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FSK3500 Physics of Biomedical Microscopy 6.0 credits

The course covers the physics and technology of microscopic imaging methods, with special emphasis on applications within the life sciences. It is similar to the second level course SK2500, except on the PhD course you also do a small project (preferrably related to your research).

Course offerings are missing for current or upcoming semesters.
Headings with content from the Course syllabus FSK3500 (Spring 2019–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

Basic optical layout of the light microscope. Aberrations. Microscope objectives. Magnification. Numerical aperture. Microscope photometry. Detectors. Noise. Contrast methods (fluorescence, phase contrast, DIC). Resolution. Fourier methods. Optical transfer functions. Three-dimensional imaging in microscopy. Sampling and reconstruction of image data. Confocal microscopy. A brief introduction to tunnel and atomic force microscopy, electron microscopy, scanning near-field optical microscopy and X-ray microscopy.

Intended learning outcomes

After completing the course the student should be able to:

  • adjust the illumination system to obtain optimal performance in transmission microscopy.
  • select a suitable light source and optical filters, and correctly adjust the illumination system for fluorescence microscopy.
  • select a suitable objective (correction, immersion etc) for various types of microscopic investigations.
  • select a suitable contrast method (phase contrast, DIC, fluorescence, darkfield etc) and correctly use this technique to obtain high-quality images.
  • calculate the expected image quality regarding resolution and signal-to-noise ratio for different practical imaging situations.
  • understand and be able to describe the physical limitations for microscope performance concerning resolution and signal-to-noise ratio.
  • describe performance for different types of microscopes by using (and in some simple cases calculating) optical transfer functions.
  • select a suitable sampling density for digital image recording in microscopy.
  • do computer processing of microscopic images to visualise three-dimensional structures.
  • perform quantitative measurements in microscopic images using a computer.

Literature and preparations

Specific prerequisites

Admitted to PhD studies in Physics or related fields of study.

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

Recommended prerequisites

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Carlsson, K. Imaging physics, KTH.
Carlsson, K. Light microscopy, KTH.
Lab. instructions.

Examination and completion

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

Grading scale

P, F


  • LAB1 - Laboratory work, 2.0 credits, grading scale: P, F
  • TEN1 - Exam, 4.0 credits, grading scale: P, 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.

Written examination (TEN1; 4 credits, grading scale P/F) and completed laboratory course (LAB1; 2 credits, grading scale P/F).

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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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

This course does not belong to any Main field of study.

Education cycle

Third cycle

Add-on studies

No information inserted


Anna Burvall (

Postgraduate course

Postgraduate courses at SCI/Applied Physics