Three-dimensional Visualization Method Research Articles

Effects of cooling rates on microstructural evolution during solidification process of liquid Ca50Zn50 alloy

A simulation study is performed on the effects of six different cooling rates on microstructural evolution during solidification process of liquid Ca50Zn50 alloy with larger atomic size difference by using the molecular dynamics method. The pair distribution function, Honeycutt-Andersen (HA) bond-type index method, cluster-type index method (CTIM-2) and three-dimensional visualization method are adopted to deeply analyze the microstructural evolution. The results show that there is a critical cooling rate (in a range of 11012 and 51011 K/s) for forming amorphous or crystal structure. When the cooling rate, such as 11014 K/s, 11013 K/s, 11012 K/s and 51011 K/s, is above the critical cooling rate, the amorphous structures are formed mainly to be the 1551, 1541 and 1431 bond-types or the icosahedron basic clustr (12 0 12 0 0 0); while the cooling rate is under the critical cooling rate, such as at 11012 K/s, the partial crystal structures are formed mainly to be the 1441 and 1661 bond-types or the bcc clusters (14 6 0 8 0 0) (containing part of hcp (12 0 0 0 6 6) and fcc (12 0 0 0 12 0) basic crystal clusters) in the system. In the cooling rate range of forming amorphous structure, the first peak of the pair distribution function g(r) is split obviously into three secondary peaks corresponding to the nearest neighbor as Zn-Zn, Ca-Zn and Ca-Ca, respectively, and with the decrease of cooling rate, the secondary peak formed by the like atoms is inereased and the secondary peak formed by unlike atoms is reduced. With the decrease of cooling rate, the Zn atoms can be easily segregated to form the larger clusters; the lower the cooling rate, the bigger the number of basic icosahedrons formed in the system, and the amorphous system is more stable. In the cooling rate range of forming crystal structure, a great number of Zn atoms are segregated to form the bulk bcc crystal structures and part of Ca atoms are segregated to form some hcp and fcc crystal clusters.

Cardiac ripple mapping: A novel three-dimensional visualization method for use with electroanatomic mapping of cardiac arrhythmias

Mapping of regular cardiac arrhythmias is frequently performed using sequential point-by-point annotation of local activation relative to a fixed timing reference. Assigning a single activation for each electrogram is unreliable for fragmented, continuous, or double potentials. Furthermore, these informative electrogram characteristics are lost when only a single timing point is assigned to generate activation maps. The purpose of this study was to develop a novel method of electrogram visualization conveying both timing and morphology as well as location of each point within the chamber being studied. Data were used from six patients who had undergone electrophysiological study with the Carto electroanatomic mapping system. Software was written to construct a three-dimensional surface from the imported electrogram locations. Electrograms were time gated and displayed as dynamic bars that extend out from this surface, changing in length and color according to the local electrogram voltage-time relationship to create a ripple map of cardiac activation. Ripple maps were successfully constructed for sinus rhythm (n = 1), atrial tachycardia (n = 3), and ventricular tachycardia (n = 2), simultaneously demonstrating voltage and timing information for all six patients. They showed low-amplitude continuous activity in four of five tachycardias at the site of successful ablation, consistent with a reentrant mechanism. Ripple mapping allows activation of the myocardium to be tracked visually without prior assignment of local activation times and without interpolation into unmapped regions. It assists the identification of tachycardia mechanism and optimal ablation site, without the need for an experienced computer-operating assistant.

Web‐based interactive 3D visualization as a tool for improved anatomy learning

Despite a long tradition, conventional anatomy education based on dissection is declining. This study tested a new virtual reality (VR) technique for anatomy learning based on virtual contrast injection. The aim was to assess whether students value this new three-dimensional (3D) visualization method as a learning tool and what value they gain from its use in reaching their anatomical learning objectives. Several 3D vascular VR models were created using an interactive segmentation tool based on the "virtual contrast injection" method. This method allows users, with relative ease, to convert computer tomography or magnetic resonance images into vivid 3D VR movies using the OsiriX software equipped with the CMIV CTA plug-in. Once created using the segmentation tool, the image series were exported in Quick Time Virtual Reality (QTVR) format and integrated within a web framework of the Educational Virtual Anatomy (EVA) program. A total of nine QTVR movies were produced encompassing most of the major arteries of the body. These movies were supplemented with associated information, color keys, and notes. The results indicate that, in general, students' attitudes towards the EVA-program were positive when compared with anatomy textbooks, but results were not the same with dissections. Additionally, knowledge tests suggest a potentially beneficial effect on learning.

