Three-dimensional Surface Mesh Research Articles

Three-dimensional surface mesh optimization and centerline extraction of vasculatures for endovascular intervention simulation

Understanding vasculatures is important for endovascular intervention simulation (EIS). A recent trend attempts to represent vasculatures with three-dimensional (3D) surface meshes by multiview image and graphics-based techniques used in optical and laser scanners. Conversion from image volume data to 3D surface meshes, however, suffers from staircases and noise. Most existing methods in geometric processing often consider mesh smoothing in their independent settings. However, this approach either is ineffective in removing the artifacts or introduces additional types of artifacts (e.g., volume shrinkage and shape distortion). We propose an effective yet vascular-oriented mesh optimization framework. We first employ a weight-adaptive vertex resampling to eliminate staircases; then, we subdivide vascular meshes to denser ones; and finally, we exploit the constrained biquadratic Bezier surface fitting to produce optimized meshes. In EIS, clinicians are interested in the centerline of surface meshes as well as surface meshes. However, centerline extraction from vascular meshes is still challenging. We adopt an existing centerline extraction approach for vascular meshes based on the observation that human blood vessels are generally composed of piecewise cylindrical shapes. Tests on vascular data illustrate that our optimization approach achieves higher quality results regarding surface smoothness compared to previous approaches. In addition, our extraction approach effectively obtains complete centerlines from real data.

SHape Analyser for Particle Engineering (SHAPE): Seamless characterisation and simplification of particle morphology from imaging data

The mechanical and rheological behaviour of particulate and granular assemblies is significantly influenced by the shape of their individual particles. We present a code that implements shape characterisation of three-dimensional particles in an automated and rigorous manner, allowing for the processing of samples composed of thousands of irregular particles within affordable time runs. The input particle geometries can be provided in one of the following forms: segmented labelled images, three-dimensional surface meshes, tetrahedral meshes or point-clouds. These can be complemented with surface texture profiles. Shape characterisation is implemented for three key aspects of shape, namely surface roughness, roundness and form. Also, simplified particle shapes are generated by the code which can be used in numerical simulations to characterise the mechanical behaviour of particulate assemblies, using numerical approaches such as the Discrete Element method and Molecular Dynamics. Combining these two features in one automated framework, the code allows not only to characterise the original granular material but also to monitor how its morphological characteristics change as the shape of the particles is simplified according to the chosen fidelity level for the application of interest. Program summaryProgram Title: SHAPE: SHape Analyser for Particle EngineeringCPC Library link to program files:https://doi.org/10.17632/7h3n5rxtf4.1Developer's respository link:https://github.com/vsangelidakis/SHAPELicensing provisions: GPLv3Programming language: MatlabNature of problem: Automatic morphological description of three-dimensional particles for material characterisation and generation of simplified particle geometries to be used in numerical simulations of their mechanical behaviour.Solution method: SHAPE [1] analyses the morphology of particles using a range of different morphological descriptors, characterising the form, roundness and roughness of each particle. An object-oriented structure is put in place to ensure a robust handling of the morphological characteristics. The simplified particle geometries are exported in a variety of different formats, supporting some of the most popular Finite Element and Discrete Element codes.

Application of PDF Software with 3D Functionalities in Radiological Models of the Skull Base: Characteristics, Experience and Solutions.

A widely known alternative for reading and exchanging digital files is the PDF file, by Adobe. This type of file has become the most used for the electronic exchange of files. It is platform-independent, suitable for the exchange of medical data in electronic academic publication. PDF can support additional resources such image, media, even, three-dimensional surface mesh models. A three-dimensional model of the base of the skull is generated from computed tomography images to provide an overview of the PDF file format, with emphasis on biomedical images. Three-dimensional representation in PDF files offers many advantages, as these images have more information than two-dimensional images, therefore, we consider this tool (3D PDF) a good alternative for the visualization, interaction and distribution of 3D content.

Quantification of nasal airflow resistance in English bulldogs using computed tomography and computational fluid dynamics.

