3D Network Analysis Research Articles

Glucokinase activity controls subpopulations of β-cells that alternately lead islet Ca2+ oscillations.

Oscillations in insulin secretion, driven by islet Ca2+ waves, are crucial for glycemic control. Prior studies, performed with single-plane imaging, suggest that subpopulations of electrically coupled β-cells have privileged roles in leading and coordinating the propagation of Ca2+ waves. Here, we used 3D light-sheet imaging to analyze the location and Ca2+ activity of single β-cells within the entire islet at >2 Hz. In contrast with single-plane studies, 3D network analysis indicates that the most highly synchronized β-cells are located at the islet center, and remain regionally but not cellularly stable between oscillations. This subpopulation, which includes 'hub cells', is insensitive to changes in fuel metabolism induced by glucokinase and pyruvate kinase activation. β-cells that initiate the Ca2+ wave ('leaders') are located at the islet periphery, and strikingly, change their identity over time via rotations in the wave axis. Glucokinase activation, which increased oscillation period, reinforced leader cells and stabilized the wave axis. Pyruvate kinase activation, despite increasing oscillation frequency, had no effect on leader cells, indicating the wave origin is patterned by fuel input. These findings emphasize the stochastic nature of the β-cell subpopulations that control Ca2+ oscillations and identify a role for glucokinase in spatially patterning 'leader' β-cells.

Quantitative 3D structural analysis of the cellular microstructure of sea urchin spines (II): Large-volume structural analysis

Biological cellular materials have been a valuable source of inspiration for the design of lightweight engineering structures. In this process, a quantitative understanding of the biological cellular materials from the individual branch and node level to the global network level in 3D is required. Here we adopt a multiscale cellular network analysis workflow demonstrated in the first paper of this work series to analyze the biomineralized porous structure of sea urchin spines from the species Heterocentrotus mamillatus over a large volume (ca. 0.32mm3). A comprehensive set of structural descriptors is utilized to quantitatively delineate the long-range microstructural variation from the spine center to the edge region. Our analysis shows that the branches gradually elongate (~50% increase) and thicken (~100% increase) from the spine center to edge, which dictates the spatial variation of relative density (from ~12% to ~40%). The branch morphology and network organization patterns also vary gradually with their positions and orientations. Additionally, the analysis of the cellular network of individual septa provides the interconnection characteristics between adjacent septa, which are the primary structural motifs used for the construction of the cellular structure in the edge region. Lastly, combining the extracted long-range cellular network and finite element simulations allows us to efficiently examine the spatial and orientational dependence of local effective Young's modulus across the spine's radius. The structural-mechanical analysis here sheds light on the structural designs of H. mamillatus’ porous spines, which could provide important insights for the design and modeling of lightweight yet strong and damage-tolerant cellular materials. Statement of SignificancePrevious investigations on the cellular structures of sea urchin spines have been mainly based on 2D measurements or 3D quantification of small volumes with limited structural parameters. This limits our understanding of the interplay between the 3D microstructural variations and the mechanical properties in sea urchin spines, which hence constrains the derivation of the underlying principles for bio-inspired designs. This work utilizes our multiscale 3D network analysis, for the first time, to quantify the 3D cellular network and its variation across large volumes in sea urchin spines from individual branch and node level to the cellular network level. The network analysis demonstrated here is expected to be of great interest to the fields of biomineralization, functional biological materials, and bio-inspired material design.

Quantitative 3D structural analysis of the cellular microstructure of sea urchin spines (I): Methodology

The mineralized skeletons of echinoderms are characterized by their complex, open-cell porous microstructure (also known as stereom), which exhibits vast variations in pore sizes, branch morphology, and three-dimensional (3D) organization patterns among different species. Quantitative description and analysis of these cellular structures in 3D are needed in order to understand their mechanical properties and underlying design strategies. In this paper series, we present a framework for analyzing such structures based on high-resolution 3D tomography data and utilize this framework to investigate the structural designs of stereom by using the spines from the sea urchin Heterocentrotus mamillatus as a model system. The first paper here reports the proposed cellular network analysis framework, which consists of five major steps: synchrotron-based tomography and hierarchical convolutional neural network-based reconstruction, machine learning-based segmentation, cellular network registration, feature extraction, and data representation and analysis. This framework enables the characterization of the porous stereom structures at the individual node and branch level (~10 µm), the local cellular level (~100 µm), and the global network level (~1 mm). We define and quantify multiple structural descriptors at each level, such as node connectivity, branch length and orientation, branch profile, ring structure, etc., which allows us to investigate the cellular network construction of H. mamillatus spines quantitatively. The methodology reported here could be tailored to analyze other natural or engineering open-cell porous materials for a comprehensive multiscale network representation and mechanical analysis. Statement of SignificanceThe mechanical robustness of the biomineralized porous structures in sea urchin spines has long been recognized. However, quantitative cellular network representation and analysis of this class of natural cellular solids are still limited in the literature. This constrains our capability to fully understand the mechanical properties and design strategies in sea urchin spines and other similar echinoderms’ porous skeletal structures. Combining high-resolution tomography and computer vision-based analysis, this work presents a multiscale 3D network analysis framework, which allows for extraction, registration, and quantification of sea urchin spines’ complex porous structure from the individual branch and node level to the global network level. This 3D structural analysis is relevant to a diversity of research fields, such as biomineralization, skeletal biology, biomimetics, material science, etc.

