The program mcfluor.c is a C program that will call the subroutine mcsubLIB.c, which executes Monte Carlo simulations using the parameters supplied by mcfluor.c.
The program is basically the same as published in Jacques SL, Monte Carlo simulations of fluorescence in turbid media, Ch. 6 in Handbook of Biomedical Fluorescence, M.A. Mycek, B.W. Pogue, publ. Marcel-Dekker, New York, NY, 2003. There are some minor changes, some because the mcsubLIB.c has been updated, for example, to allow for a mismatched boundary condition or to launch a beam at a subsurface location (to simulate a submerged optical fiber), and some changes cleaning up the code.
The run parameters are selected in the program. In the example shown here, the product of extinction coefficient and concentration is eC = 1 cm-1 = (cm-1 M-1)(M), and the energy yield is Y = 1 = 1 [J fluorescence per J excitation absorbed by fluorophore]. The results can be scaled by the actual values of eC and Y. To compile the program for execution, one simply types:
cc -o gomcsub mcsubLIB.c mcfluor.c
that yields the executable gomcsub*. Sometimes one might need to type
cc -lm -o gomcsub mcsubLIB.c mcfluor.c
to help the compiler find the math library. The details of compilation using your compiler may differ slightly. Once compiled, simply typing ./gomcsub on a Unix machine will execute the program from within the same directory where the program resides. Again, calling the program differs with the operating system being used.
The program files are
- mcfluor.c which calls mcsub.c in the library:
- mcsubLIB.c
- mcsubLIB.h
The output files are
- mcOUT101.dat = excitation files
- mcOUT102.dat = emission files for background uniform fluorescence
- mcOUT103.dat = emission files for positive-x half of asymmetric heterogeneous source
- mcOUT104.dat = emission files for negative-x half of asymmetric heterogeneous source
A MATLAB program will read these files and create the figures 1 through 6 shown below.
lookmcsubfluor.m creates the figures, and uses the following routines:
getmcsub.m reads the mcOUTxxx.dat files.
makec2f.m creates a colormap used in plotting.
Example Run
Running the compiled C program yields the 4 output files and the following printout on the console. This was a short run (controlled by selecting Nruns = 0.1) which only required 1.3 min to complete, so the data is a little noisy. The MATLAB-generated figures from the output files are shown, then the printout is listed after the figures.
 Fig. 1: Escaping fluxes Ex and Em |
 Fig. 2: Ratio of escaping Ex/Em |
 Fig. 3: Excitation |
 Fig. 4: Background fluorescence |
 Fig. 5: Off-center local fluorophore |
 Fig. 6: Off-center local fluorophore |
Output to console from example run
$ gomcsub Wed Oct 24 22:19:30 2007 ----- USER CHOICES ----- EXCITATION muax = 1.000 musx = 100.000 gx = 0.900 n1 = 1.330 n2 = 1.000 mcflag = 0 radius = 0.0000 waist = 0.0000 zfocus = 0.0000 xs = 0.0000 ys = 0.0000 zs = 0.0000 BACKGROUND FLUORESCENCE muaf = 5.000 musf = 50.000 gf = 0.000 eC = 1.000 Y = 1.000 FLUORESCENT HETEROGENEITY xh = 0.2000 yh = 0.0000 zh = 0.3000 heC = 0.1000 hY = 1.0000 hrad = 0.0100 OTHER Nruns = 0.1 @1e6 photons/run dr = 0.0100 dz = 0.0100 --------------- 3.504e-06 min/EX photon 8.342e-07 min/EM photon Total estimated completion time = 1.28 min EXCITATION est. completion time = 0.35 min 100 photons 200 photons 300 photons 400 photons 500 photons 600 photons 700 photons 800 photons 900 photons 1000 photons 2000 photons 3000 photons 4000 photons 5000 photons 6000 photons 7000 photons 8000 photons 9000 photons 10000 photons 20000 photons 30000 photons 40000 photons 50000 photons 60000 photons 70000 photons 80000 photons 90000 photons 100000 photons ------------------------------------------------------ ------------------------------------------------------ Elapsed Time for excitation = 0.361 min Wed Oct 24 22:19:52 2007 BACKGROUND FLUORESCENCE est. completion time = 0.85 min 10000 fluor photons @ ir = 1 total = 10000 10000 fluor photons @ ir = 2 total = 20000 10000 fluor photons @ ir = 3 total = 30000 10000 fluor photons @ ir = 4 total = 40000 10000 fluor photons @ ir = 5 total = 50000 10000 fluor photons @ ir = 6 total = 60000 10000 fluor photons @ ir = 7 total = 70000 10000 fluor photons @ ir = 8 total = 80000 10000 fluor photons @ ir = 9 total = 90000 10000 fluor photons @ ir = 10 total = 100000 10000 fluor photons @ ir = 20 total = 200000 10000 fluor photons @ ir = 30 total = 300000 10000 fluor photons @ ir = 40 total = 400000 10000 fluor photons @ ir = 50 total = 500000 10000 fluor photons @ ir = 60 total = 600000 10000 fluor photons @ ir = 70 total = 700000 10000 fluor photons @ ir = 80 total = 800000 10000 fluor photons @ ir = 90 total = 900000 10000 fluor photons @ ir = 100 total = 1000000 10000 fluor photons @ ir = 101 total = 1000000 1000000 fluorescent photons total Elapsed Time for background fluorescence = 0.863 min ------------------------------------------------------ FLUORESCENT HETEROGENEITY est. completion time = 0.083 min 100 photons 200 photons 300 photons 400 photons 500 photons 600 photons 700 photons 800 photons 900 photons 1000 photons 2000 photons 3000 photons 4000 photons 5000 photons 6000 photons 7000 photons 8000 photons 9000 photons 10000 photons 20000 photons 30000 photons 40000 photons 50000 photons 60000 photons 70000 photons 80000 photons 90000 photons 100000 photons Elapsed Time for fluorescent heterogeneity = 0.084 min ------------------------------------------------------ ------------------------------------------------------ Wed Oct 24 22:20:49 2007 Estimated total completion time = 1.28 min Actual total elapsed time = 1.31 min $