Teaching plan for the course unit



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General information


Course unit name: Applications of Fluorescence and Image Analysis

Course unit code: 568784

Academic year: 2021-2022

Coordinator: Florencio Serras Rigalt

Department: Department of Genetics, Microbiology and Statistics

Credits: 5

Single program: S



Prior considerations




Contact the teaching staff by mail for an appointment or for questions on the course.



Estimated learning time

Total number of hours 125


Face-to-face and/or online activities



-  Lecture





-  IT-based class





-  Laboratory session





-  Special practices




Supervised project


Independent learning




Competences to be gained during study


Basic competences

— Knowledge forming the basis of original thinking in the development or application of ideas, typically in a research context.

— Capacity to apply the acquired knowledge to problem-solving in new or relatively unknown environments within broader (or multidisciplinary) contexts related to the field of study.

— Capacity to integrate knowledge and tackle the complexity of formulating judgments based on incomplete or limited information, taking due consideration of the social and ethical responsibilities involved in applying knowledge and making judgments.

— Capacity to communicate conclusions, judgments and the grounds on which they have been reached to specialist and non-specialist audiences in a clear and unambiguous manner.

— Skills to enable lifelong self-directed and independent learning.


General competences

— Capacity to structure a reasoned discourse in a logical and rational manner, to discuss any scientific topic in front of diverse audiences.

— Capacity for critical, logical and creative thought. Capacity for analysis and synthesis.

— Capacity for interaction and transfer activities with their environment.

— Capacity to work in groups and to collaborate with other researchers.

— Capacity to read and critically interpret scientific publications related to the subject, mainly in English, and to be able to design, write and defend a research project.


Specific competences

— Capacity to understand the basic principles of fluorescence and its use in the detection of gene products and cell marking.

— Capacity to use the fluorescence microscope and confocal microscope.

— Capacity to understand image processing software like FIJI (ImageJ) and Imaris and their use in bioimage analysis.





Learning objectives


Referring to knowledge

The objective of the course is to introduce students to techniques related to the acquisition and processing of confocal microscope images.



Teaching blocks


1. Introduction to Fluorescence

1.1. Basics of fluorescence technology

1.2. Interpretation of the different spectra

1.3. Optical filters and electromagnetic spectra

1.4. Excitation, absortion and emision

2. Principles of Fluorescence Microscopy

2.1. Data analysis and image processing

2.2. Confocal Microscopy


3. Introduction to genetic markers and cell labeling

3.1. Fluorescent molecules and technology for genetic analysis.


3.2. GFP and derivatives. Genetic analysis using fluorescent tags.


3.3. Mitotic recombination and ectopic expression. FRT/FLP, CRE/LoxP, Gal4/UAS

4. Research laboratory for fluorescence labeled probes

4.1. Use of the image analysis softwares Fiji and Imaris and quantification 

4.2. Multiple labeling techniques using fluorescent probes

4.3. 3D reconstruction of developing embryos 

4.4. Cell labeling techniques

4.5. Nucleic acid dyes and organelle dyes for image analysis



Teaching methods and general organization


This is a mainly practical course with the aim to introduce the students to the techniques involving cell labeling and gene expression using confocal microscopy and image analysis. Also image processing and quantification data procedures will be introduced. A condensed course on confocal microscopy, FIJI and Imaris is included. Students will get the basic formation to conduct further experiments during their future research.

The program includes:

  • Preparation of biological material
  • Use of several fluorescent molecules with excitation wavelengths ranging from 350 to 600 nm; use of optical filters; experimental design using fluorescent markers.
  • Confocal microscopy for organelle and gene expression detection.
  • Fluorescence Recovery After Photobleaching in cultured cells to monitor protein synthesis and mobility parameters
  • Introduction to the image processing package FIJI
  • Introduction to the Microscopy Image Analysis software Imaris, for 3D and 4D imaging

Students will work in groups of 3 and must assist to all classes during the 11 days course (distributed in 3 weeks).


Distance training

The students will have to analyze their own results in extra hours. Eventually they will present the results as an oral presentation the last day (short oral communication).



Attendance at all classes is compulsory. We consider active participation in class, and leading discussions are expected.  The results of the course will be completed in a final project in the form of an oral presentation. A final exam will be given during the last session.

A contest for the best image will be encouraged at the end of the course.


Course Requirements

Active participation is expected, and questions are encouraged in both during lectures and lab exercises. Also during the final oral presentations sessions. We expect active interaction.

However, do not be intimidated - you are here to learn! Naïve questions are encouraged.

You will be asked to keep a written record of the entire course. We will give you clear guidelines (summarised in the lab Syllabus) which include a compendium of techniques, which will serve as a useful future reference.

All classes are in English.




Official assessment of learning outcomes


Oral presentation: 40%

Examination: 40%

Class participation and attendance: 20%