Interactive Three-dimensional Visualization Research Articles

MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.

Quantitative tools to compile and analyze biomolecular interactions among chemically diverse binding partners would improve therapeutic design and aid in studying molecular evolution. Here we present Mapping Areas of Genetic Parsimony In Epitopes (MAGPIE), a publicly available software package for simultaneously visualizing and analyzing thousands of interactions between a single protein or small molecule ligand (the "target") and all of its protein binding partners ("binders"). MAGPIE generates an interactive three-dimensional visualization from a set of protein complex structures that share the target ligand, as well as sequence logo-style amino acid frequency graphs that show all the amino acids from the set of protein binders that interact with user-defined target ligand positions or chemical groups. MAGPIE highlights all the salt bridge and hydrogen bond interactions made by the target in the visualization and as separate amino acid frequency graphs. Finally, MAGPIE collates the most common target-binder interactions as a list of "hotspots," which can be used to analyze trends or guide the de novo design of protein binders. As an example of the utility of the program, we used MAGPIE to probe how different antibody fragments bind a viral antigen; how a common metabolite binds diverse protein partners; and how two ligands bind orthologs of a well-conserved glycolytic enzyme for a detailed understanding of evolutionarily conserved interactions involved in its activation and inhibition. MAGPIE is implemented in Python 3 and freely available at https://github.com/glasgowlab/MAGPIE, along with sample datasets, usage examples, and helper scripts to prepare input structures.

THE COMBAT ENGAGEMENT (COMBAT EPISODE) LIFE CYCLE INTERACTIVE THREE-DIMENSIONAL VISUALIZATION CRITERIA AND INDICATORS SELECTION

The russo-Ukrainian war is generally characterized as an artillery war, since the main burden in it is the massive use of artillery. However, this war is distinguished from others by the use of various tactics, some of that repeat the tactics of the past, only at a higher technical level, and the newest tactics that have appeared thanks to the advent of modern weapons and military equipment, the which principles are based on the latest technical achievements. The specified circumstances require a careful and more detailed consideration (research) of these tactical techniques on such issues as the reasons for their occurrence, the number of participants, the course of the battle (combat episode), its result, analysis and development, practical recommendations that can be combined into a single concept of the life cycle, eliminate identified shortcomings or provide recommendations for improving individual positions in this matter. For this purpose, it is advisable to reproduce and reconstruct the life cycle of the combat engagement or combat episode that occurred. One of the means of reproducing the life cycle of a combat engagement (combat episode) is interactive three-dimensional visualization. Therefore, in order to create an interactive three-dimensional visualization model (animation) of the life cycle of a combat engagement or a combat episode, that would correspond as close as possible to real events, it is desirable to determine the criteria and indicators that characterize these events. The interactive three-dimensional visualization of the life cycle of a combat engagement or combat episode criterion can be the completeness and reliability of information, and the indicators - dynamism, evaluation of the effectiveness of combat operations and characteristics of the space (locality) in which the combat engagement (combat episode) took place.

Developing polar data-cylinders to map spatiotemporal changes in Arctic sea ice

ABSTRACT Complex ecosystems characterize the Arctic Region, which experiences rapid environmental changes due to climate change. These changes are happening spatially as much as temporally. Spatiotemporal interactive three-dimensional visualization of environmental phenomena is eye-catching, while creating the foundations for the rapid understanding of Arctic complexity. The Arctic is a circumpolar region; cylinders seem suitable visual media for related data. In this case study, the visualization of anomalies of the sea ice illustrates abnormal changes, helping the viewer/user to focus on that filtered information rather than becoming lost in a multitude of information. A holistic view of dynamic environmental changes in a stand-alone visual could impact the quick understanding, response and policymaking regarding the visualized phenomena.

NAChRDB: A Web Resource of Structure-Function Annotations to Unravel the Allostery of Nicotinic Acetylcholine Receptors.

