Running White Monte Carlo Simulation for SFDI

[Christina Negus]

Hello!

I have been using MCX to run simulations for quantitative fluorescence imaging using SFDI, here at Princess Margaret Cancer Research Centre in Toronto. I am interested in running a White Monte Carlo simulation to generate look-up tables for SFDI. However I have found no documentation depicting MCX running White Monte Carlo simulation. Does anyone have any experience in running this or have any supporting code?

Thanks in advance!

Christina 

[Qianqian Fang]

WMC is just a special case of perturbation Monte Carlo (pMC) where detected photon partial path (or other photon-specific parameters) is first stored in a baseline simulation to allow fast post-processing to plug in different mua/mus and rapidly recompute the detected photon spatial and temporal distributions.

by default, mcx stores detected partial path, along with a number of other user-specified data types, see

https://github.com/fangq/mcx/blob/v2023/mcxlab/mcxlab.m#L235-L245

once you have the partial path data of the detected photon, you can then call these functions to compute the detected weight, mean path, mean-weight, or time-of-flight,

https://github.com/fangq/mcx/blob/v2023/utils/mcxdetweight.m

https://github.com/fangq/mcx/blob/v2023/utils/mcxdettime.m

https://github.com/fangq/mcx/blob/v2023/utils/mcxdettpsf.m

https://github.com/fangq/mcx/blob/v2023/utils/mcxmeanpath.m

our python interface of mcx, pmcx, provides almost identical interface

https://github.com/fangq/mcx/blob/v2023/pmcx/pmcx/__init__.py#L36-L47

see this interactive tutorials for more info

https://colab.research.google.com/github/fangq/mcx/blob/master/mcxlab/tutorials/mcxlab_getting_started.ipynb#scrollTo=22pZIXv5dIsi

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[Christina Negus]

Hi Dr. Fang,

Thank you for your response and resources, they have been extremely helpful!

I have looked into this pMC mode and have been running simulations varying the absorption and scattering coefficients. Changing the absorption coefficient while keeping scattering coefficient constant behaves as expected. However changing the scattering coefficient behaves unexpectedly and doesn't have an effect on predicting the reflectance values. For reference I am running an initial simulation using MCX with mua = 0.01 and mus = 10, then applying pMC over ranges of mua and mus values ( mua = [0.003, 0.03, 0.3, 3, 30] and mus = [1,5,10,30,100,300]).

I am wondering if this is a limitation to using the pMC method?

Thanks again,

Christina