Uniform Local Binary Pattern Based Texture-Edge Feature for 3D Human Behavior Recognition.

PubMed

Ming, Yue; Wang, Guangchao; Fan, Chunxiao

2015-01-01

With the rapid development of 3D somatosensory technology, human behavior recognition has become an important research field. Human behavior feature analysis has evolved from traditional 2D features to 3D features. In order to improve the performance of human activity recognition, a human behavior recognition method is proposed, which is based on a hybrid texture-edge local pattern coding feature extraction and integration of RGB and depth videos information. The paper mainly focuses on background subtraction on RGB and depth video sequences of behaviors, extracting and integrating historical images of the behavior outlines, feature extraction and classification. The new method of 3D human behavior recognition has achieved the rapid and efficient recognition of behavior videos. A large number of experiments show that the proposed method has faster speed and higher recognition rate. The recognition method has good robustness for different environmental colors, lightings and other factors. Meanwhile, the feature of mixed texture-edge uniform local binary pattern can be used in most 3D behavior recognition.

A 3D THz image processing methodology for a fully integrated, semi-automatic and near real-time operational system

NASA Astrophysics Data System (ADS)

Brook, A.; Cristofani, E.; Vandewal, M.; Matheis, C.; Jonuscheit, J.; Beigang, R.

2012-05-01

The present study proposes a fully integrated, semi-automatic and near real-time mode-operated image processing methodology developed for Frequency-Modulated Continuous-Wave (FMCW) THz images with the center frequencies around: 100 GHz and 300 GHz. The quality control of aeronautics composite multi-layered materials and structures using Non-Destructive Testing is the main focus of this work. Image processing is applied on the 3-D images to extract useful information. The data is processed by extracting areas of interest. The detected areas are subjected to image analysis for more particular investigation managed by a spatial model. Finally, the post-processing stage examines and evaluates the spatial accuracy of the extracted information.

Three-dimensional information extraction from GaoFen-1 satellite images for landslide monitoring

NASA Astrophysics Data System (ADS)

Wang, Shixin; Yang, Baolin; Zhou, Yi; Wang, Futao; Zhang, Rui; Zhao, Qing

2018-05-01

To more efficiently use GaoFen-1 (GF-1) satellite images for landslide emergency monitoring, a Digital Surface Model (DSM) can be generated from GF-1 across-track stereo image pairs to build a terrain dataset. This study proposes a landslide 3D information extraction method based on the terrain changes of slope objects. The slope objects are mergences of segmented image objects which have similar aspects; and the terrain changes are calculated from the post-disaster Digital Elevation Model (DEM) from GF-1 and the pre-disaster DEM from GDEM V2. A high mountain landslide that occurred in Wenchuan County, Sichuan Province is used to conduct a 3D information extraction test. The extracted total area of the landslide is 22.58 ha; the displaced earth volume is 652,100 m3; and the average sliding direction is 263.83°. The accuracies of them are 0.89, 0.87 and 0.95, respectively. Thus, the proposed method expands the application of GF-1 satellite images to the field of landslide emergency monitoring.

A constraint logic programming approach to associate 1D and 3D structural components for large protein complexes.

PubMed

Dal Palù, Alessandro; Pontelli, Enrico; He, Jing; Lu, Yonggang

2007-01-01

The paper describes a novel framework, constructed using Constraint Logic Programming (CLP) and parallelism, to determine the association between parts of the primary sequence of a protein and alpha-helices extracted from 3D low-resolution descriptions of large protein complexes. The association is determined by extracting constraints from the 3D information, regarding length, relative position and connectivity of helices, and solving these constraints with the guidance of a secondary structure prediction algorithm. Parallelism is employed to enhance performance on large proteins. The framework provides a fast, inexpensive alternative to determine the exact tertiary structure of unknown proteins.

CMS-2 Reverse Engineering and ENCORE/MODEL Integration

DTIC Science & Technology

1992-05-01

Automated extraction of design information from an existing software system written in CMS-2 can be used to document that system as-built, and that I The...extracted information is provided by a commer- dally available CASE tool. * Information describing software system design is automatically extracted...the displays in Figures 1, 2, and 3. T achiev ths GE 11 b iuo w as rjcs CM-2t Aa nsltr(M2da 1 n Joia Reverse EwngiernTcnlg 5RT [2GRE] . Two xampe fD

Usability of stereoscopic view in teleoperation

NASA Astrophysics Data System (ADS)

Boonsuk, Wutthigrai

2015-03-01

Recently, there are tremendous growths in the area of 3D stereoscopic visualization. The 3D stereoscopic visualization technology has been used in a growing number of consumer products such as the 3D televisions and the 3D glasses for gaming systems. This technology refers to the idea that human brain develops depth of perception by retrieving information from the two eyes. Our brain combines the left and right images on the retinas and extracts depth information. Therefore, viewing two video images taken at slightly distance apart as shown in Figure 1 can create illusion of depth [8]. Proponents of this technology argue that the stereo view of 3D visualization increases user immersion and performance as more information is gained through the 3D vision as compare to the 2D view. However, it is still uncertain if additional information gained from the 3D stereoscopic visualization can actually improve user performance in real world situations such as in the case of teleoperation.

