Advanced Light Microscopy and Bioimaging

Course goals

By the end of this course, you should be able to:

1. Explain the properties of light and optical components, such as colour, filters, lenses, geometrical optics, aberration, objectives, diffraction and resolution, in the context of biological imaging
2. Explain the principles of fluorescence microscopy and confocal imaging
3. Solve quantitative problems related to geometrical optics, aberration and light microscopy
4. Construct a simple light microscope from its essential optical components
5. Discuss image formation in terms of spatial frequencies and Fourier optics
6. Recognize the main technical components in an imaging system and their role
7. Compare quantitatively advanced microscopy techniques, such as multiphoton microscopy, SPIM, TIRF, FCS, FRAP, FRET, FLIM and label-free techniques
8. Compare quantitatively super-resolution microscopy techniques, such as expansion microscopy, PALM, STORM, PAINT, SIM, STED, MINFLUX, MINSTED
9. Argue the advantages and challenges of modern light microscopy techniques 
10. Outline the main aspects in digital image analysis, both involving classical methods and AI

Content

Content of the course:
The aim of this course is to help the students build a deep understanding of modern light microscopy techniques and their use in bioimaging. The emphasis will be on the applications to cell biology and structural biology.
The course is divided in two parts. The first part covers the basics of light microscopy, with a part of the lectures in collaboration with the course “Microscopy and Image Analysis” (B-B3MIA22), although more focus on quantitative aspects is stressed. The second part covers advanced techniques, super-resolution methods and image analysis foundations.

The course consists of lectures covering the theory, accompanied by tutorials. In addition, the course provides practicals where the students have the opportunity to get hands-on experience with microscopy techniques and to assist demonstrations of different microscopes. Relation to other courses:
This course builds on the knowledge about biomolecules and cell biology acquired in year one, and the knowledge about molecular biology, biophysics and structural biology in year 2.  This research-oriented course prepares students for many other level 3 courses, bachelor thesis projects and master’s programmes in the direction of molecular cell biology & biochemistry and biophysical methods to investigate biomolecules in the context of cells and organisms.  Teaching format (estimation):
Lectures = 20%
Tutorials = 15%
Practicals = 10%
Presenting = 5%
Writing = 0%
Self-study = 50%
 

1. Digital exam about light microscopy basics (50% of the final grade)
2. Digital exam about advanced light microscopy (30% of the final grade)
3. Mini-conference about advanced light microscopy (20% of the final grade)
4. Attendance of and active participation in the practicals is obligatory. Participation in tutorials is strongly recommended.

A minimum of grade of 5.0 must be obtained for both digital exams. Given the nature of the mini-conference, there is no minimum grade for it, but also no re-take.
The final grade (weighted average of the assessments) should be at least 5.5 in order to pass the course. In case only one of the two digital exams is insufficient, a re-take for that part is possible, otherwise a final comprehensive exam determines the final grade.