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.

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.
• extract relevant information from a scientific publication and present this in the form of a seminar.

Most lectures will be given on campus and some over zoom. Recordings replacing parts of the lectures exist, for when you cannot attend.

Each student will perform four 4-hour laboratory exercises. At a specific date and time, maybe two weeks into the course, the sign-up for labs will open, so that students may sign up for the specific times that suit them best.

Each student will study a scientific paper on a subject relevant to the course, and present it at a seminar. A number of suggestions for papers will be offered but you can also choose your own, if approved by the teacher.

Each student will do a personal project, preferrably closely related to their PhD work.

Lecture 1. Basics of light microscopy: imaging ray-path and illumination ray-path, aberrations,   objective types, magnification, numerical aperture

Lecture 2. Contrast techniques: absorption, fluorescence, phase contrast, DIC, dark-field

Lecture 3. Fundamentals of radiometry and photometry, microscope photometry, detectors, noise

Lecture 4. Resolution, mathematical representation of the imaging process

Lecture 5. The Fourier transform and its interpretation, the optical transfer function OTF

Lecture 6. Continue OTF: for diffraction-limited optics, for 2D, for detectors, for imaging chain

Lecture 7. Sampling: sampling and aliasing, reconstruction calculations, multidimensional sampling

Lecture 8. Coherent imaging in microscopy, role of condenser numerical aperture

Lecture 9. Introduction to confocal microscopy

Lecture 10. Imaging properties of confocal microscopy

Lecture 11. Confocal microscopy: Limitations and errors, multi-channel detection

Lecture 12. Super resolution fluorescence microscopy: stimulated emission depletion microscopy (STED)

Lecture 13. Super resolution fluorescence microscopy: single-molecules based microscopy

Lecture 14. Problem-solving session

Lab 1. Build your own microscope with Koehler illumination (4 hours at AlbaNova)

Lab 2. Practical use of research microscopes in different imaging modes (4 hours at AlbaNova)

Lab 3A. Confocal microscopy (2 hours at AlbaNova)

Lab 3B. Super resolution fluorescence microscopy (2 hours at SCILife)

Lab 4. Analysis and visualization of results from lab 3 (4 hours via zoom)

Two compendia by Kjell Carlsson available via the course canvas page.

Students at KTH with a permanent disability can get support during studies from Funka:

Funka - compensatory support for students with disabilities

Part of the exam will be oral. There are no funka codes related to the spoken format, so if you have such disabilities your case must be handled individually. Please contact Funka or your examiner early on in the course so that Funka and examiner can agree on suitable support in good time before the exam.

P, F

• LAB1 - Laboratory work, 2.0 credits, Grading scale: P, F
• SEM1 - Seminar, 1.5 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 hp, grading scale P/F), completed laboratory course (LAB1; 2 hp, grading scale P/F) and seminar presentation (SEM1; 1.5 hp, grading scale P/F)

Laboratory Experiments ( LAB1 )

Complete all four labs (active participation) and submit a report of sufficient quality to pass pefore deadline.  You will receive feedback and have a chance to re-submit the report.

Seminar ( SEM1 )

There will be several seminars and you should attend one, where you present a paper and participate in the discussion of the other papers. The specific times, and which seminar to attend, will be determined after discussion with the students.

Examination ( TEN1 )

The examination will happen in two steps:

1. Oral exam via zoom, 30 min per student. If you pass you get the grade E on the course.

2. If you pass the oral exam, you will be offered the chance of a written home exam to improve your grade to D, C, B, or A. The home exam will be three hours long and distributed via Canvas.

As far as possible the exam will happen during the scheduled hours. If you cannot attend at the scheduled time, perhaps due to exams on other courses, contact the examiner and we will try to find a solution. 

• 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.