Depth-tunable three-dimensional display with interactive light field control

NASA Astrophysics Data System (ADS)

Xie, Songlin; Wang, Peng; Sang, Xinzhu; Li, Chenyu; Dou, Wenhua; Xiao, Liquan

2016-07-01

A software-defined depth-tunable three-dimensional (3D) display with interactive 3D depth control is presented. With the proposed post-processing system, the disparity of the multi-view media can be freely adjusted. Benefiting from a wealth of information inherently contains in dense multi-view images captured with parallel arrangement camera array, the 3D light field is built and the light field structure is controlled to adjust the disparity without additional acquired depth information since the light field structure itself contains depth information. A statistical analysis based on the least square is carried out to extract the depth information inherently exists in the light field structure and the accurate depth information can be used to re-parameterize light fields for the autostereoscopic display, and a smooth motion parallax can be guaranteed. Experimental results show that the system is convenient and effective to adjust the 3D scene performance in the 3D display.

Photometry unlocks 3D information from 2D localization microscopy data.

PubMed

Franke, Christian; Sauer, Markus; van de Linde, Sebastian

2017-01-01

We developed a straightforward photometric method, temporal, radial-aperture-based intensity estimation (TRABI), that allows users to extract 3D information from existing 2D localization microscopy data. TRABI uses the accurate determination of photon numbers in different regions of the emission pattern of single emitters to generate a z-dependent photometric parameter. This method can determine fluorophore positions up to 600 nm from the focal plane and can be combined with biplane detection to further improve axial localization.

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

PubMed

Ravikumar, Komandur Elayavilli; Wagholikar, Kavishwar B; Li, Dingcheng; Kocher, Jean-Pierre; Liu, Hongfang

2015-06-06

Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interpreting sequencing data is the assembly of information about genetic variants and their corresponding associations with other entities (e.g., diseases or medications). Even with dedicated effort to capture such information in biological databases, much of this information remains 'locked' in the unstructured text of biomedical publications. There is a substantial lag between the publication and the subsequent abstraction of such information into databases. Multiple text mining systems have been developed, but most of them focus on the sentence level association extraction with performance evaluation based on gold standard text annotations specifically prepared for text mining systems. We developed and evaluated a text mining system, MutD, which extracts protein mutation-disease associations from MEDLINE abstracts by incorporating discourse level analysis, using a benchmark data set extracted from curated database records. MutD achieves an F-measure of 64.3% for reconstructing protein mutation disease associations in curated database records. Discourse level analysis component of MutD contributed to a gain of more than 10% in F-measure when compared against the sentence level association extraction. Our error analysis indicates that 23 of the 64 precision errors are true associations that were not captured by database curators and 68 of the 113 recall errors are caused by the absence of associated disease entities in the abstract. After adjusting for the defects in the curated database, the revised F-measure of MutD in association detection reaches 81.5%. Our quantitative analysis reveals that MutD can effectively extract protein mutation disease associations when benchmarking based on curated database records. The analysis also demonstrates that incorporating discourse level analysis significantly improved the performance of extracting the protein-mutation-disease association. Future work includes the extension of MutD for full text articles.

Development of Mobile Mapping System for 3D Road Asset Inventory.

PubMed

Sairam, Nivedita; Nagarajan, Sudhagar; Ornitz, Scott

2016-03-12

Asset Management is an important component of an infrastructure project. A significant cost is involved in maintaining and updating the asset information. Data collection is the most time-consuming task in the development of an asset management system. In order to reduce the time and cost involved in data collection, this paper proposes a low cost Mobile Mapping System using an equipped laser scanner and cameras. First, the feasibility of low cost sensors for 3D asset inventory is discussed by deriving appropriate sensor models. Then, through calibration procedures, respective alignments of the laser scanner, cameras, Inertial Measurement Unit and GPS (Global Positioning System) antenna are determined. The efficiency of this Mobile Mapping System is experimented by mounting it on a truck and golf cart. By using derived sensor models, geo-referenced images and 3D point clouds are derived. After validating the quality of the derived data, the paper provides a framework to extract road assets both automatically and manually using techniques implementing RANSAC plane fitting and edge extraction algorithms. Then the scope of such extraction techniques along with a sample GIS (Geographic Information System) database structure for unified 3D asset inventory are discussed.

Development of Mobile Mapping System for 3D Road Asset Inventory

PubMed Central

Sairam, Nivedita; Nagarajan, Sudhagar; Ornitz, Scott

2016-01-01

Asset Management is an important component of an infrastructure project. A significant cost is involved in maintaining and updating the asset information. Data collection is the most time-consuming task in the development of an asset management system. In order to reduce the time and cost involved in data collection, this paper proposes a low cost Mobile Mapping System using an equipped laser scanner and cameras. First, the feasibility of low cost sensors for 3D asset inventory is discussed by deriving appropriate sensor models. Then, through calibration procedures, respective alignments of the laser scanner, cameras, Inertial Measurement Unit and GPS (Global Positioning System) antenna are determined. The efficiency of this Mobile Mapping System is experimented by mounting it on a truck and golf cart. By using derived sensor models, geo-referenced images and 3D point clouds are derived. After validating the quality of the derived data, the paper provides a framework to extract road assets both automatically and manually using techniques implementing RANSAC plane fitting and edge extraction algorithms. Then the scope of such extraction techniques along with a sample GIS (Geographic Information System) database structure for unified 3D asset inventory are discussed. PMID:26985897

3D space positioning and image feature extraction for workpiece

NASA Astrophysics Data System (ADS)

Ye, Bing; Hu, Yi

2008-03-01

An optical system of 3D parameters measurement for specific area of a workpiece has been presented and discussed in this paper. A number of the CCD image sensors are employed to construct the 3D coordinate system for the measured area. The CCD image sensor of the monitoring target is used to lock the measured workpiece when it enters the field of view. The other sensors, which are placed symmetrically beam scanners, measure the appearance of the workpiece and the characteristic parameters. The paper established target image segmentation and the image feature extraction algorithm to lock the target, based on the geometric similarity of objective characteristics, rapid locking the goal can be realized. When line laser beam scan the tested workpiece, a number of images are extracted equal time interval and the overlapping images are processed to complete image reconstruction, and achieve the 3D image information. From the 3D coordinate reconstruction model, the 3D characteristic parameters of the tested workpiece are gained. The experimental results are provided in the paper.

