Biophotonics

Code	13525
Year	1
Semester	S2
ECTS Credits	6
Workload	TP(60H)
Scientific area	Biomedical Sciences
Entry requirements	N/A
Mode of delivery	Face-to-face
Work placements	Not applicable
Learning outcomes	This curricular unit's main objective is to disseminate the principles of biophotonics and its application in biomedical sciences, as well as the underlying basic concepts of physical optics and computational optics. At the end of this curricular unit, the student should be able to understand the physical and mathematical foundations applied to biophotonics for the analysis of biological cells and tissues. A special emphasis will be given to computational techniques necessary for the implementation of biophotonics methods. The student must be able to perform optical and optoelectronic assemblies, based mainly on digital holography, with a view to analyzing biological samples. The student must also be able to use image processing techniques to reconstruct the optical phase of biological samples and analyze biophysical parameters.
Syllabus	THEORETICAL-PRACTICAL 1 MATHEMATICAL AND PHYSICAL FUNDAMENTALS 1.1 Fourier analysis and biostatistics bases 1.2 Properties electromagnetic radiation 1.3 Fundamentals of radiometry 2 OPTICAL COMPONENTS AND ELECTRONIC EQUIPMENT 2.1 Safety standards in the biophotonics laboratory 2.2 Lenses, prisms and other components 2.3 Optical fibers 2.4 Sources and detectors 2.5 Data acquisition systems 3 INTRODUCTION TO FOURIER OPTICS 3.1 Fourier transforms (TF) in two dimensions 3.2 Sampling Theorem and discrete TF 3.3 Diffraction and resolution of optical systems 3.3 Simulation of light propagation 3.4 Programming in MATLAB applied to Computational Fourier Optics 4 QUANTITATIVE PHASE IMAGING 4.1 Introduction to Digital Holographic Microscopy (MHD) 4.2 Optical assemblies in MHD 4.3 Image analysis in MHD 4.4 Phase reconstruction 4.5 Applications to cell and tissue analysis 4.6 Alternative methods: super-resolution, ETI, Fourier Ptychography.
Main Bibliography	1. COMPUTATIONAL FOURIER OPTICS: A MATLAB tutorial, David Voeltz, 1ª Ed. SPIE Press, 2011 2. A LABORATORY MANUAL IN BIOPHOTONICS, Vadim Backman et al, CRC Press, 2018 3. TISSUE OPTICS, Valery Tuchin, 3rd Ed., SPIE Press, 2015 4. DIGITAL HOLOGRAPHIC MICROSCOPY: Principles, Techniques, and Applications, Myung K. Kim, Springer, 2011 5. Óptica e Fotónica, Mário Ferreira, Lidel edições técnicas Lda. (2003) Scientific articles published in specialized journals.
Language	Portuguese. Tutorial support is available in English.