The course is designed as a mix of introductions into selected topics in the theory of transmission electron microscopy followed by practical demonstrations and hands-on exercises, which provide an opportunity to comprehend the concepts by experimenting with commonly-used image processing software. Students will be required to read and digest scientific papers for a subset of lecture topics on their own, which will subsequently be discussed jointly during student presentations with the goal to immerse them into the subject without passive consumption. The lectures cover several important concepts of the physics of image formation and analysis, which require a basic level of mathematics. An emphasis will be given to highlighting common properties between diffraction and image data and how to take advantage of tools from both techniques during the final image processing projects.

History of the TEM / Design of a TEM Lecture

Design of a TEM (cont’d) Lecture

Design of a TEM (cont’d) Lecture

Demonstration of a TEM Demo

Math refresher / Electron waves Lecture

Fourier transforms Lecture

Intro to image processing software in SBGRID Practical

Image alignment Practical

Contrast formation and transfer Lecture

Image recording and sampling Student presentation

Applications in biology Lecture

Preparation of biological samples Demo

Low-dose cryo-EM Student presentation

2D crystallography Student presentation

Overview of the single particle technique Lecture

Review of theory Lecture

Electron tomography (guest lecture) Lecture

Physical limits to cryo-EM Student presentation

Particle picking Practical

Classification techniques Student presentation

3D reconstruction Student presentation

Image processing project 1 Practical

Resolution-limiting factors Student presentation

Refinement and sources of artifacts Student presentation

Image processing project 2 Practical

A sampling of original literature Discussion

Participation 30%; Presentation, 30%; Practical Exercises 30%.

Transmission Electron Microscopy: A Textbook for Materials Science (4-vol set), by Williams and Carter (2009) Springer

Three-Dimensional Electron Microscopy of Macromolecular Assemblies, 2 edn, by J Frank (2006) Oxford University Press

Transmission Electron Microscopy: Physics of Image Formation and Microanalysis, 4th edn, by L. Reimer (1997) Springer

Introduction to Fourier Optics, 3 edn, by J Goodman (2004) Roberts & Co.