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Biological Imaging
Provider: Faculty of Science

Activity no.: 5721-22-09-31 
Enrollment deadline: 08/04/2022
PlaceDepartment of Plant and Environmental Sciences
Date and timeApril 2022 - June 2022
Regular seats20
Course fee500.00 kr.
ECTS credits7.50
Contact personAlexander Schulz    E-mail address: als@plen.ku.dk
Enrolment Handling/Course OrganiserAlexander Schulz    E-mail address: als@plen.ku.dk
Written languageEnglish
Teaching languageEnglish
Semester/BlockBlock 4
Block note25th April to 22th June 2022
Scheme groupC
Exam formWritten assignment
Exam detailsThe 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
Course workload
Course workload categoryHours
Practical exercises33.00
Theory exercises12.00


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 course is relevant for PhD students within biological, chemical, physical, medical, molecular and pharmaceutical sciences and will be coordinated with the MSc 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 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 multivariate analysis of 4D image series
Find the respective instruments in the Øresund region.

Analyse and evaluate scientific papers which utilize 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 visualize 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 completing 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).

Teaching and learning methods
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).

Provider: Department of Computer Science; Department of Plant and Environment Sciences; The Niels Bohr Institute.


UCPH discloses non-sensitive personal data to course leader/speakers, if any. In addition, we will disclose non-sensitive personal data to the other participants in the course. Non-sensitive personal data includes names, job positions, institution names & addresses, telephone numbers and e-mail addresses.

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