Three-dimensional Analysis Method Research Articles

A biplanar X-ray method for three-dimensional analysis of track formation

Tracks arise through a complex interplay between animal and substrate. Studying this dynamic process is challenging because most foot-sediment and sediment-sediment interactions are rapid and hidden from view. Herein, we describe a new method for visualizing and quantifying three-dimensional movements of both a morphologically accurate indenter and realistic sediment during track formation. Our method uses biplanar X-ray imaging and an animation-based workflow to reconstruct the trajectories of metal beads seeded throughout the sediment volume. X-rays allow sub-surface motion normally concealed by the foot and opaque matrix to be analyzed at 30 frames per second with sub-millimeter resolution. Results from two case studies of tridactyl tracks in semi-liquid mud provide novel, animated visualizations, examples of ensemble and particle-specific data, as well as measures of precision and accuracy. This methodology has the potential to mechanistically link specific track morphologies to foot movement, clarify undertrack formation, validate computational models, and set a new standard for evidence-based reconstruction of locomotion from fossil footprints. Richard G. Ellis. Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA and Structure and Motion Lab, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire, AL9 7TA United Kingdom richgellis@gmail.com Stephen M. Gatesy (correspondence author). Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA stephen_gatesy@brown.edu

Three-dimensional discontinuous deformation analysis (3-D DDA) method for particulate media applications

This paper presents a new numerical model for simulation of granular materials consisting of 3-D spheres bounded by rigid boundaries. The proposed model is based on Three-Dimensional Discontinuous Deformation Analysis (3-D DDA), a numerical method recently developed for simulation of particles in motion. Stiffness and force matrices due to body forces, point loading, inertia forces, and displacement and directional constraints are derived in detail. Moreover, an efficient model for particle contacts in 3-D is presented. In this model, sphere-sphere and sphere-boundary contacts are simply transformed into the form of point-to-plane contacts. Normal and shear contact forces as well as friction force for both sphere-sphere and sphere-plane contact types are derived by vector analysis and the penalty method. The numerical model developed herein is a simple and efficient method that can be easily coded into a computer program. The validity and capability of the model are demonstrated by numerical results obtained for several illustrative examples. Furthermore, some examples are presented and discussed to illustrate the application of the 3-D DDA to particulate media.

Spatio-temporal patterns of pre-harvest brown rot epidemics within individual peach tree canopies

Tree canopies are architecturally complex and pose several challenges for measuring and characterizing spatial patterns of disease. Recently developed methods for fine-scale canopy mapping and three-dimensional spatial pattern analysis were applied in a 3-year study to characterize spatio-temporal development of pre-harvest brown rot of peach, caused by Monilinia fructicola, in 13 trees of different maturity classes. We observed a negative correlation between an index of disease aggregation and disease incidence in the same tree (r = −0.653, P < 0.0001), showing that trees with higher brown rot incidence had lower aggregation of affected fruit in their canopies. Significant (P ≤ 0.05) within-canopy aggregation among symptomatic fruit was most pronounced for early-maturing cultivars and/or early in the epidemic. This is consistent with the notion of a greater importance of localized, within-tree sources of inoculum at the beginning of the epidemic. Four of five trees having >10 blossom blight symptoms per tree showed a significant positive spatial association of pre-harvest fruit rot to blossom blight within the same canopy. Spatial association analyses further revealed one of two outcomes for the association of new fruit rot symptoms with previous fruit rot symptoms in the same tree, whereby the relationship was either not significant or exhibited a significant negative association. In the latter scenario, the newly diseased fruit were farther apart from previously symptomatic fruit than expected by random chance. This unexpected result could have been due to uneven fruit ripening in different sectors of the canopy, which could have affected the timing of symptom development and thus led to negative spatial associations among symptoms developing over time in a tree.

