Biomedical Optics II

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Monte Carlo Modeling of
Photon Transport

2011/09/28

Radiative Transfer in Living

Tissue
How to
solve the
problem?

Maxwells
equations?

Modeling
based on
scattering
and
absorption
Monte Carlo
simulation

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Radiative
transfer
equation
2

Monte Carlo

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Monte Carlo
Simulations
The simulations treat photons as neutral particles
rather than as a wave phenomenon.
It is assumed that the photons are multiply
scattered by tissues. Sometimes, phase and
polarization are assumed to be randomized and
can be ignored.

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Introduction
Photon transport in biological tissue can be
numerically simulated by the Monte Carlo method.
The trajectory of a photon is modeled as a
persistent random walk, with the direction of each
step depending on that of the previous step.
By contrast, the directions of all of the steps in a
simple random walk are independent.
By tracking a sufficient number of photons, we can
estimate physical quantities such as diffuse
reflectance.
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Monte Carlo
The medium is random Use dice to build it

A system with known probability distributions

(scattering and absorption)
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Definition of Monte Carlo

Method
From Lux and Koblinger:
In all applications of the Monte Carlo method, a stochastic
model is constructed in which the expected value of a
certain random variable (or of a combination of several
variables) is equivalent to the value of a physical quantity
to be determined.
This expected value is then estimated by the average of
multiple independent samples representing the random
variable introduced above.
For the construction of the series of independent samples,
random numbers following the distribution of the variable
to be estimated are used.
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The photon propagation is random and determined by tissue optical properties:

1. Distance to next scattering event? Apply "dice" with properties set by the
mean free-path-length (determined by the scattering and absorption
coefficients) to set the path length before a scattering or an absorption
event occur.
2.

Direction after scattering? Apply "dice" with phase function + anisotropy

of scattering to set the scattering angles.

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Main advantage
No limitation concerning boundary conditions or
spatial localisation of inhomogeneities in the tissue
>> Flexiblility
Main disadvantage
Problem of getting good statistics, particularly if the
point of interest is located far away from the point of
entry of the light and the scattering and absorption
coefficients are high >> long CPU time
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Ensemble Averaging
It is important to realize that the Monte Carlo method estimates
ensemble-averaged quantities.
An ensemble of biological tissues is modeled for the average
characteristics of photon transport; the ensemble consists of all
instances of the tissues that are microscopically different but
macroscopically identical.
Rules are defined for photon propagation from the probability
distributions of, for example, the angles of scattering and the step
sizes.
The statistical nature requires tracking a large number of photons,
which is computationally time-consuming.
Multiple physical quantities can be simultaneously estimated,
however.
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Simplifications
In this chapter, photons are treated as waves at
each scattering site but as classical particles
elsewhere.
Coherence, polarization, and nonlinearity are
neglected.
Structural anisotropy--not to be confused with
scattering angular anisotropy--in tissue
components, such as muscle fibers or collagens, is
neglected as well.
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Three Major Sampling

Procedures
Determine the spatial interval between two
successive interaction events
Determine the scattering angle
Determine the survival of the photon

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The variables that govern Monte Carlo

The mean free path for an absorption or
scattering event
Step size (function of a and s)

The scattering angle

Deflection angle, (function of anisotropy,
g)
Azimuthal angle,

Random number generators will be used

for the selection of step size, deflection
angle and azimuthal angle for sampling
from known probability density functions
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 Consider an experiment in which a laser beam strikes a target such

as a cylindrical cuvette containing a dilute solution of scattering
particles. The scattering pattern p() is measured by a detector that
is moved in a circle around the target while always facing the target.
Hence the detector collects light scattered at various deflection
angles in a horizontal plane parallel to the table top on which the
apparatus sits. The proper definition of anisotropy is the expectation
value for cos():
It is common to express the definition of anisotropy in an equivalent
way:

