Electron Microscopy

Course Aim

This course provides an introduction into electron microscopy techniques and applications in biology. Participants will obtain the background knowledge for critical reading of current literature and will be exposed to practical exercises in image processing.

Course Description

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.

Course Contents

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%.

Prerequisites or Prior Knowledge

Undergraduate mathematics.


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

Reference Books

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.

Research Specialties