Microscopy and Image Analysis

Course goals

Course objectives
At the end of this course you will:

• know the basic physical principles underlying light and electron microscopy
• understand the workings of modern light and electron microscopes
• have hands-on experience with acquiring fixed and live imaging on an upright microscope
• understand the principles of specialized light microscopy techniques, such as confocal microscopy, TIRF microscopy, Super-resolution microscopy
• know how to choose between different microscopy approaches and labeling strategies
• have experience with analyzing, quantifying and representing microscopy data
• have experience generating paper figures using vector based software

 

Skills	Part of the course?	Explicitely examined?
Writing	X	X
Presenting	X	X
Data handling	X	X
Practical research skills	X
General research skills	X	X
Co-operation	X	X
Critical thinking	X	X
Career orientation	X
Interdisciplinarity

Content

Entry requirements
The level 2 course B-B2MGOT14 or comparable knowledge is a prerequisite. The course De Cel (B-B2CEL09) is recommended. As of 22-23 the B-B3MIA22 course replaces the B-B3LEM18 course for the biology bachelor. It is not possible to follow both. MBLS students are not allowed to follow this course and can follow MBLS-305 instead.

Study path
This course fits within the study path Cell Biology, Developmental Biology and Neurobiology. It provides a good preparation for masters such as the Master program Molecular and Cellular Life Sciences or Cancer Stem cells and Developmental Biology.

Language
This course is partially English taught (depending on the teacher). All course material and exam is in English, but the answers can be in Dutch. The report and presentation slides should be in English but the presentation can be done in Dutch.

Content
The aim of this course is to provide the students with a deep understanding of modern microscopy techniques in biology, with an emphasis on fluorescent microscopy techniques and their applications to cell biology.
The course will consist of lectures (HC) covering the theory accompanied by tutorials (WC) as well practicals where the students will have the opportunity to get hands-on experience with fluorescent microscopes. This first part will be part of the exam in week 5 of the course. Afterwards we will dive deeper into advanced microscopy techniques, which students will present to each other in groups. And finally, the students will be taught how to analyze, quantify and represent microscopy images (using ImageJ/FIJI); as well as how to assemble paper figures using vector based software (using Inkscape). 

Work formats
Lectures, seminars, practicals, presentation, self-study, writing assignment.

Grading & assessment
To pass this course, a minimum of 5,5 is mandatory. Your grade is calculated by the following components:

• Exam:                                              50%
• Presentation:                                   20%
• Image analysis report/workshop:    30%

Each individual grade should be a 5 or higher to pass. In addition, attendance of and active participation in the Practicals, the AI workshop and the final symposium is obligatory and will be registered (inspanningsverplichting).


Study material

• Murphy and Davidson, Fundamental of Light Microscopy and Electronic Imaging.

Online available through the UU library
http://onlinelibrary.wiley.com/book/10.1002/9781118382905

• Brightspace course environment, including:
  • Manual for practicals
  • Manual ImageJ and AI workshops
  • Lecture slides