ArticleJournal of neuroscience methods2021
Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images.
Article in Journal of neuroscience methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 45 citations in OpenAlex.
- Clinical Soma and Neurite Density Imaging (SANDI): Translational Microstructure Mapping on Clinical 3T MRI Scanners.Magnetic resonance in medicine · 2026Article
- Dependence of the Extra-Cellular Diffusion Coefficient on the Fractions of Neurites and Cell Bodies in Gray Matter.Magnetic resonance in medicine · 2026Article
- Axon Diameter Mapping From Myelin Water Diffusion MRI.IEEE transactions on medical imaging · 2026Article
- Monte Carlo Assessment of Accuracy for Mean Kärger Model Water Exchange Rate Estimates From Diffusional Kurtosis Time Dependence.NMR in biomedicine · 2026Article
- Passive water exchange between multiple sites can explain why apparent exchange rate constants depend on ionic and osmotic conditions in gray matter.Magnetic resonance letters · 2026Article
- Detecting Collagen Fiber Architecture after Destabilization of the Medial Meniscus Surgery Using High-Resolution Diffusion Tensor Imaging.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2026Article
- Motion and Flow Robust Free-Breathing Diffusion Kurtosis Imaging of the Kidney.NMR in biomedicine · 2025Article
- Histology-informed microstructural diffusion simulations for MRI cancer characterisation-the Histo-μSim framework.Communications biology · 2025Article
- Scattering approach to diffusion quantifies axonal damage in brain injury.Nature communications · 2025Article
- MATI: A GPU-accelerated toolbox for microstructural diffusion MRI simulation and data fitting with a graphical user interface.Magnetic resonance imaging · 2025Article
- Article
- Passive water exchange between multiple sites can explain why apparent exchange rate constants depend on ionic and osmotic conditions in gray matter.bioRxiv : the preprint server for biology · 2025Article
- In vivo cortical microstructure mapping using high-gradient diffusion MRI accounting for intercompartmental water exchange effects.NeuroImage · 2025Article
- SpinFlowSim: A blood flow simulation framework for histology-informed diffusion MRI microvasculature mapping in cancer.Medical image analysis · 2025Article
- Revealing membrane integrity and cell size from diffusion kurtosis time dependence.Magnetic resonance in medicine · 2025Article
- Predicting Mesoscopic Larmor Frequency Shifts in White Matter With Diffusion MRI-A Monte Carlo Study in Axonal Phantoms.NMR in biomedicine · 2025Article
- SpinWalk: A Monte Carlo simulator for MR-signal formation in inhomogeneous tissue.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Tuned exchange imaging: Can the filter exchange imaging pulse sequence be adapted for applications with thin slices and restricted diffusion?NMR in biomedicine · 2024Article
- In vivo mapping of cellular resolution neuropathology in brain ischemia with diffusion MRI.Science advances · 2024Article
- The effects of axonal beading and undulation on axonal diameter estimation from diffusion MRI: Insights from simulations in human axons segmented from three-dimensional electron microscopy.NMR in biomedicine · 2024Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMonte 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
methodHere 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.
resultsOur simulation of diffusion in white matter axons segmented from a mouse brain demonstrates its value in validating 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, spatially variable diffusion coefficient, and exchange. COMPARISON WITH EXISTING
methodsTo 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.
conclusionsThe 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 T
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.