NPLK17000U Biological Imaging

Volume 2024/2025

This course will introduce to all important modalities of advanced biological and biomedical imaging using photons, electrons, X-rays and neutrons, available in the Øresund region in core facilities and at synchrotron and linear accelerators (MAX IV and ESS). These modalities offer a wide zoom range and the resolution power to resolve the substructure of molecules, cells, tissues, organs and whole bodies. The couse is relevant for students of MSc. educations within biological, chemical, physical, medical, molecular and pharmaceutical sciences and will be coordinated with the PhD course "Biological Imaging". 

In particular the following topics will be treated: fluorescence microscopy, fluorescence life time imaging, super resolution microscopy, electron and cryo electron microscopy, X-ray imaging and imaging at synchrotron and linac beamlines. An important part will be the concomitant data analysis, -management and -statistics as well as image processing. 

Learning Outcome

This course aims at giving the student an understanding of biomedical imaging including the physical and optical principles of cutting-edge microscopes and beamlines. The course includes show cases at the instruments and, thus, will be an important asset for students that want to integrate biological and soft-matter imaging in their Master projects. 

After the course the student should be able to:


  • Describe properties of different light sources and their impact on biological specimens
  • Understand the principles of specimen preparation
  • Process raw data from different imaging modalities, including mulitvariate analysis of 4D image series
  • Availability of biological imaging facilities in the Øresund region


  • Analyse and evaluate scientific papers which utilise biological imaging instruments and -beam lines
  • Make a flow-chart of data management from raw image data to analysis
  • Process image series with simple software algorithms for contrast and brightness improvement, segmentation and automated analysis


  • Select appropriate imaging modalities to visualise molecular or cellular structures and processes
  • Describe the limitations of the different imaging modalities used in the course
  • Judge suitability of MAX IV or ESS to solve scientific questions of a project within Biology, Biology-Biotechnology, Computer Science, Medicine and Technology, Molecular Biomedicine, Nanoscience or Pharmaceutical Sciences while being aware of competing imaging instruments.

Relevant background material and Journal articles will be electronically available at the start of the course. Practicals will be taught at the Center for Advanced Bioimaging (CAB - FBG and Nørre Campus), and at the Center for Integrated Microscopy (CFIM - at the Panum building). An excursion to Lund (Sweden) will be undertaken to visit the MAX IV synchrotron and the linear neutron accelerator European Spallation Source (ESS).

Students interested to take this course should have a basic understanding of theory and use of wide field light microscopes, such as achieved by following cell biology, histology or anatomy courses.

Academic qualifications equivalent to a BSc degree is recommended.
Lectures, Journal Clubs, flipped classroom, practical show cases, excursions.
Please note that your laptop should be able to run MatLab or a similar data analysis program (4GB RAM)!
  • Category
  • Hours
  • Lectures
  • 28
  • Preparation
  • 130
  • Theory exercises
  • 12
  • Practical exercises
  • 33
  • Exam
  • 3
  • Total
  • 206
Continuous feedback during the course of the semester
7,5 ECTS
Type of assessment
On-site written exam, 3 hours under invigilation
Type of assessment details
The exam will consist of two parts, of which one is a multiple choice test on the fundamentals of biological imaging and the other one covers questions on the journal articles treated during the course. Part one counts 1/3, and part two 2/3.
Exam registration requirements

Approved presentation of a Journal Club article, prepared in student teams during the course.

All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship

Examination form is changed to a 30 min oral examination in case less than 10 students register for it.

It can not be dispensated for the requirement of presenting a Journal club article, and students who do not fulfil the requirements have to present a relevant Journal article at the examiners office. They will get this article a week in advance; and presentation will take approximately 15 min.

Criteria for exam assesment

See "learning outcome"