University of Gondar

Institute of Technology

Department of Biomedical Engineering

Course module

Compiled By: Zarihun Huluka (BSc in Biomedical Engineering)

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Part I: Introduction to Optics/Photonics
Optics is a branch of physics that deals with the generation, transmission and detection of optical
wave. Optical wave is part of the electromagnetic wave having wavelengths longer than x-rays
and shorter than microwaves.

Optical Engineers uses the principles of optics to design and develop optical components and
optical instruments for various applications.
Photonics is essentially the science that involves generation of a photon (light), its detection, as
well as manipulation via transmission, emission, signal processing, modulation, switching,
amplification, and sensing. Most importantly, photonics involves the proper use of light as a tool
for the benefit of humans. Most photonics applications, even though they cover all technical
applications over the entire electromagnetic spectrum, range from near-infrared light to visible
region.

Biophotonics

Biophotonics is a multidisciplinary category under photonics, which involves the fusion of

photonics and biomedical sciences. Biophotonics defined as the science of generating and
harnessing light (photons) to image, detect and manipulate biological materials. It is applied in
Medicine and Dentistry to understand, diagnosis and treatment of diseases. Biophotonics mainly
involves the interaction between light with biological tissues, and is used to study biological tissues
and biological processes at different scales that ranges from micro to nano-levels. Biophotonics

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integrates Lasers, Photonics, Nanotechnology and Biotechnology. This integrated approach
provides new dimension for diagnostics and therapeutics. This rapidly growing new discipline will
have a major impact on health care.

Applications of Photonics

Photonics have uses in almost every aspect of our life, ranging from daily life to highly innovative

science. For instance, information processing, telecommunications, light detection, metrology,

lighting, spectroscopy, photonic computing, holography, medical field (surgery, vision correction,
health monitoring and endoscopy), fighting machinery, visual art, agriculture, laser material
processing, robotics, and biophotonics. Economically significant uses of photonic devices include
fiber optic telecommunications, optical data storage, displays, optical pumping of high-power
lasers and laser printing. Prospective applications of photonics are practically limitless and include
medical diagnostics, organic synthesis, information, and communication, as well as fusion energy:
- Telecommunication: optical down-converter to microwave, and optical fiber communications
- Medical applications: laser surgery, poor eyesight correction, tattoo removal and surgical
endoscopy
- Manufacturing processes in industries: involves the use of laser in welding, cutting, drilling,
and many surface modification techniques
- Building and construction: smart structures, laser range finding, and laser leveling
- Space exploration and aviation: including astronomical telescopes
- Military operations: command and control, IR sensors, navigation, mine laying, hunt and
salvage, and discovery
- Metrology: range finding, frequency and time measurements
- Photonic computing: printed circuit boards, and quantum computing
- Micro-photonics and nanophotonics.

Biomedical applications of Optics

Photonics is a light based optical technology that is considered as the leading technology. Most
applications of photonics in health care are based on various types of light and different types of
photon tissue interactions.

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Optics has two biomedical applications; Diagnostic application (for determining diseases) and
Therapeutic (for treating diseases). This happens when light and tissue interact each other.
Where tissue affects light, it is used for diagnostic applications (Imaging and monitoring). For
example, Microscopes, Optical Coherence Tomography (OCT), Pulse Oximeter, Laser Doppler,

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Flowmetry (LDF) Glucose meter

Where light affects tissue, it is used for therapeutic applications (Cutting, coagulating, oxidizing,
etc). For example, PDT (Photodynamic therapy), Refractive error correction (LASIK)

