SK2501 Physics of Biomedical Microscopy, Extended Course 7.5 credits

Bildfysik med inriktning mot biomedicinsk mikroskopi, utökad kurs

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

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Course information

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.

Course Disposition

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Literature and preparations

Specific prerequisites *

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

Recommended prerequisites

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Equipment

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Literature

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Examination and completion

Grading scale *

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

Examination *

  • 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 *

Written examination (TEN1; 4 hp, grading scale A/B/C/D/E/Fx/F), completed laboratory course (LAB1; 2 hp, grading scale P/F) and seminar presentation (SEM1; 1.5 hp, 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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Examiner

Anna Burvall

Further information

Course web

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.

Course web SK2501

Offered by

SCI/Applied undergraduate Physics

Main field of study *

Biotechnology, Engineering Physics, Physics

Education cycle *

Second cycle

Add-on studies

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Contact

Anna Burvall (anna.burvall@biox.kth.se),

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.