The Extraction of 3D Shape from Texture and Shading in the Human Brain

PubMed Central

Georgieva, Svetlana S.; Todd, James T.; Peeters, Ronald

2008-01-01

We used functional magnetic resonance imaging to investigate the human cortical areas involved in processing 3-dimensional (3D) shape from texture (SfT) and shading. The stimuli included monocular images of randomly shaped 3D surfaces and a wide variety of 2-dimensional (2D) controls. The results of both passive and active experiments reveal that the extraction of 3D SfT involves the bilateral caudal inferior temporal gyrus (caudal ITG), lateral occipital sulcus (LOS) and several bilateral sites along the intraparietal sulcus. These areas are largely consistent with those involved in the processing of 3D shape from motion and stereo. The experiments also demonstrate, however, that the analysis of 3D shape from shading is primarily restricted to the caudal ITG areas. Additional results from psychophysical experiments reveal that this difference in neuronal substrate cannot be explained by a difference in strength between the 2 cues. These results underscore the importance of the posterior part of the lateral occipital complex for the extraction of visual 3D shape information from all depth cues, and they suggest strongly that the importance of shading is diminished relative to other cues for the analysis of 3D shape in parietal regions. PMID:18281304

Contextual Classification of Point Cloud Data by Exploiting Individual 3d Neigbourhoods

NASA Astrophysics Data System (ADS)

Weinmann, M.; Schmidt, A.; Mallet, C.; Hinz, S.; Rottensteiner, F.; Jutzi, B.

2015-03-01

The fully automated analysis of 3D point clouds is of great importance in photogrammetry, remote sensing and computer vision. For reliably extracting objects such as buildings, road inventory or vegetation, many approaches rely on the results of a point cloud classification, where each 3D point is assigned a respective semantic class label. Such an assignment, in turn, typically involves statistical methods for feature extraction and machine learning. Whereas the different components in the processing workflow have extensively, but separately been investigated in recent years, the respective connection by sharing the results of crucial tasks across all components has not yet been addressed. This connection not only encapsulates the interrelated issues of neighborhood selection and feature extraction, but also the issue of how to involve spatial context in the classification step. In this paper, we present a novel and generic approach for 3D scene analysis which relies on (i) individually optimized 3D neighborhoods for (ii) the extraction of distinctive geometric features and (iii) the contextual classification of point cloud data. For a labeled benchmark dataset, we demonstrate the beneficial impact of involving contextual information in the classification process and that using individual 3D neighborhoods of optimal size significantly increases the quality of the results for both pointwise and contextual classification.

Extracting Semantic Building Models from Aerial Stereo Images and Conversion to Citygml

NASA Astrophysics Data System (ADS)

Sengul, A.

2012-07-01

The collection of geographic data is of primary importance for the creation and maintenance of a GIS. Traditionally the acquisition of 3D information has been the task of photogrammetry using aerial stereo images. Digital photogrammetric systems employ sophisticated software to extract digital terrain models or to plot 3D objects. The demand for 3D city models leads to new applications and new standards. City Geography Mark-up Language (CityGML), a concept for modelling and exchange of 3D city and landscape models, defines the classes and relations for the most relevant topographic objects in cities and regional models with respect to their geometrical, topological, semantically and topological properties. It now is increasingly accepted, since it fulfils the prerequisites required e.g. for risk analysis, urban planning, and simulations. There is a need to include existing 3D information derived from photogrammetric processes in CityGML databases. In order to filling the gap, this paper reports on a framework transferring data plotted by Erdas LPS and Stereo Analyst for ArcGIS software to CityGML using Safe Software's Feature Manupulate Engine (FME)

Denoising imaging polarimetry by adapted BM3D method.

PubMed

Tibbs, Alexander B; Daly, Ilse M; Roberts, Nicholas W; Bull, David R

2018-04-01

In addition to the visual information contained in intensity and color, imaging polarimetry allows visual information to be extracted from the polarization of light. However, a major challenge of imaging polarimetry is image degradation due to noise. This paper investigates the mitigation of noise through denoising algorithms and compares existing denoising algorithms with a new method, based on BM3D (Block Matching 3D). This algorithm, Polarization-BM3D (PBM3D), gives visual quality superior to the state of the art across all images and noise standard deviations tested. We show that denoising polarization images using PBM3D allows the degree of polarization to be more accurately calculated by comparing it with spectral polarimetry measurements.

