First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
Course unit
SCP7081799, A.A. 2018/19

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
SC2382, Degree course structure A.Y. 2017/18, A.Y. 2018/19
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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 01/10/2018
End of activities 18/01/2019
Show course schedule 2019/20 Reg.2017 course timetable

Examination board
Board From To Members of the board
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: Foundations of optics. Matrix formalism for geometric optics. Optical instruments. Aberrations. Fourier analysis in two dimensions. Invariant linear systems. Transfer functions. Sampling theorem.
Scalar theory of diffraction. Diffraction integrals, Fourier transforms and Huygens-Fresnel principle. Angular spectrum of plane waves. Propagation of fields and spectra. Propagation of light as a linear spatial filter.
Approximation of Fresnel and Fraunhofer. Diffraction of Fraunhofer from rectangular and circular openings. Diffraction lattices.
The thin lens as a phase transformation. Image formation as a convolution. Coherent and inconsistent lighting. Analysis of optical systems in the frequency space. Function of transfer of an optical system limited by the effects of diffraction alone. Effect of aberrations on the frequency response. Coma and condition of the breasts of Abbe.
Transmitted light microscopy: Conjugated planes and optical trains; Köhler's illumination conditions; Abbe theory and resolution; phase contrast; dark field imaging; differential interference contrast.
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: impulse response of a converging lens in three dimensions; 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.
STED microscopy and super-resolution.
Digital image processing: noise and its digital filtering; deconvolution; structured illumination and super-resolution.
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; optochemogenetis; FRET, FLIM, FRAP, TIRFM; dynamics of intracellular messengers; reaction-diffusion equations, calcium waves.
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 (U.K.): Cambridge University Press, 1999. ISBN 0521642221 Cerca nel catalogo
  • Tinnefeld P, Eggelin C, Hell S (Editors), Far-Filed Optical Nanoscopy - Springer Series on Fluorescence (Book 14). New York: Springer, 2016. ISBN-13: 978-3662506875 Cerca nel catalogo

Innovative teaching methods: Teaching and learning strategies
  • Lecturing