1.
a) What are the advantages of performing image processing calculations in reciprocal space over real space? Which operations are better done in real space, and which are better done in reciprocal
space?
b) What are the major considerations in preparing biological samples for cryo-EM?
c) Explain the differences between an isosurface view, a projection, and a density section.
2.
a) What are the important considerations for the characteristics of electron detectors to be used in
high-quality data collection? Explain why the considerations you have chosen are important.
b) What are the main microscope factors that affect the quality of cryo-EM images and how are their
effects corrected?
c) What are the main sample factors that determine the quality of the final results, and how can the common problems be addressed?
3.
a) When carrying out image processing in 2D, how can (i) the signal-to-noise ratio and (ii) the contrast in cryo-EM be improved? Why is this necessary?
b) Define the point spread function (PSF) and the contrast transfer function (CTF). Explain how they are related, and explain how they can be used in cryo-EM image analysis.
4.
a) Explain the principles and image processing steps for determining a 3D density map from TEM single-particle images in the case of an unknown structure.
b) Discuss how you would establish if the details of the experimentally determined map are correct.
5. What are the key considerations in determining the in situ structure of a cellular complex that is assembled only in its native cellular environment?
Your answer should take into account sample preparation, data collection, and image processing aspects. Think about what compromises might be needed to optimize the result and explain the reasons for your choices.
6. Explain how you would fit an atomic model to a cryo-EM map and how you would validate your fit, for a map at
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