Instructions for the command prompt usage of the steady state Monte Carlo program for fluorescence propagation in a fiber-optic probe based setup

Transcription

1 Instructions for the command prompt usage of the steady state Monte Carlo program for fluorescence propagation in a fiber-optic probe based setup 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 #, $ 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, 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 directly 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 1.0 # file version 1 # number of runs # No. of photons # dz, dr (cm) # No. of dz, dr, da & dt 1

2 steadytest1exc.mco A # the output file name of #the result for excitation wavelength 0 #the number of types of fluorescence,i.e. the set of Excitation and #Emission WaveLength 460 #Excitation-->Emission 1 #the number of different wavelength #Below Specify the optical properties for each wavelength 1 # No. of layers #The 1st wavelength must be excitation wavelength 460 #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 1.0 # n for medium above # Layer # n for medium below. Sample file 2: fluorescence simulation 1.0 # file version 1 # number of runs # No. of photons # dz, dr (cm) # No. of dz, dr, da & dt steadytest1exc.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 #Excitation-->Emission #Excitation-->Emission 2 #the number of different wavelength #Below Specify the optical properties for each wavelength 1 # No. of layers #The 1st wavelength must be excitation wavelength 460 #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 1.0 # n for medium above # Layer # n for medium below. #The 2nd wavelength must be the emission wavelength 580 #The value of wavelength 2

3 steadytest1emm.mco A # output filename(not useful any more), #ASCII/Binary #n mua mus g Q.Y. d # One line for each layer 1.0 # n for medium above # Layer # n for medium below. C. Illumination and Collection Setup File (to describe the specifications of the fiber-optic probe): Illumination Parameters 1 #Beam type:0-collimated,1-diffuse 0.02 #Beam radius(cm) The radius of center null area(cm) 45 #Incident angle (degree, w.r.t. the normal axis) #Refractive index of illumination fiber #Numerical Aperture Collection Parameters 1 #Employ collecting fibers: 0-no; 1-yes 1 #The number of collecting fibers #Fiber-Radius(cm) Center-to-Center-Distance(cm) Refractive-Index Numerical- #Aperture 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 # No. of photons # dz, dr [cm] # No. of dz, dr, da. 3

4 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above # layer # 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 #Specular reflectance [-] #Diffuse reflectance [-] #Absorbed fraction [-] #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. [-] # 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 4

5 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 # 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 5

6 # 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 # No. of photons # dz, dr [cm] # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above # layer # 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: 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] 6

7 # 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] # 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 7

8 # 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 # 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 # No. of photons # dz, dr [cm] # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above 8

9 # layer # n for medium below # The above data was copied from the input parameter file Illumination Parameters 1 #Beam type:0-collimated,1-diffuse #Beam radius(cm) #Numerical Aperture Collection Parameters for current fiber #Fiber Radius(cm) Numberical Aperture Center-to-Center Distance # The above data was copied from the illumination and collection setup file Wavelength 460 #The wavelength of photons in this file # 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 9

10 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 # No. of photons # dz, dr [cm] # No. of dz, dr, da. 1 # Number of layers #n mua mus g d # One line for each layer 1 # n for medium above # layer # n for medium below Illumination Parameters 1 #Beam type:0-collimated,1-diffuse #Beam radius(cm) #Numerical Aperture Collection Parameters for current fiber #Fiber Radius(cm) Numberical Aperture Center-to-Center Distance 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 10

11 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 11