Visualization Of Three-dimensional Structures Research Articles

Comparative Analyses of Clearing Efficacies of Tissue Clearing Protocols by Using a Punching Assisted Clarity Analysis.

The advent of tissue clearing methods, in conjunction with novel high-resolution imaging techniques, has enabled the visualization of three-dimensional structures with unprecedented depth and detail. Although a variety of clearing protocols have been developed, little has been done to quantify their efficacies in a systematic, reproducible fashion. Here, we present two simple assays, Punching-Assisted Clarity Analysis (PACA)-Light and PACA-Glow, which use easily accessible spectroscopy and gel documentation systems to quantify the transparency of multiple cleared tissues simultaneously. We demonstrate the use of PACA-Light and PACA-Glow to compare twenty-eight tissue clearing protocols on rodent brains. We also show that regional differences exist in tissue transparency in the rodent brain, with cerebellar tissue consistently achieving lower clearing levels compared to the prefrontal or cerebral cortex across all protocols. This represents the largest comparative study of tissue clearing protocols to date, made possible by the high-throughput nature of our PACA platforms.

Molecular Model and Its Simplification in Teaching Stereoisomerism at Undergraduate Level

The role of molecular models in teaching chemistry is well-known. It is widely used in explaining the shape of molecules. Several authors have reported the difficulty in teaching stereochemistry/chirality. Some researchers have pleaded that the students face difficulty in solving stereochemistry problems because of poor visualization of three-dimensional structure of molecules. The present paper describes herewith the use of simple and inexpensive ball-stick molecular models in teaching stereoisomerism (conformation, configuration, and chirality in allenes) of organic molecules at undergraduate introductory organic chemistry course. It specially describes the use of simplified molecular models in determining the configuration (R or S) of the molecule.

Salamander‐Eci: An optical clearing protocol for the three‐dimensional exploration of regeneration

Salamander limb regeneration is a complex biological process that entails the orchestration of multiple cellular and molecular mechanisms in a three-dimensional space. Hence, a comprehensive understanding of this process requires whole-structure level explorations. Recent advances in imaging and optical clearing methods have transformed the study of regenerative phenomena, allowing the three-dimensional visualization of structures and entire organisms. Here we introduce Salamander-Eci, a rapid and robust optical clearing protocol optimized for the widely used axolotl model, which allows simultaneous immunohistochemistry and Click-chemistry detection with minimal volume disruption. We provide examples of its application, from whole larva to adult limbs and organs, and complement it with an image analysis pipeline for volumetric cell quantification. Further, we offer a detailed 3D quantitation of cell proliferation throughout axolotl limb regeneration. Salamander-Eci enables the comprehensive volumetric analysis of regenerative phenomena at both local and systemic levels.

Optimization of Pulmonary Vasculature Tridimensional Phenotyping in The Rat Fetus

Comparative, functional, developmental, and some morphological studies on animal anatomy require accurate visualization of three-dimensional structures. Nowadays, several widely applicable methods exist for non-destructive whole-mount imaging of animal tissues. The purpose of this study was to optimize specimen preparation and develop a method for quantitative analysis of the total pulmonary vasculature in fetal rats. Tissues were harvested at E21 and fetuses fixed overnight in 4% paraformaldehyde/phosphate buffered saline. They were treated with 25% Lugol solution for 72 hours to ensure perfusion. Four different methods were used for fetal specimen preparation; isolated lung, upper torso, direct right ventricle contrast injection, and whole body with partial thoracic skin excision. The microCT scan was performed, and pulmonary vasculature was segmented. Vessels were analyzed for diameter, length, and branching. Of the four preparation methods, only whole body with partial thoracic skin excision resulted in adequate reconstruction of the pulmonary vasculature. In silico generated 3D images gathered by micro CT showed pulmonary vasculature distributed throughout the lung, which was representative of the shape and structure of the lungs. The mean number of vessels segmented in the pulmonary tree was 900 ± 24 with a mean diameter of 134.13 µm (range 40.72–265.69 µm). While up to the 30th generation of vessels could be segmented, both for arteries and veins, the majority of branching was between the 21st and 30th generations. Passive diffusion of contrast material enables quantitative analysis of the fetal pulmonary vasculature. This technique is a useful tool to analyze the characteristics and quantify the fetal pulmonary vasculature.

