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.
- a VNC client is recommended
- otherwise familiarize yourself with no VNC
- We will provide launch and coffee breaks
Tutors: | I2PC: Carlos Oscar Sorzano Sánchez, Jose-María Carazo, Pablo Conesa, David Herreros, Jorge Jiménez, Patricia Losana, Jose Luis Vilas, Ana Cuervo. CryoEM CNB-CSIC: Francisco Javier Chichón. |
Contacts: | Lead contact: Carlos Oscar Sorzano E-mail: coss@cnb.csic.es Administrative Contact: Blanca Benitez E-mail: blanca@cnb.csic.es |
Agenda
DAY 1: Tomogram reconstruction |
16:00 – Welcome – (Jose Maria Carazo & Carlos Oscar Sorzano) |
DAY 2: Particle Picking methods |
16:00 – Particle identification: different strategies, particle filtering according to their orientation in the tomogram– (David Herreros, Jorge Jiménez) |
DAY 3: Subtomogram Averaging techniques |
16:00 – Subtomogram averaging– (Ana Cuervo, Patricia Losada) 19:00- Break 20:00 – Particle filtering using strategies based on the subtomogram averaging and mapping back subtomograms– (Ana Cuervo, Patricia Losada) 21:30 – End of session |
DAY 4: Tomogram segmentation |
16:00 – Tomogram data analysis and representation– (Javier Conesa, Javier Chichón, Jose Luis Vilas) |