Fourier transform profilometry (FTP) using an innovative band-pass filter for accurate 3-D surface reconstruction

NASA Astrophysics Data System (ADS)

Chen, Liang-Chia; Ho, Hsuan-Wei; Nguyen, Xuan-Loc

2010-02-01

This article presents a novel band-pass filter for Fourier transform profilometry (FTP) for accurate 3-D surface reconstruction. FTP can be employed to obtain 3-D surface profiles by one-shot images to achieve high-speed measurement. However, its measurement accuracy has been significantly influenced by the spectrum filtering process required to extract the phase information representing various surface heights. Using the commonly applied 2-D Hanning filter, the measurement errors could be up to 5-10% of the overall measuring height and it is unacceptable to various industrial application. To resolve this issue, the article proposes an elliptical band-pass filter for extracting the spectral region possessing essential phase information for reconstructing accurate 3-D surface profiles. The elliptical band-pass filter was developed and optimized to reconstruct 3-D surface models with improved measurement accuracy. Some experimental results verify that the accuracy can be effectively enhanced by using the elliptical filter. The accuracy improvement of 44.1% and 30.4% can be achieved in 3-D and sphericity measurement, respectively, when the elliptical filter replaces the traditional filter as the band-pass filtering method. Employing the developed method, the maximum measured error can be kept within 3.3% of the overall measuring range.

Automatic facial animation parameters extraction in MPEG-4 visual communication

NASA Astrophysics Data System (ADS)

Yang, Chenggen; Gong, Wanwei; Yu, Lu

2002-01-01

Facial Animation Parameters (FAPs) are defined in MPEG-4 to animate a facial object. The algorithm proposed in this paper to extract these FAPs is applied to very low bit-rate video communication, in which the scene is composed of a head-and-shoulder object with complex background. This paper addresses the algorithm to automatically extract all FAPs needed to animate a generic facial model, estimate the 3D motion of head by points. The proposed algorithm extracts human facial region by color segmentation and intra-frame and inter-frame edge detection. Facial structure and edge distribution of facial feature such as vertical and horizontal gradient histograms are used to locate the facial feature region. Parabola and circle deformable templates are employed to fit facial feature and extract a part of FAPs. A special data structure is proposed to describe deformable templates to reduce time consumption for computing energy functions. Another part of FAPs, 3D rigid head motion vectors, are estimated by corresponding-points method. A 3D head wire-frame model provides facial semantic information for selection of proper corresponding points, which helps to increase accuracy of 3D rigid object motion estimation.

Robust multitask learning with three-dimensional empirical mode decomposition-based features for hyperspectral classification

NASA Astrophysics Data System (ADS)

He, Zhi; Liu, Lin

2016-11-01

Empirical mode decomposition (EMD) and its variants have recently been applied for hyperspectral image (HSI) classification due to their ability to extract useful features from the original HSI. However, it remains a challenging task to effectively exploit the spectral-spatial information by the traditional vector or image-based methods. In this paper, a three-dimensional (3D) extension of EMD (3D-EMD) is proposed to naturally treat the HSI as a cube and decompose the HSI into varying oscillations (i.e. 3D intrinsic mode functions (3D-IMFs)). To achieve fast 3D-EMD implementation, 3D Delaunay triangulation (3D-DT) is utilized to determine the distances of extrema, while separable filters are adopted to generate the envelopes. Taking the extracted 3D-IMFs as features of different tasks, robust multitask learning (RMTL) is further proposed for HSI classification. In RMTL, pairs of low-rank and sparse structures are formulated by trace-norm and l1,2 -norm to capture task relatedness and specificity, respectively. Moreover, the optimization problems of RMTL can be efficiently solved by the inexact augmented Lagrangian method (IALM). Compared with several state-of-the-art feature extraction and classification methods, the experimental results conducted on three benchmark data sets demonstrate the superiority of the proposed methods.

Motion processing with two eyes in three dimensions.

PubMed

Rokers, Bas; Czuba, Thaddeus B; Cormack, Lawrence K; Huk, Alexander C

2011-02-11

The movement of an object toward or away from the head is perhaps the most critical piece of information an organism can extract from its environment. Such 3D motion produces horizontally opposite motions on the two retinae. Little is known about how or where the visual system combines these two retinal motion signals, relative to the wealth of knowledge about the neural hierarchies involved in 2D motion processing and binocular vision. Canonical conceptions of primate visual processing assert that neurons early in the visual system combine monocular inputs into a single cyclopean stream (lacking eye-of-origin information) and extract 1D ("component") motions; later stages then extract 2D pattern motion from the cyclopean output of the earlier stage. Here, however, we show that 3D motion perception is in fact affected by the comparison of opposite 2D pattern motions between the two eyes. Three-dimensional motion sensitivity depends systematically on pattern motion direction when dichoptically viewing gratings and plaids-and a novel "dichoptic pseudoplaid" stimulus provides strong support for use of interocular pattern motion differences by precluding potential contributions from conventional disparity-based mechanisms. These results imply the existence of eye-of-origin information in later stages of motion processing and therefore motivate the incorporation of such eye-specific pattern-motion signals in models of motion processing and binocular integration.

