Macromolecular Structure Visualization Tools at NCMI

2000 ◽  
Vol 6 (S2) ◽  
pp. 282-283
Author(s):  
Matthew Dougherty ◽  
Wah Chiu
Keyword(s):  
Human Factors ◽  
3D Visualization ◽  
Three Dimensional ◽  
Theoretical Models ◽  
Biological Research ◽  
Macromolecular Structure ◽  
X Ray ◽  
Visualization Tools ◽  
Types Of Information ◽  
3D Em

Sophisticated tools are needed to examine the results of cyro-microscopy. As the size and resolution of three dimensional macromolecular structures steadily improve, and the speed at with which they can be generated increases, researchers are finding they are inundated with larger datasets and at the same time are compelled to expediently evaluate these structures in unforeseen ways. Integration of EM data with other types of information is becoming necessary and routine; for example X-ray data, 3D EM reconstructions, and theoretical models, must be evaluated in concert to discount or propose hypothesis. To create such tools, the developer must take into account not only the empirical and theoretical possibilities, but also they must master the human factors and computational limits. During the last five years, the National Center for Macromolecular Imaging (NCMI) has progressed from a remedial 3D visualization capability to a collection of visualization tools allowing researchers to focus on the discovery phase of biological research.

3d Visualization Tools

2001 ◽  
Vol 7 (S2) ◽  
pp. 770-771
Author(s):  
Matthew T. Dougherty
Keyword(s):  
Electron Microscopy ◽  
Scientific Visualization ◽  
3D Visualization ◽  
Interactive Graphics ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Two Dimensional Image ◽  
Visualization Tools ◽  
Conceptual Formulation

The tutorial presents 3D visualization as implemented at NCMI: beginning with a brief overview of the history and philosophy of scientific visualization, proceeding to a description of general methodologies used throughout the field of visualization, and concluding with specific applications in electron microscopy, confocal microscopy and x-ray diffraction. The majority of the tutorial uses biological examples of visualization to demonstrate concepts and tools.History and Philosophy: Effective scientific visualization presents data in a simple, accurate conceptual formulation. Over the last one hundred years there has been a sea change in its economics caused by digital computers: beginning with calculated tables that were manually plotted, proceeding to two dimensional image graphics, and most recently multivariate 3D interactive graphics. The capability of scientific visualization has been greatly facilitated by the evolution of computers; particularly over the last ten years the 3D visualization of biological structures is quickly becoming a necessity for analysis, conceptualization, and presentations.

scholarly journals The use of three-dimensional visualization tools to detect deficiencies in geometric roadway designs

2014 ◽  
Vol 20 (1) ◽  
pp. 54-69 ◽  
Author(s):  
Aurenice da Cruz Figueira ◽  
Ana Paula C. Larocca ◽  
José Alberto Quintanilha ◽  
Felipe Issa Kabbach Jr
Keyword(s):  
3D Visualization ◽  
Three Dimensional ◽  
Geometric Design ◽  
Application Software ◽  
The Road ◽  
Road Project ◽  
Visualization Tools ◽  
Design Deficiencies ◽  
The Impact ◽  
Geometric Designs

The use of three-dimensional (3D) visualization technologies in the field of transportation sciences has contributed not only to the assessment of the impact of a road project on its surroundings but also to the development and study of elements of the geometric design itself. The present study aimed to assess the effectiveness of the use of 3D visualization tools in the detection of poor compatibility between the horizontal and vertical alignments of a road project. The assessment was performed by conducting tests with groups of participants who were students from a civil engineering course with no experience in the development of geometric roadway designs. These participants each assessed two road stretches: one stretch with unflawed coordination between the vertical and horizontal alignments of the road and another stretch in which this coordination had been intentionally distorted. It was used an application software for roadway geometric designs that allowed the creation of a video of the trajectory of the targeted road. Subsequently, the participants answered a questionnaire that aided the interpretation of the results regarding the design deficiencies in road layouts perceived from the 3D visualization of the roadways.