Nicotinic acetylcholine receptors (nAChRs) comprise a large and ancient family of allosteric ion channels mediating synaptic transmission. The vast knowledge about nAChRs has become difficult to navigate. NAChRDB is a web-accessible resource of curated residue-level functional annotations of neuromuscular nAChRs. Interactive three-dimensional (3D) visualization and sequence alignment give further context to this rich and growing collection of experimental observations and computational predictions. NAChRDB is freely available at https://crocodile.ncbr.muni.cz/Apps/NAChRDB/, with interactive tutorials and regular updates to the content and web interface. No installation or user registration is required. NAChRDB is accessible through any modern internet browser on desktops and mobile devices. By providing immediate and systematic access to practical knowledge gained through decades of research, NAChRDB represents a powerful educational tool and helps guide discovery by revealing gaps in current knowledge and aiding the interpretation of results of molecular and structural biology experiments or computational studies.

Facilitating Student Understanding through Incorporating Digital Images and 3D-Printed Models in a Human Anatomy Course

Combining classical educational methods with interactive three-dimensional (3D) visualization technology has great power to support and provide students with a unique opportunity to use them in the study process, training, and/or simulation of different medical procedures in terms of a Human Anatomy course. In 2016, Rīga Stradiņš University (RSU) offered students the 3D Virtual Dissection Table “Anatomage” with possibilities of virtual dissection and digital images at the Department of Morphology. The first 3D models were printed in 2018 and a new printing course was integrated into the Human Anatomy curriculum. This study was focused on the interaction of students with digital images, 3D models, and their combinations. The incorporation and use of digital technologies offered students great tools for their creativity, increased the level of knowledge and skills, and gave them a possibility to study human body structures and to develop relationships between basic and clinical studies.

Immersive 5G Virtual Reality Visualization Display System Based on Big-Data Digital City Technology

The virtual reality visual display system creates a realistic virtual product display system, allowing users to swim in a three-dimensional virtual environment and perform interactive operations, fully simulating the process of shopping selection and payment in reality, so that users have an immersive feeling. The purpose of this article is to realize the design of an immersive 5G virtual reality visual display system through big-data digital city technology. This paper uses big-data digital city technology to design and implement an immersive virtual reality visualization system from the three-dimensional display mode of vision, hearing, and touch, creating a real and interactive three-dimensional visualization environment for users to have a more intuitive visual experience. The experimental results of this paper show that the smoothness of the virtual reality visualization system test can reach 60FPS, the excellent rate reaches nearly 33%, and the model scene-realistic feedback excellent rate is about 62.5%.

Information Graph Visualization Using AlgoView Software Tool

One of the approaches to the study of the information structure of algorithms is the analysis of information graphs. These are complex objects, the understanding of the structure of which can significantly facilitate their visualization. However, it is difficult to visualize large graphs, while maintaining clarity of the information structure of the algorithm is generally very difficult. Therefore, we are developing a tool for three-dimensional interactive visualization of information graphs called AlgoView, designed to facilitate this task. At the moment, AlgoView is embedded as a visualizer on separate pages of the AlgoWiki Open encyclopedia of parallel algorithmic features, and in the near future it is planned to obtain a stand-alone version of this system.

Moving beyond two-dimensional screens to interactive three-dimensional visualization in congenital heart disease.

Beginning with the discovery of X-rays to the development of three-dimensional (3D) imaging, improvements in acquisition, post-processing, and visualization have provided clinicians with detailed information for increasingly accurate medical diagnosis and clinical management. This paper highlights advances in imaging technologies for congenital heart disease (CHD), medical adoption, and future developments required to improve pre-procedural and intra-procedural guidance.