Visualization of three-dimensional structures shed by an oscillating beam

Piezoelectric fans have been studied extensively and are seen as a promising technology for thermal management due to their ability to provide quiet, reliable cooling with low power consumption. The fluid mechanics associated with a piezoelectric fan are similar to that for a flapping bird wing, which are known to be complex. This paper is the first to investigate the three-dimensional fluid mechanics of an unconfined fan operating in its first vibration frequency mode. A custom built experimental facility was developed to capture the fan's flow field using two-dimensional phase locked Particle Image Velocimetry (PIV). The fluid-structure interaction was also captured through unique two-way coupled three-dimensional simulations of an oscillating beam in which the beam is actuated by a shear force at its resonant frequency and interacts with the surrounding air. This forgoes the need for temporal beam displacement data from experiments as in previous studies, allowing the numerical technique to be used independently. A finite element method is used for the simulations which allows the two-way coupling while maintaining computational efficiency. A three dimensional λ2 criterion constructed from interpolated PIV measurements as well as numerical data was used to identify a horse shoe vortex in the vicinity of the fan and its evolution into a hairpin vortex before it breaks up due to a combination of vortex shedding and flow along the fan blade. The experimental and numerical data are comparatively in agreement, confirming that the methods presented are valid for capturing the complex flow fields generated by this fluid-structure interaction. The results provide both a fundamental understanding on the formation and break-up of vortices from an oscillating beam, and demonstrate a validated approach which can be applied in the development of high efficiency piezoelectrically driven air moving devices and extended to the study of flapping bird and UAV wings.

Advantages and limitations of X-ray and computed tomography systems for the study of the skeleton in meagre (Argyrosomus regius)

Several methods and procedures exist for the diagnosis of skeletal disorders in fish. X-ray is one of the most reliable diagnosis technologies for medium-sized and large animals, whereas external examination is only of value in animals with extreme and prominent deformities. In small fish (e.g. juveniles or larvae), whole mount staining with alizarin red and/or alcian blue is advisable, although soft-tissue X-ray may be also used. Under this context, the study of the fish skeleton and its morphological and developmental disorders requires an accurate visualization of three-dimensional structures, but few widely applicable methods exist for non-destructive whole-volume imaging of animal tissues. In this sense, computed tomography (CT) has been recently suggested as an alternative or complementary imaging method for the early diagnosis of skeletal deformities, as well as a valuable tool for the current research on the causes and prevention of these anatomical disorders. In this study, we have analysed the skeleton of a 9.3 kg meagre (Argyrosomus regius) by means of standard X-rays (SEDECAL APR-VET 20 KW) and computerized X-ray tomography (HiSpeed Zx/i, General Electric Healthcare) and compared both imaging methods. The vertebral column of the examined specimen was composed by 24 vertebral bodies (including the urostyle) with a regional variation in the morphology of centrums along the vertebral axis. Both imaging methodologies allowed the clear visualization and identification of bony structures composing the skeleton of the meagre. In addition, the CT also allowed performing axial cuts of the meagre in which it was possible to differentiate tissues of different density (e.g. muscle, fat, bone), due to their different attenuation of the X-rays measured in Hounsfield scale. A general view of the potential of such imaging techniques, considering both their advantages and limitations is discussed.

