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?

• Two or three morning lectures

• Hands-on single particle analysis

• Lunch

• Open afternoons / Time for additional workshops

• Evening lectures / Hands-on processing

• Dinner

• Open program after dinner

Note: The programme is always tentative and each day’s programme will be adapted to the actual needs of The 9th Brazil School for Single Particle Cryo-EM.