Laser Scanning Up-Conversion Luminescence Microscopy for Imaging Cells Labeled with Rare-Earth Nanophosphors

Because of the ability to selectively reveal the objects of interest with subcellular resolution, fluorescence microscopy provides widespread applications from basic biological research to clinical diagnosis. However, challenges still remain in reducing the degree of photobleaching and increasing the contrast between signal and noise. Herein, we found that rare-earth nanophosphors exhibit a unique up-conversion luminescence mechanism and imaging modality and developed a new three-dimensional visualization method of laser scanning up-conversion luminescence microscopy (LSUCLM) with little photobleaching and no background fluorescence, by introducing a reverse excitation dichroic mirror and the confocal pinhole technique. Moreover, we demonstrated the up-conversion emission imaging of thin films containing embedded rare-earth nanophosphors and cells multilabeled with the nanophosphors and organic dyes. These data show that LSUCLM not only shares noninvasive benefits and deep penetration of two-photon microscopy but also offers some distinct advantages, such as little photobleaching of both organic dyes and rare-earth nanophosphors, no background fluorescence from either endogenous fluorophores or colabeled fluorescent probes, and excellent compatibility with conventional confocal microscopy.

Use of Confocal Microscopy as a Nondestructive Method in the Study of Ink Jet Dot Formation

The formation of the printing ink dot on the substrate is the final and the most critical phase in the printing process. The ink distribution on the printing surface and the drying mechanism depend on ink characteristics as well as on many other factors, for example, surface energy, roughness, sizing, and porosity. Suitable dot gain and high circularity (near unity) of printed dots predict the final print quality. High deviation from ideal circularity could cause undesired phenomena like wicking and bleeding. The aim of the present study is to determine ink dot formation by three different microscopic methods, optical microscopy (OM), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). The main goal of the authors research was to evaluate the applicability of CLSM as a nondestructive method for three-dimensional visualization in the analysis of ink dot formation on UV ink jet prints. To validate the feasibility of such means in a three-dimensional context, the images obtained are compared to those obtained by traditional two-dimensional imaging systems such as OM and SEM. The authors show that the CLSM produces a replica of the cross-sectioned dot profile as seen in SEM. This means that the CLSM technique can be used to rapidly assess the dot profile without physical sectioning.

3-D Visualization and Identification of Biological Microorganisms Using Partially Temporal Incoherent Light In-Line Computational Holographic Imaging

We present a new method for three-dimensional (3-D) visualization and identification of biological microorganisms using partially temporal incoherent light in-line (PTILI) computational holographic imaging and multivariate statistical methods. For 3-D data acquisition of biological microorganisms, the band-pass filtered white light is used to illuminate a biological sample. The transversely and longitudinally diffracted pattern of the biological sample is magnified by microscope objective (MO) and is optically recorded with an image sensor array interfaced with a computer. Three-dimensional reconstruction of the biological sample from the diffraction pattern is accomplished by using computational Fresnel propagation method. Principal components analysis and nonparametric inference algorithms are applied to the 3-D complex amplitude biological sample for identification purposes. Experiments indicate that the proposed system can be useful for identifying biological microorganisms. To the best of our knowledge, this is the first report on using PTILI computational holographic microscopy for identification of biological microorganisms.

Service-oriented Technology Roadmap (SoTRM) using patent map for R&D strategy of service industry

As a consequence of the service economy, R&D of the service industry has become more essential nowadays. Therefore, technology roadmaps are required for selection and concentration of services and related technologies. However, now there are problems and challenging issues as follows. First, there is no objective and systematic method or analysis tool to evaluate emerging technologies for services. Second, current technology roadmaps do not provide technology’s priority oriented to the service side. Therefore, we propose a patent map and a Service-oriented Technology Roadmap using the patent map, i.e. SoTRM. Our patent map is a three-dimensional visualization method and analysis tool based on keywords, which contributes to evaluating emerging technologies for services. It does not only overcome the subjectivity of experts, but it also discovers technologies missed out by experts initially. And SoTRM is a technology roadmap customized for the service industry. Based on four layers of patents, keywords, technologies, and services, the layer of service-oriented technologies provides the order of technologies in a service-oriented aspect. It also gives guidelines to assign roles in R&D to public and private sectors. As a result, we provide an objective and systematic framework required to form a technology roadmap oriented to services for R&D strategy of the service industry. Eventually, it helps decision makers from public and private sectors to select and concentrate on the first things among services and the related technologies in R&D of the service industry, and thereby to find the direction of distributing investment funds into technologies for services.

