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Biological Imaging - Basic Module
Provider: Faculty of Science

Activity no.: 5721-25-09-31There are 24 available seats 
Enrollment deadline: 19/04/2025
PlaceDepartment of Plant and Environmental Sciences
Date and time23.04.2025, at: 09:00 - 21.05.2025, at: 16:00
Regular seats25
Course fee1,000.00 kr.
ECTS credits5.00
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 noteThe first 5 weeks of block 4
Scheme groupC
Scheme group noteCourse Location: PLEN-CPSC Ø-labs, CAB, CFIM
Grading scaleCompleted/ Not completed
Criteria for exam assessmentType of assessment: Short report of the images recorded as the showcases
Course workload
Course workload categoryHours
Lectures20.00
Practical exercises16.00
Theory exercises12.00
Preparation92.00
Sum140.00
Content
This tool box course is part of the former course “Biological Imaging” up to 2024. It gives the academic qualifications to three different 2.5 ECTS options - Biological Mass Spectrometry Imaging (PLEN), Biological X-ray and Neutron Imaging (PLEN), and Biological IR and Raman Imaging (IGN) , which can be chosen immediately after this course or at a later time point.

Aim and content
All research areas using light microscopic imaging.
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 three Advanced Biological Imaging modules, namely X-ray imaging, Mass Spectroscopic imaging, and IR / Raman imaging (see course numbers X, Y, Z)

Formel requirements
Passed Bachelor in Biomedical, Chemical or Computer Sciences

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 relevant instruments and, thus, will be an important asset for students that want to integrate biological imaging in their projects.

After the course the student should be able to:

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:
•Analyze 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.

Literature
Relevant background material and journal articles will be electronically available at the start of the course

Target group
PhD students within Life and Biomedical Sciences

Teaching and learning methods
Lectures, Journal Clubs, flipped classroom, and practical show cases. 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).

Lecturers

Tim B. Dyrby, DTU
Guest lecture on preclinical and clinical MRI

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Collaborating Department:
Faculty of Science / Dpt. of Plant and Environmental Sciences 
Faculty of Science / Dpt. of Biology
Faculty of Science / Dpt. of Computer Science
Faculty of Science / Dpt. of Chemistry
Faculty of Health and Medical Science / Dpt. of Biomedical Sciences
Faculty of Health and Medical Science / Dpt. of Drug Design and Pharmacology

Remarks

Course fee: All PhD students (including Danish Universities) are charged for instrument-time (time fees) at the core facilities CAB and CFIM: DKK 1000

PhD students enrolled at UCPH: Please provide us with "stedkode" and "alias" when you register by choosing "Enroll" at the upper right corner of the course description, so that UCPH Accounting Department can make an internal transfer regarding payment of the course fee.

PhD students enrolled at other universities than UCPH: After you have registered by choosing "Enroll" in the upper right corner of the course description, please pay the course fee via this link 
https://eventsignup.ku.dk/bio-imaging-basic-5721  Payment via creditcard or Mobilepay only.

The registration is binding, and the course fee is non-refundable in case of participant cancellation after enrolment deadline 19 April 2025.

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NB. applicants outside UCPH applying for PhD courses for the first time: press "login for others" in upper right corner of website. Then choose "forgot password" and enter your mail. A password will be sent to your mail which enables you to make a login and enroll at the course.

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