Computational fluid dynamics for non-experts: Development of a user-friendly CFD simulator (HNVR-SYS) for natural ventilation design applications

Measuring the ventilation rate is crucial to ensuring the control of thermal comfort, energy saving, and emission of pollutants in greenhouses and animal houses. This is more difficult in naturally ventilated (NV) buildings because of the dynamic and complex air flow patterns caused by wind and buoyancy effects. In this study, a user-friendly computational fluid dynamics (CFD) simulator is developed to analyse internal airflow patterns and ventilation rates of NV buildings, with the initial focus on agricultural buildings. The user-friendly CFD automation program, developed using the freely available open-source OpenFOAM and ParaView visualization toolkit, is aimed at non-CFD experts to help them obtain practical CFD solutions quickly. Users simply input building and ventilating configurations, outdoor wind conditions, topographical conditions, and information regarding plants or animals through user-friendly graphical user interfaces. General CFD processes are automated, and the quality of each process is controlled. After executing the program, a three-dimensional interactive visualization module is used for post-processing. It can ensure the flexibility and manageability of the model by automating predeveloped procedures in a user-interactive manner, thereby reducing time and effort. This paper describes the development process of automation interfaces.

Widespread white matter microstructural abnormalities in bipolar disorder: evidence from mega- and meta-analyses across 3033 individuals

Fronto-limbic white matter (WM) abnormalities are assumed to lie at the heart of the pathophysiology of bipolar disorder (BD); however, diffusion tensor imaging (DTI) studies have reported heterogeneous results and it is not clear how the clinical heterogeneity is related to the observed differences. This study aimed to identify WM abnormalities that differentiate patients with BD from healthy controls (HC) in the largest DTI dataset of patients with BD to date, collected via the ENIGMA network. We gathered individual tensor-derived regional metrics from 26 cohorts leading to a sample size of N = 3033 (1482 BD and 1551 HC). Mean fractional anisotropy (FA) from 43 regions of interest (ROI) and average whole-brain FA were entered into univariate mega- and meta-analyses to differentiate patients with BD from HC. Mega-analysis revealed significantly lower FA in patients with BD compared with HC in 29 regions, with the highest effect sizes observed within the corpus callosum (R2 = 0.041, Pcorr < 0.001) and cingulum (right: R2 = 0.041, left: R2 = 0.040, Pcorr < 0.001). Lithium medication, later onset and short disease duration were related to higher FA along multiple ROIs. Results of the meta-analysis showed similar effects. We demonstrated widespread WM abnormalities in BD and highlighted that altered WM connectivity within the corpus callosum and the cingulum are strongly associated with BD. These brain abnormalities could represent a biomarker for use in the diagnosis of BD. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.

Interactive three-dimensional visualization of network intrusion detection data for machine learning

The threat of cyber-attacks is on the rise in the digital world today. As such, effective cybersecurity solutions are becoming increasingly important for detecting and combating cyber-attacks. The use of machine learning techniques for network intrusion detection is a growing area of research, as these techniques can potentially provide a means for automating the detection of attacks and abnormal traffic patterns in real-time. However, misclassification is a common problem in machine learning for intrusion detection, and the improvement of machine learning models is hindered by a lack of insight into the reasons behind such misclassification. This paper presents an interactive method of visualizing network intrusion detection data in three-dimensions. The objective is to facilitate the understanding of network intrusion detection data using a visual representation to reflect the geometric relationship between various categories of network traffic. This interactive visual representation can potentially provide useful insight to aid the understanding of machine learning results. To demonstrate the usefulness of the proposed visualization approach, this paper presents results of experiments on commonly used network intrusion detection datasets.

