CH-416 / 3 credits

Teacher: Rivera Fuentes Pablo

Language: English


This course will introduce basic concepts of fluorescence spectroscopy and microscopy applied to the observation of biological systems. The course will focus on the design, preparation and implementation of small-molecule and protein-based probes.



fluorescence, labeling, imaging, cell biology, photophysical properties, proteins, sensors

Learning Prerequisites

Recommended courses

Basic chemistry and biology courses

Important concepts to start the course

Electronic absorption and fluorescence; molecular orbitals; basic concepts of electron donating and accepting funtional groups; structure of proteins, basic understanding of the central dogma of molecular biology, basic cell biology.

Learning Outcomes

By the end of the course, the student must be able to:

  • Predict the approximate photophysical properties of imaging agents (molecules, proteins) based on their chemical structures and physical environment.
  • Classify the main fluorescence imaging modalities based on the samples that they can handle and the information that can be obtained from them.
  • Assess / Evaluate the suitability of bioconjugation and tagging strategies for specific imaging agents and biological targets.
  • Identify the connections between chemical reactions, supramolecular interactions and photophysical properties in fluorescence sensing.
  • Assess / Evaluate research papers that describe bioimaging experiments and explain them orally to a multidisciplinary audience.

Transversal skills

  • Assess one's own level of skill acquisition, and plan their on-going learning goals.
  • Demonstrate the capacity for critical thinking
  • Communicate effectively with professionals from other disciplines.
  • Identify the different roles that are involved in well-functioning teams and assume different roles, including leadership roles.
  • Access and evaluate appropriate sources of information.
  • Design and present a poster.
  • Make an oral presentation.
  • Summarize an article or a technical report.

Teaching methods

In this course, students learn to design efficient fluorescence bioimaging experiments. To achieve this objective, a combination of teaching methods is implemented, including regular lectures, case studies, analysis of recent papers, and design of experiments for “real-world” problems. Constant work in small teams and ungraded weekly quizzes are implemented to help students learn by themselves and manage large amounts of multidisciplinary information throughout the course.

Expected student activities

Lecture attendance, participation in interactive sequences, design and presentation of a poster, participation in weekly online quizzes, participation in a final oral presentatation at the end of the semester, if applicable, participation in instrument demonstrations.

Assessment methods

Oral exam. Oral presentation and weekly quizzes provide additional points.


Office hours No
Assistants Yes
Forum No
Others Although no official office hours are provided, students are always welcome to send their question by e-mail, Moodle, or ask in person before, during and after class.



J. R. Lakowicz. Principles of Fluorescence Spectroscopy. Kluwer Academic / Plenum Publishers. 2006.


P. J. Walla. Modern Biophysical Chemistry: Detection and Analysis of Biomolecules. Wiley-VCH. 2014.


M. Chalfie; S. R. Kain (Eds.) Green Fluorescent Protein: Properties, Applications, and Protocols.
Wiley-Interscience. 2006.


R. W. Sabnis. Handbook of Fluorescent Dyes and Probes. John Wiley & Sons, Inc. 2015.


A. P. Demchenko. Introduction to Fluorescence Sensing. Springer Science. 2009.

Ressources en bibliothèque


Slides and handouts will be available on Moodle before class.

Moodle Link

In the programs

  • Semester: Fall
  • Exam form: Oral (winter session)
  • Subject examined: Chemical biology of cell imaging
  • Lecture: 3 Hour(s) per week x 14 weeks
  • Semester: Fall
  • Exam form: Oral (winter session)
  • Subject examined: Chemical biology of cell imaging
  • Lecture: 3 Hour(s) per week x 14 weeks
  • Exam form: Oral (winter session)
  • Subject examined: Chemical biology of cell imaging
  • Lecture: 3 Hour(s) per week x 14 weeks

Reference week


Monday, 10h - 13h: Lecture INM201