Biomedical Engineering BEng/MEng

Microscopy and Optics 3 ENG3038

  • Academic Session: 2020-21
  • School: School of Engineering
  • Credits: 10
  • Level: Level 3 (SCQF level 9)
  • Typically Offered: Semester 1
  • Available to Visiting Students: Yes
  • Available to Erasmus Students: Yes

Short Description

The course will give students a fundamental understanding of a variety of microscopic and spectroscopic methodologies used to study biological systems. After completing the course students will understand the principles of operation for these methods and be able to identify the most suitable for studying a given sample. This understanding will be achieved through a combination of lectures and practical laboratory sessions.


The course will consist of 20 lectures and 3 laboratory sessions

Requirements of Entry

Mandatory Entry Requirements


Recommended Entry Requirements


Excluded Courses





70% Examination

30% Lab reports

Main Assessment In: December

Course Aims

The aimsof this course are to:

■ provide a fundamental understanding of the principles underlying optical detection using modern microscopic and spectroscopic technologies;

■ provide students with knowledge and skills allowing them to identify suitable techniques for a given biological sample and application.

Intended Learning Outcomes of Course

By the end of this course students will be able to:

■ demonstrate an appreciation of the theory and practical use of a microscope and how to optimize its use for studying different samples with different illumination techniques e.g. bright field (Kohler illumination), dark field, DIC;

■ describe fluorescence processes, fluorescence probes, and the factors influencing the qualitative and quantitative detection of fluorescence;

■ be aware of the principles of a number of modern, advanced fluorescence techniques including confocal fluorescence microscopy, fluorescence correlation spectroscopy (FCS), Total Internal Reflection Fluorescence Microscopy (TIRF), Fluorescence Lifetime Imaging Microscopy (FLIM);

■ identify an appropriate fluorescence technique for a given sample and application;

■ be aware of the principles of Raman spectroscopy including surface enhanced Raman spectroscopy, and compare Raman and Fluorescence techniques for characterizing biological samples;

■ describe the use of evanescence wave theory and surface Plasmon resonance, alone and in combination with microscopy, for biological samples analysis.;

■ describe how scanning electron microscopy and atomic force microscope work; and list the main information that can be obtained by them for a given type of sample.

Based on the laboratory sessions students will be able to:

■ choose the appropriate optical components for both an optical microscope and a fluorescence microscope for a given sample;

■ set up and operate a microscope and optimize acquisition conditions (for example, align it's illumination); 

■ design an experiment to understand the factors that influence qualitative and quantitative fluorescence measurements;

■ record, analysis and present experimental results in a report format.

Minimum Requirement for Award of Credits

Students must submit at least 75% by weight of the components (including examinations) of the course's summative assessment.