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Parallel, multi-purpose Monte Carlo code for simulation of light propagation in segmented tissues

Wojtkiewicz Stanislaw, Liebert Adam

Biocybernetics and Biomedical Engineering

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2021

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Vol. 41, no. 4

1303--1321

EN

We have developed a massive-parallel, multi-purpose Monte Carlo (MC) code for simulation of light propagation in complex structures modelled with e.g. magnetic resonance images. The code is designed to execute parallel threads on a Linux-based cluster of computers equipped with multiple graphical processing units (GPU) utilizing NVidia CUDA technology. We show steps one can take to implements such code itself. Furthermore, we provide methodology of building a MRI-based head model and populating it with realistic optical properties at excitation and fluorescence emission wavelengths during inflow of fluorescence agent (indocyanine green – ICG). The proposed code provides following original features: (i) Simulation of fluorescence light propagation in media with spatial distribution of multiple different fluorophores characterized by concentration, quantum yield and fluorescence lifetime. (ii) The fluorescence light tracking does not need extra photon tracking and works in parallel with tracking photons at the excitation wavelength, introducing execution time overhead of 0.02% only. (iii) Calculation of high-resolution spatial distributions of sensitivity factors mapping voxels absorption change to parameters measured on a model surface: statistical parameters (moments) of the distribution of time of flight of photons. (iv) Random number generators states are preserved between runs to greatly improve calculation time of the sensitivity factors. (v) Simulation of fluorescence lifetime wide field imaging in diffusively scattering media. The code is designed to handle big models, divided into e.g. 200 million voxels or more, which other methods struggle to handle. Simulations on a human head model with 0.3 mm voxel size require 2 GB of a GPU memory only. This is supported by developed non-standard floating-point data storage format. The proposed code is cross-validated with field-leading MC and finite element methods on the same hardware environment for varying model sizes and temporal resolutions. Tests revealed competitive execution time and high temporal resolution of boundary data for high spatial resolution of MRI-based head model.

2

Functional brain imaging by multi-wavelength time-resolved near infrared spectroscopy

Torricelli A., Contini D., Pifferi A., Spinelli L., Cubeddu R.

Opto-Electronics Review

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2008

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Vol. 16, No. 2

131-135

EN

We present a description of evolution of time-resolved systems developed at the Department of Physics, Politecnico di Milano for tissue oximetry and functional brain imaging. From a single source and 4-channel set-up we have upgraded to a potentially 18-sources and 64-channel device. An example of sensitivity of the latest set-up is reported for a motor task experiment. A short discussion on the next generation time-resolved instrumentation for functional studies is also presented.

3

Accelerated Monte Carlo method for computation of photon migration by matrix description of photon direction

Pluciński J.

Optica Applicata

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2005

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Vol. 35, nr 4

977-983

EN

A new accelerated Monte Carlo method that uses matrix description of photon migration (instead of vector description) for computation of photon migration in highly scattering media is presented. This method requires two multi-clock floating-point instructions (one division and one square root operation) less for each scattering event than the standard method. Theoretical considerations show that the new method reduces calculation time about 4% for personal computers with a one-pipeline floating-point coprocessor, or more on computers having multi-pipeline floating-point units. Tests performed on selected types of personal computers have shown a few percent (from 2.5% to 6%) decrease in computation time when the new method was used.

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Modelling of light propagation in the adult head for optical brain function mesurement

Okada E.

Biocybernetics and Biomedical Engineering

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2002

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Vol. 22, no. 4

135-147

EN

Near infrared (NIR) spectroscopy and imaging are now established techniques for measurements of change in oxygenation and haemo-dynamics within the brain. However, scattering of the light in biological tissue causes ambiguity in the spatial sensitivity profiles and the partial optical path lenght in the brain. The light propagation in the adult head model of which optical properties are chosen from the reported data of in vitro experiments is validated by time-resolved measurements of the human foreheads. The apparent optical properties estimated by a least squares fit of the diffusion model to the temporal point spread function for the adult head model agree with the experimental results. The heterogeneity of the head scarcely affects the total optical path lenght. However the partial optical path lenght in the brain and the spatial sensitivity profiles which can not be directly obtained by experiment are considerably affected by the heterogeneity of tissue, especially the presence of low scattering subarachnoid space surrounding the brain.