Introduce the student to the fundamentals of optical imaging and tomography at the micro/nano-scale to the macroscopic level, presenting the physical basis, introducing the mathematical tools, discussing instrumental implementations, togetther with photonics advancements, and describing examples of applications, with particular emphasis on biophysical and biomedical topics.

- Knowledge and understanding

The students will improve knowledge and understanding on wave physics, diffraction and diffusion, light-matter interaction, linear algebra and inverse problems, with specific application to the problem of optical microscopy and optical tomography in diffusive media.

- Apply knowledge and understanding

The students will be able to design autonomously an optical system for microscopy and imaging. The students will be able to evaluate the resolution and contrast in optical microscopy and diffuse tomography systems. The students will be challenged to solve – in the project activity – a problem of tomographic reconstruction implying the application of knowledge on the physics of diffuse optics, modelling of real photonics systems and methods for solving inverse problems.

- Making Judgements

Given a specific optical imaging system, the students will be able to precisely analyse the resolution and contrast.

The students will be required to judge the plausibility of their own project results as well as, in common discussions, of the outcomes of other teams.

- Lifelong learning skills

The students will be capable to understand how to take into account, and how to overcome the effects of diffraction and diffusion in a biological sample.

The students will be faced with the key difference between theoretical models and practical implementation, as well as the ability of problem solving, team-working and workflow organization.

Optical microscopy and nanoscopy:

• Point spread function in an optical microscope and 3D imaging theory.
• Classical microscopy techniques (bright-field, darkfield, phase contrast, fluorescence).
• Optical sectioning with spatial gating (Confocal microscopy, Structured illumination miroscopy, 2-photon microscopy).
• Tomographic imaging (Filtered back projection algorithm and Optical Projection Tomography).
• Optical sectioning with temporal gating (Optical Coherence Tomography).
• Circumventing the resolution limit with optical nanoscopy (Stimulated Emission Depletion and Photo-Activated Localization Microscopy).
• Applications of microscopy and super-resolution microscopy in biophysics and biomedicine.

Diffuse Optical Tomography:

• Diffuse optics, time-resolved techniques, frequency-resolved techniques.
• Applications: optical mammography, cerebral oximetry, functional imaging of brain activity, non-invasive tissue spectroscopy.
• Photon density waves.
• Diffuse Optical Tomography in the linear (Born approximation) and non-linear regime.
• Inverse Problems.
• Photoacoustics tomography
• Applications and new perspectives.

Basic knowledge on wave physics, linear algebra, diffusion equation for highly scattering media.

Knowledge and understanding of the Fourier Transform.

The final assessment will be based on a written test with open questions on the topics of the course and of the project activity.