Map-reading Strategy to Diagnose Root Perforations Near Metallic Intracanal Posts by Using Cone Beam Computed Tomography

Introduction To determine the diagnostic hypothesis on the basis of periapical radiography (PR) is a great challenge for radiologists and endodontists. Visualization of three-dimensional structures, available with cone beam computed tomography (CBCT), favors precise definition of the problem and treatment planning. However, metallic artifact effect of intracanal posts might also induce untrue images. The aim of this article is to suggest a map-reading strategy to diagnose root perforations near metallic intracanal posts (ICPs) by using CBCT. Methods and Results The incapacity to locate correctly the position of root perforation might lead to clinical failures. One strategy to minimize metallic artifact in root perforation associated with ICP is to obtain sequential axial slices of each root, with an image navigation protocol from coronal to apical (or from apical to coronal), with axial slices of 0.2 mm/0.2 mm. This map reading provides valuable information showing dynamic visualization toward the point of communication between the root canals and the periodontal space, associated with radiolucent areas, suggesting root perforation. Conclusions The accurate management of CBCT images might reveal abnormality that is unable to be detected in conventional PR. A map-reading approach reduces problems related to detection of root perforations near metallic artifacts. The final diagnosis should always be made in conjunction with the clinical findings.

MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues

BackgroundComparative, functional, and developmental studies of animal morphology require accurate visualization of three-dimensional structures, but few widely applicable methods exist for non-destructive whole-volume imaging of animal tissues. Quantitative studies in particular require accurately aligned and calibrated volume images of animal structures. X-ray microtomography (microCT) has the potential to produce quantitative 3D images of small biological samples, but its widespread use for non-mineralized tissues has been limited by the low x-ray contrast of soft tissues. Although osmium staining and a few other techniques have been used for contrast enhancement, generally useful methods for microCT imaging for comparative morphology are still lacking.ResultsSeveral very simple and versatile staining methods are presented for microCT imaging of animal soft tissues, along with advice on tissue fixation and sample preparation. The stains, based on inorganic iodine and phosphotungstic acid, are easier to handle and much less toxic than osmium, and they produce high-contrast x-ray images of a wide variety of soft tissues. The breadth of possible applications is illustrated with a few microCT images of model and non-model animals, including volume and section images of vertebrates, embryos, insects, and other invertebrates. Each image dataset contains x-ray absorbance values for every point in the imaged volume, and objects as small as individual muscle fibers and single blood cells can be resolved in their original locations and orientations within the sample.ConclusionWith very simple contrast staining, microCT imaging can produce quantitative, high-resolution, high-contrast volume images of animal soft tissues, without destroying the specimens and with possibilities of combining with other preparation and imaging methods. Such images are expected to be useful in comparative, developmental, functional, and quantitative studies of morphology.

The development of interactive online learning tools for the study of Anatomy

Background: The study of human anatomy is a core component of health science programs. However large student enrolments and the content-packed curricula associated with these programs have made it difficult for students to have regular access to cadaver laboratories.Methods: Adobe Flash MX™ was used with cadaver digital photographs and textbook-derived illustrations to develop interactive anatomy images that were made available to undergraduate health science students enrolled in first-year combined anatomy and physiology (ANP) courses at the University of Ottawa. Colour coding was used to direct student attention, facilitate name-structure association, improve visualization of structure contours, assist students in the construction of anatomical pathways, and to reinforce functional or anatomical groupings. The ability of two-dimensional media to support the visualization of three-dimensional structure was extended by developing the fade-through image (students use a sliding bar to move through tissues) as well as the rotating image in which entire organs such as the skull were photographed at eight angles of rotation. Finally, students were provided with interactive exercises that they could repeatedly try to obtain immediate feedback regarding their learning progress.Results: Survey data revealed that the learning and self-testing tools were used widely and that students found them relevant and supportive of their self-learning. Interestingly, student summative examination outcomes did not differ between those students who had access to the online tools and a corresponding student group from the previous academic year who did not.Conclusion: Interactive learning tools can be tailored to meet program-specific learning objectives as a cost-effective means of facilitating the study of human anatomy. Virtual interactive anatomy exercises provide learning opportunities for students outside the lecture room that are of especial value to visual and kinesthetic learners.