Interactive 3D stereoscopic digital‐image analysis of the basilar artery bifurcation

The goal of this study was to analyze morphometrical variations of the basilar artery bifurcation (BAB), so that physicians could map out a patients anatomical structure prior to delicate neurosurgical procedures. The CT-angio files of 98 patients ranging from 12 to 78 years of age were retrieved. These files were evaluated using Gradual Angiographic Image Data Analyzer (GAIDA) software, where a new interactive three-dimensional (3D) stereoscopic visualization method was used to reconstruct computer images of the BAB complex. Subsequently the measurements of the BAB angles and BAB distances in relation to the dorsum sellae (DS), posterior clinoid processes (PCPs), and posterior biclinoid plane (PBP) were carried out. The average BAB angle was determined to be 117.7 degrees (30.93 degrees -172.2 degrees ). The three types of BAB were classified as type T with a BAB angle greater than 145 degrees (mean 154.4 degrees ), type Y for an angle being equal or less than 145 degrees but greater than 100 degrees (mean 121.5 degrees ) and type V for angles less than 100 degrees (mean 83.28 degrees ). The mean distances between BAB and DS (9.55 mm), BAB and left PCP (12.97 mm), and BAB and right PCP (13.01 mm), BAB and PBP (2.2 mm) were evaluated. Furthermore, the BAB is of great importance when examining basilar artery aneurysm development, particularly at the point of greatest hemodynamic stress, as well as the BAB distances in relation to the bony landmarks used for different approach methods in neurosurgical procedures.

Adipogenesis in Obesity Requires Close Interplay Between Differentiating Adipocytes, Stromal Cells, and Blood Vessels

The expansion of adipose tissue mass seen in obesity involves both hyperplasia and hypertrophy of adipocytes. However, little is known about how adipocytes, adipocyte precursors, blood vessels, and stromal cells interact with one another to achieve adipogenesis. We have developed a confocal microscopy-based method of three-dimensional visualization of intact living adipose tissue that enabled us to simultaneously evaluate angiogenesis and adipogenesis in db/db mice. We found that adipocyte differentiation takes place within cell clusters (which we designated adipogenic/angiogenic cell clusters) that contain multiple cell types, including endothelial cells and stromal cells that express CD34 and CD68 and bind lectin. There were close spatial and temporal interrelationships between blood vessel formation and adipogenesis, and the sprouting of new blood vessels from preexisting vasculature was coupled to adipocyte differentiation. CD34(+) CD68(+) lectin-binding cells could clearly be distinguished from CD34(-) CD68(+) macrophages, which were scattered in the stroma and did not bind lectin. Adipogenic/angiogenic cell clusters can morphologically and immunohistochemically be distinguished from crown-like structures frequently seen in the late stages of adipose tissue obesity. Administration of anti-vascular endothelial growth factor (VEGF) antibodies inhibited not only angiogenesis but also the formation of adipogenic/angiogenic cell clusters, indicating that the coupling of adipogenesis and angiogenesis is essential for differentiation of adipocytes in obesity and that VEGF is a key mediator of that process. Living tissue imaging techniques provide novel evidence of the dynamic interactions between differentiating adipocytes, stromal cells, and angiogenesis in living obese adipose tissue.

A Three-Dimensional Visualization of Air Bubbles in Bubbely Flows

A three-dimensional visualization method (3D-BTV) for bubble measurements was developed to measure bubble shapes and velocities in a liquid. The 3D-BTV method is based on the combination the 3D shadow graph method and 3D super resolution particle tracking velocimetry. The proposed method was verified by virtual experiments and the real measurements of air bubble motions in the water, respectively. In this study, it can be realized that The 3D-BTV method has capability to measure the both bubble shapes and motions in the 3D space with highly temporal-spatial resolution in comparison with the previous technique.