Evaluation of Ultrasonic Fiber Structure Extraction Technique Using Autopsy Specimens of Liver

NASA Astrophysics Data System (ADS)

Yamaguchi, Tadashi; Hirai, Kazuki; Yamada, Hiroyuki; Ebara, Masaaki; Hachiya, Hiroyuki

2005-06-01

It is very important to diagnose liver cirrhosis noninvasively and correctly. In our previous studies, we proposed a processing technique to detect changes in liver tissue in vivo. In this paper, we propose the evaluation of the relationship between liver disease and echo information using autopsy specimens of a human liver in vitro. It is possible to verify the function of a processing parameter clearly and to compare the processing result and the actual human liver tissue structure by in vitro experiment. In the results of our processing technique, information that did not obey a Rayleigh distribution from the echo signal of the autopsy liver specimens was extracted depending on changes in a particular processing parameter. The fiber tissue structure of the same specimen was extracted from a number of histological images of stained tissue. We constructed 3D structures using the information extracted from the echo signal and the fiber structure of the stained tissue and compared the two. By comparing the 3D structures, it is possible to evaluate the relationship between the information that does not obey a Rayleigh distribution of the echo signal and the fibrosis structure.

3D spherical-cap fitting procedure for (truncated) sessile nano- and micro-droplets & -bubbles.

PubMed

Tan, Huanshu; Peng, Shuhua; Sun, Chao; Zhang, Xuehua; Lohse, Detlef

2016-11-01

In the study of nanobubbles, nanodroplets or nanolenses immobilised on a substrate, a cross-section of a spherical cap is widely applied to extract geometrical information from atomic force microscopy (AFM) topographic images. In this paper, we have developed a comprehensive 3D spherical-cap fitting procedure (3D-SCFP) to extract morphologic characteristics of complete or truncated spherical caps from AFM images. Our procedure integrates several advanced digital image analysis techniques to construct a 3D spherical-cap model, from which the geometrical parameters of the nanostructures are extracted automatically by a simple algorithm. The procedure takes into account all valid data points in the construction of the 3D spherical-cap model to achieve high fidelity in morphology analysis. We compare our 3D fitting procedure with the commonly used 2D cross-sectional profile fitting method to determine the contact angle of a complete spherical cap and a truncated spherical cap. The results from 3D-SCFP are consistent and accurate, while 2D fitting is unavoidably arbitrary in the selection of the cross-section and has a much lower number of data points on which the fitting can be based, which in addition is biased to the top of the spherical cap. We expect that the developed 3D spherical-cap fitting procedure will find many applications in imaging analysis.

Building change detection via a combination of CNNs using only RGB aerial imageries

NASA Astrophysics Data System (ADS)

Nemoto, Keisuke; Hamaguchi, Ryuhei; Sato, Masakazu; Fujita, Aito; Imaizumi, Tomoyuki; Hikosaka, Shuhei

2017-10-01

Building change information extracted from remote sensing imageries is important for various applications such as urban management and marketing planning. The goal of this work is to develop a methodology for automatically capturing building changes from remote sensing imageries. Recent studies have addressed this goal by exploiting 3-D information as a proxy for building height. In contrast, because in practice it is expensive or impossible to prepare 3-D information, we do not rely on 3-D data but focus on using only RGB aerial imageries. Instead, we employ deep convolutional neural networks (CNNs) to extract effective features, and improve change detection accuracy in RGB remote sensing imageries. We consider two aspects of building change detection, building detection and subsequent change detection. Our proposed methodology was tested on several areas, which has some differences such as dominant building characteristics and varying brightness values. On all over the tested areas, the proposed method provides good results for changed objects, with recall values over 75 % with a strict overlap requirement of over 50% in intersection-over-union (IoU). When the IoU threshold was relaxed to over 10%, resulting recall values were over 81%. We conclude that use of CNNs enables accurate detection of building changes without employing 3-D information.

LIDAR Point Cloud Data Extraction and Establishment of 3D Modeling of Buildings

NASA Astrophysics Data System (ADS)

Zhang, Yujuan; Li, Xiuhai; Wang, Qiang; Liu, Jiang; Liang, Xin; Li, Dan; Ni, Chundi; Liu, Yan

2018-01-01

This paper takes the method of Shepard’s to deal with the original LIDAR point clouds data, and generate regular grid data DSM, filters the ground point cloud and non ground point cloud through double least square method, and obtains the rules of DSM. By using region growing method for the segmentation of DSM rules, the removal of non building point cloud, obtaining the building point cloud information. Uses the Canny operator to extract the image segmentation is needed after the edges of the building, uses Hough transform line detection to extract the edges of buildings rules of operation based on the smooth and uniform. At last, uses E3De3 software to establish the 3D model of buildings.

An MR-based Model for Cardio-Respiratory Motion Compensation of Overlays in X-Ray Fluoroscopy

PubMed Central

Fischer, Peter; Faranesh, Anthony; Pohl, Thomas; Maier, Andreas; Rogers, Toby; Ratnayaka, Kanishka; Lederman, Robert; Hornegger, Joachim

2017-01-01

In X-ray fluoroscopy, static overlays are used to visualize soft tissue. We propose a system for cardiac and respiratory motion compensation of these overlays. It consists of a 3-D motion model created from real-time MR imaging. Multiple sagittal slices are acquired and retrospectively stacked to consistent 3-D volumes. Slice stacking considers cardiac information derived from the ECG and respiratory information extracted from the images. Additionally, temporal smoothness of the stacking is enhanced. Motion is estimated from the MR volumes using deformable 3-D/3-D registration. The motion model itself is a linear direct correspondence model using the same surrogate signals as slice stacking. In X-ray fluoroscopy, only the surrogate signals need to be extracted to apply the motion model and animate the overlay in real time. For evaluation, points are manually annotated in oblique MR slices and in contrast-enhanced X-ray images. The 2-D Euclidean distance of these points is reduced from 3.85 mm to 2.75 mm in MR and from 3.0 mm to 1.8 mm in X-ray compared to the static baseline. Furthermore, the motion-compensated overlays are shown qualitatively as images and videos. PMID:28692969

a Tool for Crowdsourced Building Information Modeling Through Low-Cost Range Camera: Preliminary Demonstration and Potential

NASA Astrophysics Data System (ADS)

Capocchiano, F.; Ravanelli, R.; Crespi, M.

