Introduction to

Biomedical Optics: From

Theory to Applications
Polarization

Dr. Uttam M. Pal,

Assistant Professor of Biomedical Engineering,
Department of Sciences and Humanities,
IIITDM Kancheepuram - Chennai
Polarization
• Light is polarized when its electric fields oscillate in a single plane,
rather than in any direction perpendicular to the direction of
propagation.

[1] Physics: Principles with Application, D. Giancoli, 2014 Pearson Education, Inc.
2
Polarization
• Polarized light will not be transmitted through a polarized film
whose axis is perpendicular to the polarization direction.

[1] Physics: Principles with Application, D. Giancoli, 2014 Pearson Education, Inc.
3
Polarization
• When light passes through a polarizer, only the component parallel
to the polarization axis is transmitted. If the incoming light is plane-
polarized, the outgoing intensity is:

[1] Physics: Principles with Application, D. Giancoli, 2014 Pearson Education, Inc.
4
Polarization
• This means that if initially unpolarized light passes through crossed
polarizers, no light will get through the second one.

[1] Physics: Principles with Application, D. Giancoli, 2014 Pearson Education, Inc.
5
Polarization
• This means that if initially unpolarized light passes through crossed
polarizers, no light will get through the second one.

[1] Physics: Principles with Application, D. Giancoli, 2014 Pearson Education, Inc.
6
Polarization

How can the same window be opaque and transparent?

Image courtesy: Wikipedia

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Tissue Polarization
• Weakly scattering (Transparent)
• Cornea
• Crystalline lens
• Vetreous humor Slit lamp image of the cornea, iris and lens
(showing mild cataract)
• Aqueous humor of the front chamber of ye
• Strongly scattering (Opaque or Turbid)
• Skin
• Brain
• Vessel wall
• Eye sclera
• Blood
• Lymph

[1] Wikipedia
9
Depolarization Strongly scattering
𝑰𝑯 𝑰𝑽 Weakly scattering
𝑰+𝟒𝟓° 𝑰−𝟒𝟓°

Alternative Stokes Parameter

Stokes Parameter
𝐼 𝐼𝐻 + 𝐼𝑉
𝑄 𝐼 − 𝐼𝑉
𝜃 𝑆= = 𝐻
𝑈 𝐼+45° − 𝐼−45°
Depolarized
𝑉 𝐼𝑅 − 𝐼𝐿

Linearly polarized

0 < 𝐷𝑂𝐿𝑃 < 1

Fully Fully linearly

Unpolarized DOP: Degree of polarization polarized
depolarized
DOLP: Degree of linear polarization
DOCP: Degree of circular polarization
1) Arif et al., JBP, 2021

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Quantifying Depolarization (Experimental Setup)

1) Arif et al., JBP, 2021

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Fun Trivia: Which Photons will sustain the original
Polarization?

Ballistic!

[1] Guy Satat, How to See Through Tissue, MIT Media Lab
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 Circular Polarization
0° phase shift 180° phase shift
a) b)

Interference between two optical waves is determined by the relative phase

between the waves1

The superimposed waves are 90° phase shifted2

[1] Bigio, Irving J.; Fantini, Sergio. Quantitative Biomedical Optics (Cambridge Texts in Biomedical Engineering) (p. 102).
Cambridge University Press. Kindle Edition.
[2] Wikipedia
13
Circular Polarization

Left circularly polarized OR Right circularly polarized

Left circularly polarized!

The superimposed waves are 90° phase shifted

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Polarimetric Tool: Circular Polarization
• Quantify degree of circular polarization (DOCP) while operating at 850 nm and 940 nm
• Breast biopsy tissues from N = 8 patients.
𝐼 𝐼𝐻 + 𝐼𝑉 𝐼𝐻 + 𝐼𝑉 𝐼𝐻 + 𝐼𝑉
𝑄 𝐼 − 𝐼𝑉 𝐼 − 𝐼𝑉 𝐼 − 𝐼𝑉 𝑉2 𝑉
𝑆= = 𝐻 = 𝐻 = 𝐻 𝐷𝑂𝐶𝑃 = =
𝑈 𝐼𝑁 − 𝐼𝑀 𝐼𝑁 − 𝐼𝑀 𝐼𝑁 − 𝐼𝑀 𝐼 𝐼
𝑉 𝐼𝑅 − 𝐼𝐿 2𝐼𝑅 − (𝐼𝐻 + 𝐼𝑉 ) 𝐼 − 2P(0°, 45°) 0 < 𝐷𝑂𝐶𝑃 < 1
45°
Unpolarized Fully circularly
polarized
0°
𝜙
Elliptical