Stenotic nares, edematous intranasal turbinates, mucosal swelling, and an elongated, thickened soft palate are common sources of airflow resistance for dogs with brachycephalic airway syndrome. Surgery has focused on enlarging the nasal apertures and reducing tissue of the soft palate. However, objective measures of surgical efficacy are lacking. Twenty-one English bulldogs without previous surgery were recruited for this prospective, pilot study. Computed tomography was performed using conscious sedation and without endotracheal intubation using a 128 multidetector computed tomography scanner. Raw multidetector computed tomography data were rendered to create a three-dimensional surface mesh model by automatic segmentation of the air-filled nasal passage from the nares to the caudal soft palate. Three-dimensional surface models were used to construct computational fluid dynamics models of nasal airflow resistance from the nares to the caudal aspect of the soft palate. The computational fluid dynamics models were used to simulate airflow in each dog and airway resistance varied widely with a median 36.46 (Pa/mm)/(l/s) and an interquartile range of 19.84 to 90.74 (Pa/mm)/(/s). In 19/21 dogs, the rostral third of the nasal passage exhibited a larger airflow resistance than the caudal and middle regions of the nasal passage. In addition, computational fluid dynamics data indicated that overall measures of airflow resistance may significantly underestimate the maximum local resistance. We conclude that computational fluid dynamics models derived from nasal multidetector computed tomography can quantify airway resistance in brachycephalic dogs. This methodology represents a novel approach to noninvasively quantify airflow resistance and may have utility for objectively studying effects of surgical interventions in canine brachycephalic airway syndrome.

A Hyperelastic Two-Scale Optimization Model for Shape Matching

We suggest a novel shape matching algorithm for three-dimensional surface meshes of disk or sphere topology. The method is based on the physical theory of nonlinear elasticity and can hence handle large rotations and deformations. Deformation boundary conditions that supplement the underlying equations are usually unknown. Given an initial guess, these are optimized such that the mechanical boundary forces that are responsible for the deformation are of a simple nature. We show a heuristic way to approximate the nonlinear optimization problem by a sequence of convex problems using finite elements. The deformation cost, i.e., the forces, is measured on a coarse scale, while ICP-like matching is done on the fine scale. We demonstrate the plausibility of our algorithm through examples taken from different datasets.

Volume preserving smoothing of triangular isotropic three-dimensional surface meshes

The present paper deals with the volume preserving smoothing of triangular isotropic meshes over three-dimensional surfaces. The adopted approach is based on Laplacian smoothing combining in an alternating manner positive and negative weights in consecutive cycles of the smoothing. Since the aim is to improve the shape of individual elements of the mesh rather than to get rid of a noise, the weights are derived in a very simple way using a “do not harm” concept. The paper also extends the smoothing methodology from meshes on closed surfaces to meshes on open surfaces and discusses how the concept can be applied to meshes over surfaces with sharp features and curvature discontinuities. The performance and capabilities of the presented smoothing approach are demonstrated on several examples.

A novel specimen-specific methodology to optimise the alignment of long bones for experimental testing

The choice of coordinate system and alignment of bone will affect the quantification of mechanical properties obtained during in-vitro biomechanical testing. Where these are used in predictive models, such as finite element analysis, the fidelic description of these properties is paramount. Currently in bending and torsional tests, bones are aligned on a pre-defined fixed span based on the reference system marked out. However, large inter-specimen differences have been reported. This suggests a need for the development of a specimen-specific alignment system for use in experimental work. Eleven ovine tibiae were used in this study and three-dimensional surface meshes were constructed from micro-Computed Tomography scan images. A novel, semi-automated algorithm was developed and applied to the surface meshes to align the whole bone based on its calculated principal directions. Thereafter, the code isolates the optimised location and length of each bone for experimental testing. This resulted in a lowering of the second moment of area about the chosen bending axis in the central region. More importantly, the optimisation method decreases the irregularity of the shape of the cross-sectional slices as the unbiased estimate of the population coefficient of variation of the second moment of area decreased from a range of (0.210–0.435) to (0.145–0.317) in the longitudinal direction, indicating a minimisation of the product moment, which causes eccentric loading. Thus, this methodology serves as an important pre-step to align the bone for mechanical tests or simulation work, is optimised for each specimen, ensures repeatability, and is general enough to be applied to any long bone.