Biophotonics in Medical diagnosis

 Laser optical, photonic and biophotonic principles revolutionize diagnostic investigational

and clinical medicine. Light-based technologies are often contact free, have little impact
on the integrity of living matter and can therefore easily be applied in situ. Many old
examples of the introduction of optical sensors in medicine exist, for example in
recirculation of indicator substances and flow measurements in vivo and a multitude of in-
vitro applications for analytical purposes.
 Advanced optical technologies in medicine now help to detect and monitor cellular
biochemistry and function, tissue characteristics and integrity of organs. They do so by the
application of lasers (including femtosecond lasers), photonic and biophotonic metrology
and imaging in diagnostic and analytical medicine.
 Tissue, cells, proteins and DNA are labeled with optical tags and their fluorescence or
incandescence is measured and modifications interpreted according to the physiological or
pathological (functional) situation.
 Fluorescence spectroscopy, light absorption and scattering analysis, angle-resolved low
coherence interferometer and spontaneous biophotonic activity also offer opportunities for
non-invasive tissue or blood/body fluid analysis.
 Sophisticated laser technology has allowed the visualization of vasculature and other
structures of the retina and the optic nerve head to diagnose ocular diseases precisely.
Visualization of changes in ocular capillaries also allows the diagnosis of general vascular
disorders. Examples for such diagnostic tools are laser scanning systems, laser polarimetry,

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 optical coherence tomography, all of which allow to obtain precise information about the
retinal vessels, the retina, the retinal pigment epithelium and the choroid.
 Furthermore metabolic products like lipofuscin can be used to judge disease processes in
the retina and help to determine the dignity of tumors of the choroid. Further improvement
of the resolution of imaging techniques allow progress into the cellular or molecular level.
 The combination of optical with endoscopical methods allows the evaluation of
dysfunction of swallowing and phonation. The simulation and analysis of deglutition and
phonation is performed as a basis to optimize reconstructive surgery in tumor patients.

Biophotonics in Medical therapy

 In the field of therapy, sensor controlled laser systems have the potential to optimize the
outcome of surgery and to minimize complications especially when bone has to be cut.
 Osteotomies performed with laser systems promise improved results. The effect of lasers
is based on photoablation.
 However, when using a laser system it is hard to control the depth of the cut. Therefore it
is desirable to develop closed-loop control systems that allow performing safe laser
osteotomy without damaging internal and surrounding tissues.
 The aim of the control mechanism is to detect different tissue structures during the
application of laser energy. Emissions caused by the interaction of laser light and tissue
surfaces are registered to stop laser tissue ablation as soon as the characteristics change,
i.e. when the bone has been cut through, so as not to destroy the surrounding soft tissues.
The interaction of laser and tissue cause’s optical and acoustic emissions such as burn- or
pyrolysis lights, thermal radiation, air- and structure-borne sounds. Photodiodes,
pyrometers, microphones and piezoelectric accelerometers are suitable for detecting such
emissions.
 Sensor controlled laser systems are a focus in the field of therapy. They have been already
applied in experimental trials with living tissues as well as in humans. Another focus is the
destruction of tumor tissue and intraluminal calculi by medical lasers. Tumors are
nowadays destroyed by photodynamic therapy and by vaporization using various laser
sources.

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 The development of sensors for malignant tissue in combination with laser sources for
specific, efficient and safe tissue destruction is investigated. New materials, laser sources
and application devices need to be developed for more cost-efficient use and wider
distribution in medical therapy.
 Calculi, in various clinical settings, are efficiently fragmented also using tissue-stone
discriminating technology. Pancreatic stones are particularly difficult to sense and to
destroy, and their spectroscopic and mechanical characteristics need to be reinvestigated.
 Refractive corneal surgery uses advanced wave-front analysis techniques to provide
algorithms, which are used for treatment of refractive errors with excimer and femtosecond
lasers. The further development of laser techniques will enable the reliable treatment of
myopia as well as hyperopic and astigmatism.
 One of the great dreams of mankind is artificial vision, which through opto-mechanical
stimulation allows the provision of sight for ocular blindness. The space could allow for
supplementation of the visual pathway with useful information in diseases which normally
would cause blindness. In the future, direct stimulation of the visual cortex with electrical
signals from video systems might even bypass the eye and allow for a new era of artificial
vision.

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Part II: Light-tissue interaction

Light can interact with biological tissues in numerous ways. These interactions modify the
characteristics of the re-emitted light, which can be measured to provide information about the
tissue. Measuring the intensity of the reemitted light as a function of its wavelength is the basis of
spectral analysis.

