• 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. 

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.

The first lecture will be in person. After that we will alternate digital and in person lectures. 

Each week you will have one digital lecture consisting of multiple video recordings to watch and one in person meeting to discuss the video's content and perform exercise.

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

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

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

Lecture 2b. Fundamentals of radiometry and photometry, microscope photometry, detectors, noise

Lecture 3a. Resolution, mathematical representation of the imaging process

Lecture 3b. The Fourier transform and its interpretation, the optical transfer function OTF

Lecture 4a. Continue OTF: for diffraction-limited optics, for 2D, for detectors, for imaging chain

Lecture 4b. Sampling: sampling and aliasing, reconstruction calculations, multidimensional sampling

Lecture 5. Coherent imaging in microscopy, role of condenser numerical aperture

Lecture 6a. Introduction to confocal microscopy

Lecture 6b. Imaging properties of confocal microscopy

Lecture 6c. Confocal microscopy: Limitations and errors, multi-channel detection

Lecture 7a. Super resolution fluorescence microscopy: stimulated emission depletion microscopy (STED)

Lecture 7b. Super resolution fluorescence microscopy: single-molecules based microscopy

Lecture 8. 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 3. Confocal microscopy + Super resolution fluorescence microscopy (4 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.

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.

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. 

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.

Learning outcomes 1-3

(P) complete all labs and report and evaluate the results in a comprehensive way

Learning outcome 4 [SK2501 only]

(P) present a research paper and actively participate in the seminar

Learning outcome 5

(Fx) almost fulfil the requirements for (E)

(E) asses how some of the image quality measures are affected by microscopy parameters, and choose suitable microscopy systems and parameters in some cases.

(D) fulfil the requirements for (E) and partly those for (C)

(C) asses how most of the image quality measures are affected by microscopy parameters, and choose suitable microscopy systems and parameters in most cases

(B) fulfil the requirements for (C) and partly those for (A)

(A) asses how the image quality measures are affected by microscopy parameters, and choose suitable microscopy systems and parameters

Yes

• 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.