Smooth anisotropic sources with application to three-dimensional surface mesh generation

Isotropic sources are extended to take anisotropy into account in order to obtain a smooth anisotropic sizing field for anisotropic mesh generation. Different types of anisotropic sources are described to represent boundary layers on surfaces and in volume that guarantee a smooth anisotropic field. This allows to us resolve multiple boundary layer intersections properly and naturally provides a smooth transition between the anisotropic boundary layer sizing and the isotropic region. Furthermore, the interaction between a smooth anisotropic sizing field and curvature is studied, and estimates of the tangential size spacing are provided for first and second order approximation of the geometry to ensure smoothness of the sizing field. It is also shown that, in order to get a smooth size variation, volumetric and surface meshing can not be decoupled. The filtering of the sources in order to obtain a computationally efficient method is described. Numerical examples demonstrate our method.

Despinning Orbital Debris Before Docking Using Laser Ablation

Many regions of Earth orbit are ideal for satellites that provide commonly used services, including communication, television, and navigation. However, defunct satellites, spent upper stages, and other space debris are crowding these vital regions of space, resulting in the need for methods for their removal. For remediation methods that depend on docking with the debris, eliminating the residual spin of the debris before docking is desirable, and perhaps necessary. The purpose of this work is to model the use of laser ablation to despin large space debris objects before surface contact. With a three-dimensional surface mesh of a known debris geometry, an assumed initial spin for the debris, and an offboard location for the laser, a targeting algorithm computes which faces are targetable at each instant based on geometric constraints. The location that generates the most desirable change in angular momentum is then targeted at each instant while integrating the equations of motion over time. The effects of nonoptimal targeting distance, incidence angle, surface ablation physics, and laser power are considered in the evaluation of total time to despin the debris object. It is shown that the time required to despin a representative object with a 250 W pulsed laser is on the order of days.

Rapid three-dimensional surface mesh segmentation based on region dilation

Three-dimensional laser scanned surface segmentation is an important step for computer-aided broken objection patching. Current methods still have high time consuming problem in practical applications. In order to solve this problem, we propose the rapid three-dimensional (3-D) surface segmentation based on region dilation. The procedure includes three steps of point cloud meshing, candidate region generating, and insignificant region eliminating. Some experiments are implemented on the 3-D surface with a Roland LPX-250 3-D laser scanner to testify the feasibility and performance of the proposed algorithm compared with other methods.

Head-to-head comparison of contrast-enhanced magnetic resonance imaging and electroanatomical voltage mapping to assess post-infarct scar characteristics in patients with ventricular tachycardias: real-time image integration and reversed registration

Substrate-based ablation of ventricular tachycardia (VT) relies on electroanatomical voltage mapping (EAVM). Integration of scar information from contrast-enhanced magnetic resonance imaging (CE-MRI) with EAVM may provide supplementary information. This study assessed the relation between electrogram voltages and CE-MRI scar characteristics using real-time integration and reversed registration. Fifteen patients without implantable cardiac defibrillator (14 males, 64 ± 9 years) referred for VT ablation after myocardial infarction underwent CE-MRI. Contours of the CE-MRI were used to create three-dimensional surface meshes of the left ventricle (LV), aortic root, and left main stem (LM). Real-time integration of CE-MRI-derived scar meshes with EAVM of the LV and aortic root was performed using the LM and the CARTO surface registration algorithm. Merging of CE-MRI meshes with EAVM was successful with a registration error of 3.8 ± 0.6 mm. After the procedure, voltage amplitudes of each mapping point were superimposed on the corresponding CE-MRI location using the reversed registration matrix. Infarcts on CE-MRI were categorized by transmurality and signal intensity. Local bipolar and unipolar voltages decreased with increasing scar transmurality and were influenced by scar heterogeneity. Ventricular tachycardia reentry circuit isthmus sites were correlated to CE-MRI scar location. In three patients, VT isthmus sites were located in scar areas not identified by EAVM. Integration of MRI-derived scar maps with EAVM during VT ablation is feasible and accurate. Contrast-enhanced magnetic resonance imaging identifies non-transmural scars and infarct grey zones not detected by EAVM according to the currently used voltage criteria and may provide important supplementary substrate information in selected patients.