The energy of a photon is proportional to the frequency of the light wave, f, or inversely
proportional to its wavelength (f = c/A; c = speed of light). Photons of a shorter wavelength (higher
frequency) have more energy than those of longer wavelengths (lower frequency). As light
interacts with tissue structures, part or all of their energy may be transferred to the tissue, changing
its energy (or wavelength) of the re-emitted photons.

A portion of the light will be reflected. The remainder will be transmitted into the tissue, where it
may undergo one of various fundamental interactions. For example, here we consider four types
of interactions most important for diagnostic tissue spectroscopy.

1. Elastic scattering (single scattering and diffuse scattering)

2. Absorption
3. Fluorescence
4. Raman scattering.

All of these interactions are dependent on the structural and biochemical composition of the tissue.

1. Elastic scattering

An elastic scattering event redirects an incident light ray without changing its wavelength. The
extent to which light is scattered is a function of the density of particles, the particle size, and the
ratio of the refractive indices of the particles relative to the medium. Thus, the scattered light
provides information about structures within the medium, predominantly those structures that have
the highest refractive index mismatch relative to their surroundings.

2. Absorption

The intensity of this scattered light can be further reduced due to the presence of absorption.
Molecules and atoms can absorb incident light, converting the light's energy into internal energy.

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The energy of visible and UV light can elevate the electrons in molecules and atoms to excited
(higher) energy states. These energy states exist as discrete levels, and can be excited only by
photons of a frequency that corresponds to that energy level. See the following figure below. The
structure of the molecule determines which incident frequencies will be absorbed.

3. Fluorescence

In many cases light absorbed by a molecule is converted into heat. However, an absorbed photon
can also be re-emitted as fluorescence. Fluorescence emission typically occurs at a lower energy
(longer wavelength) than the absorption energy of the incident photons. See the following figure
below. The difference in wavelength between the incident light and fluorescence is known as the
Stokes shift.

Fluorescence tends to be more dominant in the UV than in the IR. Fluorescence spectra in tissue
can be used to identify fluorophores and monitor their concentrations. Various tissue fluorophores
include metabolic substances such as nicotinamide adenine dinucleotide (NADH) and flavins,
aromatic amino acids such as tryptophan, tyrosine and phenylalanine, structural proteins such as
collagen and elastin, several porphyrins, and lipids such as ceroid and lipofuscin. Each of these
fluorophores has specific wavelengths for excitation and emission.

4. Raman Scattering

Raman spectroscopy is a technique that measures the frequency shift and intensity of light in-
elastically scattered from molecules. In Raman scattering, a specific form of inelastic scattering

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important in probing biological tissue, the internal energy process is molecular vibration
(occasionally rotation. The incident wave sets the molecule into motion, and the energy of the
scattered photons is reduced by this amount of energy. This change in energy manifests itself as a
shift in frequency, which corresponds to the transfer of energy to or from the sample's vibrational
or rotational modes. The intensity pattern of the scattered light produces a fingerprint of the
scattering molecule. In the Raman effect, spectral information is encoded as frequency shifts in
the scattered light; every molecule has its own distinct set of vibrations, hence its own
characteristic frequency shifts. Raman frequency shifts are always the same, regardless of the
wavelength of the incident light. This gives an important degree of flexibility in generating a
Raman spectrum; UV, visible, or IR excitation light can all be used, and in each case the Raman
fingerprints will be the same. The incident wavelength can thus be tailored to the specific
application, in contrast to many spectroscopic techniques.

Figure 1.1: Fundamental light-tissue interactions

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There are four major categories of light-tissue interactions that lead to alteration of the tissue
structure /composition (for therapeutic application):
1. Photochemical interaction: Absorption of light by molecules present or added to tissue.
2. Photothermal interaction: Biological effects due to deposition of thermal energy in
tissue.
3. Photoablative interaction: in UV, photons possess sufficient energy to cause photo-
dissociation of bio-polymers and subsequent desorption of fragments (a substance is
released from or through a surface).
4. Photomechanical interaction: occurs at high fluence rates where dielectric breakdown of
tissue is induced which can lead to plasma formation. Rapid plasma expansion generates a
shock wave which can rupture tissue.
The biological tissue interaction is determined by the laser irradiance or power density [W/cm2].
For example, lasers used for medical applications must have fluences ranging from 1 J/cm2 to
1000 J/cm2.

