Teaching plan for the course unit



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General information


Course unit name: Fluorescence Microscopy Techniques

Course unit code: 569907

Academic year: 2021-2022

Coordinator: Carles Rentero Alfonso

Department: Faculty of Medicine

Credits: 3

Single program: S



Estimated learning time

Total number of hours 75


Face-to-face and/or online activities



-  Lecture

Face-to-face and online




-  Lecture with practical component

Face-to-face and online




-  Group tutorial

Face-to-face and online




-  IT-based class

Face-to-face and online




-  Laboratory session




Supervised project


Independent learning




Competences to be gained during study


— Basic knowledge of the  physical and biological bases of fluorescence microscopy techniques.

— Understanding of available fluorophores for fluorescence microscopy.

— Ability to use state of the art techniques in confocal microscopy.

— Ability to perform experimental design for time-lapse microscopy.

— Capacity to perform FRAP (Fluorescence Recovery After Photobleaching) and FRET (Fluorescence Resonance Energy Transfer) experimental design and analysis.

— Capacity to perform flow cytometry experimental design and analysis.





Learning objectives


Referring to knowledge

— Describe fluorescence microscopy’s physical and biological background.

— Explain confocal microscopy basis.

— Describe the main available fluorophores.

— Describe different cellular molecular detection strategies.

— Recognise the main fluorescent proteins and its applications.

— Acquire an overview of available image analysis software.

— Learn about FRET, FRAP and related approaches.

— Acquire an overview of new super-resolution microscopy techniques.

— Learn basic concepts in image analysis using ImageJ/FIJI.

— Learn basic principles of flow cytometry.



Teaching blocks


1. Characteristics of visual information in biomedicine; Basic and optical principles; 2D and 3D resolution; Light sources; Fluorescence; Fluorochromes; Fluorescence microscopy; Photobleaching: applications

2. Bioimaging; Fluorescent labelling in proliferation and apoptosis; Monitoring gene function by fluorescent genetic markers; Multiple fluorescent labelling; New generation of fluorescent molecules; Loss and gain of gene function studies with fluorescence microscopy; Applications in biomedical research; Brainbow: genetic design for non invasive cell tracing

3. Microscopy of living cells; How to maintain living cells under a microscope; Molecular labelling with fluorescence; Transmitted light contrast techniques; Capture of images in time intervals (time lapse microscopy)

4. Fluorescence photobleaching; Study of molecular dynamics; FRAP (Fluorescence recovery after photobleaching) and iFRAP (inverse FRAP); FLIP (Fluorescence loss in photobleaching); Fluorescent labelling; How to perform an experiment of photobleaching: microscope settings, parameters to consider; Image analysis and kinetic parameters

5. Resonance energy transfer between molecules in fluorescent microscopy (FRET, Fluorescence resonance energy transfer); Study of molecular interaction; Concepts; Methodology: acceptor photobleaching method; Labelling molecular FRET pairs; How to perform an experiment with FRET microscopy: settings, microscope parameters to take into account; Image analysis, representation and interpretation of results



Teaching methods and general organization


Lectures introduce all the theory of the teaching blocks of the subject, during both the theoretical lectures and the theoretical classes with a practical component.

Laboratory training
Practical sessions take place at the Microscopy Units of the Scientific and Technological Centres of the Faculty of Biology and the Faculty of Medicine (Hospital Clínic campus).

Computer training
To introduce students to the use of ImageJ/FIJI software.



Official assessment of learning outcomes


Students are assessed on their acquisition of theoretical and practical knowledge. Attendance, participation in proposed activities and acquired abilities are also evaluated.


Examination-based assessment

Students are assessed on their acquisition of theoretical and practical knowledge. Attendance, participation in proposed activities and acquired abilities are also evaluated.



Reading and study resources

Consulteu la disponibilitat a CERCABIB


Current Protocols in Cell Biology. John Wiley and Sons. Somerset, NJ. ISSN 1934-3639. 2012. http://www.currentprotocols.com/WileyCDA/Section/id-810292.html


Live Cell Imaging: A Laboratory Manual

Robert D. Goldman, David L. Spector, Jason R. Swedlow (Editor)

Cold Spring Harbor Laboratory Press; 2 edition (December 30, 2009)


Live Cell Imaging: Methods and Protocols (Methods in Molecular Biology) [Hardcover]

Dmitri B. Papkovsky (Editor)

Humana Press; 1st Edition. edition (December 17, 2009)