Segmentation method for three-dimensional visualization of microscopic objects imaged with a confocal laser scanning microscope

This paper is a revision of a paper presented at the SPIE conference on Medical Imaging 2005: Physiology, Function, and Structure from Medical Images, Feb. 2005, San Diego, California. The paper presented there appears (unrefereed) in SPIE Proceedings Vol. 5746. Segmentation, or separating an image into distinct objects, is the key to creating 3-D renderings from serial slice images. This is typically a manual process requiring trained persons to tediously outline and isolate the objects in each image. We describe a template-based semiautomatic segmentation method to aid in the segmentation process and 3-D reconstruction of microscopic objects recorded with a confocal laser scanning microscope (CLSM). The simple and robust algorithm is based on the creation of a user-defined object template, followed by automatic segmentation of the object in each of the remaining image slices. The user guides the process by selecting the initial image slice for the object template, and labeling the object of interest. The algorithm is applied to mathematically defined shapes to verify the performance of the software. The algorithm is then applied to biological samples, including neurons in the common housefly. It is the quest to further understand the visual system of the housefly that provides the opportunity to develop this segmentation algorithm. Further application of this algorithm may extend to other registered and aligned serial section datasets with high contrast objects.

Three-dimensional (3D) visualization and microstructure-based modeling of deformation in a Sn-rich solder

We report on three-dimensional (3D) microstructure visualization and finite-element method modeling of deformation in Sn–3.5Ag alloy. The 3D virtual microstructure accurately represented the alignment, aspect ratio, and distribution of the Ag 3 Sn second phase. The 3D microstructure-based approach is more accurate than unit cell models for simulating and understanding material behavior.

VISUALIZATION, RECONSTRUCTION, AND INTEGRATION OF NEURONAL STRUCTURES IN DIGITAL BRAIN ATLASES

Brain atlases are used in neuroanatomy to define the spatial layout of neuronal structures. Their digital variant can serve as a database and common reference frame for integrating data from different biological experiments. This article presents an overview of methods for three-dimensional visualization of neuroanatomical image data, reconstructing neuronal structures from image data, creating digital brain atlases, and registering data in an atlas. This enables analysis of spatial relations between individual structures imaged in different experiments as well as between these structures and the atlas.

Three methods that improve the visual quality of colour anaglyphs

Anaglyphs are one of the most economical methods for three-dimensional visualization. This method, however, suffers from severe drawbacks such as loss of colour and extreme discomfort for prolonged viewing. We propose several methods for anaglyph enhancement that rely on stereo image registration, defocusing and nonlinear operations on synthesized depth maps. These enhancements substantially reduce unwanted ghosting artefacts, improve the visual quality of the images, and make comfortable viewing of the same sequence possible in three-dimensional as well as the two-dimensional mode of the same sequence.

Method for three-dimensional visualization of neurodegeneration in cupric-silver stained serial rat brain slices

The spatial distribution of neurodegeneration in brains is difficult to visualize when working from 2-D serial slices. In studies where repetitive operant behavior measurements are made over several weeks following organic solvent exposure, definitive evidence of degeneration in brain structures may have been significantly cleared by the time the tissue is prepared histologically. The only remaining evidence that injury has occurred may be nothing more than neuronal and cellular debris. By choosing stains that are specific for this type of residual and/or indicative of specific pathology, a 3-D representation of the spatial distribution of the neuronal and cellular debris fields within the organ can be highlighted and displayed. We present a method for visualizing the spatial distribution of neuronal degeneration that can result from low-level organic solvent exposure scenarios. A cupric-silver stain highly specific for neuronal degeneration is used to identify neuronal debris fields in 73 serial slices of brains of rodents that were exposed to toluene vapors. Serial brain sections stained with cupric-silver are scanned at 600 dpi using a gray-scale protocol. Using commercially available software, scans are assembled into 3-D images showing both topographical and internal anatomical details. The reassembled images are further processed into stereo pairs. Gray-scale scans are compared to the original sections to establish gray-scale ranges for healthy and damaged tissue and artifact staining.

