autumn 2022
FYS-3029 Optical nanoscopy - 10 ECTS

Application deadline

Applicants from Nordic countries: 1 June for the autumn semester and 1 December for the spring semester. Applicants from outside the Nordic countries: 1 October for the spring semester and 15 April for the autumn semester.  

Type of course

The course is available as a singular course. The course is also available to exchange students and Fulbright-students. The course will only be taught if there is a sufficient number of students. If you are interested in following the course, please contact the student advisor as soon as possible  

Admission requirements

Admission requirements are a Bachelor's degree in physics or similar education, including specialization in physics worth the equivalent of not less than 80 ECTS credits. Local admission, application code 9371 - singular courses at Master's level. 

Course overlap

If you pass the examination in this course, you will get an reduction in credits (as stated below), if you previously have passed the following courses:

FYS-8029 Optical nanoscopy 8 stp

Course content

The objective of this course is to provide education and training on state-of-the-art optical super-resolution imaging techniques. The emerging field of super-resolution optical microscopy is commonly referred to as optical nanoscopy. The focus will be on structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM) techniques.

The course will provide theoretical and practical training on the state-of-the art optical nanoscopy techniques. The teaching will be given as lectures, demonstrations, and practical sessions. Students will be provided opportunities to image their own sample (within limitations) using state-of-the-art SIM and dSTORM microscopes to be installed at UiT. Optical nanoscopy has had an impact in several disciplines. Similarly, this course is planned to be cross-disciplinary and it is suitable for candidates with different backgrounds, such as physics, biology, medicine, fisheries, pharmacy, who are interested to learn or use the emerging field of optical nanoscopy.

The contents of the course are:

  • Introduction to fluorescence based optical imaging techniques
  • Diffraction limit and its implication in bio-imaging application
  • Overview of existing optical nanoscopy techniques
  • Opportunities and limitations of different optical nanoscopy techniques, (SIM, STED, dSTORM).
  • Theory and background of direct stochastic optical reconstruction microscopy (dSTORM)
  • Theory and background of Structured illumination microscopy
  • Practical hands-on training on using dSTORM to acquire super-resolved optical images, small groups (each consisting of 3-5 students)
  • Practical hands-on training on using SIM to acquire super-resolved optical images of live and fixed cells, small groups (each consisting of 3-5 students)
  • Training on data analysis and post-acquisition image processing for 3D image rendering for SIM and d-STORM using Image J/Fiji or Volocity

The course will provide brief overview on image formation and microscopy before venturing into the arena of super-resolution optical microscopy.  The course will be given at both Master and PhD level. For Master level, cell staining, image acquisition, 3-D data rendering will not be mandatory and practical hands-on training will be less extensive. Practical training on SIM and dSTORM will be more extensive at PhD levels.  

Recommended prerequisites

FYS-1002 Electromagnetism, FYS-1003 Basic experimental physics

Objectives of the course

Knowledge - The student can:

  • understand the implication of diffraction limits of conventional fluorescence microscopy
  • evaluate the advantages and limitation of various optical nanoscopy techniques
  • understand the underlying principles of SIM and dSTORM

Skills - The student can:

  • gain basic skills to use and operate commercial SIM and d-STORM system to acquire super-resolved optical images
  • gain practical skills on image rendering using Fiji/ImageJ/Volocity

General competence - The student can:

  • familiarize with optical microscope and fluorescence imaging techniques
  • appreciate the multi-disciplinary research opportunities available at the cross-roads of biology and physics  

Language of instruction and examination

The language of instruction is English and all of the syllabus material is in English. Examination questions will be given in English, but may be answered either in English or a Scandinavian language.

Teaching methods

Lectures: 20 hours

Exercises: 20 hours

The course will be given in two extensive modules, each consisting of one week.  

Information to incoming exchange students

This course is open for inbound exchange student who meets the admission requirements. Please see the Admission requirements' section.

Do you have questions about this module? Please check the following website to contact the course coordinator for exchange students at the faculty:


Examination: Date: Weighting: Grade scale:
Off campus exam 21.11.2022 14:00 (Hand in) 4/10 A–E, fail F
Oral exam 01.12.2022 09:00
6/10 A–E, fail F

Coursework requirements:

To take an examination, the student must have passed the following coursework requirements:

Lab course Approved – not approved
UiT Exams homepage

More info about the coursework requirements

Coursework requirements: Participation in laboratory course.

Re-sit examination

There is no access to a re-sit examination in this course
  • About the course
  • Campus: Tromsø |
  • ECTS: 10
  • Course code: FYS-3029
  • Tidligere år og semester for dette emnet