Mage: A Tool for Developing Interactive Instructional Graphics

Mage is a graphics program developed for visualization of three-dimensional structures of proteins and other macromolecules. An application of the Mage program is reported here for developing interactive instructional graphics files (kinemages) of much smaller scale. Examples are given illustrating features of VSEPR models, permanent dipoles, model crystal structures, radius ratios, hybridization, point group symmetry, and vibrational modes. This article demonstrates some of the advantages of the Mage program: (i) construction of instructional Mage data files is straightforward and results in clear, geometrically correct images; (ii) Mage images may be viewed directly from a Java-capable Web page; (iii) several other formats may be converted to kinemages in order to use the Mage applet. This paper also discusses a related student activity.

Direct visualization of flow-induced microstructure in dense colloidal gels by confocal laser scanning microscopy

Unconstrained uniaxial compression (or squeeze flow) of high volume fraction gels of fluorescent silica particles of diameter 832 nm results in the formation of voids (at φ=0.26) and cracks (at φ=0.40) that are of scale 10–100 μm. This evidence of inhomogeneous material deformation was obtained by direction visualization of three-dimensional structure by confocal laser scanning microscopy. Flow-induced void and crack microstructures are quantified by locating all particle centroids with quantitative image processing, by performing Voronoi volume tessellation with computational geometry and by analyzing the particle number density fluctuations as a function of averaging volume. Average short-range real space structural measures, such as the pair correlation function, are little changed by the flow. However, the probability distribution of excess normalized Voronoi polyhedra volume is profoundly extended by squeeze flow, particularly at large polyhedra volumes. Comparison of the Voronoi polyhedra volume distributions and particle bond distributions indicates that: (1) in the low φ gel, large flow-induced voids are formed by the reorganization of the existing quiescent voids without significant effect on the local structure; and (2) in the high φ gel, cracks are formed by reorganization of the local structure itself. Analysis of the number density fluctuations shows that the gels respond to applied squeeze flow deformation with structural distortion on the length scale of 5–10 particle diameters.Unconstrained uniaxial compression (or squeeze flow) of high volume fraction gels of fluorescent silica particles of diameter 832 nm results in the formation of voids (at φ=0.26) and cracks (at φ=0.40) that are of scale 10–100 μm. This evidence of inhomogeneous material deformation was obtained by direction visualization of three-dimensional structure by confocal laser scanning microscopy. Flow-induced void and crack microstructures are quantified by locating all particle centroids with quantitative image processing, by performing Voronoi volume tessellation with computational geometry and by analyzing the particle number density fluctuations as a function of averaging volume. Average short-range real space structural measures, such as the pair correlation function, are little changed by the flow. However, the probability distribution of excess normalized Voronoi polyhedra volume is profoundly extended by squeeze flow, particularly at large polyhedra volumes. Comparison of the Voronoi polyhedra volume dis...

Virtual reality: new method of teaching anorectal and pelvic floor anatomy.

A clear understanding of the intricate spatial relationships among the structures of the pelvic floor, rectum, and anal canal is essential for the treatment of numerous pathologic conditions. Virtual-reality technology allows improved visualization of three-dimensional structures over conventional media because it supports stereoscopic-vision, viewer-centered perspective, large angles of view, and interactivity. We describe a novel virtual reality-based model designed to teach anorectal and pelvic floor anatomy, pathology, and surgery. A static physical model depicting the pelvic floor and anorectum was created and digitized at 1-mm intervals in a CT scanner. Multiple software programs were used along with endoscopic images to generate a realistic interactive computer model, which was designed to be viewed on a networked, interactive, virtual-reality display (CAVE or ImmersaDesk). A standard examination of ten basic anorectal and pelvic floor anatomy questions was administered to third-year (n = 6) and fourth-year (n = 7) surgical residents. A workshop using the Virtual Pelvic Floor Model was then given, and the standard examination was readministered so that it was possible to evaluate the effectiveness of the Digital Pelvic Floor Model as an educational instrument. Training on the Virtual Pelvic Floor Model produced substantial improvements in the overall average test scores for the two groups, with an overall increase of 41 percent (P = 0.001) and 21 percent (P = 0.0007) for third-year and fourth-year residents, respectively. Resident evaluations after the workshop also confirmed the effectiveness of understanding pelvic anatomy using the Virtual Pelvic Floor Model. This model provides an innovative interactive educational framework that allows educators to overcome some of the barriers to teaching surgical and endoscopic principles based on understanding highly complex three-dimensional anatomy. Using this collaborative, shared virtual-reality environment, teachers and students can interact from locations world-wide to manipulate the components of this model to achieve the educational goals of this project along with the potential for virtual surgery.

