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Instruction for the command prompt usage of the steady state Monte Carlo program for objective lens based illumination and detection from a layer tissue with an embedded spherical tumor target You will need to find a C compiler to create an executable file first. If you use an Unix/Linux/Apple computer, you could download the public-domain package for MCML and use its make file to compile this code. The manual for MCML will also help you understand the principle of Monte Carlo modeling and the .mci file. A. How to run the program in Windows: Click “Start” button on the task bar in Windows, then select “Run…” menu and type in “cmd” in the blank edit box then hit “Enter” key, a command window will pop up. Change to the directory where all the exe files and sample files are located by typing “cd XXX”. XXX refers to the directory name, in which special characters, such as @, #, $ and spaces, are not allowed, because of the restriction of DOS file names. If all the files still have their original names, the following command can be used to run a steady-state Monte Carlo simulation: mcmlforinstruction tissue.mci illcoll_setup.txt The first argument “mcmlforinstruction.exe” is the exe file of the Monte Carlo program, the second argument “tissue.mci” is the input parameter file for tissue model and the third argument “illcoll_setup.txt” is the file containing illumination and collection setup information. It will be similar in an Unix/Linux/Apple computer to run the executable file in a shell or terminal window after the file is compiled and built. B. Input Parameter File: Sample file 1 shows a sample input parameter file (“tissue.mci”), in which the texts after a “#” symbol are comments. Most data lines have been explained well by the comments at the end of the lines. This sample file can be revised to run other simulations. Be aware that “No. of layers” should match the actual number of layers for which optical properties are specified. In addition, “the number of types of fluorescence” and “the number of different wavelength” should be 0 and 1 respectively for reflectance simulation, and 1 and 2 for fluorescence simulation. For reflectance simulation, only the first set of optical properties (as shown in bold font at the end of the file) will be used; while for fluorescence simulation, totally the first two sets of optical properties will be used. Because only one set of optical properties is specified in the current file, another set of optical property that will be used for the emission wavelength need to be added at the end. The user only needs to copy and paste the bolded paragraph and change appropriate numbers for the second set of optical properties. Read Sample file 2 for fluorescence simulation. Sample file 1: reflectance simulation #### # Template of input files for Monte Carlo simulation (mcml). # Anything in a line after "#" is ignored as comments. # Space lines are also ignored. # Lengths are in cm, mua and mus are in 1/cm. ####

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1.0 # file version 1 # number of runs 1000 # No. of photons 0 0 0 0.06 50 150 0.8 #Sphere parameters: radius, x,y,z,mua, mus,g 0.025000 0.030000 # dz, dr 120 20 1 # No. of dz, dr & da 0.025 0.025 #dx,dy 101 101 #nx,ny. No. of dx,dy skin_Ref.mco A # the output file name of the result for excitation wavelength 1 #the number of types of fluorescence,i.e. the set of Excitation and Emission WaveLength 405 #Excitation-->Emission 1 #the number of different wavelength #Below Specify the optical properties for each wavelength 2 # No. of layers #The 1st wavelength must be excitation wavelength 405 #The value of wavelength nonsense A # output filename(not useful any more), ASCII/Binary #n mua mus g Q.Y. d # One line for each layer 1.462000 # n for medium above. 1.4 12 500 0.8 0.8 0.05 #Layer 1 1.4 9 360 0.8 0.75 0.45 #Layer 2 1.338000 # n for medium below.

Sample file 2: fluorescence simulation #### # Template of input files for Monte Carlo simulation (mcml). # Anything in a line after "#" is ignored as comments. # Space lines are also ignored. # Lengths are in cm, mua and mus are in 1/cm. #### 1.0 # file version 1 # number of runs 1000 # No. of photons 0 0 0 0.06 50 150 0.8 #Sphere parameters: radius, x,y,z,mua, mus,g 0.025000 0.030000 # dz, dr 120 20 1 # No. of dz, dr & da 0.025 0.025 #dx,dy 101 101 #nx,ny. No. of dx,dy skin_Ref.mco A # the output file name of the result for excitation wavelength 1 #the number of types of fluorescence,i.e. the set of Excitation and Emission WaveLength 405 540 #Excitation-->Emission 2 #the number of different wavelength #Below Specify the optical properties for each wavelength

