Course detail

Microscopic Imaging Technology

FEKT-MPC-MZTAcad. year: 2022/2023

The course will be a detailed overview of the principle and practice of light microscopy. The emphasis of the course will be on the correct and appropriate use of the light microscope. Course covers optical microscope theory and also advanced optical and imaging techniques.

Learning outcomes of the course unit

The student is able to:
- describe spatial transfer of the electromagnetic wave,
- list and explain meaning of its parameters,
- define the main optical laws,
- apply Fresnel coefficients for specific case,
- describe simple optical system by matrix notation,
- describe the principle of light microscope,
- discuss the function of specific microscopy components,
- revise basic optical abberations and their influence on image quality,
- compare the properties of polarization, dark-field, phase and Nomarsky contrast microscopy techniques,
- describe the fluorescence microscope and its application,
- describe the confocal microscope and its application,
- explain physical principle of two-photon microscopy,
- explain TIRF microscopy,
- discuss, compare and select the optimal light detecion method,
- choose appropriate microscopy technique for specific application.


Student should be able to define basic optical laws and should be able to mathematicaly describe electromagnetic field. The mathematical background from matrix theory is also required.


Not applicable.

Recommended optional programme components

Not applicable.


D. B. Murphy Fundamentals of light microscopy and electronic imaging, Wiley-Liss, 2001
P. Mouroulis Visual Instrumentation, McGraw-Hill, 1999
J. Kuběna, Úvod do optiky, MU Brno 1994, skriptum
Murphy,D.B.: Fundamentals of light microscopy and electronic imaging, Wiley, 2011 (CS)
Sharma, K.K.: Optics: Principles and Applications, Academic Press, 2006 (CS)

Planned learning activities and teaching methods

Techning methods include lectures and practical laboratories. Course is taking advantage of e-learning (Moodle) system. Students have to write 10 assignment during the course.

Assesment methods and criteria linked to learning outcomes

Laboratory work: 0 - 40 points
Final exam: 0 - 60 points
Final exam is focused on testing the knowledge from the light microscopy imaging.

Language of instruction


Work placements

Not applicable.

Course curriculum

1. Fundamentals of wave and geometry optic.
2. Fresnel coefficients.
3. Matrix description of the optic systems.
4. Eye as an optical system.
5. Basic microscopy design concept.
6. CCD, CMOS sensors, photomultiplier, Avalanche diode, hybrid detectors its principle and parameters.
7. Dark field microscopy.
8. Phase contrast microscopy.
9. Stereomicroscopy.
10. Nomarsky differential interference contrast microscopy.
11. Hoffman modulation contrast microscopy.
12. Fluorescence microscopy.
13. Laser scanning (confocal) microscopy.
14. 2-photon and multi-photon microscopy. TIRF microscopy.
15. Optical coherent microscopy.
16. Selected fluorescence microscopic techniques.
17. Advanced and superresolution techniques - STED, STORM/PALM, SIM.
18. Basic of electron microscopy.


The main aim of this course is to provide basic orientation in the light microscopy imaging, selected imaging techniques, its principles and its medical and biological applications.

Specification of controlled education, way of implementation and compensation for absences

Labs are obligatory. The properly excused missed laboratory exercise is to be replaced after agreement with the teacher during last week of the semester.

Classification of course in study plans

  • Programme MPC-BTB Master's, 2. year of study, winter semester, 5 credits, compulsory

Type of course unit



39 hours, optionally

Teacher / Lecturer

Laboratory exercise

26 hours, compulsory

Teacher / Lecturer