45°
+90°
Circular

1) Arif et al., JBP, 2021

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Stokes Parameter: Summary Light intensity measured with
the following optical device in
Alternative Stokes Parameter front of the detector
Stokes Parameter
❖ IH = Horizontal linear polarization
𝐼 𝐼𝐻 + 𝐼𝑉 ❖ IV = Vertical linear polarization
𝑄 𝐼 − 𝐼𝑉 ❖ I+45◦ = 45° linear polarization
𝑆= = 𝐻
𝑈 𝐼+45° − 𝐼−45°
❖ I-45◦ = -45° linear polarizer
𝑉 𝐼𝑅 − 𝐼𝐿
❖ IR = a right circular analyzer
❖ IL = left circular analyzer
S0 = the total irradiance
S1 = the excess in intensity of light transmitted by a horizontal polarizer over light
transmitted by a vertical polarizer

S2 = the excess in intensity of light transmitted by a 45° polarizer over light

transmitted by a 135° polarizer

S3 = the excess in intensity of light transmitted by a RCP filter over light transmitted
by a LCP filter

What we mean when we say ‘unpolarized light’: All three of

these excess quantities are zero
[1] Valery Tuchin, Tissue Optics, SPIE, 2014
[2] David Littleman lectures 16
Jones Vector
• Describes the polarization state of a wave
• Lets define the polarization state of a field as a 2D vector— (Jones
vector)
• Containing the two complex amplitudes:

[1] David Littleman lectures

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 Jones Vector (Contd.)

Ey

Ex

Horizontal polarization Vertical polarization +45° polarization

[1] David Littleman lectures

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 Jones Vector (Contd.)

Ey

Ex

In exponential form: 90° Phase shift is expressed by exp(-iπ/2)

Right circularly polarized light

Euler's Formula

Left circularly polarized light

With 90° phase shift

Circularly polarized light source

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
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Quantifying State of Polarization: Summary

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
20
 Effect on Polarization State: Jones Matrix
• To model the effect of a medium on light's polarization state, we use Jones
matrices.
• Since polarization state can be written as a (Jones) vector, one can use
matrices, A, to transform them from the input polarization, E0, to the output
polarization, E1.
1 0
 
0 0 E1 = AxE0
Ey (Jones Vector)
Ax (Jones Matrix)
(Jones Vector)  Ex   1 0  Ex 
 Ex    =   
   Ex   0   0 0  Ey 
E0 E1  
Ex  Ey   0
Input polarization Output polarization
state state

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 Effect on Polarization State: Jones Matrix
1 0 0 0
   
0 0 0 1

(Jones Vector)
Ax (Jones Matrix)
Ay (Jones Matrix)
(Jones Vector) (Jones Vector) (Jones Vector)
 Ex   Ex   Ex   0 
  E0 E1      
 Ey   0  Ey  E0 E1  Ey 
Input polarization Output polarization Input polarization Output polarization
state state state state

Jones Matrix Jones Matrix

for x-polarizer for y-polarizer

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Optical Device: Half Plate
E1 A E0 E1
 1   1 0 1 1
  =     
 − 1  0 − 11  −1
Transmission axis

E0
 1
 
 1

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
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 Effect on Polarization State: Jones Matrix
1 0 
1 0   
   0 −1
 0 −1 (Jones Matrix)
(Jones Vector)
A (Jones Matrix)
A
(Jones Vector) (Jones Vector) (Jones Vector)
 1 1 1  1
  E0 E1      
 1  −1  −1 E0 E1  1
45˚ LP -45˚ LP -45˚ LP 45˚ LP

Jones Matrix for 45˚ => -45˚ Jones Matrix for -45˚ => 45˚

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Optical Device: Quarter Waveplate
E1 A E0
 1   1 0 1
  =   
 j   0 j 1 1
 
Transmission axis  j

 1
 
 1

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
25
 Effect on Polarization State: Jones Matrix
1 0
1 0  
  0 j
0 j (Jones Matrix)
(Jones Vector)
A (Jones Matrix)
A
(Jones Vector) (Jones Vector) (Jones Vector)
 1 1 1  1 
  E0 E1      
 1  j  −1 E0 E1 − j
45˚ LP RCP -45˚ LP LCP

Jones Matrix for 45˚ => RCP Jones Matrix for -45˚ => LCP

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Optical Systems have Multiple Optical Devices:
Jones Vector

Order is counter-intuitive, but matters!