3D Interactive Visualization Method of Urban Waterlogging Based on Cesium

Abstract. Urban waterlogging, as a common natural disaster in China, seriously restricted the development of society. Nowadays, while the computer technology is developing continuously, the urban waterlogging model is also constantly improved. These models can simulate the process of urban waterlogging, but the simulation results are not intuitive. So it is difficult for users to understand how the model works. Therefore, it is important to find a way to show the simulation results so that people can see the waterlogging simulation intuitively. Cesium, as a three-dimensional visualization platform, can reproduce the process of the urban waterlogging. It will make sense if we could show the simulation results on the Cesium platform. Nowadays, many studies focus on both urban waterlogging and visualization methods. However, there are fewer studies on the combination of the two, especially the interactive visualization of urban waterlogging under parameter adjustment. Therefore, this paper mainly focuses on urban three-dimensional interactive visualization method based on Cesium.On the one hand, the three-dimensional visualization of the urban waterlogging simulation facilitates the intuitive expression of the simulation results. Without visualization, the results of the simulation are only some complicated and unintuitive figures for most non-experts. On the other hand, visualization based on the Cesium platform can better adapt to the cross-platform application. It can better meet the needs of different terminal devices of different users for the visualization platform, so that users can obtain the disaster information more accurately, consistently and intuitively. It is conducive for management departments to respond to sudden disasters more quickly and efficiently.This research aims to propose a three-dimensional dynamic interactive visualization method for urban waterlogging. Particularly, we hope to find out how to integrate urban waterlogging model and 3D visualization platform. With this 3D visualization platform, we can combine the advantages of the SWMM (Storm Water Management Model) and Cesium platform. Using this platform, it will be easier and more effective to respond to disasters for the masses and management departments.The following two issues are resolved in this study: i) How do model parameters affect the urban waterlogging simulation and visualization results? ii) How to integrate SWMM and Cesium 3D visualization platform?In order to address the above research objectives, we will apply the following methodologies: i) We will analyse the parameters of the SWMM for the urban waterlogging visualization. Under the premise of understanding the development process of the urban waterlogging, we will analyse the modelling principle of the urban waterlogging, the mechanism of each part of the model separately. Then, we will find out the method of determining the model parameters of urban waterlogging and its influence on the simulation visualization results. ii) We will study integration methods of urban waterlogging model and 3D visualization platform. We will analyse the mechanism and process of urban waterlogging. We will also calculate the urban waterlogging process data by the SWMM, and establish a three-dimensional visualization platform by the node.js and Cesium, which can dynamically show the process of urban waterlogging. iii) We will complete the design and implementation of the interactive visualization platform of urban waterlogging. According to the above research, taking the Xianlin Campus of Nanjing Normal University as an example, we will build a dynamic interactive visualization system of urban waterlogging simulation based on Cesium. We will also verify the effectiveness of the system by comparing it with actual flood situation.With this study, we expect to answer how model parameters affect the urban waterlogging simulation and visualization results. As expected results, we plan to build an interactive visualization system of urban waterlogging simulation based on Cesium, publish the flood calculation results into the 3D scene. This will make urban waterlogging process shown in the 3D scene. This visualization system is designed for different users, including specialists, government and individual. It means that you can use the system easily even if you are non-cartographers or non-IT-specialists.

The Role of Portable Documentation Format in Three-Dimensional Interactive Visualization in Maxillofacial Prosthetics.

Although digital technology has advanced the visualization of treatment planning and rehabilitation in prosthodontics, the field of maxillofacial prosthetics is in vital need of an accessible document for exchange of interactive three-dimensional (3D) model visualization without requiring installation of any additional software. This article introduces a 3D data documentation method for effective interactive digital visualization in maxillofacial prosthetics using a portable documentation format (PDF).

Collaboration between interactive three-dimensional visualization and computer aided detection of pulmonary embolism on computed tomography pulmonary angiography views.

This paper explores the benefits of interactive three-dimensional (3D) visualization of stimuli using a computer aided detection (CAD) system of pulmonary embolisms (PEs), on computed tomography pulmonary angiography (CTPA) views. We designed a new CAD method that prompts the PE sites on CTPA views; we then utilized two interactive approaches of 3D visualization to assess CAD performance. This collaboration allows different methodologies to be used to assess PE-CAD performance, by comparison with the common method in which radiologists are prompted with CAD stimuli directly on the CTPA views. Both 3D approaches are based on the voxel size of the CTPA examination, and consider the acquisition settings. A set of ten retrospective CTPA cases were collected, with different acquisition parameters, in terms of voxel size and spatial resolution. 3D visualization CAD performance was examined by an experienced radiologist. Both 3D visualization methods proved to have a constructive impact on improving CAD performance. The rate of true positive (TP) responses increased by 27%; while the rate of false positive (FP) responses dropped by 31%. We concluded that evaluation of PE-CAD performance utilizing interactive 3D visualization could increase or ascertain the correct rate of TP stimuli, as well as noticeably reduce FP responses.