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2 # No. of layers #The 1st wavelength must be excitation wavelength 405 #The value of wavelength nonsense A # output filename(not useful any more), ASCII/Binary #n mua mus g Q.Y. d # One line for each layer 1.462000 # n for medium above. 1.4 12 500 0.8 0.8 0.05 #Layer 1 1.4 9 360 0.8 0.75 0.45 #Layer 2 1.338000 # n for medium below. 540 #The value of wavelength skin_Fiber_emm.mco A # output filename(not useful any more), ASCII/Binary #n mua mus g Q.Y. d # One line for each layer 1.462000 # n for medium above. 1.4 2.8 200 0.8 0.00000 0.05 #Layer 1 1.4 5 315 0.8 0.00000 0.45 #Layer 2 1.338000 # n for medium below.

C. Illumination and Collection Setup File: The following figures were adopted from the following reference to facilitate the explanation of the relevant parameters: C. Zhu and Q. Liu, “Numerical investigation of lens based setup for depth sensitive diffuse reflectance measurements in an epithelial cancer model,” Opt Express 20, 29807-29822 (2012).

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#178427 - $15.00 USD Received 22 Oct 2012; revised 3 Dec 2012; accepted 12 Dec 2012; published 21 Dec 2012(C) 2012 OSA 31 December 2012 / Vol. 20, No. 28 / OPTICS EXPRESS 29810

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Illumination Parameters 2 #Beam type:0-Collimated,1-Diffuse,2-4f-system 1.27 1.17 #Radius of beam(cm):r in Fig.1; Radius of center null area(cm): R in Fig.1 0 0 #Beam radial and angular profile: 0-uniform, 1-Gaussian 0 #Incident angle (degree, w.r.t. the normal axis). This will not be used when the beam type is 2 3.5 # Distance between the tissue surface and the lens 2 in Fig.1. 3.5 # Focal length of the illumination lens, i.e. Lens 2 in Fig.1. 0.35 # Not used for objective lens 35 # Not used for objective lens 1.27 # If the beam type is 2, this value is the radius of illumination lens 2 in Fig.1 1 #Refractive index of medium between the tissue surface and lens 1.47 #Refractive index of source fiber if type is not 2. 1 #Not used for objective lens 1.27 # Radius of the collimating lens for detection, i.e. Lens 2 In Fig.3 3.5 # Focal length of the collimating lens used for detection, i.e. Lens 3 in Fig.3 0.22 # Numerical Aperture of the Illumination Fiber. This is needed when the beam type is 1 Collection Parameters

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1 #Employ collecting fibers 1 #The number of collecting fibers. The number must be set to 1 when beam type is 2 or 3. #Fiber-Radius(cm) Center-to-Center-Distance(cm) Refractive-Index Numerical-Aperture Tilt-Angle; The S-D must be set to 0 when beam type is 2 0.02 0 1.47 0.22 0

D. Output file: Most output data has been normalized to unit weight of incident photons, unit depth, unit radial distance or unit angle. Sample output file 1 for the excitation wavelength (reflectance) for all photons A1 # Version number of the file format. #### # Data categories include: # InParm, RAT, # A_l, A_z, Rd_r, Rd_a, Tt_r, Tt_a, # A_rz, Rd_ra, Tt_ra #### # User time: 1 sec = 0.00 hr. Simulation time of this run. InParm # Input parameters. cm is used. steadytest1exc.mco A # output file name, ASCII. 1000 # No. of photons 0.01 0.01 # dz, dr [cm] 100 100 1 # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above 1.37 0.1 100 0.9 10 # layer 1 1.37 # n for medium below

# The above data was copied from the input parameter file # All the statistics were normalized by the total weight of incident photons (in our case, it is the number of incident photons). RAT #Reflectance, absorption, transmission. 0.0326342 #Specular reflectance [-] 0.626154 #Diffuse reflectance [-] 0.341215 #Absorbed fraction [-] 0.281236 #Absorbed fraction due to surviving photons[-] 0 #Transmittance [-]

