Type of course

Master course for biology students - principally aimed at MSc-students specializing in Molecular Environmental Biology. The course is limited to 8 students due to constraints with the equipment. Minimum number of students is 3. Students from Molecular Environmental Biology and other Master disciplines at the department (AMB) will be prioritized.

The admission will take place during the first lecture. First lecture is mandatory.

Course content

Large multidimensional image datasets are nowadays routinely captured for biological analysis at a variety of scales, from macroscopic field studies to microscopic cellular studies. A common challenge is the state-of-the-art analysis of image-based data.

With the course, we will introduce a variety of image-based analysis techniques based on the use of different spectral qualities of light. We will have a focus on light microscopy, including examples from phase contrast and fluorescence microscopy. The theoretical part of the course will cover the essentials for safe and appropriate use of the techniques, while strong emphasis will be on the practical part. In the first practical part, the students will be able to familiarize themselves with different techniques with pre-defined exercises. We will also treat related topics such as sample preparation (including sectioning and staining techniques) and the professional documentation of the results by microphotography. We will also cover upcoming hybrid techniques that use optical principles (with or without magnifying lenses) to trace macroscopic traits or movements, such as hyperspectral macroscopy or video tracking and cover basic aspects of the analysis of images derived from these techniques. In the second practical part, each student will pick an object or technique of their choice and design a small individual project to apply the acquired knowledge. The results of these individual mini-projects will be presented by each student to his peers and to other interested audience in a small workshop.

Objectives of the course

Knowledge; Students who have completed this course can

• explain the principle of light microscopy
• list different techniques to visualize organisms
• assess the potential and the limitations of different optical imaging techniques
• apply state-of-the-art procedures of image analysis
• avoid incorrect image manipulation

Skills; Students who have completed this course can:

• are comfortable and knowledgeable in working with microscopes
• perform maintenance on a microscope
• prepare objects for microscopical analysis
• use modern software to document microscopic structures
• design robust experiments with appropriate controls
• apply tools to create and execute individual or automated unbiased image analysis work flows
• design a poster of their work using PowerPoint

General competence; Students who have completed this course can

• appreciate optical techniques, including light microscopy as tool for classical and modern biological research
• formulate a research question, choose the appropriate methods and perform the experiments independently
• design engaging posters describing scientific results
• convey the essence of their project to others
• engage in critical discussions with their fellow students

Language of instruction and examination

Teaching methods

Lectures and seminars 15 hours, laboratory and computer exercises 50 hours, poster design and workshop (incl. colloquium) 10 hours, preparation of course materials 5 hours, own project 20 hours.

Specific safety training regarding the use of microscopy equipment and other equipment is given in the course.