Meshless Local Petrov-Galerkin Method for Three-Dimensional Heat Transfer Analysis

A meshless local Petrov-Galerkin (MLPG) method is proposed to obtain the numerical solution of nonlinear heat transfer problems. The moving least squares scheme is generalized to construct the field variable and its derivatives continuously over the entire domain. The essential boundary conditions are enforced by the direct scheme. By defining a radiation heat transfer coefficient, the nonlinear boundary value problem is solved as a sequence of linear problems each time updating the radiation heat transfer coefficient. The matrix formulation is used to drive the equations for a three dimensional nonlinear coupled radiation heat transfer problem. By using the MPLG method, along with the linearization of the nonlinear radiation problem, a new numerical approach is proposed to find the solution of the coupled heat transfer problem. A numerical study of the dimensionless size parameters for the quadrature and support domains is conducted to find the most appropriate values to ensure convergence of the nodal temperatures to the correct values quickly. Numerical examples are presented to illustrate the applicability and effectiveness of the proposed methodology for the solution of one-, two-, and three-dimensional heat transfer problems involving radiation with different types of boundary conditions. In each case, the results obtained using the MLPG method are compared with those given by the finite element method (FEM) method for validating the results.

Three-dimensional analysis of tooth dimensions in the MSX1-missense mutation

A novel, 3D technique to measure the differences in tooth crown morphology between the MSX1 cases and non-affected controls was designed to get a better understanding of dental phenotype-genotype associations. Eight Dutch subjects from a single family with tooth agenesis, all with an established nonsense mutation c.332 C > A, p. Ser 111 Stop in exon 1 of MSX1, were compared with unaffected controls regarding several aspects of tooth crown morphology of incisor and molar teeth. A novel method of quantitative three-dimensional analysis was used to detect differences. Statistically significant shape differences were observed for the maxillary incisor in the MSX1 family compared with the controls on the following parameters: surface area, buccolingual dimension, squareness, and crown volume (P ≤ 0.002). Molar crown shape was unaffected. A better understanding of dental phenotype-genotype associations may contribute to earlier diagnosis of some multiple-anomaly congenital syndromes involving dental anomalies. A "shape database" that includes associated gene mutations resulting from developmental syndromes may facilitate the genetic identification of hypodontia cases.

A Novel Method for Three-Dimensional Analysis of Endoscopic Spatial Relationships of Pterygopalatine Fossa Structures and Associated Regions

Background: The spatial orientation rules of the important skull base structures are essential for performing endoscopic surgery. However, there is no satisfactory three-dimensional (3-D) anatomy study available to the surgeon at present. The aims of this study are to construct a new method to learn the spatial orientation of anatomical features under endoscopy and to help the surgeon establish a 3-D image of skull base structures in his mind. Methods: A modified MicronTracker navigation system was used to measure the pitch angle, direction angle and distance from the reference points to various anatomical landmarks of the pterygopalatine fossa and related structures (PPFRS) at the skull base in 10 fresh cadavers (20 sides). Results: The location data of the positions of the major landmarks were acquired and a digital model of the anatomical structures of the PPFRS was built, which can be moved, whirled or demonstrated easily. Conclusion: It is practical to measure the positions of the anatomical structures of the PPFRS with a modified binocular vision-based MicronTracker navigation system. It is a valuable exploration tool to help the surgeon establish the orientation of surgical landmarks in his mind by the 3-D parameters and model.

Optical Sectioning and Confocal Imaging and Analysis in the Transmission Electron Microscope

Aberration correction in the transmission electron microscope has led to a reduction in the depth of focus for imaging. The depth of focus in a state-of-the-art scanning transmission electron microscope system, which is currently just a few nanometers, creates an opportunity to explore the three-dimensional structure of a sample by focusing on specific layers, an approach known as optical sectioning. In this article, we review the performance of optical sectioning in the scanning transmission electron microscope. Limitations in the simple optical sectioning approach are used to motivate discussion of confocal electron microscopy. Three imaging modes in scanning confocal electron microscopy have been investigated both theoretically and experimentally, and are reviewed here. The method of implementing a confocal arrangement in a microscope is discussed, along with its comparative performance with other methods for three-dimensional imaging and analysis. Finally, current and future potential applications are discussed.

Investigation of pore parameters of woven fabrics by theoretical and image analysis methods

Fluid permeability property is an important performance feature of fabrics and must be considered during the designing processes of products. Since the rate of fluid flow through a textile is a function of viscosity, density, pressure gradient of fluid, and the pore properties of fabric, it is necessary to define pore properties by controlling the structural parameters of fabric for a certain area of use. Due to the complexity of fabric structure, modeling of pore structure and predicting the pore parameters are difficult. In this study, the interyarn porosity, pore size, and pore-size distribution of cotton woven fabrics were calculated by using two-dimensional (2D) and three-dimensional (3D) geometrical pore models and image analysis method. The effect of weave types and weft settings on the pore parameters and air permeability of fabrics were investigated, and the advantages of 2D, 3D geometrical pore models and image analysis method were compared.

