ITA | ENG
B014003 - PHYSICS FOR BIOENGINEERING
Main information
Teaching Language
Course Content
Suggested readings
Learning Objectives
Prerequisites
Teaching Methods
Further information
Type of Assessment
Course program
Academic Year 2015-16
Coorte 2015 - Second Cycle Degree in INGEGNERIA BIOMEDICA
Course year
First year - First Semester
Belonging Department
Information Engineering (DINFO)
Course Type
Single education field course
Scientific Area
FIS/01 - EXPERIMENTAL PHYSICS
Credits
6
Teaching Hours
48
Teaching Term
21/09/2015 ⇒ 18/12/2015
Attendance required
No
Type of Evaluation
Final Grade
Course Content
show
Course program
show
Lectureship
Teaching Language
Italian
Course Content
Advanced optical microscopy - Principles and biomedical applications
Suggested readings (Search our library's catalogue)
- Optics; Eugene Hecht.
- Introduction to Optical Microscopy; Jerome Mertz.
- PDF of the slides presented during the lectures.
- Introduction to Optical Microscopy; Jerome Mertz.
- PDF of the slides presented during the lectures.
Learning Objectives
Knowledge in optical microscopy, non-linear microscopy and super-resolution techniques.
Prerequisites
Basic knowledge on geometrical optics and electromagnetic wave.
Teaching Methods
- Lectures.
- Experiences in research laboratory.
- Experiences in research laboratory.
Further information
None
Type of Assessment
- Reports on experiments conducted in the research laboratory.
- Presentation of a scientific article related to topics presented during the course.
- Presentation of a scientific article related to topics presented during the course.
Course program
COURSE PROGRAM:
1. Electromagnetic Waves - Equation of electromagnetic waves - planar and spherical waves - waves in dielectrics: dependence of the refractive index on the frequency - electromagnetic wave spectrum - Energy conservation and Poynting vector - Momentum of an electromagnetic wave.
2. Radiation-matter interaction- Reflection and refraction - Dispersion of light - Group velocity- Huygens-Fresnel principle - Interference - Diffraction.
3. Geometrical Optics - Geometrical optics approximation - Reflection - Refraction - Lens - Properties of several optical devices - The human eye.
4. Image formation - 2f system, 4f system, Magnification, Resolution and Point Spread Function - Numerical Aperture of a lens.
5. Molecular Spectra and light-molecule interaction - Electronic structure of a molecule - Absorption - Scattering - Fluorescence - Intersystem crossing and Photo-bleaching.
6. Fluorescent probes and labeling techniques - Endogenous and exogenous dyes- Fluorescent proteins and transfection techniques - Brainbow technology- Functional imaging: voltage sensitive dyes and calcium probes.
7. Wide field microscopy - Microscope scheme- Illumination systems - Detection Systems - Bright-field microscopy - Dark-field microscopy - Phase contrast microscopy - Fluorescence Microscopy - Biological application.
8. Laser scanning microscopy - Confocal microscope - Spatial resolution and optical sectioning - Scanning systems - Detectors (photodiodes - APD- photomultipliers) - Biomedical application.
9. TIRFM - FLIM - FRET microscopy - Total internal reflection (TIR) and evanescent wave - Total Internal Reflection Fluorescence Microscopy (TIRFM) - Fluorescence lifetime - Fluorescence Lifetime Microscopy (FLIM) - Molecular interaction and energy transfer - Foster Resonance Energy Transfer (FRET) - Biological applications.
10. Light sheet microscopy - Basic principle - Spatial resolution and field of view - Clearing of biological tissues - Biological applications.
11. Two-Photon fluorescence microscopy - Non-linear microscopy - Two photons absorption- Spatial resolution - Penetration depth- pulsed laser sources - Biological applications: high resolution imaging in tissues.
12. Second-harmonic generation microscopy - Second-harmonic generation - Coherent sommation - Emission angle - Biological applications: Imaging of ordered structures.