2017-11-01

Within the construction sector, Building Information Models (BIMs) are more and more used thanks to the several benefits that they offer in the design of new buildings and the management of the existing ones. Frequently, however, BIMs are not available for already built constructions, but, at the same time, the range camera technology provides nowadays a cheap, intuitive and effective tool for automatically collecting the 3D geometry of indoor environments. It is thus essential to find new strategies, able to perform the first step of the scan to BIM process, by extracting the geometrical information contained in the 3D models that are so easily collected through the range cameras. In this work, a new algorithm to extract planimetries from the 3D models of rooms acquired by means of a range camera is therefore presented. The algorithm was tested on two rooms, characterized by different shapes and dimensions, whose 3D models were captured with the Occipital Structure SensorTM. The preliminary results are promising: the developed algorithm is able to model effectively the 2D shape of the investigated rooms, with an accuracy level comprised in the range of 5 - 10 cm. It can be potentially used by non-expert users in the first step of the BIM generation, when the building geometry is reconstructed, for collecting crowdsourced indoor information in the frame of BIMs Volunteered Geographic Information (VGI) generation.

Case study of 3D fingerprints applications

PubMed Central

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition. PMID:28399141

Case study of 3D fingerprints applications.

PubMed

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition.

Semantic World Modelling and Data Management in a 4d Forest Simulation and Information System

NASA Astrophysics Data System (ADS)

Roßmann, J.; Hoppen, M.; Bücken, A.

2013-08-01

Various types of 3D simulation applications benefit from realistic forest models. They range from flight simulators for entertainment to harvester simulators for training and tree growth simulations for research and planning. Our 4D forest simulation and information system integrates the necessary methods for data extraction, modelling and management. Using modern methods of semantic world modelling, tree data can efficiently be extracted from remote sensing data. The derived forest models contain position, height, crown volume, type and diameter of each tree. This data is modelled using GML-based data models to assure compatibility and exchangeability. A flexible approach for database synchronization is used to manage the data and provide caching, persistence, a central communication hub for change distribution, and a versioning mechanism. Combining various simulation techniques and data versioning, the 4D forest simulation and information system can provide applications with "both directions" of the fourth dimension. Our paper outlines the current state, new developments, and integration of tree extraction, data modelling, and data management. It also shows several applications realized with the system.

Automatic 3D power line reconstruction of multi-angular imaging power line inspection system

NASA Astrophysics Data System (ADS)

Zhang, Wuming; Yan, Guangjian; Wang, Ning; Li, Qiaozhi; Zhao, Wei

2007-06-01

We develop a multi-angular imaging power line inspection system. Its main objective is to monitor the relative distance between high voltage power line and around objects, and alert if the warning threshold is exceeded. Our multi-angular imaging power line inspection system generates DSM of the power line passage, which comprises ground surface and ground objects, for example trees and houses, etc. For the purpose of revealing the dangerous regions, where ground objects are too close to the power line, 3D power line information should be extracted at the same time. In order to improve the automation level of extraction, reduce labour costs and human errors, an automatic 3D power line reconstruction method is proposed and implemented. It can be achieved by using epipolar constraint and prior knowledge of pole tower's height. After that, the proper 3D power line information can be obtained by space intersection using found homologous projections. The flight experiment result shows that the proposed method can successfully reconstruct 3D power line, and the measurement accuracy of the relative distance satisfies the user requirement of 0.5m.

Towards 3D Matching of Point Clouds Derived from Oblique and Nadir Airborne Imagery

NASA Astrophysics Data System (ADS)

Zhang, Ming

Because of the low-expense high-efficient image collection process and the rich 3D and texture information presented in the images, a combined use of 2D airborne nadir and oblique images to reconstruct 3D geometric scene has a promising market for future commercial usage like urban planning or first responders. The methodology introduced in this thesis provides a feasible way towards fully automated 3D city modeling from oblique and nadir airborne imagery. In this thesis, the difficulty of matching 2D images with large disparity is avoided by grouping the images first and applying the 3D registration afterward. The procedure starts with the extraction of point clouds using a modified version of the RIT 3D Extraction Workflow. Then the point clouds are refined by noise removal and surface smoothing processes. Since the point clouds extracted from different image groups use independent coordinate systems, there are translation, rotation and scale differences existing. To figure out these differences, 3D keypoints and their features are extracted. For each pair of point clouds, an initial alignment and a more accurate registration are applied in succession. The final transform matrix presents the parameters describing the translation, rotation and scale requirements. The methodology presented in the thesis has been shown to behave well for test data. The robustness of this method is discussed by adding artificial noise to the test data. For Pictometry oblique aerial imagery, the initial alignment provides a rough alignment result, which contains a larger offset compared to that of test data because of the low quality of the point clouds themselves, but it can be further refined through the final optimization. The accuracy of the final registration result is evaluated by comparing it to the result obtained from manual selection of matched points. Using the method introduced, point clouds extracted from different image groups could be combined with each other to build a more complete point cloud, or be used as a complement to existing point clouds extracted from other sources. This research will both improve the state of the art of 3D city modeling and inspire new ideas in related fields.

