The 9th Brazil School for Single Particle Cryo-EM will follow the successful pattern of the previous school in this series that was interrupted by five years due to the Covid-19 pandemic.
The course participants will learn the processing of single particles from optimizing the data collection and automatic particle selection, through the pre-processing, 2D-3D particle alignments, 3D reconstruction, 4D image analysis of data-sets with mixed populations, up to the interpretation of the data and fitting of known X-ray structures.
The Multivariate-Statistical-Analysis (MSA) plays a crucial role in most aspects of the data processing. This year, special emphasis will also be placed on new fundamental insights in the Foundations of Physics that surfaced with the advanced use of new sensors that allow the detection of each individual electron arriving in the sensor.
Continuous parallel stereo pictures of a SARS-Cov2 spike protein where every neighbouring pair of images form a stereo pair
The SARS-Cov2 spike protein is here coloured by a new local-information density metric that emphasises the local stability of the Spike-protein trimer
Check the Brazil School Website for details about the previous editions of The Brazil School for Single Particle Cryo-EM.
Venue: Eco-Resort Refúgio Cheiro de Mato / Mairiporã – SP
Target Audience
• Recommended for undergraduate and graduate students (Master’s and PhD), postdoctoral researchers and professionals in the fields of physics, chemistry, engineering and materials science.
Registration Fee
- Shared double room: 7.800,00 (BRL)
Includes: registration, lodging, meals and shuttle service (see detailed info on the registration menu)
REGISTRATIONS ARE NOW OPEN
General Information
- Language: The official language of The 9th Brazil School for Single Particle Cryo-EM is English.
- Computer Requirements: Participants are strongly encouraged to bring a well-equipped gaming (mini) computer to install the necessary software, which they can later use in their own lab. A document detailing the required computing hardware will be provided soon.
- Dataset Suggestion: Participants should consider bringing one (large) dataset of particular interest for practical work during the school.
Main Lecture Topics
Distributed over various speakers and various lectures:
- Specimen preparation for single-particle Cryo-EM.
- Optimizing the EM data collection.
- Filtering and data normalization.
- Basic Linear Algebra.
- What hardware is needed for the processing of large Cryo-EM data sets?
- How to coherently organise your data.
- What is Information in measurements (and not just in EM)?
- The Fourier transform in 1D – 2D – 3D.
- What is 4D processing?
- Properties of the Fourier transform.
- Multivariate Statistical Analysis.
- Unsupervised automatic classification.
- The principles of Eigen-Filtering.
- Automatic Particle selection.
- Is particle selection by AI (“Artificial Intelligence”) a good idea?
- CTF correction using the cos2 approach.
- Alignment using correlation functions.
- Multi-reference alignments in 2D.
- Multi-reference alignments in 3D.
- Angular reconstitution: a-posteriori Euler angle determination.
- What are Maximum Likelihood approaches?
- Exact-Filter Three-dimensional reconstruction.
- Projection matching.
- Alignment refinements.
- 3D refinements.
- 1D/2D/3D resolution and Information criteria.
- 3D fitting of known X-ray structures (Chimera, Coot).
- Refining towards different 3D structures simultaneously (“4D” analysis).
- Using image processing software (IMAGIC-4D, plus any other useful software).
- Parallel processing using MPI.
- Are GPUs good for Cryo-EM data processing?
- What are the advantages of Single-Electron counting?
- What are the theoretical limits of Single-Electron counting?
Guest speakers
International lecturers and instructors:
- Michael Schatz, Germany
- Pavel Afanasyev, Switzerland
- Deborah Mendonça, Spain
- Rodrigo Portugal, Brazil
- Gabriela Noske, Brazil
- Gabriel Schleder, Brazil
- Elena Orlova, USA
- Misha Kudryashev, Germany
*Important: Speakers and the schedule are subject to change up until the day of the event.
Organization
Scientific Coordinator
Marin van Heel
Local Committee
CNPEM – School Administration