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Advanced Courses III

Code 15044
Year 1
Semester S2
ECTS Credits 5
Workload TP(40H)
Scientific area Biomedicina/Medicina/Bioquímica
Entry requirements Bachelor's degree or legal equivalent
Learning outcomes On completion of the course, the student should:
- Be familiar with the various basic and advanced fluorescence microscopy techniques used in biomedical research.
- Know the various basic and advanced fluorescence microscopy techniques used in biomedical research.
- Know how to select the appropriate image acquisition mode for the intended purpose.
- Have acquired the basics of image analysis methods such as digitisation, image enhancement, segmentation and feature classification.
- Carry out manual and automatic measurements using image analysis tools.
- Carry out object tracking.
- Understand the applications and limitations of each technique.
- Know and apply the fundamental notions of ethics in image analysis.
Syllabus Introduction to Fluorescence Microscopy
Optical Sectioning
Live Cell Imaging
Super-Resolution Microscopy
Hands-On Microscopes (Axio Observer Z1, Axio Imager Z2, Confocal LSM 710)
Introduction to Image Analysis
Introduction to FIJI (Is Just ImageJ)
Hands-On FIJI (Fluorescence Intensity Analysis, Lesion Area & Colocalisation)
Introduction to ZEN Microscopy Software
Introduction to Imaris
Hands-On Imaris (Tracking Analysis)
How to Analyse Large Images: QuPath Software
Introduction to Huygens
Hands-On Huygens (Widefield 3D Image Deconvolution)
Main Bibliography - Fluorescence Microscopy: From Principles to Biological Applications, 2nd Edition. Ulrich Kubitscheck (Editor) ISBN: 978-3-527-33837-5 June 2017 Wiley-Blackwell
- Bioimage Data Analysis, Edited by Kota Miura, Wiley-VCH. ePDF ISBN: 978-3-527-80092-6
- Quantitative Imaging in Cell Biology, Methods in Cell Biology, Volume 123 (2014). Editors Jennifer C. Waters & Torsten Wittmann

Teaching Methodologies and Assessment Criteria The course consists of theoretical sessions, hands-on practical sessions on the microscopes assigned to the microscopy laboratory, and theoretical-practical image analysis sessions. The theoretical sessions provide the theoretical basis for fluorescence microscopy techniques and the basic concepts of image acquisition and analysis in biomedical research. The theoretical-practical image analysis sessions enable the application of the concepts presented in the theoretical sessions and the use of available tools to build workflows suitable for a given research objective. Assessment involves the individual application of knowledge in contexts that students will be able to transpose into their research projects.
Language Portuguese. Tutorial support is available in English.
Last updated on: 2024-06-19

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