Efficient GPU-based Monte-Carlo simulation of diffusion in real astrocytes reconstructed from confocal microscopy

Khieu-Van Nguyen 1, * Edwin Hernández-Garzón 1 Julien Valette 1
* Corresponding author
1 LMN - Laboratoire des Maladies Neurodégénératives - UMR 9199
MIRCEN - Service MIRCEN : DRF/JACOB, UP11 - Université Paris-Sud - Paris 11, CNRS - Centre National de la Recherche Scientifique : UMR 9199
Abstract : The primary goal of this work is to develop an efficient Monte-Carlo simulation of diffusion-weighted signal in complex cellular structures, such as astrocytes, directly derived from confocal microscopy. In this study, we first use an octree structure for spatial decomposition of surface meshes. Octree structure and radius-search algorithm help to quickly identify the faces that particles can possibly encounter during the next time step, thus speeding up the Monte-Carlo simulation. Furthermore, we propose to use a three-dimensional binary marker to describe the complex cellular structure and optimize the particle trajectory simulation. Finally, a GPU-based version of these two approaches is implemented for more efficient mod-eling. It is shown that the GPU-based binary marker approach yields unparalleled performance, opening up new possibilities to better understand intracellular diffusion, validate diffusion models, and create dictionaries of intracellular diffusion signatures.
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Khieu-Van Nguyen, Edwin Hernández-Garzón, Julien Valette. Efficient GPU-based Monte-Carlo simulation of diffusion in real astrocytes reconstructed from confocal microscopy. Journal of Magnetic Resonance, Elsevier, 2018, 296, pp.188-199. ⟨10.1016/j.jmr.2018.09.013⟩. ⟨cea-02155389⟩

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