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

Ideally combined with A410 Molecular Electron Tomography (Skoglund)