First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
Course unit
SCP7081799, A.A. 2019/20

Information concerning the students who enrolled in A.Y. 2018/19

Information on the course unit
Degree course Second cycle degree in
SC2382, Degree course structure A.Y. 2017/18, A.Y. 2019/20
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Degree course track PHYSICS OF MATTER [002PD]
Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination BIOPHOTONICS
Website of the academic structure
Department of reference Department of Physics and Astronomy
Mandatory attendance No
Language of instruction English
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Teacher in charge FABIO MAMMANO FIS/07

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines FIS/01 Experimental Physics 6.0

Course unit organization
Period First semester
Year 2nd Year
Teaching method frontal

Type of hours Credits Teaching
Hours of
Individual study
Lecture 6.0 48 102.0 No turn

Start of activities 30/09/2019
End of activities 18/01/2020
Show course schedule 2019/20 Reg.2017 course timetable

Examination board
Board From To Members of the board
2 BIOPHOTONICS 01/10/2019 30/11/2020 MAMMANO FABIO (Presidente)
BORTOLOZZI MARIO (Membro Effettivo)
1 BIOPHOTONICS 01/10/2018 30/11/2019 MAMMANO FABIO (Presidente)
BORTOLOZZI MARIO (Membro Effettivo)

Prerequisites: Biological Physics
Target skills and knowledge: The course aims to provide in-depth knowledge of Fourier optics, bright field microscopy, contrast generation, conventional and confocal fluorescence microscopy, super-resolution, digital image processing, molecular probes and cell signal detection. The course is specifically designed to provide students with the ability to design optical microscopy experiments for a wide range of potential biological applications.
Examination methods: Written and an oral exam. The written part concerns topics developed during the course. The oral exam consists in the presentation by the student of one or more original articles related to optical super-resolution techniques.
Assessment criteria: The evaluation of the student's preparation will be based on the understanding of the topics developed, on the acquisition of the concepts and methodologies proposed and on the ability to apply them in an autonomous and conscious way.
Course unit contents: Electromagnetic wave propagation: plane waves, spherical waves, phase velocity, irradiance, wave packets, group velocity, coherence length, interference.
Scalar diffraction theories: the Kirchhoff formulation, the Rayleigh-Somrnerfeld formulation, the Huygens-Fresnel principle.
Geometrical optics: Optical path length, the principle of Fermat, ideal imaging systems, matrix methods in paraxial imaging, cardinal points and planes.
Apertures and stops, image-forming instruments, brightness and illumination of images, intensity fluctuations, detection noise.
The Debye integral representation of focused fields, irradiance distribution near focus (three-dimensional point spread function). Resolving power: the Rayleigh criterion. Minimum angular separation, visual acuity, phototransduction.
Transmitted light microscopy: angular spectrum of plane waves, diffraction gratings, abbe theory and resolution. Phase contrast, dark field, and differential interference contrast microscopy.
Fluorescence microscopy: molecular spectra, Jablonski diagram, Stokes' shift, life time and quantum efficiency, saturation of the excited state. Structure of the conventional fluorescence microscope.
Confocal microscopy: lateral resolution and axial resolution in the classical limit; optical sectioning and volume reconstruction; physical principles and applications of 2-photon excitation; advantages and disadvantages of different confocal systems.
Stimulated emission depletion (STED) nanoscopy and super-resolution.
Selected biophotonics applications: optical recording of changes in ion concentration. Optical sensors of Ca2+ ions, protons and other physiologically relevant ionic species. Imaging of Ca2+ at one and two wavelengths; local control of the concentration of Ca2+ and other active molecular species by UV photolysis of caged compounds; FRET, FRAP.
Intravital microscopy: biosensors, optochemogenetics, photodynamic therapy of cancer.
Planned learning activities and teaching methods: Taught lessons
Additional notes about suggested reading: Lecture notes
Textbooks (and optional supplementary readings)
  • Born M, Wolf E, Principles of Optics - 7th expanded edition. Cambridge, UK: Cambridge University Press, 1999. ISBN: 9780521642224 Cerca nel catalogo
  • Mertz, J, Introduction to Optical Microscopy. Cambridge, UK: Cambridge University Press, 2019. ISBN: 9781108428309 Cerca nel catalogo
  • Saleh B, Teich M, Fundamentals of Photonics, 2 Volume Set, 3rd Edition. New York, USA: John Wiley & Sons, Inc., 2019. ISBN: 9781119506874 Cerca nel catalogo