# Absorption as a function of layer contributed by photons that eventually escape from the top surface AR_l #Absorption due to diffusely reflectance as a function of layer. [-]

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… # Absorption as a function of depth contributed by photons that eventually escape from the top surface AR_z #AR[0], [1],..AR[nz-1]. [1/cm] Absorption due to diffusely reflected photons

…

# Absorption as a function of layer contributed by all photons A_l #Absorption as a function of layer. [-]

# Absorption as a function of depth contributed by all photons A_z #A[0], [1],..A[nz-1]. [1/cm]

# Reflectance as a function of radial distance contributed by all photons Rd_r #Rd[0], [1],..Rd[nr-1]. [1/cm2]

# Reflectance as a function of the exit angle (relative to the normal axis) contributed by all photons Rd_a #Rd[0], [1],..Rd[na-1]. [sr-1]

# Transmittance as a function of radial distance contributed by all photons Tt_r #Tt[0], [1],..Tt[nr-1]. [1/cm2]

# Transmittance as a function of the exit angle (relative to the normal axis) contributed by all photons Tt_a #Tt[0], [1],..Tt[na-1]. [sr-1]

# Absorption as a function of both radial distance and depth contributed by all photons # A[r][z]. [1/cm3] # A[0][0], [0][1],..[0][nz-1] # A[1][0], [1][1],..[1][nz-1] # ... # A[nr-1][0], [nr-1][1],..[nr-1][nz-1] A_rz

# Absorption as a function of both radial distance and depth contributed by photons that eventually escape from the top surface # AR[r][z]. [1/cm3] # AR[0][0], [0][1],..[0][nz-1] # AR[1][0], [1][1],..[1][nz-1] # ... # AR[nr-1][0], [nr-1][1],..[nr-1][nz-1] AR_rz

7

# Reflectance as a function of both radial distance and depth contributed by all photons # Rd[r][angle]. [1/(cm2sr)]. # Rd[0][0], [0][1],..[0][na-1] # Rd[1][0], [1][1],..[1][na-1] # ... # Rd[nr-1][0], [nr-1][1],..[nr-1][na-1] Rd_ra

# Transmittance as a function of both radial distance and depth contributed by all photons # Tt[r][angle]. [1/(cm2sr)]. # Tt[0][0], [0][1],..[0][na-1] # Tt[1][0], [1][1],..[1][na-1] # ... # Tt[nr-1][0], [nr-1][1],..[nr-1][na-1] Tt_ra

Sample output file 2 for the emission wavelength (fluorescence) for all photons Fluorescence #Fluorescence Data A1 # Version number of the file format. #### # Data categories include: # InParm, RAT, # A_l, A_z, Rd_r, Rd_a, Tt_r, Tt_a, # A_rz, Rd_ra, Tt_ra #### # User time: 1 sec = 0.00 hr. Simulation time of this run. InParm # Input parameters. cm is used. steadytest1exc.mco A # output file name, ASCII. 1000 # No. of photons 0.01 0.01 # dz, dr [cm] 100 100 1 # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above 1.37 0.1 100 0.9 10 # layer 1 1.37 # n for medium below

# The above data was copied from the input parameter file

# All the statistics were normalized by the total weight of incident photons (in our case, it is the number of incident photons). #Fluorescence Result for wavelength equal to 580nm is as Follows:

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AFFb---Fluorescence Absorption, Flourescence measured at top surface,Flourescence measured at bottom surface. 0 #Fluorescence Absorption[-] 0 #Flourescence measured at top surface[-] 0 #Flourescence measured at bottom surface[-]

# Absorption as a function of layer contributed by all fluorescent photons FA_l #Absorption of fluorescence photon as a function of layer. [-]

# Absorption as a function of depth contributed by all fluorescent photons The absorped fluorescence photon in each depth interval FA_z #FA[0], [1],..A[nz-1]. [1/cm]

# Fluorescence detected on the top of the medium as a function of radial distance contributed by all fluorescent photons The exit fluorescence photon(from the top surface) in each radious interval F_r #F[0], F[1],..F[nr-1]. [1/cm2]

# Fluorescence detected on the top of the medium as a function of the exit angle (relative to the normal axis) contributed by all fluorescent photons The exit fluorescence photon(from the top surface) in each angle interval F_a #F[0], F[1],..F[na-1].