Widespread white matter microstructural differences in schizophrenia across 4322 individuals: results from the ENIGMA Schizophrenia DTI Working Group

The regional distribution of white matter (WM) abnormalities in schizophrenia remains poorly understood, and reported disease effects on the brain vary widely between studies. In an effort to identify commonalities across studies, we perform what we believe is the first ever large-scale coordinated study of WM microstructural differences in schizophrenia. Our analysis consisted of 2359 healthy controls and 1963 schizophrenia patients from 29 independent international studies; we harmonized the processing and statistical analyses of diffusion tensor imaging (DTI) data across sites and meta-analyzed effects across studies. Significant reductions in fractional anisotropy (FA) in schizophrenia patients were widespread, and detected in 20 of 25 regions of interest within a WM skeleton representing all major WM fasciculi. Effect sizes varied by region, peaking at (d=0.42) for the entire WM skeleton, driven more by peripheral areas as opposed to the core WM where regions of interest were defined. The anterior corona radiata (d=0.40) and corpus callosum (d=0.39), specifically its body (d=0.39) and genu (d=0.37), showed greatest effects. Significant decreases, to lesser degrees, were observed in almost all regions analyzed. Larger effect sizes were observed for FA than diffusivity measures; significantly higher mean and radial diffusivity was observed for schizophrenia patients compared with controls. No significant effects of age at onset of schizophrenia or medication dosage were detected. As the largest coordinated analysis of WM differences in a psychiatric disorder to date, the present study provides a robust profile of widespread WM abnormalities in schizophrenia patients worldwide. Interactive three-dimensional visualization of the results is available at www.enigma-viewer.org.

Building dynamic 3D visualizations through ontology-guided interactions with domain knowledge and simulation models

We need to find better ways of allowing non-computing experts to construct visualizations of dynamic models within familiar domain-specific contexts. Current methods used to construct these customized views, however, are expensive since content experts must employ engineers to code the mathematical model that defines the dynamic behaviour of the scenario. Engineers must then somehow visualize the output of the model. These tasks are typically performed with engineering software tools or just pure computer programming. We define an interface and interaction model that compresses this engineering overhead, thus narrowing the user interface gap between mathematical modelling and three-dimensional interactive visualization design and consumption. We present an interaction theory and corresponding software prototype. Both are discussed using a human cardiovascular system case study.

Three-dimensional visualization of ensemble weather forecasts – Part 2: Forecasting warm conveyor belt situations for aircraft-based field campaigns

Abstract. We present the application of interactive three-dimensional (3-D) visualization of ensemble weather predictions to forecasting warm conveyor belt situations during aircraft-based atmospheric research campaigns. Motivated by forecast requirements of the T-NAWDEX-Falcon 2012 (THORPEX – North Atlantic Waveguide and Downstream Impact Experiment) campaign, a method to predict 3-D probabilities of the spatial occurrence of warm conveyor belts (WCBs) has been developed. Probabilities are derived from Lagrangian particle trajectories computed on the forecast wind fields of the European Centre for Medium Range Weather Forecasts (ECMWF) ensemble prediction system. Integration of the method into the 3-D ensemble visualization tool Met.3D, introduced in the first part of this study, facilitates interactive visualization of WCB features and derived probabilities in the context of the ECMWF ensemble forecast. We investigate the sensitivity of the method with respect to trajectory seeding and grid spacing of the forecast wind field. Furthermore, we propose a visual analysis method to quantitatively analyse the contribution of ensemble members to a probability region and, thus, to assist the forecaster in interpreting the obtained probabilities. A case study, revisiting a forecast case from T-NAWDEX-Falcon, illustrates the practical application of Met.3D and demonstrates the use of 3-D and uncertainty visualization for weather forecasting and for planning flight routes in the medium forecast range (3 to 7 days before take-off).