scholarly journals Creation and observation of Hopfions in magnetic multilayer systems

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Noah Kent ◽  
Neal Reynolds ◽  
David Raftrey ◽  
Ian T. G. Campbell ◽  
Selven Virasawmy ◽  
...  
Keyword(s):  
Magnetic Circular Dichroism ◽  
Three Dimensional ◽  
Perpendicular Magnetic Anisotropy ◽  
Theoretical Models ◽  
Magnetic Multilayer ◽  
Multilayer Systems ◽  
Transmission Microscopy ◽  
X Ray ◽  
Three Dimensional Objects ◽  
Magnetic Skyrmions

AbstractAmong topological solitons, magnetic skyrmions are two-dimensional particle-like objects with a continuous winding of the magnetization, and magnetic Hopfions are three-dimensional objects that can be formed from a closed loop of twisted skyrmion strings. Theoretical models suggest that magnetic Hopfions can be stabilized in frustrated or chiral magnetic systems, and target skymions can be transformed into Hopfions by adapting their perpendicular magnetic anisotropy, but their experimental verification has been elusive so far. Here, we present an experimental study of magnetic Hopfions that are created in Ir/Co/Pt multilayers shaped into nanoscale disks, known to host target skyrmions. To characterize three-dimensional spin textures that distinguish Hopfions from target skyrmions magnetic images are recorded with surface-sensitive X-ray photoemission electron microscopy and bulk-sensitive soft X-ray transmission microscopy using element-specific X-ray magnetic circular dichroism effects as magnetic contrast. These results could stimulate further investigations of Hopfions and their potential application in three-dimensional spintronics devices.

scholarly journals Three-dimensional imaging of inhomogeneous lithologies using X-ray computed tomography: characterization of drill core from the Borrowdale Volcanic Group

2012 ◽  
Vol 76 (8) ◽  
pp. 2931-2938 ◽  
Author(s):  
D. L. Engelberg ◽  
R. A. D. Pattrick ◽  
C. Wilson ◽  
R. McCrae ◽  
P. J. Withers
Keyword(s):  
Computed Tomography ◽  
3D Visualization ◽  
Three Dimensional ◽  
X Ray ◽  
Volcanic Group ◽  
Tomography System ◽  
Thin Sectioning ◽  
Calcite Veins ◽  
X Ray Computed

AbstractX-ray computed tomography augmented by elemental microanalysis has been used to characterize two drill cores from the Borrowdale Volcanic Group, west Cumbria, UK. Information about the three-dimensional (3D) distribution of mineral phases was obtained non-destructively, and regions of interest were extracted for thin sectioning and elemental analysis. This revealed the presence of pyrite and other iron- and iron-titanium-bearing minerals. X-ray computed tomography is a very useful tool for 3D visualization, but the limitations of the tomography system used made it difficult to distinguish between regions with similar compositions, such as the different layers within the calcite veins. Methods by which these limitations might be overcome are briefly discussed.

Spatial Architecture of Nitrifying Bacteria Biofilm Immobilized on Polyurethane Foam in an Automatic Biodetector for Water Toxicity

2010 ◽  
Vol 16 (5) ◽  
pp. 550-560 ◽  
Author(s):  
Andrzej Woznica ◽  
Jagna Karcz ◽  
Agnieszka Nowak ◽  
Aleksander Gmur ◽  
Tytus Bernas
Keyword(s):  
Polyurethane Foam ◽  
Laser Scanning ◽  
Spatial Organization ◽  
3D Visualization ◽  
Three Dimensional ◽  
Bacterial Biofilm ◽  
Laser Scanning Microscopy ◽  
Nitrifying Bacteria ◽  
Confocal Laser ◽  
X Ray

