I2PC – Instruct-RI Hubs hybrid course on Electron Tomography and Subtomogram Averaging. Madrid, December 10 – 13, 2024

VENUE

Hybrid course.
December 10 – 13, 2024 from 16:00 to 21:30 CET.
You do not need to install any special software to connect. A modern browser should be enough.

Overall aims and course outline

By using image processing algorithms, it becomes possible to pinpoint the macromolecules of interest within the electron tomograms. Subsequently, researchers can extract small subtomograms from these locations and identify similar particles, facilitating their averaging and the recognition of diverse conformations. This process, referred to as subtomogram averaging, has played a pivotal role in elucidating an increasing number of macromolecular structures, achieving resolutions ranging from 20 to 3 A.

The course is designed to offer a comprehensive overview of the whole image processing workflow in Electron Tomography (ET). This includes tasks such as aligning the tilt series, reconstructing 3D tomograms, identifying particles, performing subtomogram averaging or even to perform a tomogram segmentation, all inside Scipion integration framework.  

With the experience gained in the organisation of virtual and in-person courses, we intend to organise this course in a hybrid format. We will be able to accommodate up to 20 individuals for in-person attendance. However, other 20 participants will attend remotely. In total, we can host 40 attendees. 

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 coffee breaks

Tutors: I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, Jorge Jiménez & Jose Luis Vilas.
CryoEM CNB-CSIC: Francisco Javier Chichón.
Contacts: Lead contact:  Carlos Oscar Sorzano
E-mail: coss@cnb.csic.es
Administrative Contact: Blanca Benitez & Oscar Saiz
E-mail: blanca@cnb.csic.es; oscar.saiz@cnb.csic.es

Agenda

 Times are expressed in CET time Zone

DAY 1: 

From movies to tomograms

15:00 – Welcome – (José Maria Carazo & Carlos Oscar Sorzano)
15:15 – Introduction to Electron Tomography – (José Luis Vilas)
15:35 – Course Introduction (Machines & Scipion) – (Pablo Conesa)
16:00 – Import Tilt Series, Automatic alignment – (José Luis Vilas)
17:00 – 15 minutes break
17:15 – CTF estimation and correction – (José Luis Vilas)
18:30 – Tomogram reconstruction – (José Luis Vilas)
20:00 – eTomo – (José Luis Vilas)
20:30 – End of session

DAY 2: 

From tomograms to subtomograms: Picking

15:00 – Non-directional picking with cryolo and SPA leap – (Pablo Conesa)
17:00- 15 minutes break
17:15 – Dynamo – (Pablo Conesa)
20:30 – End of session

DAY 3: 

Processing subtomograms

 15:00 – Classic Subtomogram averaging – (Jorge Jiménez)
16:00 – Subtomogram averaging with RELION5 (I) – (Jorge Jiménez)
17:00- 15 minutes break
19:00 – Subtomogram averaging with EMAN (I) – (Jorge Jiménez)
20:30 – End of session

DAY 4: 

Tomogram interpretation

15:00 – Tomogram segmentation: SuRVos– (Javier Chichón)
20:30 – End of course. Wrap up

Registration Fee

ACOMMODATIONS

REGISTRATION

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