Cross Institutional Bioimaging PhD Course

Next time: Fall semester 2019, 9 lectures

Example of the course program for the Spring semester 2018.

Locations: Copenhagen, Odense, Århus, Kng. Lyngby. (Transportation expenses are not covered by the course)

Language: English
Level of course: PhD course

No. of contact hours 72
Capacity limits: 20



Objectives of the course:

The Cross Institutional Bioimaging Ph.D. course is interdisciplinary and cross-institutional and will be given by a series of lecturers who are experts within each their field of bioimaging. The course will take place at different institutions in order to expose the students to different research groups, their researchers and experimental research facilities. The course will thus give the students a unique opportunity of orienting him or herself within an active and diverse field of interdisciplinary science within bioimaging.

The course is relevant for PhD students within medicine, physics, chemistry, biochemistry, molecular biology, nano-bioscience, pharmaceutical sciences, agricultural science or biology. The emphasis of the course is a tour of all bioimaging techniques available in Denmark and will cover subjects like live cell imaging, spinning disk microscopy, electron microscopy, photoactivated localization microscopy, single particle techniques, structured illumination, stimulated emission depletion microscopy, imaging of neurons and cell migration. 

Time schedule for the course in 2018:

The course starts January 30th 2018, and consecutive Tuesdays for 9 weeks at 4 different universities and by different lecturers. Each day of the course covers around 8 hours, from 09:30-17:30. In general, the morning session will consist of a set of lectures and the afternoon session will predominantly involve either the student's active participation in experiments, specific numerical exercises, or inspection of the local experimental facilities. Program.

Course credit and evaluation

The workload of the course corresponds to 9 ECTS points, the total workload includes reading material for each lecture and the preparation of the final talk (presentation). Credit for the course requires the student's presence at 7 of 9 lectures. For missed lectures students will have to write 3 page reports on the topic of the missed lecture. Also the students presence on the exam is mandatory.

The course is evaluated with: Internal oral examination with co-examiner assessed passed/not passed at KU and SDU depending where for students it is more convenient. 20 minutes presentation of a project and 15 minutes questions from examiners and from a student opponent. Each student has to be an opponent for one presentation of another student. In the presentation each student has to present a description of an experiment using one of the applications described in the course and include an image analysis strategy. The task for the presentation will be given in advance (on the last lecture day the 20th of March).

In order to get credits for the course, every student has to be present at all the other students' talks in their session (at KU / SDU) on the exam day.

Registration and transportation: Registration is open by email to



PhD course for students with Master Degree in Physics, Engineering, Life Science, Biology, Medicine Accepted at a PhD program

Course responsible:

Eva Arnspang Christensen and Jonathan Brewer (SDU)


(AU) Lene Niemann Nejsum, Morten Nielsen, Victoria Birkedal

(DTU) Rasmus Reinhold Paulsen, Anders Nymark Christensen, Anders Bjorholm Dahl

(KU) Clara Prats, Klaus Qvortrup, Henrik H. El Ali, Sune Darkner, Jon Sporring

(SDU) Eva Arnspang Christensen, Martin Hedegaard, Jonathan Brewer

Will be announced every week during the course.

Course homepage:
All materials will be published on the open black board platform (SDU).

If you have any questions, please contact Vita Solovyeva, Email:


Short lecture description

Electron microscopy:  Klaus Qvortrup

The course provides an introduction to the essential grounding in the basic principles of electron microscopy, covering topics such as electron optics, electromagnetic lenses, principles of transmission and scanning electron microscopy, electron sources, vacuum systems, specimen-electron interactions and diffraction. The state-of-the-art facilities available at CFIM allow for a strong practical element of demonstrations of both cryo- and room temperature electron microscopy. The course will be run by experienced microscopists in a relaxed atmosphere with the aim of promoting discussion and exchange of ideas between students and tutors. 

Single particle & Fluorescent Proteins: Morten Nielsen

In this lecture we will focus on how to study receptor trafficking using imaging technologies. We will go through methods to follow endocytic receptors from the surface and through the endo-lysosomal system and demonstrate how we analyse if receptors are transcytosed in polarised endothelial and epithelial cells. 

Confocal Microscopy: Clara Prats

Students will be introduced to the Principles and Essentials of Single Point Scanning Microscopy.  Lectures and hands-on practical exercises will be combined to teach the students the critical components of a Confocal Microscope and, how to properly construct imaging light paths and settings to avoid artifacts and collect proper bioimaging data

The basic principals of non invasive imaging modalities and their in vivo applications in preclinical research: Henrik H. El Ali

The course session provides an introduction to the technique of non invasive 3D imaging modalities (such as PET/SPECT/CT/MRI) and what applications it can be used for in the field of molecular imaging. The aim is to provide the students with basic knowledge about the different non invasive imaging techniques and how to use/select right technique for different applications.

The basic physical principles, instrumentations including data acquisition and image formation, post-processing, displaying of the images will be covered in the morning session.  In the afternoon session, factors affecting image quality and quantification will be discussed. In addition, hands-on practical exercises related to clinical and preclinical applications will be provided to promote discussion and exchange of ideas between students about the selection of “best” imaging technique application for their own research field. In the end of the course session the students will improve their ability to understand the limitation of the different imaging technologies and be able to properly select the imaging technique that best answer their scientific question.

Fluorescence Microscopy, two photon and Image Analysis Jonathan Brewer & Eva Arnspang Christensen

Photoactivatable localization microscopy (PALM) is a recent developed technique which is optimal for membranes. It takes benefit from activating a subset of the fluorophores at each timepoint in the sample and reconstituting the full image from mapped positions in a series of images. K-space image correlation spectroscopy is a technique in which the bulk diffusion coefficient is calculated after conventional epi fluorescence or TIRF imaging.

Image Analysis   Jon Sporring, Sune Darkner 

Image Analysis Rasmus Reinhold Paulsen, Anders Nymark Christensen, Anders Bjorholm Dahl

Super-resolution, STED, ICS and Raman Eva Arnspang Christensen, Jonathan Brewer & Martin Hedegaard

Confocal Raman imaging is a label free imaging technique based entirely on molecular vibrations. This course will include an introduction to basic working principles and choice of instrumentation including lasers, microscopes and spectrometers. In addition, there will be an introduction to pre-processing and analysis of Raman imaging data.