Adaptive generation of multimaterial grids from imaging data for biomedical Lagrangian fluid–structure simulations

Abstract

Spatial discretization of complex imaging-derived fluid-solid geometries, such as the cardiac environment, is a critical but often overlooked challenge in biomechanical computations. This is particularly true in problems with Lagrangian interfaces, where the fluid and solid phases share a common interface geometrically. For simplicity and better accuracy, it is also highly desirable for the two phases to have a matching surface mesh at the interface between them. We outline a method for solving this problem, and illustrate the approach with a 3D fluid-solid mesh of the mouse heart. An MRI perfusion-fixed dataset of a mouse heart with 50μm isotropic resolution was semi-automatically segmented using a customized multimaterial connected-threshold approach that divided the volume into non-overlapping regions of blood, tissue and background. Subsequently, a multimaterial marching cubes algorithm was applied to the segmented data to produce two detailed, compatible isosurfaces, one for blood and one for tissue. Both isosurfaces were simultaneously smoothed with a multimaterial smoothing algorithm that exactly conserves the volume for each phase. Using these two isosurfaces, we developed and applied novel automated meshing algorithms to generate anisotropic hybrid meshes on arbitrary biological geometries with the number of layers and the desired element anisotropy for each phase as the only input parameters. Since our meshes adapt to the local feature sizes and include boundary layer prisms, they are more efficient and accurate than non-adaptive, isotropic meshes, and the fluid-structure interaction computations will tend to have relative error equilibrated over the whole mesh.

A chicken embryo cardiac outflow tract atlas for registering changes due to abnormal blood flow

“…A step beyond a 2D heart atlas is a 3D heart atlas developed with 3D subdivision techniques [22–24]. A 3D atlas has the advantage of incorporating data from any plane of imaging [25].…”

In situ casting and imaging of the rat airway tree for accurate 3D reconstruction

“…The airways of the TLC image were semi-automatically segmented using intensity threshold-based approaches described by Carson et al [24] in conjunction with interactive segmentation using Digital Data Viewer (DDV) (http://cgc-code.org/). A 3D median filter was applied to the segmented TLC airway data to improve surface boundary continuity.…”

Geochemical and Geomechanical Effects on Wellbore Cement Fractures: Data Information for Wellbore Reduced Order Model

“…The CFD models were driven using different pressure gradients along 2 cm long cement sample with three different working fluids; (1) DI water at 20 o C with 20 kPa, (2) CO 2 saturated brine at 50 o C with 20 kPa and 200 kPa, and (3) supercritical CO 2 at 50°C with 20 kPa, 200 kPa, and 1 MPa. The fracture geometries for all the three cases were segmented based on the approach described by Carson et al (Carson et al 2010b;Carson et al 2010c). Briefly, the images were masked to remove any background noise and then intensity-based thresholding followed by visual validation was performed.…”