Fast 3D 1H MRSI of the Corticospinal Tract in Pediatric Brain

PubMed Central

Kim, Dong-Hyun; Gu, Meng; Cunningham, Charles; Chen, Albert; Baumer, Fiona; Glenn, Orit A.; Vigneron, Daniel B.; Spielman, Daniel Mark; Barkovich, Anthony James

2010-01-01

Purpose: To develop a 1H magnetic resonance spectroscopic imaging (MRSI) sequence that can be used to image infants/children at 3T and by combining it with diffusion tensor imaging (DTI) tractography, extract relevant metabolic information corresponding to the corticospinal tract (CST). Materials and Methods: A fast 3D MRSI sequence was developed for pediatric neuroimaging at 3T using spiral k-space readout and dual band RF pulses (32 × 32 × 8 cm field of view [FOV], 1 cc iso-resolution, TR/TE = 1500/130, 6:24 minute scan). Using DTI tractography to identify the motor tracts, spectra were extracted from the CSTs and quantified. Initial data from infants/children with suspected motor delay (n = 5) and age-matched controls (n = 3) were collected and N-acetylaspartate (NAA) ratios were quantified. Results: The average signal-to-noise ratio of the NAA peak from the studies was ≈22. Metabolite profiles were successfully acquired from the CST by using DTI tractography. Decreased NAA ratios in those with motor delay compared to controls of ≈10% at the CST were observed. Conclusion: A fast and robust 3D MRSI technique targeted for pediatric neuroimaging has been developed. By combining with DTI tractography, metabolic information from the CSTs can be retrieved and estimated. By combining DTI and 3D MRSI, spectral information from various tracts can be obtained and processed. PMID:19097091

RGB-D SLAM Based on Extended Bundle Adjustment with 2D and 3D Information

PubMed Central

Di, Kaichang; Zhao, Qiang; Wan, Wenhui; Wang, Yexin; Gao, Yunjun

2016-01-01

In the study of SLAM problem using an RGB-D camera, depth information and visual information as two types of primary measurement data are rarely tightly coupled during refinement of camera pose estimation. In this paper, a new method of RGB-D camera SLAM is proposed based on extended bundle adjustment with integrated 2D and 3D information on the basis of a new projection model. First, the geometric relationship between the image plane coordinates and the depth values is constructed through RGB-D camera calibration. Then, 2D and 3D feature points are automatically extracted and matched between consecutive frames to build a continuous image network. Finally, extended bundle adjustment based on the new projection model, which takes both image and depth measurements into consideration, is applied to the image network for high-precision pose estimation. Field experiments show that the proposed method has a notably better performance than the traditional method, and the experimental results demonstrate the effectiveness of the proposed method in improving localization accuracy. PMID:27529256

Combining heterogenous features for 3D hand-held object recognition

NASA Astrophysics Data System (ADS)

Lv, Xiong; Wang, Shuang; Li, Xiangyang; Jiang, Shuqiang

2014-10-01

Object recognition has wide applications in the area of human-machine interaction and multimedia retrieval. However, due to the problem of visual polysemous and concept polymorphism, it is still a great challenge to obtain reliable recognition result for the 2D images. Recently, with the emergence and easy availability of RGB-D equipment such as Kinect, this challenge could be relieved because the depth channel could bring more information. A very special and important case of object recognition is hand-held object recognition, as hand is a straight and natural way for both human-human interaction and human-machine interaction. In this paper, we study the problem of 3D object recognition by combining heterogenous features with different modalities and extraction techniques. For hand-craft feature, although it reserves the low-level information such as shape and color, it has shown weakness in representing hiconvolutionalgh-level semantic information compared with the automatic learned feature, especially deep feature. Deep feature has shown its great advantages in large scale dataset recognition but is not always robust to rotation or scale variance compared with hand-craft feature. In this paper, we propose a method to combine hand-craft point cloud features and deep learned features in RGB and depth channle. First, hand-held object segmentation is implemented by using depth cues and human skeleton information. Second, we combine the extracted hetegerogenous 3D features in different stages using linear concatenation and multiple kernel learning (MKL). Then a training model is used to recognize 3D handheld objects. Experimental results validate the effectiveness and gerneralization ability of the proposed method.

Polarized light microscopy for 3-dimensional mapping of collagen fiber architecture in ocular tissues.

PubMed

Yang, Bin; Jan, Ning-Jiun; Brazile, Bryn; Voorhees, Andrew; Lathrop, Kira L; Sigal, Ian A

2018-04-06

Collagen fibers play a central role in normal eye mechanics and pathology. In ocular tissues, collagen fibers exhibit a complex 3-dimensional (3D) fiber orientation, with both in-plane (IP) and out-of-plane (OP) orientations. Imaging techniques traditionally applied to the study of ocular tissues only quantify IP fiber orientation, providing little information on OP fiber orientation. Accurate description of the complex 3D fiber microstructures of the eye requires quantifying full 3D fiber orientation. Herein, we present 3dPLM, a technique based on polarized light microscopy developed to quantify both IP and OP collagen fiber orientations of ocular tissues. The performance of 3dPLM was examined by simulation and experimental verification and validation. The experiments demonstrated an excellent agreement between extracted and true 3D fiber orientation. Both IP and OP fiber orientations can be extracted from the sclera and the cornea, providing previously unavailable quantitative 3D measures and insight into the tissue microarchitecture. Together, the results demonstrate that 3dPLM is a powerful imaging technique for the analysis of ocular tissues. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemistry of wood in 3D: new infrared imaging

Treesearch

Barbara L. Illman; Julia Sedlmair; Miriam Unger; Casey Crooks; Marli Oliveira; Carol Hirschmugl

2015-01-01

Chemical detection, mapping and imaging in three dimensions will help refine our understanding of wood properties and durability. We describe here a pioneering infrared method to create visual 3D images of the chemicals in wood, providing for the first time, spatial and architectural information at the cellular level without liquid extraction or prior fixation....

