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Graduate courses

Departments' graduate courses for PhD-students.


Syllabus for

Academic year
TIF045 - Molecular microscopy
Syllabus adopted 2014-02-24 by Head of Programme (or corresponding)
Owner: MPBIO
7,5 Credits
Grading: TH - Five, Four, Three, Not passed
Education cycle: Second-cycle
Major subject: Bioengineering, Engineering Physics

This course round is cancelled

Teaching language: English
Open for exchange students

Course module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 Summer course No Sp
0105 Project 7,5c Grading: TH   7,5c    

In programs



Bitr professor  Annika Enejder


In order to be eligible for a second cycle course the applicant needs to fulfil the general and specific entry requirements of the programme that owns the course. (If the second cycle course is owned by a first cycle programme, second cycle entry requirements apply.)
Exemption from the eligibility requirement: Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling these requirements.

Course specific prerequisites

Fundamental knowledge in optics is advantageous but not required, as a voluntary introduction seminar will be given.


The course provides theoretical as well as practical know-how in modern microscopy, inviting the student to the nano-scale worlds of physics, chemistry, bio- and material sciences. An overview over the different light-matter interaction mechanisms in the focal volume will be given, and how this information is passed on as an image from the micro- to the macro-world by an optical system. In particular, we will address how structures and single molecules can be selectively imaged using various microscopy techniques.

Learning outcomes (after completion of the course the student should be able to)

  • explain how a 3-dimensionell, highly resolved image is created in a modern microscope;
  • identify important components of a microscope after hands-on training, including sources and detectors;
  • set up and use a modern microscope typically found at the bio-labs today: wide-field, dark-field, polarization, DIC and fluorescence microscopes will be available for practical training.
  • describe the wide range of light-matter interaction processes occurring in the sample probe volume forming the actual image contrast;
  • identify suitable microscopy technique for different biological samples from the many novel microscopy techniques currently emerging within the exciting inter-disciplinary field of physics and molecular cell biology: FRET, FLIM, TIRF, TERS, multi-photon fluorescence microscopy, Second and Third Harmonic Generation microscopy, Coherent anti-Stokes Raman scattering (CARS) microscopy, etc.;
  • prepare and handle biological samples for microscopy;
  • plan, perform, present and criticize research projects conducted in groups of 2-3 students using a research microscopy technique.


The topics of the course are:

  1. An introduction to the fundamentals of optics and photonics also for non-physicists.
  2. The theory of image formation in a microscope
  3. Three dimensional microscopy: wide-field/deconvolution, confocal, structured illumination and non-linear microscopy
  4. The Microscopy Workshop - microscopy in practice
    a. The anatomy of a modern microscope: the optics, different objectives, polarizers, filters and the DIC prism
    b. The anatomy of a modern microscope: from light sources to detectors
    c. Hands-on training: Koehler illumination, wide-field, dark-field, polarization, DIC and fluorescence microscopy
  5. The physics in the microscope probe volume
    a. Visualizing the invisible - contrast mechanisms: absorption, refractive index, polarization, electron density etc.
    b. Molecular microscopy: fluorescence, vibrational and non-linear effects
  6. Fluorescence microscopy in contemporary cell biology: sample preparation, fluorescent markers such as GFP and emerging alternatives, applications also including advanced techniques such as FLIM and FRET.
  7. Research projects involving for instance one of the following techniques:
    a. Multi-photon fluorescence microscopy
    b. Fluorescence lifetime imaging - FLIM
    c. CARS - Coherent anti-Stokes Raman scattering microscopy
    d. Second and Third Harmonic Generation microscopy
    e. Surface plasmon resonance and nano-particle imaging
    f. Video-rate fluorescence microscopy
  8. Oral presentations of the research project, including scientific discussions
  9. Scanning-probe microscopy techniques


The teaching will be given as lectures by invited experts on the different topics. The most recent research literature will be discussed in Journal Clubs. Computer exercises using the "Virtual Microscope" will provide an understanding for the fundamental properties of light propagation and optics in a microscope. This will be combined with practical exercises in conjunction with the Microscopy Workshop and a research project. The research project will be presented orally in a whole-class setting. Attendance on all activities is compulsory, which will be met by a flexible schedule. The number of attendants is limited to 20 students for practical reasons.


Material will be handed out at the lectures and can also be downloaded from "Introduction to Optical Microscopy, Digital Imaging, and Photomicrography"

For the interested reader: Handbook of Biological Confocal Microscopy (Kluwer Academic Publishers), James B. Pawley (Editor), 2006


A home exam, covering the basic concepts, will be handed out after the first four weeks. The results of this exam will together with the performance and presentation of the research projects, including active participation in the discussions, form either of the grades fail, 3, or 4. If the students want to candidate for a grade 5, an oral exam has to be passed clearly showing deep insights and interest in all topics covered by the course.

Page manager Published: Thu 04 Feb 2021.