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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 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.

 

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.

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