AbstractWe describe the architecture of nitrifying bacteria biofilms immobilized on a three-dimensional (3D) polyurethane foam that permits efficient water flow through a bioreactor. The 3D spatial organization of immobilized bacterial colonies is characterized on three resolution levels with X-ray tomography, light confocal microscopy, and scanning electron microscopy (SEM). Using these techniques we demonstrate biofilm distribution in the foam and the existence of several modes of binding of bacteria to the foam. Computed X-ray tomography permits observation of the distribution of the biofilm in the whole open cellular polyurethane material volume and estimation of biofilm volume. SEM and confocal laser scanning microscopy techniques permit 3D visualization of biofilm structure. Three distinct immobilization patterns could be observed in the open cellular polyurethane material: (1) large irregular aggregates of bacterial biofilm that exist as irregular biofilm fragments, rope-like structures, or biofilm layers on the foam surface; (2) spherical (pom-pom) aggregates of bacteria localized on the external surface of biofilm; and (3) biofilm threads adherent to the surface of polyurethane foam. Finally, we demonstrate that immobilized bacteria exhibit metabolic activity and growth.

scholarly journals 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Marina Eckermann ◽  
Jasper Frohn ◽  
Marius Reichardt ◽  
Markus Osterhoff ◽  
Michael Sprung ◽  
...  
Keyword(s):  
Lung Tissue ◽  
Phase Contrast ◽  
3D Visualization ◽  
Diffuse Alveolar Damage ◽  
Three Dimensional ◽  
Cone Beam ◽  
X Ray ◽  
Multi Scale ◽  
Beam Geometry ◽  
Third Dimension

We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.

scholarly journals Three-dimensional Non-destructive Visualization of Teeth Enamel Microcracks Using X-ray Micro-computed Tomography

2021 ◽  
Author(s):  
Irma Dumbryte ◽  
Arturas Vailionis ◽  
Edvinas Skliutas ◽  
Saulius Juodkazis ◽  
Mangirdas Malinauskas
Keyword(s):  
Computed Tomography ◽  
Deep Learning ◽  
3D Visualization ◽  
Three Dimensional ◽  
Potential Effect ◽  
Micro Computed Tomography ◽  
X Ray ◽  
Tooth Structure ◽  
Structure Damage ◽  
Non Destructive

Abstract Although the topic of tooth fractures has been extensively analyzed in the dental literature, there is still insufficient information on the potential effect of enamel microcracks (EMCs) to the underlying tooth structures. For precise examination of tooth structure damage in the area of EMCs (i.e. whether it crosses the dentin-enamel junction (DEJ) and reaches dentin or pulp), volumetric (three-dimensional (3D)) evaluation of EMCs is necessary. The aim of this study was to present an X-ray micro-computed tomography (μCT) as a technique suitable for 3D non-destructive visualization and qualitative analysis of different severity teeth EMCs. Extracted human maxillary premolars were examined using a μCT instrument ZEISS Xradia 520 Versa. In order to separate (segment) cracks from the rest of the tooth a Deep Learning Tool was utilized within the ORS Dragonfly software. The scanning technique used allowed for the recognition and detection of EMCs that are not only visible on the outer surface but also those that are deeply buried inside the tooth. The 3D visualization combined with Deep Learning segmentation enabled evaluation of EMC dynamics as it extends from the cervical to the occlusal part of the tooth, and precise examination of EMC position with respect to the DEJ.

Detection of complex vascular system in bamboo node by X-ray μCT imaging technique

Holzforschung ◽  
2014 ◽  
Vol 68 (2) ◽  
pp. 223-227 ◽  
Author(s):  
Guanyun Peng ◽  
Zehui Jiang ◽  
Xing’e Liu ◽  
Benhua Fei ◽  
Shumin Yang ◽  
...  
Keyword(s):  
Vascular System ◽  
3D Visualization ◽  
Final Height ◽  
Three Dimensional ◽  
Vascular Bundles ◽  
X Ray ◽  
Novel Approach ◽  
3D Network ◽  
Computed Microtomography ◽  
X Ray Computed