[1] David Littleman lectures
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Multiplying Jones Matrix

LPx LPy

0
E0 E1 =  
0

Ax Ay
 1 0  0 0   0 0 
AyAx =    =  
 0 0  0 1   0 0 
Transfer Function

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Multiplying Jones Matrix

LPx LP45˚ LPy

0 0  E x   0 
E0 E1 =  1  ,in  =  1 
0  E y ,in   E x ,in 
2   2 

Ax A45˚ Ay
1 1
 0 0  2  1 0   0
1
0

AyA45˚Ax =   2   =
 0 1  1 1  0 0   0
 2 
2 2
Transfer Function
θ = 45˚
[1] https://www.fiberoptics4sale.com/blogs/wave-
optics/102261126-jones-matrix-calculus 29
Optical System Setup on Optical Breadboard

https://www.youtube.com/watch?v=pR4r7gMyN5U&ab_channel=Thorlabs
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Polarization: Applications

Schematics of the experimental setup:89,93 vertical polarized light from a laser

diode (639 nm, 30 mW) is directed toward the sample at an angle 55 deg from
Schematic illustrations of experimental setup for the normal through a half wave plate (HWP) via mirror; the light is then altered
measuring the degree of circular polarization (DOCP) by a QWP into a state of right circular polarized and/or right elliptically polarized,
value from tissue slice on a microscopy slide and focused onto the surface of the tissue by a lens; the source–detector
separation d, as well as the angle of detection θ can be varied to change the
sampling volume
[1] Nishizawa, N, Al-Qadi, B, Kuchimaru, T. Angular optimization for cancer identification with circularly polarized light.
J. Biophotonics. 2021
[2] A. Doronin and I. Meglinski, “Online object oriented Monte Carlo computational tool for the needs of biomedical 31
optics,” Biomed. Opt. Express 2(9), 2461–2469 (2011)
Jones Matrix: Summary

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
32
Optical Systems have Multiple Optical Devices:
Jones Vector

Order is counter-intuitive, but matters!

[1] David Littleman lectures
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 Multiple Optical Devices: Mueller Matrices
Instead of input Jones Instead of output Jones
vector, we use input Stokes vector, we use output
vector Stokes vector

Stokes vector (S): Mueller matrix (M):

Jones vector: Jones matrix: I  m11 m12 m13 m14 
   
 Ex   a11 a12  Q  m21 m22 m23 m24 
    m
 Ey 
U  m32 m33 m34 
 a21 a22     31 
V  m m44 
   41 m42 m43
[1] David Littleman lectures
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Jones Vector/Stokes Vector
(unpolarized)

Jones Vector Stokes Vector

• Fully polarized light source • Fully polarized, partially polarized,
sadfadfadf and unpolarized light source
• Compact form • Detailed form
• More useful for coherent light • When phase of the light source
beams (maintains same phase fluctuates as it propagates
throughout the propagation) fsadfsadfsd
• Only combination of fully • Can describe light with arbitrarily
polarized light source complicated combination of
polarized and unpolarized light

35
https://www.bog5.in.ua/lection/wave_optics_lect/lect5_wave_eng.html
Jones Matrices and Mueller Matrices

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
36
 Mueller Matrix (Example 1)

LP-45°
1 1 0 −1 0  1  1
𝐼 𝐼𝐻 + 𝐼𝑉       
0 0 0 0 0 0 0
𝑄 𝐼 − 𝐼𝑉 = 0.5 = 0 . 5
𝑆=
𝑈
= 𝐻
𝐼+45° − 𝐼−45° 0 = S0 S1 
−1 0 1 0 0
 
 − 1
 
  0    0
𝑉 𝐼𝑅 − 𝐼𝐿
0  0 0 0 0  
 
Unpolarized light M1 Output intensity is 0.5 times the
initial intensity and polarized in -45°
source

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Mueller Matrix (Example 2)

LPx LPy
1 0
   
0 0
0 = S0 S1 = 0
   
0 0
   
Unpolarized light M1 M2
source 0 0 0 0
 
0 0 0 0
M2M1 = = 0 0 0 0
 
0 0 0 0 


Transfer Function

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Thank You

39
Backup Slides

40
Polarization Systems: Linear Polarizer

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
41
Polarization Systems: Linear Polarizer and Analyzer

If the transmission axis of

Analyzer is rotated by 90° to
that of the Polarizer

Analyzer is the Linear Polarizer that can be rotated

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
42
Can you draw the optical schematic with
polarization?

A piece of waxed paper between crossed polarizers

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
43
Polarization Systems: Linear Polarizers and Quarter
waveplate

[1] Eugene Hecht, Optics, 5th Edition, Pearson Education India, 2012
44