The exposure time (s):- is also responsible for the variety of interaction mechanisms:
When exposure times 1min-1ms: thermal interactions

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When exposure times 1ms-1ns: photoablation
When exposure times > 1s: photochemical interactions

When exposure times <1ns: plasma-induced ablation and photodisruption. The differences
between those two are due to different energy densities (Plasma-induced ablation based on
ionization, photodisruption based on mechanical effects).

1. Photochemical interaction
Light can induce chemical effects and reactions within macromolecules or tissues. For example,
Photodynamic therapy (PDT):- spectrally adapted chromophores are injected into the body.
Monochromatic irradiation (usually red) may then trigger photochemical reactions, resulting in
certain biological transformations. A chromophore which is capable of causing light-induced
reactions in other non-absorbing molecules is called photosensitizer (PS)(organic dyes).
2. Photothermal interaction
Thermal interaction: large group of interaction types where the increase in local temperature is the
significant parameter change. The damage done to the tissue depends on the temperature that is
reached, and the duration at which it is held at that temperature.
For the energy in the photons to end up as heat in tissue, two things must happen:
i. Absorption: The absorption of a photon promotes the molecule A to an excited state
A*.
A + hv A*
ii. Deactivation (non-radiative decay): Collisions with some partner M lead to a
deactivation of A* and an increase in the kinetic energy of M. An increase in the kinetic
energies of the molecules is, on a macro-scale, an increase in the temperature of the
tissue.
A* + M (KE) A + M (KE + ∆KE), KE is the kinetic energy
i.e

3. Photoablative interaction
It involves the use of UV light. It is based on the fact that material is decomposed when exposed
to high intense laser irradiation. It is very predictable and precise in the etching process. Let us

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assume that two atoms A and B are bound by a common electron. Absorption of a UV photon may
promote them to an excited state (AB)*.
i. Excitation:
AB + hv (AB)*
ii. Dissociation: If the energy gain exceeds the bond energy, the two atoms may dissociate
at the very next vibration.
(AB)* A + B + KE
i.e

4. Photomechanical interaction
Photomechanical effects include plasma-induced ablation and
photodisruption.
 Plasma-induced ablation:
- For very high power densities in solids and fluids optical breakdown occurs. The physical effects
of that are plasma formation and shock wave generation.
 Photodisruption:
- If optical breakdown occurs,inside soft tissues, cavitation and jet formation can also take place
(more mechanical).
Plasma is one of the four fundamental states of matter (the others being solid, liquid, and gas).
Ionization is the process by which an atom or a molecule acquires a negative or positive charge
by gaining or losing electrons to form ions. It can result from the loss of an electron after collisions
with sub atomic particles, with other atoms, or through the interaction with light.

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Ionization with subsequent electron avalanche (plasma formation – accumulation of free e- and
ions): a free e- absorbs a photon and accelerates. The accelerated e- collides with another atom and
ionizes it, resulting in two free electrons. And so forth.

Plasma-induced ablation
If the applied electric field forces ionization of tissue optical breakdown occurs leading to well-
defined removal of tissue.
i.e

Dielectric breakdown refers to plasma generation by intense electric field. Optical breakdown
refers to the fact that this field is generated using light (UV, VIS and IR).

Photodisruption
At higher pulse energies shock waves and other mechanical side effects (CAVITATION
BUBBLES and JET FORMATION) become significant and might determine the global effect
upon the tissue. Shock wave generation is associated with the expansion of the plasma (damage
at subcellular level due to short displacement length 1-4 mm). Cavitation occurs when focusing
the laser beam not on the surface of a tissue but into it. Cavitation bubbles consist of gaseous
vapors (water and carbon oxides) which diffuse again into the surrounding tissue. If cavitations
collapse in fluids and near a solid boundary, a jet formation is achieved.

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i.e

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