bme 101 biomedical optics and lasers
DESCRIPTION
BME 101 Biomedical Optics and Lasers. Instructor: Irene Georgakoudi TA: Cherry Greiner Class meeting time: T/Th: 10:30 -11:45 AM Office hours: Tuesdays, 3:00-4:30 PM Blackboard site: http://blackboard.tufts.edu Reading material on reserve (Tisch): - PowerPoint PPT PresentationTRANSCRIPT
BME 101 Biomedical Optics and Lasers
Instructor: Irene Georgakoudi
TA: Cherry GreinerClass meeting time: T/Th: 10:30 -11:45 AM
Office hours: Tuesdays, 3:00-4:30 PM
Blackboard site: http://blackboard.tufts.eduReading material on reserve (Tisch):
Handbook of Biomedical Photonics, Tuan Vo Dinh
Introduction to Biophotonics, Prasad
Biological spectroscopy, Campbell
Electo-optics library: Optics, Hecht
Evaluation• 10% Class participation• 30% Homeworks/Lab reports (due every Tuesday)
• 15% Midterm exam• 25% Final exam• 20% Final paper and presentation
– 10-15 page paper on specific molecular imaging method and its impact on a clinical problem
» Introduction» Theoretical background of method» Background on clinical problem» Instrumentation» Methods/Results» Advantages/Disadvantages» Suggested improvements
What is biomedical optics?
• Biomedical optics is typically defined as the area of study of methods/technologies based on the use of visible light (applications cover UV-NIR) for:– Improving basic understanding of biological
processes (from gene to tissue level)– Enhancing the detection and treatment of
human diseases (from acne to atherosclerosis and cancer)
Syllabus
• Basic principles
• Spectroscopic methods
• Microscopy and Imaging
• Photodynamic Therapy/Flow Cytometry
Basic Principles
• Light matter interactions– Basic wave definitions– Schrodinger’s equation
-Bonds and orbitals
-Biological chromophores
kzttz o cos,
Basic Principles
• Laser basics– Principles of operation
• Stimulated emission• Critical inversion• Pumping schemes
– Major laser components– Laser beam properties– Diode lasers
Cell and Tissue basics• Cell basics
– Major cellular components– Origins of intrinsic cellular
optical signals
• Tissue basics– Major epithelial types– Connections to disease and optical
sources of contrast
Spectroscopic methods
• Absorption• Scattering• Fluorescence
Epithelium
Connective Tissue
Spectroscopic methods• Basic Theoretical principles
• Instrumentation
• Applications
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Source
Polarizer
Filters
BeamSplitter
CCD
Tissue
Polarizer
Mirror
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1.5
EnlargedNuclei, %
mm
mm40-50
30-40
20-30
10-20
Non-dysplasticmucosaAdenoma
AdenomaAdenoma
NormalNormal
0 2 4 6 8 10
20
18
16
14
12
10
8
6
4
2
0y (cm)
x (c
m)
Colon cancer
Breast cancer
800 1000 1200 1400 1600 1800
-0.5
0
0.5
1
Raman Shift (cm-1)
Inte
nsi
ty (
a.u
.)
DataFitResidual
atherosclerosis
Microscopy and Imaging• Basic Principles
4-Pi microscopyMitochondrial network of live bacterial cell
80 nm res
From organelles to cells
Triple stained endothelialCell of pulmonary artery
From
cel
ls
to ti
ssue
s
Engineered tissue:Fibroblast (red) in collagen matrix (green)Endogenous signal
From
tissues to
animals
Tumors and blood vessels imaged in vivo
Confocal in vivo H&E “En face” SECTION of human skin
From
anim
als to
hum
ans
Optical imaging of cell-matrix interactions
Excitation wavelength: 488 nmGreen channel: 485-490 nm (scattering)Red channel: 500-620 nm (GFP fluorescence)Stack size: 238x238x125 mImages acquired using 63X, 1.2 NA, water immersion objective
Collagen gel embedded with GFP-expressing fibroblasts
Leica TCS SP2 confocal microscope
Photodynamic Therapy
• Basic Principles
• Applications
1O2
3O2
C ollisionalQuenching
Ground StateTriplet Oxygen
Excited stateSinglet oxygen
Type II: Oxygen radicals
Type I: Free radicals
C YTOTOXIC ITY
Ground State So
Exited SingletState S1
Excited Triplet State T1A
bsorption
Fluorescence
Phosphorescence
1O2
3O2
C ollisionalQuenching
Ground StateTriplet Oxygen
Excited stateSinglet oxygen
Type II: Oxygen radicals
Type I: Free radicals
C YTOTOXIC ITY
Ground State So
Exited SingletState S1
Excited Triplet State T1A
bsorption
Fluorescence
Phosphorescence
Maculardegeneration
Flow Cytometry
• Basic Instrumentations
• Advanced Methods
• Reading assignment:
• Introduction to biophotonics, ch. 1 and 2.1
• Lecture notes
• Also posted on the blackboard site:– Calculus review– Electromagnetic waves review
Biomedical opticsExploiting interactions of light with matter
Wavelengths used typically: 300-900 nm
Why biomedical optics?