# Fluorescence detected on the bottom of the medium as a function of radial distance contributed by all fluorescent photons The exit fluorescence photon(from the bottom surface) in each radious interval Fb_r #Fb[0], Fb[1],..Fb[nr-1]. [1/cm2]

# Fluorescence detected on the bottom of the medium as a function of the exit angle (relative to the normal axis) contributed by all fluorescent photons The exit fluorescence photon(from the bottom surface) in each angle interval Fb_a #Fb[0], Fb[1],..Fb[na-1].

# Fluorescence detected on the top of the medium as a function of the radial distance of origination contributed by all fluorescent photons The fluorescence(measured at top surface) vs originating position r FFrom_r #FFrom[0], [1],..FFrom[nr-1]. [1/cm]

# Fluorescence detected on the top of the medium as a function of the depth of origination contributed by all fluorescent photons The fluorescence(measured at top surface) vs occuring position z FFrom_z #FFrom[0], [1],..FFrom[nz-1]. [1/cm]

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# Fluorescence detected on the bottom of the medium as a function of the radial distance of origination contributed by all fluorescent photons The fluorescence(measured at bottom surface) vs originating position r FbFrom_r #FbFrom[0], [1],..FbFrom[nr-1]. [1/cm]

# Fluorescence detected on the bottom of the medium as a function of the depth of origination contributed by all fluorescent photons The fluorescence(measured at bottom surface) vs occuring position z FbFrom_z #FbFrom[0], [1],..FbFrom[nz-1]. [1/cm]

# Absorption as a function of both radial distance and depth contributed by all fluorescent photons # FA[r][z]. [1/cm3] # FA[0][0], [0][1],..[0][nz-1] # FA[1][0], [1][1],..[1][nz-1] # ... # FA[nr-1][0], [nr-1][1],..[nr-1][nz-1] FA_rz---the absorption array of fluorescent photon

# Fluorescence detected on the top of the medium as a function of both radial distance and exit angle (relative to the normal axis) contributed by all fluorescent photons # F[r][angle]. [1/(cm2sr)]. # F[0][0], [0][1],..[0][na-1] # F[1][0], [1][1],..[1][na-1] # ... # F[nr-1][0], [nr-1][1],..[nr-1][na-1] F_ra---the exit fluorescence(top surface) vs radius and angle

# Fluorescence detected on the bottom of the medium as a function of both radial distance and exit angle (relative to the normal axis) contributed by all fluorescent photons # Fb[r][angle]. [1/(cm2sr)]. # Fb[0][0], [0][1],..[0][na-1] # Fb[1][0], [1][1],..[1][na-1] # ... # Fb[nr-1][0], [nr-1][1],..[nr-1][na-1] Fb_ra---the exit fluorescence(bottom surface) vs radius and angle

# Fluorescence detected on the top of the medium as a function of the radial distance and depth of origination contributed by all fluorescent photons # FFrom[r][z]. [1/(cm2sr)]. # FFrom[0][0], [0][1],..[0][nz-1] # FFrom[1][0], [1][1],..[1][nz-1] # ... # FFrom[nr-1][0], [nr-1][1],..[nr-1][nz-1] FFrom_rz----2D distribution of fluorescence generating sites

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# Fluorescence detected on the bottom of the medium as a function of the radial distance and depth of origination contributed by all fluorescent photons # FbFrom[r][z]. [1/(cm2sr)]. # FbFrom[0][0], [0][1],..[0][nz-1] # FbFrom[1][0], [1][1],..[1][nz-1] # ... # FbFrom[nr-1][0], [nr-1][1],..[nr-1][nz-1] FbFrom_rz

Sample output file 3 for the excitation wavelength (reflectance) for photons collected by fibers A1 # Version number of the file format. #### # Data categories include: # InParm, RAT, # A_l, A_z, Rd_r, Rd_a, Tt_r, Tt_a, # A_rz, Rd_ra, Tt_ra #### # User time: 1 sec = 0.00 hr. Simulation time of this run. InParm # Input parameters. cm is used. steadytest1exc.mco A # output file name, ASCII. 1000 # No. of photons 0.01 0.01 # dz, dr [cm] 100 100 1 # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above 1.37 0.1 100 0.9 10 # layer 1 1.37 # n for medium below