Analisis Jaringan 3-Dimensi Untuk Penentuan Rute Evakuasi di Gedung Bertingkat

Accessibility of evacuation routes in the multi-storey building is an important thing to notice. The number of floors and rooms in multi-storey buildings which are too many often makes the building users have difficulty, especially for users who do not know the ins and outs of the building well. Not only the difficulty in finding evacuation routes to exit the building quickly in emergency times, but also to find a certain room during normal times. Nowadays, the Network Analysis capabilities in Geographic Information System (GIS) have become more reliable, even able to accommodate 3 Dimensional aspect (3D) which is often known as 3D Network Analysis. Therefore, this research intends to apply 3D Network Analysis for developing the navigation and evacuation management system in the KLMB (Klinik Lingkungan dan Mitigasi Bencana) Building Faculty of Geography UGM which has 6 floors. Generally, the implementation of this research can be divided into 4 main stages, namely Data Collection Stage, 3D Network Dataset Preparation Stage, 3D Network Analysis Implementation Stage, and Test & Evaluation Stage. Through application of the 3D Network Analysis, this research successfully obtained a navigation and evacuation management system in the ArcScene (ArcGIS) software environment which is quite effective and easy to use to help navigation and determination of the fastest evacuation route in the KLMB building. This system can also be used to help the evacuation simulation as a form of disaster mitigation in the KLMB Building.

3D NETWORK ANALYSIS FOR INDOOR SPACE APPLICATIONS

Abstract. Indoor space differs from outdoor environments, since it is characterized by a higher level of structural complexity, geometry, as well as topological relations. Indoor space can be considered as the most important component in a building’s conceptual modelling, on which applications such as indoor navigation, routing or analysis are performed. Therefore, the conceptual meaning of sub spaces or the activities taking place in physical building boundaries (e.g. walls), require the comprehension of the building’s indoor hierarchical structure. The scope of this paper is to perform 3D network analysis in a building’s interior and is structured as follows: In Section 1 the definition of indoor space is provided and indoor navigation requirements are analysed. Section 2 describes the processes of indoor space modeling, as well as routing applications. In Section 3, a case study is examined involving a 3D building model generated in CityEngine (exterior shell) and ArcScene (interior parts), in which the use of commercially available software tools (ArcGIS, ESRI), in terms of indoor routing and 3D network analysis, are explored. The fundamentals of performing 3D analysis with the ArcGIS Network Analyst extension were tested. Finally a geoprocessing model was presented, which was specifically designed to be used to interactively find the best route in ArcScene. The paper ends with discussion and concluding remarks on Section 4.

GEOGRAPHICAL INFORMATION SYSTEM (GIS) MAP FOR FIRE AND RESCUE APPLICATION

The purpose of the Fire and Rescue Service is to protect human life, our property, and Earth natural resources from fire and other emergencies. With fluctuation in demands, the Fire and Rescue Service must be equipped with the best techniques, training regime and equipment to meet public expectations. Mitigation, preparedness and risk management have taken on new benefit with challenges faced by the fire service today. Fast response cannot be achieved without good planning and preparedness. This 3D network analysis model identifies the shortest path from the Fire and Rescue Service position to the source of emergency. The second objective was to design wireless fire detection systems to help fire-fighters to pinpoint the emergency call location, assess the potential consequences, and determine the most efficient strategy. The 3D model was built by Google Sketch Pro 8 and the 3D network analysis and it was mainly conducted in the ESRI’s ArcGIS software. The 3D network analysis was based on distance measurements instead of GNSS coordinates. The distance of each path will be measured on the site personally for maximum accuracy. The fire detection systems prototype hardware will be equipped with smoke sensor, image sensor, a transmitter and a receiver.

Integration of CityGML and Oracle Spatial for implementing 3D network analysis solutions and routing simulation within 3D-GIS environment

3D navigation within a 3D-GIS environment is increasingly getting more popular and spreading to various fields. In the last decade, especially after the 9/11 disaster, evacuating the complex and tall buildings of today in case of emergency has been an important research area for scientists. Most of the current navigation systems are still in the 2D environment and that is insufficient to visualize 3D objects and to obtain satisfactory solutions for the 3D environment. Therefore, there is currently still a lack of implementation of 3D network analysis and navigation for indoor spaces in respect to evacuation. The objective of this paper is to investigate and implement 3D visualization and navigation techniques and solutions for indoor spaces within 3D-GIS. For realizing this, we have proposed a GIS implementation that is capable of carrying out 3D visualization of a building model stored in the CityGML format and perform analysis on a network model stored in Oracle Spatial. The proposed GUI also provides routing simulation on the calculated shortest paths with voice commands and visual instructions.

CORRECTION OF FAULTY LINES IN MUSCLE MODEL, TO BE USED IN 3D BUILDING NETWORK CONSTRUCTION

Abstract. This paper describes the usage of MUSCLE (Multidirectional Scanning for Line Extraction) Model for automatic generation of 3D networks in CityGML format (from raster floor plans). MUSCLE (Multidirectional Scanning for Line Extraction) Model is a conversion method which was developed to vectorize the straight lines through the raster images including floor plans, maps for GIS, architectural drawings, and machine plans. The model allows user to define specific criteria which are crucial for acquiring the vectorization process. Unlike traditional vectorization process, this model generates straight lines based on a line thinning algorithm, without performing line following-chain coding and vector reduction stages. In this method the nearly vertical lines were obtained by scanning the images horizontally, while the nearly horizontal lines were obtained by scanning the images vertically. In a case where two or more consecutive lines are nearly horizontal or nearly vertical, raster data become unmanageable and the process generates wrongly vectorized lines. In this situation, to obtain the precise lines, the image with the wrongly vectorized lines is diagonally scanned. By using MUSCLE model, the network models are topologically structured in CityGML format. After the generation process, it is possible to perform 3D network analysis based on these models. Then, by using the software that was designed based on the generated models, a geodatabase of the models could be established. This paper presents the correction application in MUSCLE and explains 3D network construction in detail.