Highlights Archives - I2PC - Instruct Image Processing Center

Cryo-EM Facilities Meeting 2026

Workshop Information

Meeting Information

Venue	Hybrid
Location	National Center for Biotechnology (CNB), Madrid, Spain
Date	October 29–30, 2026
Contact	I2PC – Instruct Image Processing Center

Aim

This meeting will gather feedback and showcase how different facilities are using Scipion in Cryo-EM centers. The event will include talks and discussion time to share experiences, review operational methodologies, present new developments, and improve the community’s daily workflow.

Conditions

The workshop will take place at the Spanish National Centre for Biotechnology (CNB) in Madrid and can be attended in person or remotely. No programming skills are required. Online sessions will use CSIC Conecta; please check your browser at conecta.csic.es .

Program

The detailed agenda is currently being finalized and will be announced shortly. We start the day at:

Thursday 29 October – Hybrid
10:00 – 10:30	Welcome and assistant’s introduction
10:30 – 11:00	Scipion SPA in a live acquisition with several workflows; an overview – Alberto Garcia [CNB-CSIC-Madrid]
11:00 – 11:30	SBGrid: Research Computing Support for Structural Biology – Using Scipion in SBGrid – Estrella Fernandez [SBGrid Consortium, Boston]
11:30 – 12:00	Coffee break
12:00 – 12:30	Screening feedback with in live processing. Beyond the in live pipeline – Alberto Garcia [CNB-CSIC-Madrid]
12:30 – 13:00	TBA
13:00 – 14:00	Lunch
14:00 – 14:30	TBA
14:30 – 15:00	TBA
15:00 – 15:30	TBA
15:30 – 16:00	TBA
Friday 30 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	Cryo-EM in CNPEM – Rodrigo Villares [CNPEM, Campinas]
11:00 – 11:30	Implementing On-the-Fly Tomography Data Processing with Scipion3 at DCI Lausanne – Emiko Uchikawa [Dubochet Center for Imaging (DCI), Lausanne]
11:30 – 12:00	The CryoEM CNB-CSIC facility setup; EMHub, IRODS, FandanGO
12:00 – 12:30	Coffee break
12:30 – 13:00	Cryo-EM for Translational Biomedicine: Insights from the IBMB-CSIC Platform – Pablo Guerra [Ibmb – Barcelona]
13:00 – 13:30	The Screening Gateway: Building Portugal’s First Talos 12 Cryo-EM Facility – Dmitry Semchonok [ITQB Lisboa]
13:30 – 14:00	Integrating Scipion into the European Synchrotron Infrastructure – Ludovic Broche [ESRF Grenoble]
14:00	Lunch

Registration is free for all attendees.

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.

Venue

National Center for Biotechnology (CNB), Madrid, Spain
Madrid, June 22- 26, 2026

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, BCU/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€

Acommodations

Hotel Chamartín The One (****): Calle Agustín de Foxá, s/n 28036 Chamartín, Madrid. Reservas: reservas@hotelchamartintheone.com
Hotel Exe Plaza (****): Paseo de la Castellana 191, Madrid, 28045, España. Reservas: reservas@hotelexeplaza.com
Hotel Crisol Via Castellana (****): Paseo de la Castellana, 220, Madrid, 28046, España. Reservas: reservas@hotelviacastellana.com
VP Jardín de Tres Cantos (***): Avenida de los Encuartes, 17, Tres Cantos, 28760, España. tc@vphoteles.com

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/

Online registration will close on 31 May 2026 at 12:00 PM

Day 1
10:30 – 11:00	Badge Pick-up & Welcome
11:00 – 13:00	Movie alignment, screening Movie alignment, CTF estimation and micrograph curation
13:00 – 14:00	Lunch Break
14:00 – 16:00	Strategies for particle picking
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 & 3D classification
11:00 – 11:30	Coffee break
11:30 – 13:00	3D Refinement
13:00 – 14:00	Lunch Break
14:00 – 16:00	Advaced methods for 3D classification & Refinement (I)
16:00 – 16:30	Coffee break
16:30 – 17:30	Advaced methods for 3D classification & Refinement (II)
17:30	End of day

Day 3
09:30 – 11:00	Postprocessing: Sharpening, local resolution, anisotropy assessment and validation metrics (I)
11:00 – 11:30	Coffee break
11:30 – 13:00	Postprocessing: Sharpening, local resolution, anisotropy assessment and validation metrics (II)
13:00 – 14:00	Lunch Break
14:00 – 16:00	Asymmetric features and symmetry expansion.
16:00 – 16:30	Coffee break
16:30 – 17:30	Asymmetric features and localized reconstruction.

Day 4
09:30 – 10:15	Introduction to model building in cryo-EM
10:15 – 11:00	Getting the initial model (homology, AlphaFold and ModelAngelo)
11:00 – 11:30	Coffee break
11:30 – 12:00	Structure analysis: Structure comparison
12:00 – 13:00	Rigid fitting; Introduction to flexible fitting (Coot)
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 an alternative structure

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 maps and structures to EMDB
12:00 – 12:30	Structure analysis: chain contacts
12:30 – 13:00	Structural search
13:00	Lunch Break and end of the day

Scipion for facilities Workshop. October 29 – 30, 2026