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Basis for the Monte Carlo

method
The Monte Carlo method as its name implies
(throwing the dice) relies on the random sampling
of a probability density function based on a computer
generated random number
Need to understand definitions for probability
density functions and probability distributions

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Scattering and Absorption

Probability
d

Beer-Lambert law

I0

I(d)

I (d ) I 0 e d , ( represents scattering or absorption coefficient)

The probability of the photon passing through the medium

without scattering or absorption is:

Within any infinitesimal interval ds, the probability of being

scattered or absorbed is:
ds
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Henyey-Greenstein Phase
Function
Henyey and Greenstein (1941) devised an expression which mimics
the angular dependence of light scattering by small particles, which
they used to describe scattering of light by interstellar dust clouds.
The Henyey-Greenstein scattering function has proven to be useful
in approximating the angular scattering dependence of single
scattering events in biological tissues.

Which is approximately used by Henyey-Greenstein function

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Homework 1: reproduce this plot with Matlab.

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Definition of Problem
The problem to be solved begins with an
infinitely narrow photon beam, also
referred to as a pencil beam, that is
perpendicularly incident on a multilayered scattering medium (Figure 3.1);
various physical quantities are computed
as responses.
The pencil beam can be represented by
an impulse (Dirac delta) function of
space, direction, and time; thus, the
responses are termed impulse responses
or Greens functions.
Although never infinitely wide in reality,
a layer can be so treated if it is much
wider than the photon distribution.
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Optical Properties
Each layer is described by the following
parameters:
thickness ,
refractive index ,
absorption coefficient ,
scattering coefficient ,
scattering anisotropy .

The top and the bottom ambient media are each

described by a refractive index.
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Coordinates

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How to sample random

variables
Consider a random variable x needed for a Monte
Carlo simulation. Then there is a probability
density function p(x) of x , which defines x over
the interval such that: a x b

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Sample random
variables
The probability that x will fall in
the interval [a, x1] is given by the
distribution function F(x1),
defined as:
x1

F ( x1 ) p ( x)dx
a

where x1 is a random variable.

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Sample random
variables
By using a computer random number generator,
one can obtain a random number in the range [0,
1]. The probability density function for this
random number is 1 in the range [0, 1].
The corresponding probability distribution is
1

F (1 ) p ( )d 1 [0,1]
a

where p(x)=1, a<x<b.

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This means that the random number picked gives

the integrated value of p(x), that is :
x1

1 F ( x1 ) p ( x)dx
a

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For generality, we replace the variables, 1 and x1

by the continuous variables, and x:
x

p ( x)dx
a

This is the basic equation for sampling x from p(x)

based using a randomly generated number, over
the interval [0,1]

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Generation of Random Numbers

p x dx

Cumulative density function(CDF)

then the sampling can be calculaed by

P 1 ( ), is a uniform random number in 0,1

p(x )

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P( ) a p( x )dx

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Selecting the step size, s

The step size of the photon is calculated based on
sampling the probability for the photons mean free
path
If step size too small, MC is inefficient, but if step
size is too large, poor approximation of real photon
travel
Choose step size from probability density function
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The total attenuation coefficient

Recall that the probability of interaction of a photon
with a medium per unit path length is:
P[s1,s1+ds1]=tds1

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The total attenuation coefficient

The probability of interaction of a photon with a
medium per unit path length is related to the gradient
of transmission:

dT ( s1 )
t ds1
T ( s1 )

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The total attenuation coefficient

The probability distribution function (from Beers
law) is defined as:

P ( s s1 ) T ( s1 ) exp( t s1 )
P ( s s1 ) 1 T ( s1 ) 1 exp( t s1 )

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Final expression
Solving for s yields:

ln
s
t

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Sampling the Step Size

Cumulative distribution function of step size :
P s 1 exp( t s )
Inverse distribution method :
1 exp( t s )
Sampled step size :
ln 1
ln
s
or s
t
t
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Sampling the Scattering Angle