# The above data was copied from the input parameter file Illumination Parameters 1 #Beam type:0-Collimated,1-Diffuse 0.020000 #Beam radius(cm) 1.452000 #Numerical Aperture Collection Parameters for current fiber #Fiber Radius(cm) Numberical Aperture Center-to-Center Distance 0.020000 0.200000 1.452000

# The above data was copied from the illumination and collection setup file Wavelength 460 #The wavelength of photons in this file

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# All the statistics were normalized by the total weight of incident photons (in our case, it is the number of incident photons). RAT---The diffuse reflectance and absorped fraction at excitation wavelength 0 #The diffuse reflectance detected in this fiber 0 #The absorped fraction detected in this fiber attributed to surviving photons

# Absorption as a function of layer contributed by photons that eventually escape from the top surface and collected by the current fiber AR_l #Absorption due to diffusely reflectance collected by the fiber as a function of layer. [-]

# Absorption as a function of depth contributed by photons that eventually escape from the top surface and collected by the current fiber AR_z #AR[0], [1],..AR[nz-1]. [1/cm] Absorption due to diffusely reflected photons

# Absorption as a function of both radial distance and depth contributed by photons that eventually escape from the top surface and collected by the current fiber # AR[r][z]. [1/cm3] # AR[0][0], [0][1],..[0][nz-1] # AR[1][0], [1][1],..[1][nz-1] # ... # AR[nr-1][0], [nr-1][1],..[nr-1][nz-1] AR_rz

Sample output file 4 for the emission wavelength (fluorescence) for photons collected by fibers Fluorescence #Fluorescence Data A1 # Version number of the file format. #### # Data categories include: # InParm, RAT, # A_l, A_z, Rd_r, Rd_a, Tt_r, Tt_a, # A_rz, Rd_ra, Tt_ra #### # User time: 1 sec = 0.00 hr. Simulation time of this run. InParm # Input parameters. cm is used. steadytest1exc.mco A # output file name, ASCII. 1000 # No. of photons 0.01 0.01 # dz, dr [cm] 100 100 1 # No. of dz, dr, da. 1 # Number of layers

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#n mua mus g d # One line for each layer 1 # n for medium above 1.37 0.1 100 0.9 10 # layer 1 1.37 # n for medium below Illumination Parameters 1 #Beam type:0-Collimated,1-Diffuse 0.020000 #Beam radius(cm) 1.452000 #Numerical Aperture Collection Parameters for current fiber #Fiber Radius(cm) Numberical Aperture Center-to-Center Distance 0.020000 0.200000 1.452000 Wavelength 580 #The wavelength of photons in this file

# The above data was copied from the input parameter file

# All the statistics were normalized by the total weight of incident photons (in our case, it is the number of incident photons). AFFb---Fluorescence collected by the fiber at top surface 0 #Fluorescence collected by the fiber at top surface

# Fluorescence detected on the top of the medium as a function of the radial distance of origination contributed by photons collected by the current fiber The fluorescence(measured at top surface) vs originating position r FFrom_r #FFrom[0], [1],..FFrom[nr-1]. [1/cm]

# Fluorescence detected on the top of the medium as a function of the depth of origination contributed by photons collected by the current fiber The fluorescence(measured at top surface) vs occuring position z FFrom_z #FFrom[0], [1],..FFrom[nz-1]. [1/cm]

# Fluorescence detected on the top of the medium as a function of the radial distance and depth of origination contributed by photons collected by the current fiber # FFrom[r][z]. [1/(cm2sr)]. # FFrom[0][0], [0][1],..[0][nz-1] # FFrom[1][0], [1][1],..[1][nz-1] # ... # FFrom[nr-1][0], [nr-1][1],..[nr-1][nz-1] FFrom_rz----2D distribution of fluorescence generating sites

instruction for the command prompt usage of the steady ... · instruction for the command prompt...

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