Three‐Dimensional Analysis of the Islet Vasculature

The pancreatic islets of Langerhans are highly vascularized structures scattered throughout the pancreas that contain a capillary network 5-10 times denser than that of the exocrine pancreas. A simple method for three-dimensional (3D) analysis of this intricate intraislet vasculature has been difficult because of the intrinsic opacity of the pancreas. We developed a whole-mount imaging technique that allows relatively easy visualization of the islet vasculature. In combination with confocal microscopy and the use of 3D imaging software, we were able to readily reconstruct the 3D architecture of an islet, allowing delineation of the islet volume, length of the intraislet vessels, and the number of vessel branch-points. This technique allows for straightforward 3D image analysis that may help toward understanding islet function.

Quantitative Evaluation of Papilledema from Stereoscopic Color Fundus Photographs

To derive a computerized measurement of optic disc volume from digital stereoscopic fundus photographs for the purpose of diagnosing and managing papilledema. Twenty-nine pairs of stereoscopic fundus photographs and optic nerve head (ONH) centered spectral domain optical coherence tomography (SD-OCT) scans were obtained at the same visit in 15 patients with papilledema. Some patients were imaged at multiple visits in order to assess their changes. Three-dimensional shape of the ONH was estimated from stereo fundus photographs using an automated multi-scale stereo correspondence algorithm. We assessed the correlation of the stereo volume measurements with the SD-OCT volume measurements quantitatively, in terms of volume of retinal surface elevation above a reference plane and also to expert grading of papilledema from digital fundus photographs using the Frisén grading scale. The volumetric measurements of retinal surface elevation estimated from stereo fundus photographs and OCT scans were positively correlated (correlation coefficient r(2) = 0.60; P < 0.001) and were positively correlated with Frisén grade (Spearman correlation coefficient r = 0.59; P < 0.001). Retinal surface elevation among papilledema patients obtained from stereo fundus photographs compares favorably with that from OCT scans and with expert grading of papilledema severity. Stereoscopic color imaging of the ONH combined with a method of automated shape reconstruction is a low-cost alternative to SD-OCT scans that has potential for a more cost-effective diagnosis and management of papilledema in a telemedical setting. An automated three-dimensional image analysis method was validated that quantifies the retinal surface topography with an imaging modality that has lacked prior objective assessment.

A Morphological Analysis Method for Geological Bodies and Its Application on Three-dimensional Visualization Environment

Aiming at the spatial shape analysis of complex geological bodies in stereoscopic quantitative prediction of concealed ore bodies, a three-dimensional morphological analysis method for geological bodies based on 3-dimensional raster model under visualization environment was put forward by combining mathematical morphology with Euclidean distance transform theory. Firstly, the 3-dimensional visualization models for geological bodies were constructed on the basis of the 3-dimensional geological modeling (3DGM) technology; Secondly, the algorithm for extracting the surface shape trend of geological body with the 3-dimensional raster model was proposed by using mathematical morphology filtering. By the combination of morphological filtering, global set operation and three-dimensional Euclidean distance transform, the models for the quantitative analysis and extraction of the shape undulance were established. Lastly, as a case study, the three-dimensional morphological analysis method was applied in analyzing quantitatively the Xinwuli magmatic body in Fenghuangshan ore field in Tongling, Anhui Province. By means of the calculation model of Euclidean distance field, the quantitative extraction of the shape trend and shape undulance as the quantitative indexes of geological ore-controlling factors were achieved after building the 3D raster models of the magmatic body. The results show that the morphological analysis method is feasible to calculate various morphological parameters of complex geological bodies and extract quantitative indexes of geological ore-controlling factors successfully for stereoscopic quantitative predication of concealed ore bodies.