Henyey-Greenstein phase function:
1 g2
p(cos )
, 0,
2
3/2
2(1 g 2 g cos )

Sampled scattering angle:

2
1

g
2
1 g

cos 2 g
1 g 2 g

2 1

if

g0

if

g 0

Sampling the Azimuthal

Scattering Angle

[0, 2
1
p
2
2
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Moving the Photon Packet

x x x si
y y y si
z z z si
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Absorption

a
W
W
t
W W W

Update of Photon Propagation

Direction
'x
'y

sin ( x z cos y sin )

1

2
z

sin ( y z cos x sin )

1

2
z

x cos ,
y cos ,

'z 1 z2 sin cos z cos .

If z 1, then 'x sin cos , 'y sin sin , 'z sgn z cos .
Note : Prescatte ring photon propagation k has polar and azimuthal angles 0 , 0 .

To transform from global coordinates x, y , z to local coordinates x ' , y ' , z ' ,

(1) Rotate x, y , z about z for 0 to get intermediate coordinates x * , y * , z * .
(2) Rotate x * , y * , z * about y * for 0 to get x ' , y ' , z ' .

Postscattering photon propagation k ' along z has polar and azimuthal angles , in x ' , y ' , z ' .
Alternative solution exists.

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Please go to Jianan Qus ppt: 13b.pdf and 13c.pdf.

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Monte Carlo Program

int main ()
{
albedo = mu_s / (mu_s + mu_a);
rs = (n-1.0)*(n-1.0)/(n+1.0)/(n+1.0); /* specular reflection */
crit_angle = sqrt(1.0-1.0/n/n);
/* cos of critical angle */
bins_per_mfp = 1e4/microns_per_bin/(mu_a+mu_s);
for (i = 1; i <= photons; i++){
launch ();
while (weight > 0) {
move ();
absorb ();
scatter ();
}
}
print_results();
return 0;
}
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Monte Carlo Program

void launch() /* Start the photon */
{
x = 0.0; y = 0.0; z = 0.0;
u = 0.0; v = 0.0; w = 1.0;
weight = 1.0 - rs;
}
void bounce () /* Interact with top surface */
{
double t, temp, temp1,rf;
w = -w;
z = -z;
if (w <= crit_angle) return;

/* total internal reflection */

t
= sqrt(1.0-n*n*(1.0-w*w));
/* cos of exit angle */
temp1 = (w - n*t)/(w + n*t);
temp = (t - n*w)/(t + n*w);
rf = (temp1*temp1+temp*temp)/2.0;
/* Fresnel reflection */
rd += (1.0-rf) * weight;
weight -= (1.0-rf) * weight;
}
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Monte Carlo Program

void move() /* move to next scattering or absorption event */
{
double d = -log((rand()+1.0)/(RAND_MAX+1.0));
x += d * u;
y += d * v;
z += d * w;
if ( z<=0 ) bounce();
}
void absorb () /* Absorb light in the medium */
{
int bin=z*bins_per_mfp;
if (bin >= BINS) bin = BINS-1;
heat[bin] += (1.0-albedo)*weight;
weight *= albedo;
if (weight < 0.001){ /* Roulette */
bit -= weight;
if (rand() > 0.1*RAND_MAX) weight = 0; else weight /= 0.1;
bit += weight;
}
} College of Engineering, Peking University

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Monte Carlo Program

void scatter() /* Scatter photon and establish new direction */
{
double x1, x2, x3, t, mu;
for(;;) {
x1=2.0*rand()/RAND_MAX - 1.0;
x2=2.0*rand()/RAND_MAX - 1.0;
if ((x3=x1*x1+x2*x2)<=1) break;
}
if (g==0) { /* isotropic */
u = 2.0 * x3 -1.0;
v = x1 * sqrt((1-u*u)/x3);
w = x2 * sqrt((1-u*u)/x3);
return;
}

