Biological Imaging - Basic Module
PhD School at the Faculty of SCIENCE at University of Copenhagen
This is a toolbox course where 80% of the seats are reserved to PhD students enrolled at the Faculty of SCIENCE at UCPH and 20% of the seats are reserved to PhD students from other Danish Universities/faculties (except CBS). Seats will be allocated on a first-come, first-served basis and according to the applicable rules.
Anyone can apply for the course, but if you are not a PhD student at a Danish university (except CBS), you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to applicants on the waiting list.
Aim and Content
This course will introduce to all important modalities of advanced biological and biomedical imaging using electromagnetic and other light sources. These modalities offer a wide magnification range 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.
In particular the following topics will be treated: digital images, resolution power, contrast demands within fluorescence microscopy, fluorescence life time imaging, super resolution microscopy, electron and cryo electron microscopy.
An important part will be the dos and don’ts of imaging, data analysis, -management and –statistics as well as image processing.
Biological Imaging’s basic module gives the knowledge background of two Advanced Biological Imaging modules, namely X-ray imaging, and IR / Raman imaging.
Learning outcomes
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 relevant instruments and, thus, will be an important asset for students that want to integrate biological imaging in their projects.
Intended learning outcome for the students who complete the course:
Knowledge:
• 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
Skills:
• 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
Competences:
• Select appropriate imaging modalities to visualize molecular or cellular structures and processes;
• Describe the limitations of the different imaging modalities used in the course; to solve scientific questions of a project within Biology, Biology-Biotechnology, Computer Science, Medicine and Technology, Molecular Biomedicine, Nanoscience or Pharmaceutical Sciences.
Target Group
PhD students within Life, Biomedical, Biochemical and Food Sciences.
Recommended Academic Qualifications
Passed Bachelor in Biomedical, Chemical or Computer Sciences.
Research Area
Imaging research in all topics of the target group.
Teaching and Learning Methods
Lectures, Journal Clubs, flipped classroom, and practical showcases. The laptop should be able to run Python or a similar data analysis program (4GB RAM).
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).
Type of Assessment
Short written report on the images recorded at the showcases.
Literature
Relevant background material and journal articles will be electronically available at the start of the course.
Course coordinator
Alexander Schulz (Professor)
Guest Lecturers
Tim B. Dyrby, DTU: Guest lecture on preclinical and clinical MRI.
Pippa Hawes, Roland Fleck: Guest lectures on electron microscopy (coordinated by CFIM).
Dates
26 April-28 May 2027 (the first 5 weeks of block 4).
Expected frequency
Once a year
Course location
Lectures in lecture halls as allocated on North Campus or Frederiksberg Campus, Showcases at UCPH’s core facilities CAB and CFIB.
Course fee and participant fee
PhD courses offered at the Faculty of SCIENCE have course fees corresponding to different participant types.
In addition to the course fee, there might also be a participant fee.
If the course has a participant fee, this will apply to all participants regardless of participant type - and in addition to the course fee.
Course fee
• Participant fee: DKK 1.000
• PhD student enrolled at SCIENCE: DKK 0
• PhD student from Danish PhD school Open market: DKK 0
• PhD student from Danish PhD school not Open market: DKK 6.000
• PhD student from foreign university: DKK 6.000
• Master's student from Danish university: DKK 0
• Master's student from foreign university: DKK 6.000
• Non-PhD student employed at a university (e.g., postdocs): DKK 6.000
• Non-PhD student not employed at a university (e.g., from a private company): DKK 16.800
You will receive an email with a link and instructions for payment after completing the course
Cancellation policy
• Cancellations made up to two weeks before the course starts are free of charge.
• Cancellations made less than two weeks before the course starts will be charged a fee of DKK 3.000
• Participants with less than 80% attendance cannot pass the course and will be charged a fee of DKK 5.000
• No-show will result in a fee of DKK 5.000
• Participants who fail to hand in any mandatory exams or assignments cannot pass the course and will be charged a fee of DKK 5.000