Three-dimensional visualization of ensemble weather forecasts – Part 1: The visualization tool Met.3D (version 1.0)

Abstract. We present "Met.3D", a new open-source tool for the interactive three-dimensional (3-D) visualization of numerical ensemble weather predictions. The tool has been developed to support weather forecasting during aircraft-based atmospheric field campaigns; however, it is applicable to further forecasting, research and teaching activities. Our work approaches challenging topics related to the visual analysis of numerical atmospheric model output – 3-D visualization, ensemble visualization and how both can be used in a meaningful way suited to weather forecasting. Met.3D builds a bridge from proven 2-D visualization methods commonly used in meteorology to 3-D visualization by combining both visualization types in a 3-D context. We address the issue of spatial perception in the 3-D view and present approaches to using the ensemble to allow the user to assess forecast uncertainty. Interactivity is key to our approach. Met.3D uses modern graphics technology to achieve interactive visualization on standard consumer hardware. The tool supports forecast data from the European Centre for Medium Range Weather Forecasts (ECMWF) and can operate directly on ECMWF hybrid sigma-pressure level grids. We describe the employed visualization algorithms, and analyse the impact of the ECMWF grid topology on computing 3-D ensemble statistical quantities. Our techniques are demonstrated with examples from the T-NAWDEX-Falcon 2012 (THORPEX – North Atlantic Waveguide and Downstream Impact Experiment) campaign.

Spatiotemporal Volumetric Analysis of Dynamic Plantar Pressure Data

The purposes of this study were (i) to develop a three-dimensional interactive visualization tool for exploring plantar pressure time series and spatiotemporal statistical volumes and (ii) to demonstrate the benefits of volumetric analyses using various running and walking data sets. A data exploration tool was developed in Python using the open-source Visualization Toolkit. Multiple-pressure isosurfaces were computed and were then rendered with interactive rotation and adjustable thresholds and transparencies. Plantar pressure data were collected: (i) from two running subjects, one with a heel-loading pattern and one with a forefoot-loading pattern; (ii) from one individual while running straight and then while performing a cutting maneuver; and (iii) from one subject walking at three different speeds. All data were spatiotemporally aligned, and mean volumes were computed. Statistical volumes were also computed for the walking data set, and significance was assessed topologically using techniques from three-dimensional brain imaging. After converting raw plantar pressure data into a rapidly readable format, volumetric renderings were presented in ∼50 ms, a negligible time lag for interactive data exploration. We observed that consideration of only spatial two-dimensional variables yielded "impulse illusions" that could be resolved most effectively with three-dimensional renderings. For all data sets, we found that dynamic foot behavior was clearest through interactive three-dimensional exploration. Plantar pressure data contain high-quality biomechanical information in their original three-dimensional form. The main benefit of the proposed visualization technique is that it affords qualitatively rich and unique holistic explorations of dynamic foot behavior.

Development of the excretory system in the polyplacophoran mollusc,Lepidochitona corrugata: The protonephridium

A single pair of protonephridia is the typical larval excretory organ of molluscs. Their presence in postlarval developmental stages was discovered only recently. We found that the protonephridia of the polyplacophoran mollusc, Lepidochitona corrugata, achieve their most elaborate differentiation and become largest during the postlarval period. This study describes the protonephridia of L. corrugata using light and electron microscopy and interactive three-dimensional visualization. We focus on the postlarval developmental period, in which the protonephridia consist of three parts: the terminal part with the ultrafiltration sites at the distal end, the voluminous protonephridial kidney, and the efferent nephroduct leading to the nephropore. The ultrafiltration sites show filtration slits between regularly arranged thin pedicles. The ciliary flame originates from both the terminal cell and the duct cells of the terminal portion. The efferent duct also shows ciliation. The most conspicuous structures, the protonephridial kidneys, are voluminous swellings composed of reabsorptive cells ("nephrocytes"). These cells exhibit strong vacuolization and an infolding system increasing the basal surface. The protonephridial kidneys, previously not reported at such a level of organization in molluscs, strikingly resemble (metanephridial) kidneys of adult molluscan excretory systems.