Abstract Bamboo is one of the world’s fastest growing plants. They reach a final height of 15–40 m during a period of 40–120 days. The full height is reached by intercalary growth of each node. However, it is very difficult to detect the complex vascular system in a bamboo node using traditional methods. X-ray computed microtomography (μCT) is a noninvasive novel approach to the three-dimensional (3D) visualization and quantification of biological structures. In the present article, μCT has been applied to provide insights into the internal structure of bamboo node, where three branches are connected. The picture obtained could hardly be obtained by any other means. The bamboo nodal characteristics of three transverse and axial sections are presented. The complex 3D network of vascular bundles has been directly obtained for the first time.

scholarly journals Three-dimensional pore structure visualization and characterization of paper using X-ray computed tomography

TAPPI Journal ◽  
2017 ◽  
Vol 16 (09) ◽  
pp. 519-530 ◽  
Author(s):  
Yves Defrenne ◽  
Vasili Zhdankin ◽  
Sahana Ramanna ◽  
Shri Ramaswamy ◽  
Bandaru Ramarao
Keyword(s):  
Experimental Data ◽  
Computed Tomography ◽  
Pore Structure ◽  
3D Visualization ◽  
Complex Structure ◽  
Three Dimensional ◽  
Structure Characterization ◽  
X Ray ◽  
Pore Size Distributions ◽  
X Ray Computed

Porous biomaterials such as paper and board have a complex structure that influences their mechanical, optical, and transport properties and thereby their performance during manufacturing and end uses. Reconstruction of the three-dimensional (3D) pore spaces in paper was obtained by X-ray computed tomography and used to study the structure and its impact on properties. A set of laboratory-made paper samples of varying freeness was prepared, and the 3D structures of the samples were visualized and characterized. Tomographic reconstruction images were processed using techniques such as anisotropic diffusion, minimum error thresholding, and isolated voxel removal to enhance image quality. The pore structures were analyzed to determine porosity, fiber-pore interfacial surface area, geometric tortuosity, and pore size distributions (using a sphere growing algorithm). These properties were compared with experimental data and were found to be in good agreement. The results from 3D visualization and characterization were then compared with experimental data of various samples using conventional pore structure characterization techniques, such as mercury intrusion porosimetry.

scholarly journals Three-dimensional non-destructive visualization of teeth enamel microcracks using X-ray micro-computed tomography

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Irma Dumbryte ◽  
Arturas Vailionis ◽  
Edvinas Skliutas ◽  
Saulius Juodkazis ◽  
Mangirdas Malinauskas
Keyword(s):  
Computed Tomography ◽  
3D Visualization ◽  
Three Dimensional ◽  
Potential Effect ◽  
Micro Computed Tomography ◽  
X Ray ◽  
Tooth Structure ◽  
Maxillary Premolars ◽  
Non Destructive ◽  
3D Evaluation

AbstractAlthough the topic of tooth fractures has been extensively analyzed in the dental literature, there is still insufficient information about the potential effect of enamel microcracks (EMCs) on the underlying tooth structures. For a precise examination of the extent of the damage to the tooth structure in the area of EMCs, it is necessary to carry out their volumetric [(three-dimensional (3D)] evaluation. The aim of this study was to validate an X-ray micro-computed tomography ($$\mu $$ μ CT) as a technique suitable for 3D non-destructive visualization and qualitative analysis of teeth EMCs of different severity. Extracted human maxillary premolars were examined using a $$\mu $$ μ CT instrument ZEISS Xradia 520 Versa. In order to separate crack, dentin, and enamel volumes a Deep Learning (DL) algorithm, part of the Dragonfly’s segmentation toolkit, was utilized. For segmentation needs we implemented Dragonfly’s pre-built UNet neural network. The scanning technique which was used made it possible to recognize and detect not only EMCs that are visible on the outer surface but also those that are buried deep inside the tooth. The 3D visualization, combined with DL assisted segmentation, enabled the evaluation of the dynamics of an EMC and precise examination of its position with respect to the dentin-enamel junction.

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