Light-tissue Interaction

6 EC

Semester 1, period 1

5354LITI6Y

Owner Master Physics and Astronomy (joint degree)
Coordinator Dierck Hillmann
Part of Master Physics and Astronomy (joint degree), track Biophysics and Biophotonics, Master Physics and Astronomy (joint degree), track General Physics and Astronomy,

Course manual 2025/2026

Course content

Our subject is the physics of the interaction of light with biological tissue, with focus on imaging techniques and diagnostics applications.

We will cover the physical fundamentals of light absorption and scattering properties, and their relation to physiological and metabolic parameters of the tissue. Different theories for scattering and absorption will be discussed. For single particle scattering theories, Rayleigh, Mie and geometrical scattering will be treated. Light propagation in bulk tissue is treated using the Radiative Transport Equation (RTE), the diffusion approximation and using Monte Carlo simulations of light transport. 

General properties of imaging (transfer functions, confocal imaging, rigorous diffraction theory for single scattering), speckle and flow techniques will be covered.

Clinically used (imaging) methods are discussed: Optical Coherence Tomography, Fluorescence & Raman spectroscopy,  nonlinear microscopy, dynamic light scattering, etc. 

The course will contain practical (lab) work and programming exercises in Matlab or Python. 

Study materials

Syllabus

  • Comprised of book chapters, scientific articles, and class notes.

Practical training material

  • Exercises during class and homework assignments.

Software

  • Links to open source calculators.

  • Programming language and IDE of choice, ideally Python or Matlab 

Other

  • Materials will be made available in Canvas.

Objectives

  • The physical processes of light-tissue interaction, absorption and scattering. Knowing the important biological compounds that absorb and scatter visible and near infra-red light along with their descriptive physical quantities (absorption and scattering efficiencies, cross sections, coefficients and phase function). Familiarity with theories and methods to describe scattering (Rayleigh, Mie and geometrical scattering); models to describe scattering and absorption single particles and suspensions of particles as tissue models. Knowledge about the main imaging methodologies and when they are applied.
  • Understand the derivation of optical properties such as the scattering cross section, coefficient and phase functions. Explain the physics behind absorption flattening and dependent scattering as function of volume fraction. Understand the sampling process in Monte Carlo simulations. Derive the diffusion approximation from the radiative transport equation. Understand physical mechanisms of absorption and scattering (elastic, Raman, fluorescence, phosphorescence). Understand the main imaging parameters, transfer functions, and diffraction, and their impact on imaging scenarios.
  • Apply the theoretical and practical concepts to biomedical optics applications, e.g. Optical Coherence Tomography (EM wave propagation, interference, single scattering); Single Fiber Reflectance Spectroscopy (optical properties, Monte Carlo simulations).
  • Connect the role of tissue organization in absorption and scattering processes; connect the role of speckle in OCT measurements, physical phenomena like ‘glare in the eye’ and dynamic light scattering to estimate blood flow velocity.
  • Judge selected research papers on the topics discussed in class.

Teaching methods

  • Lecture
  • Self-study
  • Fieldwork/excursion
  • Computer lab session/practical training

Will be announced.

Learning activities

Activity

Number of hours

Zelfstudie

168

Attendance

  • Some course components require compulsory attendance. If compulsory attendance applies, this will be indicated in the Course Catalogue which can be consulted via the UvA-website. The rationale for and implementation of this compulsory attendance may vary per course and, if applicable, is included in the Course Manual.

    • Assessment

    Item and weight Details

    Final grade

    0.5 (50%)

    Tentamen

    		Must be ≥ 6

    0.25 (25%)

    Lab 1

    0.25 (25%)

    Lab 2

    Final grade after retake

    0.5 (50%)

    Hertentamen

    		Must be ≥ 6

    0.25 (25%)

    Lab 1

    0.25 (25%)

    Lab 2

    Fraud and plagiarism

    The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

    Course structure

    Class Onderwerpen Studiestof
    1  Maxwell’s equations, Kramers Kronig dispersion relations, absorption efficiency/cross
    section/coefficient.     		  class slides
    2  Discrete random media; absorption by suspensions vs. absorption by solutions. Pair correlation
    function.     		 class slides
    Research paper: Duysens, absorption of suspensions vs. solutions. Derivation up to eq. 4.
    Research paper: Finlay et al, effect of pigment packing. Modern derivation of Duysens’ idea. 
    3  Optical properties of blood, light scattering by single particles, scattering
    efficiency/coefficient/cross section; phase function; scattering anisotropy. Independent scattering
    (no interference) by more than one particle.     		  class slides
    vd Hulst Chapter 2 – general formalism of light scattering. 
    4  Optical properties of blood, light scattering by single particles, scattering
    efficiency/coefficient/cross section; phase function; scattering anisotropy. Independent scattering
    (no interference) by more than one particle. Probabilistic interpretation, expectation value of the
    path length.    		  class slides
    Chandrasekhar - Appendix III page 81: explains how a Bernoulli distribution converges to a
    Poisson distribution for large number of particles.
    Rayleigh Scattering.pdf - Chapter 6 of Van der Hulst, light scattering by small particles - scattering
    by particles smaller compared to wavelength
    5  Scattering by a dilute medium (independent scattering), definition of extinction coefficient (all losses:
    absorption + scattering); effective medium, effective refractive index    		  class slides
    vdHulst Chapter 4 – wave propagation in medium containing independent scatterers.
    Research paper: Wang et al, vertex propagor model for photon transport. Only the 1D part.
    6    
    7    
    8    

    Additional information

    The first weeks, covering introductory topics, imaging, and imaging techniques, are joint with the Biomedical Optics course (Master program Biomedical Technology and Physics, Faculty of Science, VU).

    Lectures are given by experts in the respective fields. Some of the topics will be covered in an inverted/flipped classroom.

    We will facilitate laboratory tours if possible.

    Contact information

    Coordinator

    • Dierck Hillmann