English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Zendy Plus

Presents the zaia usage as premium feature

ZAIA

Presents the pdf analysis as premium feature

PDF Analysis

Insights

Presents the summarisation as premium feature

Summarisation

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the access of premium content as premium feature

Premium Content

Zendy Tools

Zendy Open

Background: Monte Carlo simulations of diffusion are commonly used as a modelvalidation tool as they are especially suitable for generating the diffusionMRI signal in complicated tissue microgeometries.  New method: Here we describe the details of implementing Monte Carlosimulations in three-dimensional (3d) voxelized segmentations of cells inmicroscopy images. Using the concept of the corner reflector, we largely reducethe computational load of simulating diffusion within and exchange betweenmultiple cells. Precision is further achieved by GPU-based parallelcomputations.  Results: Our simulation of diffusion in white matter axons segmented from amouse brain demonstrates its value in validating biophysical models.Furthermore, we provide the theoretical background for implementing adiscretized diffusion process, and consider the finite-step effects of theparticle-membrane reflection and permeation events, needed for efficientsimulation of interactions with irregular boundaries, spatially variablediffusion coefficient, and exchange.  Comparison with existing methods: To our knowledge, this is the first MonteCarlo pipeline for MR signal simulations in a substrate composed of numerousrealistic cells, accounting for their permeable and irregularly-shapedmembranes.  Conclusions: The proposed RMS pipeline makes it possible to achieve fast andaccurate simulations of diffusion in realistic tissue microgeometry, as well asthe interplay with other MR contrasts. Presently, RMS focuses on simulations ofdiffusion, exchange, and T1 and T2 NMR relaxation in static tissues, with apossibility to straightforwardly account for susceptibility-induced T2* effectsand flow.

Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in three-dimensional cell segmentations of microscopy images