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2022

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.

 

Scipion at facilities workshop. October 4th, 2022

Dates: 4th October 2022
Venue: Hybrid Meeting (Brno/Remote)
The face-to-face meeting will take place at the CEITEC facilities (Kamenice 753/5, Brno, 625 00).
CEITEC Website: https://www.ceitec.eu/

Aim : The aim of this meeting is to mainly get feedback and showcase how facilities are using Scipion and show what scipion offers to a Cryo-em facility. There will be talks but also plenty of time for discussion.

Target Audience: Cryo em facility staff wanting to do or already doing on-the-fly processing.

Conditions: The workshop will be hybrid:  online and presential (in Brno) for both attendees and speakers.
No programming skills are required.

Program: This program is tentative and may be subjected to changes depending on the attendees. Anyone is welcome to present their infrastructure.

9.00 Welcome
9.15 Brief update on Scipion for facilities CNB
9.45-13.00 Examples of setup, use, hardware and software architecture: ESRF, CNB, Francis Crick, SciLife Lab, NIEHS, UCSF (there will be a 20 minutes break)
13.00 Lunch
14.00 Discussion: Usability, maintainability, IT support, needs, reporting.
16.00 Brainstorming
16.45 Conclusions
17.00 End

REGISTRATION

Registration will be free for all attendees.
Fill  your application here. 

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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

I2PC Seminar Series on Image Processing 2022

Following the tradition, I2PC (Instruct Image Processing Center) is organizing the third edition of seminar series on cryoEM and cryoET methods for image processing. 
The aim of the seminar series is to gather expert developers and users in a same  framework where the algorithms can gain visibility and users can understand the applications and mechanisms of the presented algorithms. 

The webinars will be online and they are absolutely free (registration is not required). You can join the session through next link 

https://conectaha.csic.es/b/bla-rkh-dqa-rpn

The contents and speakers will be 

  • April 21th. (14:00 London, Dublin,  15:00 Madrid, Berlin, Paris, 9:00 New York)
    Sjors Scheres – New developments in RELION-4.0.
    MRC Laboratory of Molecular Biology 
  • May 12th   (16:00 London, Dublin,  17:00 Madrid, Berlin, Paris, 11:00 New York, 9:00 New Mexico)
    Thomas C. Terwilliger. AlphaFold changes everything.
    Los Alamos National Laboratory
  • May 26th (14:00 London, Dublin,  15:00 Madrid, Berlin, Paris, 9:00 New York)
    Daniel Marchan and Marcos Gragera. Stream processing for facilities. 
    BioComputing Unit CNB/CSIC. 
  • June 9th (14:00 London, Dublin,  15:00 Madrid, Berlin, Paris, 9:00 New York)
    Carsten Sachse. Statistical methods for the cryo-EM toolbox. Forschungszentrum Jülich GmbH.
    Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons. 
  • June 23th (14:00 London, Dublin,  15:00 Madrid, Berlin, Paris, 9:00 New York)
    Min Xu. AITom: Open-source AI platform for cryo-electron tomography data analysis. 
    School of Computer Science. Carnegie Mellon University
  • June 30th(14:00 London, Dublin,  15:00 Madrid, Berlin, Paris, 9:00 New York)
    Carlos Óscar Sorzano. Validation tools in cryoEM.
    BioComputing Unit CNB/CSIC. 

The seminar series will continue in September with next speakers, the exact day and time will be announced in summer

  • Dmitry Lyumkis – Laboratory of Genetics, The Salk Institute of Biological Sciences
  • Jorge Jimenez –  BioComputing Unit CNB/CSIC. 
  • Lorenz Lamm – Helmholtz Pioneer Campus, Helmholtz Munich

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.

I2PC Seminar series on Image processing

Dear EM community,

From I2PC we are proud to announce the second part of our seminar
series on Image processing, addressed to Electron Tomography Methods.

The aim of the seminar series is to gather expert developers and
users in a same framework where the algorithms can gain visibility and users
can understand the applications and mechanisms of the presented algorithms. The
webinars will be online at 16:00 GTM+1 (Berlin, Paris, Madrid) and they are
free without registration of cost. You can join the session through next link.

https://conectaha.csic.es/b/bla-rkh-dqa-rpn

The contents (speakers are free to present other contents) and
speakers will be

3rd
June. DeepFinder.Emmanuel Moebel.
CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, France

10th June. NOVACTF. Beata
Turonova. Max-Planck Institute of Biophysics, Germany.

17th
June.PySeg. Antonio Martínez-Sánchez.Universidad de Oviedo, Spain.

24th June. cryoCARE. Tim Oliver Buchholz.Max
Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany

8th
July. Dynamo. Daniel Castaño. Dynamo.
Biozentrum, University of Basel. Switzerland

With best wishes

I2PC Team

I2PC – Instruct virtual course on Single Particle Analysis by CryoEM. Madrid, 18 – 20 April, 2022

Venue

Remote course
18 – 20 April, 2022 from 09.30-18.00 CET

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.

For logistic reasons and travelling restrictions, 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 I2PC. Although the course is online we will try to keep the interactions 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 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), Roberto Melero (RM), Daniel Marchán (DM), Estrella Fernández (EF), David Herreros (DH), Pablo Conesa (PC), Yunior Fonseca (YF)

Program

Day 1: Data processing

9:30       Morning:

  • Movie alignment, Screening micrographs and CTF
  • Particle picking and screening

13:00    Lunch Break

14:00    Afternoon:

  • Particle picking and screening
  • 2D classification
17:00    End of day

Day 2:

9:30       Morning:

  • Initial volume
  • 3D classification

13:00    Lunch Break

14:00    Afternoon:

  • 3D classification
  • 3D reconstruction
17:00    End of day
   

Day 3: 

9:30       Morning:

  • Validation and analysis

13:00    Lunch Break

14:00    Afternoon:

  • General discussion, open questions

17:00    End of day

 * Virtual machines and I2PC staff will be available
until 17:30 for those who want to access.

REGISTRATION

Registration Fee: 50€ 
Fill  your application here (Regitration closed). 

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

Copyright © 2011-2025 Instruct Image Processing Center I2PC. All rights reserved.