• Major advantages: non-invasive; high resolution• Continuous or repetitive monitoring• Study/characterize process/disease in natural
environment (no artifacts)• More sensitive/accurate monitoring• Real-time information
– Triage with therapy– Accurate dosimetry– Psychological impact
A bit of optics history
It all started with the Greeks…
Plato (427-347 BC)
Believer of extramission theory: Eye emits a “fire” providing man the capability of vision by seizing objects
It all started with the Greeks…
Aristotle (384-322 BC)
Light emitted by a source is captured by the eyes when reflected by an object
• Euclid (circa 325-265 BC)• Treatise entitled
“Catoptrics”• Foundations of geometric
optics• First law of reflection
It all started with the Greeks…
Galen of Pergamum (Claudius Gelenus: 130-201 AD)
• Described anatomical details of the eye
• Identified lens as principle eye instrument
• Believed in extramission theory
It all started with the Greeks…
Philosophers from the Middle-East followed…
Mohammad ibn Zakariya al-Razi (864-930AD)
• Also known as Rhazes • Observed that pupil
contracts in response to light
Philosophers from the Middle-East followed…
Abu Ali al-Hasan ibn al-Haytham (965-1040 AD)
• Also known as Alhazen• Considered by some as the father of
Optics• Wrote comprehensive treatise on
optics (Katib-al-Manazir/Book on Optics), translated in Latin in 1270– Proved that extramission theory is not
correct– Detailed description of human eye – Theory of vision which prevailed until
17th century– Discussed primary and secondary light
sources, light propagation and colors– Studied spherical and parabolic mirrors– Laws of reflection and refraction
Western philosophers/scientists
Leonardo da Vinci (1452-1519 AD)
• Initially believed in extramission, but later changed his view in support of external light sources based on experiments he performed with ox eyes
Western philosophers/scientists
Johannes Kepler (1571-1630)
• Established retinal image formation theory based on experiments with ox eyes
• Law of refraction for small angles of incidence
Theories on nature of light:Light as a particle vs. Light as a wave
• Only corpuscular theory of light prevalent until 1660
• Francesco Maria Grimaldi (Bologna) described diffraction in 1660
Light as a particle
Sir Isaac Newton (1642-1727)• Embraces corpuscular theory of
light because of inability to explain rectilinear propagation in terms of waves
• Demonstrates that white light is mixture of a range of independent colors
• Different colors excite ether into characteristic vibrations---sensation of red corresponds to longer ether vibration
Light as a wave
Christiaan Huygens (1629-1695)Huygens’ principle (Traite de la
Lumière, 1678):Every point on a primary
wavefront serves as the source of secondary spherical wavelets, such that the primary wavefront at some later time is the envelope of these wavelets. Wavelets advance with speed and frequency of primary wave at each point in space
http://id.mind.net/~zona/mstm/physics/waves/propagation/huygens1.html
Light as a wave
Thomas Young (1773-1829)
1801-1803: double slit experiment, showing interference by light from a single source passing though two thin closely spaced slits projected on a screen far away from the slits
http://vsg.quasihome.com/interfer.htm
Light as a waveAugustine Fresnel (1788-
1827)
1818: Developed mathematical wave theory combining concepts from Huygens’ wave propagation and wave interference to describe diffraction effects from slits and small apertures
Electromagnetic wave nature of light
• Michael Faraday (1791-1865)
• 1845: demonstrated electromagnetic nature of light by showing that you can change the polarization direction of light using a strong magnetic field
Electromagnetic theory
• James Clerk Maxwell (1831-1879)
• 1873: Theory for electromagnetic wave propagation
• Light is an electromagnetic disturbance in the form of waves propagated through the ether
Quantum mechanics• 1900: Max Planck postulates that
oscillating electric system imparts its energy to the EM field in quanta
• 1905: Einstein-photoelectric effect– Light consists of individual energy quanta, photons,
that interact with electrons like particle• 1900-1930 it becomes obvious that concepts
of wave and particle must merge in submicroscopic domain
• Photons, protons, electrons, neutrons have both particle and wave manifestations– Particle with momentum p has associated
wavelength given by p=h/• QM treats the manner in which light is
absorbed and emitted by atoms
Max Planck
Niels Bohr
Louis de Broglie
Schrödinger
Heisenberg
Wave definitions
Classical Description of Light
Wave Equation (derived from Maxwell’s equations)
Any function that satisfies this eqn is a wave
It describes light propagation in free space and in time
operatorLaplacian
fieldinductionmagnetic
fieldelectricE
lightofspeedc
wheretc
t
E
cE
2
2
2
22
2
2
22
,
1
1
B
BB
(see calculus review handout)
Classical Description of Light Plane Wave Solution
One useful solution is for plane wave
frequencyangular
vectornpropagatioornumberwavek
where
eBB
eEeeEEtrki
o
trkio
tirkio
,
E
B
r
Classical description of lightConsidering only the real part of the previous solution to make things simpler, we have for the electric field propagating along one dimension, z
kzttz o cos,
(or distance)
0
Period
time
angle) to timeconverts(2
2
)angle todistance converts(2
)/(1
)(sec
)(
frequencyangular
wavenumberk
Hzorscyclesfrequencyc
ondsperiod
meterswavelength
Light as a wave: Basic concepts• Phase of a wave is the offset of
the wave from a reference point o
• We typically talk about a phase shift
• When light interacts with matter (e.g. as it travels through a biological specimen), its speed of propagation slows down. The wave emanating from the specimen exhibits a phase shift when compared with the initial wave
• The refractive index , n, and the thickness of a specimen determine by how much the wave is retarded
Green-incident waveBlue-wave after passing through specimen shifted by /4
in vacuumlight of speed where, cc
n
Phase==t-kz
Monochromatic (only onewavelength/frequency)waves traveling in phase
Monochromatic (only onewavelength/frequency)waves traveling out of phase
Phase==t-kz
Coherent Light
Incoherent Light
Incoherent Light
Constructiveinterference
Destructiveinterference