/*new direction*/

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Monte Carlo Program

mu = (1-g*g)/(1-g+2.0*g*rand()/RAND_MAX);
mu = (1 + g*g-mu*mu)/2.0/g;
if ( fabs(w) < 0.9 ) {
t = mu * u + sqrt((1-mu*mu)/(1-w*w)/x3) * (x1*u*w-x2*v);
v = mu * v + sqrt((1-mu*mu)/(1-w*w)/x3) * (x1*v*w+x2*u);
w = mu * w - sqrt((1-mu*mu)*(1-w*w)/x3) * x1;
} else {
t = mu * u + sqrt((1-mu*mu)/(1-v*v)/x3) * (x1*u*v + x2*w);
w = mu * w + sqrt((1-mu*mu)/(1-v*v)/x3) * (x1*v*w - x2*u);
v = mu * v - sqrt((1-mu*mu)*(1-v*v)/x3) * x1;
}
u = t;
}

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Monte Carlo Program

void print_results() /* Print the results */
{
int i;
printf("%s\n%s\n\nScattering = %8.3f/cm\nAbsorption = %8.3f/cm\n",t1,t2,mu_s,mu_a);
printf("Anisotropy = %8.3f\nRefr Index = %8.3f\nPhotons = %8ld",g,n,photons);
printf("\n\nSpecular Refl
= %10.5f\nBackscattered Refl = %10.5f",rs,rd/(bit+photons));
printf("\n\n Depth
Heat\n[microns] [W/cm^3]\n");
for (i=0;i<BINS-1;i++){
printf("%6.0f %12.5f\n",i*microns_per_bin, heat[i]/microns_per_bin*1e4/(bit+photons));
}
printf(" extra %12.5f\n",heat[BINS-1]/(bit+photons));
}

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Monte Carlo Program

char t1[80] = "Small Monte Carlo by Scott Prahl (http://omlc.ogi.edu)";
char t2[80] = "1 W/cm^2 Uniform Illumination of Semi-Infinite Medium";
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#define BINS 101
double mu_a = 5;
/* Absorption Coefficient in 1/cm */
double mu_s = 95;
/* Scattering Coefficient in 1/cm */
double g = 0.25;
/* Scattering Anisotropy -1<=g<=1 */
double n = 1.5;
/* Index of refraction of medium */
double microns_per_bin = 20;/* Thickness of one bin layer */
long i, photons = 100000;
double x,y,z,u,v,w,weight;
double rs, rd, bit, albedo, crit_angle, bins_per_mfp, heat[BINS];

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Summary
Monte Carlo can simulate photon transport in
biological tissue
Three steps: move, absorb, scatter
Weight defines its alive or dead
The trajectory of a photon is modeled as a
persistent random walk. The directions are
independent.

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Further readings
http://
omlc.ogi.edu/classroom/ece532/class4/index.html
Tiny_mc.c, Small_mc.c, mc321.c:
http://omlc.ogi.edu/software/mc/
MCML download:
http://labs.seas.wustl.edu/bme/Wang/mc.html

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Homework
1. Plot the Henyey Greenstein Function with different g.
2. Write a program (in C or MATLAB) to describe a simple
random walk in x-y plane. The direction is uniformly
random in 360 degrees, and the walking step size follows
the same way of a photon transportation in a medium
with =100 /cm. Plot your result and hand in your
program. (up to 20 steps)
3. Rewrite the tiny_mc.c program to Matlab.

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Experiment: Monte Carlo

Simulation

Fiber

=633nm
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Biomedical Optics II

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Experiment: Monte Carlo

Simulation

Fiber

=633nm
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Experiment: Monte Carlo

Simulation

Fiber

=633nm
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Experiment report
Using g = 0.9, and the measured scattering coefficient as
well as other parameters, apply Monte Carlo simulation
(next experiment), then compare your simulated result
with your measured data.

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