13. Vibrational Microscopy - Rayleigh Scattering Vs. Raman Scattering - Raman spectroscopy - Raman Microscopy - Coherent Antistokes Raman Scattering (CARS) microscopy - Stimulated Raman Scattering (SRS) microscopy - Biological applications.
14. Super-resolution techniques- Deconvolution microscopy - 4Pi microscopy - Stimulated Emission Depletion (STED) microscopy - Photo-Activable Localization Microscopy (PALM) - Stochastic Optical Reconstruction Microscopy (STORM) - Biological applications.
15. Optical aberrations - Chromatic aberrations - Spherical aberrations - Wave front distortion- Zernike polynomials - Quantification and correction of aberrations.
16. Experiences in research laboratory :
1) In vivo imaging of neuronal plasticity using non-linear two-photon microscopy.
2) Imaging and manipulation of the electrical conduction system of the whole heart.
3) High resolution imaging of the whole brain using confocal light sheet microscopy.
1. Electromagnetic Waves - Equation of electromagnetic waves - planar and spherical waves - waves in dielectrics: dependence of the refractive index on the frequency - electromagnetic wave spectrum - Energy conservation and Poynting vector - Momentum of an electromagnetic wave.
2. Radiation-matter interaction- Reflection and refraction - Dispersion of light - Group velocity- Huygens-Fresnel principle - Interference - Diffraction.
3. Geometrical Optics - Geometrical optics approximation - Reflection - Refraction - Lens - Properties of several optical devices - The human eye.
4. Image formation - 2f system, 4f system, Magnification, Resolution and Point Spread Function - Numerical Aperture of a lens.
5. Molecular Spectra and light-molecule interaction - Electronic structure of a molecule - Absorption - Scattering - Fluorescence - Intersystem crossing and Photo-bleaching.
6. Fluorescent probes and labeling techniques - Endogenous and exogenous dyes- Fluorescent proteins and transfection techniques - Brainbow technology- Functional imaging: voltage sensitive dyes and calcium probes.
7. Wide field microscopy - Microscope scheme- Illumination systems - Detection Systems - Bright-field microscopy - Dark-field microscopy - Phase contrast microscopy - Fluorescence Microscopy - Biological application.
8. Laser scanning microscopy - Confocal microscope - Spatial resolution and optical sectioning - Scanning systems - Detectors (photodiodes - APD- photomultipliers) - Biomedical application.
9. TIRFM - FLIM - FRET microscopy - Total internal reflection (TIR) and evanescent wave - Total Internal Reflection Fluorescence Microscopy (TIRFM) - Fluorescence lifetime - Fluorescence Lifetime Microscopy (FLIM) - Molecular interaction and energy transfer - Foster Resonance Energy Transfer (FRET) - Biological applications.
10. Light sheet microscopy - Basic principle - Spatial resolution and field of view - Clearing of biological tissues - Biological applications.
11. Two-Photon fluorescence microscopy - Non-linear microscopy - Two photons absorption- Spatial resolution - Penetration depth- pulsed laser sources - Biological applications: high resolution imaging in tissues.
12. Second-harmonic generation microscopy - Second-harmonic generation - Coherent sommation - Emission angle - Biological applications: Imaging of ordered structures.
13. Vibrational Microscopy - Rayleigh Scattering Vs. Raman Scattering - Raman spectroscopy - Raman Microscopy - Coherent Antistokes Raman Scattering (CARS) microscopy - Stimulated Raman Scattering (SRS) microscopy - Biological applications.
14. Super-resolution techniques- Deconvolution microscopy - 4Pi microscopy - Stimulated Emission Depletion (STED) microscopy - Photo-Activable Localization Microscopy (PALM) - Stochastic Optical Reconstruction Microscopy (STORM) - Biological applications.
15. Optical aberrations - Chromatic aberrations - Spherical aberrations - Wave front distortion- Zernike polynomials - Quantification and correction of aberrations.
16. Experiences in research laboratory :
1) In vivo imaging of neuronal plasticity using non-linear two-photon microscopy.
2) Imaging and manipulation of the electrical conduction system of the whole heart.
3) High resolution imaging of the whole brain using confocal light sheet microscopy.