Three-Dimensional Reciprocal-Lattice Analysis Using Azimuth-Scan Reflection High-Energy Electron Diffraction: Determination of Complex Crystal Orientations of Al Grains on Si(111) Surface

We have applied a three-dimensional (3D) reciprocal-lattice analysis method using a typical reflection high-energy electron diffraction (RHEED) system – all RHEED patterns in scanning sample-surface azimuth are converted into 3D reciprocal-lattice space. This analysis method can determine complex crystal orientations of nanoclusters, islands, and grains with multiple domains, which are difficult to obtain from a small number of non-converted two-dimensional RHEED patterns. For an Al-deposited Si(111) surface followed by annealing, we successfully determined new crystal orientations of Al grains: Al(001), Al(012) and Al(011) ∥ Si(111) with Al[100] ∥ Si<01̄1>. The typical acquisition time of 3D RHEED patterns is 10–20 min, which is shorter than that by a standard X-ray diffraction system with φ and ω scans for 3D reciprocal-lattice mapping. This is one of the advantages of this analysis method, in addition to the convenient observation of in situ vacuum-fabricated nanocrystals on substrate surfaces with high sensitivity.

Transmissive color filtering using plasmonic multilayer structure

A transmission type plasmonic multilayer filter is theoretically investigated using three-dimensional rigorous coupled wave analysis (RCWA) method. The design rule of the resonance properties associated with the weakly localized surface plasmon modes in metal/insulator/metal waveguide arrays is discussed. The optical performances with respect to the geometrical parameters of the plasmonic structure are evaluated. Through manipulating the geometric parameters of the metal/insulator/metal waveguide, the optical properties of the filter can be engineered.

Introducing a Novel Analysis Technique for Osseointegrated Dental Implants Retrieved 29 Years Postsurgery

To investigate osseointegration of oral implants, which were retrieved from a patient after 29 years in situ, we use novel three-dimensional analysis methods and visualization techniques that supplement conventional two-dimensional analysis. The sample processing involved nondecalcification and embedment in resin. Conventional two-dimensional histomorphometrical methods were conducted. Additionally, the quantification was extended to three-dimensional by using synchrotron radiation micro-computed tomography (SRµCT) technique and two relevant visualization methods for the three-dimensional data were introduced. The three-dimensional results involved three-dimensional quantification and visualization of two implant samples with methods beyond state-of-the-art. Traditional two-dimensional histomorphometrical results revealed a mean bone-implant contact (BIC) of about 50%. In most samples, bone area (BA) was lower inside the treads compared with out-folded mirror images, which were confirmed by the three-dimensional quantification. The BIC along four selected regions showed highest percentages in the bottom/valley region and lowest in the thread-peak region. Qualitative observations revealed ongoing bone remodeling areas in all samples. The apical hole demonstrated high osseointegration. The novel techniques including an animation and an out-folding of BIC and BA enabled a simultaneous visualization of the three-dimensional material obtained from SRµCT data. However, the two-dimensional histological sections were needed for qualitative and quantitative evaluation of osseointegration and, thus, both methods are considered equally important.

Intracranial depth electrodes implantation in the era of image-guided surgery

The advent of modern image-guided surgery has revolutionized depth electrode implantation techniques. Stereoelectroencephalography (SEEG), introduced by Talairach in the 1950s, is an invasive method for three-dimensional analysis on the epileptogenic zone based on the technique of intracranial implantation of depth electrodes. The aim of this article is to discuss the principles of SEEG and their evolution from the Talairach era to the image-guided surgery of today, along with future prospects. Although the general principles of SEEG have remained intact over the years, the implantation of depth electrodes, i.e. the surgical technique that enables this method, has undergone tremendous evolution over the last three decades, due the advent of modern imaging techniques, computer systems and new stereotactic techniques. The use of robotic systems, the constant evolution of imaging and computing techniques and the use of depth electrodes together with microdialysis probes will open up enormous prospects for applying depth electrodes and SEEG both for investigative use and for therapeutic use. Brain stimulation of deep targets and the construction of "smart" electrodes may, in the near future, increase the need to use this method.

