The aim of this meeting is to gather feedback and showcase how different facilities are using Scipion, demonstrating its capabilities and benefits for Cryo-EM centers. The event will feature talks and ample time for discussion, aiming to share experiences with Scipion, discuss operational methodologies, and highlight new developments that can enhance our community’s daily workflow.

Conditions:

The workshop will be held on October 30 and 31 at the Spanish National Centre for Biotechnology (CNB) in Madrid, Spain. It can be attended either in person or remotely. No programming skills are required. We will use the CSIC Conecta video conferencing system for the online sessions — please verify your browser works at https://conecta.csic.es/.

Program:

We start the day at:

AGENDA

Thursday 30th October – Hybrid
10:00 – 10.30 Welcome and assistant’s introduction
10:30 – 11:00 An Unattended Image Processing Pipeline for On-the-Fly Quality Assessment and 3D Exploration in Cryo-EM – Daniel Marchán (CNB-CSIC, Madrid)
11:00 – 11:30 Deployment of Scipion in clusters (with and without containers)  – Lola Sánchez, Mikel Iceta and Irene Sanchez (CNB-CSIC, Madrid)
11:30 – 12:00 Coffee break
12:00 – 12:30

Mario Borgnia (NIEHS/NIH – Genome Integrity and Structural Biology)
12:30 – 13:00

Enhancing screening in acquisition time scipion-em-smartscope – Alberto García (CNB-CSIC, Madrid)
13:00 – 14:00 Lunch
14:00 – 14:30 nextPYP: a web-based platform for monitoring cryo-EM and cryo-ET sessions in real-time  – Alberto Bartesaghi (Duke University – Computer Science and Biochemistry)
14:30 – 15:00 The CryoEM CNB-CSIC facility setup: EMhub, iRODS, OSCEM – Lola Sánchez and Irene Sánchez (CNB-CSIC, Madrid)
15:00 – 15:30 Facilitating cryo-EM single-particle and tomography data analysis with EMhub- José Miguel (St. Jude Children’s Research Hospital, Memphis)
15:00 – 15:15 Discussion and conclusions
Friday 31st October – Hybrid
10.00 – 10:30 Live image processing with ScipionTomo for facilities – José Luis Vilas and Jorge Jiménez (CNB-CSIC, Madrid)
10:30 – 11:00 Balancing CryoSPA and CryoET: Building Skills and Innovation in a BSL-2 Facility – Carolin Seuring (Cryo-EM Technology Platform at CSSB Hamburg)
11:00 – 11:30 Four years of progress at the cryo-EM facility of Switzerland – Emiko Uchikawa (Dubochet Center for Imaging (DCI), Lausanne)
11:30 – 12:00 Using Scipion in SBGrid – Estrella Fernández (SBGrid Consortium, Boston)
12:00 – 12:30 Coffee break
12:30 – 13:00 Cryo-EM in CNPEM – Rodrigo Villares Portugal (CNPEM, Campinas)
13:00 – 13:30 Advancing Cryo-EM Services at ESRF with Scipion – Isai Kandiah (ESRF, Grenoble)
13:30 – 14:00 Discussion and conclusions
14:00 Lunch
Registration

Registration will be free for all attendeess

Further details, such as class locations, meeting links, title updates, and instructions for reaching the centre, will be provided in the weeks leading up to the workshop.

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

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