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SK2501 Physics of Biomedical Microscopy, Extended Course 7.5 credits

This course is an extended version of SK2500 which includes a seminar on modern microscopy methods and applications recently published.

About course offering

For course offering

Autumn 2024 Start 28 Oct 2024 programme students

Target group

For all programs as long as it can be included in your programme.

Part of programme

Master's Programme, Engineering Physics, åk 1, TFYE, Conditionally Elective

Master's Programme, Engineering Physics, åk 2, TFYE, Conditionally Elective


P2 (7.5 hp)


28 Oct 2024
13 Jan 2025

Pace of study


Form of study

Normal Daytime

Language of instruction


Course location


Number of places

Places are not limited

Planned modular schedule


For course offering

Autumn 2024 Start 28 Oct 2024 programme students

Application code



For course offering

Autumn 2024 Start 28 Oct 2024 programme students


Anna Burvall (,


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Course coordinator

No information inserted


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Headings with content from the Course syllabus SK2501 (Autumn 2023–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

  • The basic layout of the light microscope as consisting of a microscope objective and an eye-piece, and their properties such as aberrations, magnification, numerical aperture, and field of view.
  • Different methods for obaining contrast in a microscope, such as absorption, fluorescence, and phase-contrast methods.
  • Different image-quality measures such as resolution, contrast, signal-to-noise ratio (SNR), modulation transfer function (MTF), sampling density, field of view, and depth of field.
  • Layout of the illumination systems, particularly Köhler illumination for transmission and epi-fluorescence microscopy, and how the illumination system can be used to optimize image quality. 
  • How properties of the microscope and illumination system affect image quality such as resolution and contrast, mainly via Fourier methods including point-spread functions (PSF) and optical transfer functions (OTF, MTF).
  • How the choice of detector affects image quality measures such as signal-to-noise (SNR) and sampling. How to sample to avoid loss of information and artefacts. Some microscope photometry.
  • The basic layout for confocal microscopy and hence three-dimensional imaging, including resolution and sampling in different dimensions.
  • The basics of nanoscopy and imaging beyond the classical resolution limit. 

Intended learning outcomes

After completing the course the student should be able to:

  • adjust the microscope and the illumination system to obtain optimal performance in transmission and fluorescence microscopy.
  • select suitable contrast methods and microscope objectives for standard microscopic samples.
  • perform and report quantitative microscopic measurements, including image computer processing and 3D visualization.
  • extract and comprehensively present relevant information from a scientific publication.
  • assess how different image quality measures are affected by physical limits connected to choices of microscopes and imaging parameters, and use this knowledge to choose suitable settings in new imaging experiments.

Literature and preparations

Specific prerequisites

English B / English 6

Recommended prerequisites

Basic knowledge of waves, geometrical optics and photometry (course SK1100 or similar). Elementary knowledge of the Fourier transform.


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Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

A, B, C, D, E, FX, F


  • LAB1 - Laboratory Experiments, 2.0 credits, grading scale: P, F
  • SEM1 - Seminar, 1.5 credits, grading scale: P, F
  • TEN1 - Examination, 4.0 credits, grading scale: A, B, C, D, E, FX, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Other requirements for final grade

The course is examined through a combination of oral and written examination (TEN1; 4 credits, grading scale A/B/C/D/E/Fx/F), as well as approved labs (LAB1; 2 credits, grading scale P/F), and a seminar presentation (SEM1; 1.5 credits, grading scale P/F). The grade for TEN1 determines the grade for the course.

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination



Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study

Biotechnology, Engineering Physics, Physics

Education cycle

Second cycle

Add-on studies

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Anna Burvall (,