Course Introduction to Fluorescence Microscopy

ECTS: 3.9

Course leader: Lene Niemann Nejsum

Language: English

Graduate school: Faculty of Health

Graduate program: ClinFO

Course fee: 4,680.00 DKK

Status: Course is open for application

Semester: Spring 2024

Application deadline: 19/12/2023

Cancellation deadline: 02/01/2024

Course type: Classroom teaching

Start date: 16/01/2024

Administrator: Anne Fabricius

Day 4 and 5 are special

Please note that there will only be 2 hours per group on day 4 or 5 (23 and 24 January); it is not two whole days of teaching! The groups will be decided on course start.

Title: Introduction to Fluorescence Microscopy C267/07

is being offered by the Graduate School of Health, Aarhus University, 2024

Criteria for participation:
University degree in medicine, dentistry, nursing, or master’s degree in other fields and/or postgraduate research fellows (PhD students and research-year medical students).

You must submit a written application when signing up for the course. Please note, that everyone will be placed on waiting list and the seats will be given upon the approval of your application by the course leader.

The aim is to give the participants an overview of basic fluorescence microscopy techniques, sample preparation, image acquisition and imaging analysis.

Learning outcomes:
The students will obtain basic knowledge of different fluorescence microscopy techniques, sample preparation, image acquisition and image analysis. This should enable students to prepare samples for fluorescence microscopy, choose the appropriate microscope setup, acquire images, analyze images and generate publication figures. This will enable students to participate in research projects involving fluorescence microscopy.


  • Overview of basic light and fluorescence microscopy methods including white light microscopy, wide-field fluorescence microscopy and confocal microscopy as well as optics, cameras and photodetectors.
  • Introduction to sample preparation of cells and paraffin embedded tissue sections for fluorescence microscopy (hands on).
  • Introduction to image analysis using ImageJ Fiji; this includes working with multicolor images, background handling and fluorescence quantification (hands on) and
  • Practical demonstration of wide-field fluorescence image acquisition using an inverted, automated microscope.
  • There will be a mandatory home assignment equivalent to 6 h

Recommended knowledge for participation:
This is an introductory course, so no experience with fluorescence microscopy is necessary.     


Head of course:
Lene Niemann Nejsum

Assistant Professor Frédéric H. Login, PhD student Benjamin Bach Green  and PhD student Amalie Grønning 

Time and date:


Note, on the 23-24/1, it will only be 2 h per student.

Venue: Bartholin Læsesal and adjacent laboratories. Forum AUH.

Course fee:
Participation in the course is without cost for:

  • PhD students, Research Year students and Research Honours Programme students from Aarhus University
  • PhD students enrolled at partner universities of the Nordoc collaboration
  • PhD students from other institutions in the open market agreement for PhD courses