Comparing 2D Vector Field Visualization Methods: A User Study

We present results from a user study that compared six visualization methods for two-dimensional vector data. Users performed three simple but representative tasks using visualizations from each method: 1) locating all critical points in an image, 2) identifying critical point types, and 3) advecting a particle. Visualization methods included two that used different spatial distributions of short arrow icons, two that used different distributions of integral curves, one that used wedges located to suggest flow lines, and line-integral convolution (LIC). Results show different strengths and weaknesses for each method. We found that users performed these tasks better with methods that: 1) showed the sign of vectors within the vector field, 2) visually represented integral curves, and 3) visually represented the locations of critical points. Expert user performance was not statistically different from nonexpert user performance. We used several methods to analyze the data including omnibus analysis of variance, pairwise t-tests, and graphical analysis using inferential confidence intervals. We concluded that using the inferential confidence intervals for displaying the overall pattern of results for each task measure and for performing subsequent pairwise comparisons of the condition means was the best method for analyzing the data in this study. These results provide quantitative support for some of the anecdotal evidence concerning visualization methods. The tasks and testing framework also provide a basis for comparing other visualization methods, for creating more effective methods and for defining additional tasks to further understand the tradeoffs among the methods. In the future, we also envision extending this work to more ambitious comparisons, such as evaluating two-dimensional vectors on two-dimensional surfaces embedded in three-dimensional space and defining analogous tasks for three-dimensional visualization methods.

Measuring membrane potential and electric field of brainstem neurons in vitro by confocal microscopy

A method of measuring transmembrane potential and electric field of neural cells cultured in vitro is described in this paper. The high resolution and scanning speed of the method make it considerable to be used to observe the viability of the neurons cultured on opaque substrate. Rhodamine 123 was used to stain the cells in order to display different intensity corresponding to transmembrane potential. The fluorescence data were collected by confocal laser scanning microscopy (CLSM). Then the data were processed to create the graphs of transmembrane potential and electric field. This is the first paper describes a reliable method for three-dimensional visualization of potential voltage of neurons at the best of our knowledge.

Induction of vascular networks in adult organs: implications to proangiogenic therapy.

Most therapeutic proangiogenic approaches rely on the premise that a single factor (e.g., VEGF) can induce new vascular loops properly connected to the existing vasculature of an ill-perfused organ (e.g., the ischemic myocardium). To gain insights into VEGF-driven neovascularization in the adult, in general, and to uncover inherent obstacles in VEGF-based therapeutic angiogenesis, we have used a transgenic system for conditional "on" and "off" switching of VEGF expression in selected adult organs and analytical methods for three-dimensional visualization of the induced vascular network. VEGF induces massive accumulation of endothelial progenitor cells and their subsequent coalescence into new vascular loops. Continual ramification of the vasculature and fusion of adjacent vessels culminate in formation of hemangioma-like vessels. In the absence of guiding cues, abnormal branching patterns and random connections with the existing network are formed. Following cessation of the VEGF stimulus, the acquired network undergoes extensive hemodynamic remodeling acting to "normalize" its architecture. Premature withdrawal of VEGF leads to regression of most acquired vessels, thus challenging the utility of therapeutic approaches relying on short stimulus duration. Overproduction of VEGF leads also to highly disruptive edema, thereby emphasizing the need to uncouple VEGF-induced permeability from its angiogenic activity. This genetic switch system thus highlights remaining problems critical for the implementation of proangiogenic therapy.

Parallel unfolding and visualization of curved surfaces extracted from large three-dimensional volumes

Although many three-dimensional (3D) medical imaging visualization methods exist, 3D volume slicing remains the most commonly used technique for visualizing medical data from modali- ties such as CT, MRI, and PET. We propose to extend the possibili- ties of oblique slicing to developable curved surfaces that can be flattened and displayed in two dimensions without deformation. Such surfaces can be used to follow curved anatomical structures while preserving distance metrics at visualization time. They may also be useful for the staging of tumors, i.e., to evaluate the spatial extension of a tumor. We propose an out of core algorithm that runs in parallel on a multi-PC architecture and is able to extract surfaces from very large 3D datasets such as the visible human data set (man: 13 GB, woman: 49 GB). Experimental performance results are presented which demonstrate that parallel surface extraction is scalable and has a reasonable overhead compared with traditional oblique planar slicing. Surface extraction is made available to the public as one of the services offered by EPFLs visible human web server (http://visiblehuman.epfl.ch). © 2002 SPIE and IS&T.

Structural Details in Soybeans: A New Three‐dimensional Visualization Method

ABSTRACT: A new combination of sample preparation, imaging and image processing techniques allowing new insights into the structure of biological objects has been developed as a method for the visualization and quality evaluation. This method is for the first time transferred to soybeans (Glycine soja L.) of the Nattousyoryu variety as an example of food and agricultural produce using volume rendering of thin slice microscopy images. By this method, soybeans are displayed as three‐dimensional data representations for visualization. Internal structures like the dormant cotyledon leafs are visualized and highlighted.