3D Profile Variety Measurement of Pectoral Fin in Fish Fast Start

Fast-starts are brief, sudden accelerations used by fish during predator-prey encounters. In this paper, a three-dimensional (3D) test and analysis method is critical to understand the function of the pectoral fin during maneuvers. An experiment method based on Fourier Transform Profilometry for 3D pectoral fin profile variety during fish maneuvers is proposed. This method was used in a carp fast-start during prey. Projecting the moiré fringes onto a carp pectoral fin it will produce the deformed fringe patterns contain 3D information. A high speed camera captures these time-sequence images. By Fourier transform, filter, inverse Fourier transform and unwrap these phase maps in 3D phase space, the complex pectoral fin profile variety were really reconstructed. The present study provides a new method to quantify the analysis of kinetic characteristic of the pectoral fin during maneuvers.

Three-Dimensional FEM Analysis of Sensitive Mechanism of Airflow Level Posture Sensor Based on Thermoelectric Coupling

Using ANSYS program, the finite element simulation based on thermoelectric coupling is conducted by a series of procedures, such as three-dimensional model building of airflow level posture sensor according to the actual size of the proportion, network modifying, loads applying and equation solving. The sensitive mechanism of airflow level posture sensor is explained by finite element method. The numerical results show that compared with two-dimensional modeling, the simulation result of three-dimensional modeling and thermoelectric analysis methods are more comprehensive and accurate, which provides more reliable basis for practical research of the airflow level posture sensor.

Study on the Airflow Level Posture Sensor Based on Fluid-Solid Coupling

Using ANSYS program, the finite element simulation based on Fluid-Solid coupling is conducted by a series of procedures, such as three-dimensional model building of airflow level posture sensor according to the actual size of the proportion, network modifying, loads applying and equation solving. The flow field in three-dimensional hermetic chamber of sensitive element of airflow level posture sensor is calculated. The numerical results show that: 1) The velocity difference of air flow at two heat source changes with the tilt angle, the difference between airflow velocity increases with the increase of the tilt angle. 2)Compared with two-dimensional modeling, the simulation result of three-dimensional modeling and fluid-solid analysis methods are more comprehensive and accurate, which provides more reliable basis for practical research of the airflow level posture sensor.

Three-dimensional Morphological Analysis for Geological Bodies and Application

To address the spatial Morphological analysis of complex geological bodies in stereoscopic quantitative prediction of concealed ore bodies, a three-dimensional morphological analysis method for geological bodies based on 3-dimensional raster model under visualization environment was put forward by combining mathematical morphology with Euclidean distance transform theory. Firstly, the 3-dimensional visualization models for geological bodies were constructed on the basis of the 3-dimensional geological modeling (3DGM) technology; Secondly, the algorithm for extracting the surface shape trend of geological body with the 3-dimensional raster model was proposed by using mathematical morphology filtering. By the combination of morphological filtering, global set operation and three-dimensional Euclidean distance transform, the models for the quantitative analysis and hierarchical extraction of the shape undulance were established. Lastly, as a case study, the three-dimensional morphological analysis method was applied in analyzing quantitatively the Xinwuli magmatic body in Fenghuangshan ore field in Tongling, Anhui Province. By means of the calculation model of Euclidean distance field, the quantitative extraction of the shape trend and shape undulance as well as the angle between geological interface and trend surface, as the quantitative indexes of geological ore-controlling factors, were achieved after building the 3D raster models of the magmatic body. The results show that the morphological analysis method is feasible to calculate various morphological parameters of complex geological bodies and extract quantitative indexes of geological ore-controlling factors successfully for stereoscopic quantitative predication of concealed ore bodies.

Direct visualization of the charge transfer in conjugated polymers

Ion-induced charge-transfer states in conjugated polyelectrolytes were experimentally investigated by Justin M. Hodgkiss and his co-workers [J Am Chem Soc, 2009, 131(25): 8913]. In this work, charged and neutral conjugated polyelectrolytes were further studied with quantum chemistry methods. The calculation result shows that the absorption spectra are roughly in visible and ultraviolet light regions, and the two absorption peaks are located in the wavelength span 300–400 nm for charged polyelectrolytes. However, in neutral conjugated polyelectrolytes, the peaks of the absorption spectra showed a blue shift compared with those of the charged polyelectrolytes. Charge transfer (CT) properties of the studied compounds were also investigated with both the three-dimensional real-space analysis method of transition and charge difference densities, and the two-dimensional real-space analysis method of transition density matrices based on the simulated absorption spectra. The calculation results revealed the charge transfer in conjugated polyelectrolytes on the excitation states.