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Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images
Journal of Neuroscience Methods ( IF 3 ) Pub Date : 2020-12-03 , DOI: 10.1016/j.jneumeth.2020.109018
Hong-Hsi Lee 1 , Els Fieremans 1 , Dmitry S Novikov 1
Affiliation  

Background

Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries.

New method

Here we describe the details of implementing Monte Carlo simulations in three-dimensional (3d) voxelized segmentations of cells in microscopy images. Using the concept of the corner reflector, we largely reduce the computational load of simulating diffusion within and exchange between multiple cells. Precision is further achieved by GPU-based parallel computations.

Results

Our simulation result of diffusion in the exemplified white matter axons segmented from a mouse brain demonstrates its power and value in validations of biophysical models. Furthermore, we provide the theoretical background for implementing a discretized diffusion process, and consider the finite-step effects of the particle-membrane reflection and permeation events, needed for efficient simulation of interactions with irregular boundaries, variable diffusion coefficient, and exchange.

Comparison with existing methods

To our knowledge, this is the first Monte Carlo pipeline for MR signal simulations in a substrate composed of numerous realistic cells, accounting for their permeable and irregularly-shaped membranes.

Conclusions

The proposed RMS pipeline makes it possible to achieve fast and accurate simulations of diffusion in realistic tissue microgeometry, as well as the interplay with other MR contrasts. Presently, RMS focuses on simulations of diffusion, exchange, and T1 and T2 NMR relaxation in static tissues, with a possibility to straightforwardly account for susceptibility-induced T2* effects and flow.



中文翻译:

逼真的微观结构模拟器 (RMS):在显微镜图像的三维细胞分割中扩散的蒙特卡罗模拟

背景

扩散的蒙特卡罗模拟通常用作模型验证工具,因为它们特别适用于在复杂的组织微观几何结构中生成扩散 MRI 信号。

新方法

在这里,我们描述了在显微镜图像中对细胞进行三维 (3 d ) 体素化分割时实施蒙特卡罗模拟的细节。使用角反射器的概念,我们大大减少了模拟多个细胞内的扩散和交换的计算负荷。基于 GPU 的并行计算进一步实现了精度。

结果

我们对从小鼠大脑分割的示例性白质轴突中扩散的模拟结果证明了其在生物物理模型验证中的能力和价值。此外,我们提供了实现离散扩散过程的理论背景,并考虑了粒子膜反射和渗透事件的有限步长效应,这是有效模拟与不规则边界、可变扩散系数和交换的相互作用所必需的。

与现有方法的比较

据我们所知,这是第一个在由许多真实细胞组成的基板中进行 MR 信号模拟的 Monte Carlo 管道,考虑到它们具有可渗透性和不规则形状的膜。

结论

所提出的 RMS 管道可以在现实组织微观几何中实现快速和准确的扩散模拟,以及与其他 MR 对比的相互作用。目前,RMS 专注于模拟静态组织中的扩散、交换以及T 1T 2 NMR 弛豫,有可能直接解释磁化性诱导的2*效果和流量。

更新日期:2020-12-30
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