Virtual Reality

PURPOSE: A clear understanding of the intricate spatial relationships among the structures of the pelvic floor, rectum, and anal canal is essential for the treatment of numerous pathologic conditions. Virtual-reality technology allows improved visualization of three-dimensional structures over conventional media because it supports stereoscopic-vision, viewer-centered perspective, large angles of view, and interactivity. We describe a novel virtual reality-based model designed to teach anorectal and pelvic floor anatomy, pathology, and surgery. METHODS: A static physical model depicting the pelvic floor and anorectum was created and digitized at 1-mm intervals in a CT scanner. Multiple software programs were used along with endoscopic images to generate a realistic interactive computer model, which was designed to be viewed on a networked, interactive, virtual-reality display (CAVE® or ImmersaDesk®). A standard examination of ten basic anorectal and pelvic floor anatomy questions was administered to third-year (n = 6) and fourth-year (n = 7) surgical residents. A workshop using the Virtual Pelvic Floor Model was then given, and the standard examination was readministered so that it was possible to evaluate the effectiveness of the Digital Pelvic Floor Model as an educational instrument. RESULTS: Training on the Virtual Pelvic Floor Model produced substantial improvements in the overall average test scores for the two groups, with an overall increase of 41 percent (P= 0.001) and 21 percent (P= 0.0007) for third-year and fourth-year residents, respectively. Resident evaluations after the workshop also confirmed the effectiveness of understanding pelvic anatomy using the Virtual Pelvic Floor Model. CONCLUSION: This model provides an innovative interactive educational framework that allows educators to overcome some of the barriers to teaching surgical and endoscopic principles based on understanding highly complex three-dimensional anatomy. Using this collaborative, shared virtual-reality environment, teachers and students can interact from locations world-wide to manipulate the components of this model to achieve the educational goals of this project along with the potential for virtual surgery.

Classes of polyhedra defined by jet graphics

The uniform polyhedra form a fascinating set of objects for display on graphics output devices. When animated on graphics screens they help in visualization of three-dimensional structures and in understanding the geometrical properties and relationships between the various polyhedra. However, the coordinates of the vertices of these objects—the Platonic solids, the Archimedean solids, the Johnson solids and the starred regular polyhedra—are mostly very difficult and tedious to determine algebraically. When the objective is simply to display these solids on a graphics screen, rather than explicit coordinate calculation, another approach can be adopted: the use of jet graphics software. Turtle graphics provides a compact method of describing and displaying the two-dimensional analogies of these solids, and this research investigated to what extent three-dimensional turtle graphics, also known as jet graphics, could describe and also display the regular three-dimensional polyhedra. A number of methods applicable to many of the solids were invented. In particular, methods were found that apply to the infinite classes of prisms and anti-prisms, pyramids and dipyramids, cupolas, bicupolas and gyrobicupolas as well as some starred versions of these polyhedra. A new class of polyhedra, the star antiprisms, are shown to be facially equilateral only for the case when the parallel faces correspond to pentagrams. A single iterative algorithm for the finite class of convex regular polyhedra was found. However, this method applies to all Platonic solids except the icosahedron, and generalizes the Petrie polygon rings to form new infinite classes of polyhedra such as Petrie-prisms. A recursive algorithm is described which correctly displays all regular polyhedra and is generalizable to semiregular and other classes of polyhedra.