Computational fluid dynamics simulation of transcatheter aortic valve degeneration☆☆☆

Studied under clinical trials, transcatheter aortic valves (TAV) have demonstrated good short-term feasibility and results in high-risk surgical patients with severe aortic stenosis. However, their long-term safety and durability are unknown. The objective of this study is to evaluate hemodynamic changes within TAV created by bioprosthetic leaflet degeneration. Computational fluid dynamics (CFD) simulations were performed to evaluate the hemodynamics through TAV sclerosis (35% orifice reduction) and stenosis (78% orifice reduction). A three-dimensional surface mesh of the TAV within the aortic root was generated for each simulation. Leaflets were contained within an open, cylindrical body without attachment to the sinus commissures representing the stent. A continuous surface between the annulus and TAV excluded the geometry of the native calcified leaflets and prevented paravalvular leak. Unsteady control volume analysis throughout systole was used to calculate leaflet shear stress and total force on the TAV. Sclerosis increased total force on the TAV by 63% (0.602-0.98 N). Advancement of degeneration from sclerosis to stenosis was accompanied by an 86% increase in total force (1.82 N) but only a 32% increase in peak wall shear stress on the leaflets. Of the total force exerted on the TAV, 99% was in the direction of axial flow. Shear stresses on the TAV were greatest during peak systolic flow with stress concentrations on the tips of the leaflets. In the normal TAV, the aortic root geometry and physiologic flow dominate location and magnitude of shear stress. Following leaflet degeneration, the specific geometry of the stenosis dictates the profile of axial velocity leaving the TAV and shear stress on the leaflets. A dramatic increase in peak leaflet shear stress was observed (115 Pa stenosis vs. 87 Pa sclerosis and 29 Pa normal). CFD simulations in this study provide the first of its kind data quantifying hemodynamics within stenosed TAV. Stenosis leads to significant forces of TAV during systole; however, diastolic forces predominate even with significant stenosis. Substantial changes in peak shear stress occur with TAV degeneration. As the first implanted TAV begin to stenose, the authors recommend watchful examination for device failure.

Three-Dimensional Surface Mesh Segmentation Using Curvedness-Based Region Growing Approach

A new parameter-free graph morphology based segmentation algorithm is proposed to address the problem of partitioning a 3D triangular mesh into disjoint sub- eshes that correspond to the physical parts of the underlying object. Curvedness, which is a rotation and translation invariant shape descriptor, is computed at every vertex in the input triangulation. Iterative graph dilation and morphological filtering of the outlier curvedness values result in multiple, disjoint, maximally connected sub-meshes such that each sub-mesh contains a set of vertices with similar curvedness values, and vertices in disjoint sub-meshes have significantly different curvedness values. Experimental evaluations using the triangulations of a number of complex objects demonstrate the robustness and the efficiency of the proposed algorithm and the results prove that it compares well with a number of state-of-the-art mesh segmentation algorithms.

Augmented virtuality based on stereoscopic reconstruction in multimodal image-guided neurosurgery: methods and performance evaluation

Displaying anatomical and physiological information derived from preoperative medical images in the operating room is critical in image-guided neurosurgery. This paper presents a new approach referred to as augmented virtuality (AV) for displaying intraoperative views of the operative field over three-dimensional (3-D) multimodal preoperative images onto an external screen during surgery. A calibrated stereovision system was set up between the surgical microscope and the binocular tubes. Three-dimensional surface meshes of the operative field were then generated using stereopsis. These reconstructed 3-D surface meshes were directly displayed without any additional geometrical transform over preoperative images of the patient in the physical space. Performance evaluation was achieved using a physical skull phantom. Accuracy of the reconstruction method itself was shown to be within 1 mm (median: 0.76 mm +/- 0.27), whereas accuracy of the overall approach was shown to be within 3 mm (median: 2.29 mm +/- 0.59), including the image-to-physical space registration error. We report the results of six surgical cases where AV was used in conjunction with augmented reality. AV not only enabled vision beyond the cortical surface but also gave an overview of the surgical area. This approach facilitated understanding of the spatial relationship between the operative field and the preoperative multimodal 3-D images of the patient.