A dental vision system for accurate 3D tooth modeling.

PubMed

Zhang, Li; Alemzadeh, K

2006-01-01

This paper describes an active vision system based reverse engineering approach to extract the three-dimensional (3D) geometric information from dental teeth and transfer this information into Computer-Aided Design/Computer-Aided Manufacture (CAD/CAM) systems to improve the accuracy of 3D teeth models and at the same time improve the quality of the construction units to help patient care. The vision system involves the development of a dental vision rig, edge detection, boundary tracing and fast & accurate 3D modeling from a sequence of sliced silhouettes of physical models. The rig is designed using engineering design methods such as a concept selection matrix and weighted objectives evaluation chart. Reconstruction results and accuracy evaluation are presented on digitizing different teeth models.

Line segment extraction for large scale unorganized point clouds

NASA Astrophysics Data System (ADS)

Lin, Yangbin; Wang, Cheng; Cheng, Jun; Chen, Bili; Jia, Fukai; Chen, Zhonggui; Li, Jonathan

2015-04-01

Line segment detection in images is already a well-investigated topic, although it has received considerably less attention in 3D point clouds. Benefiting from current LiDAR devices, large-scale point clouds are becoming increasingly common. Most human-made objects have flat surfaces. Line segments that occur where pairs of planes intersect give important information regarding the geometric content of point clouds, which is especially useful for automatic building reconstruction and segmentation. This paper proposes a novel method that is capable of accurately extracting plane intersection line segments from large-scale raw scan points. The 3D line-support region, namely, a point set near a straight linear structure, is extracted simultaneously. The 3D line-support region is fitted by our Line-Segment-Half-Planes (LSHP) structure, which provides a geometric constraint for a line segment, making the line segment more reliable and accurate. We demonstrate our method on the point clouds of large-scale, complex, real-world scenes acquired by LiDAR devices. We also demonstrate the application of 3D line-support regions and their LSHP structures on urban scene abstraction.

[Rapid identification of micro-constituents in monoammonium glycyrrhizinate raw materials by high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry].

PubMed

Yang, Xue-Dong; Tang, Xu-Yan; Sang, Lin

2012-11-01

To establish a method for rapid identification of micro-constituents in monoammonium glycyrrhizinate by high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry. HPLC preparative chromatograph was adopted for determining the optimal method for high-pressure solid phase extraction under optimal conditions. 5C18-MS-II column (20.0 mm x 20.0 mm) was used as the extraction column, with 35% acetonitrile-acetic acid solution (pH 2. 20) as eluent at the speed of 16 mL x min(-1). The sample size was 0.5 mL, and the extraction cycle was 4.5 min. Then, extract liquid was analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS) after being concentrated by 100 times. Under the optimal condition of high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry, 10 components were rapidly identified from monoammonium glycyrrhizinate raw materials. Among them, the chemical structures of six micro-constituents were identified as 3-O-[beta-D-glucuronopyranosyl-beta-D-glucuronopyranosyl]-30-0-beta-D-apiopyranosylglycyrrhetic/3-O- [P-D-glucuronopyranosyl-beta-D-glucuronopyranosyl]-30-O-beta-D-arabinopyranosylglycyrrhetic, glycyrrhizic saponin F3, 22-hydroxyglycyrrhizin/18alpha-glycyrrhizic saponin G2, 3-O-[beta-D-rhamnopyranosyl]-24-hydroxyglycyrrhizin, glycyrrhizic saponin J2, and glycyrrhizic saponin B2 by MS(n) spectra analysis and reference to literatures. Four main chemical components were identified as glycyrrhizic saponin G2, 18beta-glycyrrhizic acid, uralglycyrrhizic saponin B and 18alpha-glycyrrhizic acid by liquid chromatography, MS(n) and ultraviolet spectra information and comparison with reference substances. The method can be used to identify chemical constituents in monoammonium glycyrrhizinate quickly and effectively, without any reference substance, which provides basis for quality control and safe application of monoammonium glycyrrhizinate-related products.

Extraction of Urban Trees from Integrated Airborne Based Digital Image and LIDAR Point Cloud Datasets - Initial Results

NASA Astrophysics Data System (ADS)

Dogon-yaro, M. A.; Kumar, P.; Rahman, A. Abdul; Buyuksalih, G.

2016-10-01

Timely and accurate acquisition of information on the condition and structural changes of urban trees serves as a tool for decision makers to better appreciate urban ecosystems and their numerous values which are critical to building up strategies for sustainable development. The conventional techniques used for extracting tree features include; ground surveying and interpretation of the aerial photography. However, these techniques are associated with some constraint, such as labour intensive field work, a lot of financial requirement, influences by weather condition and topographical covers which can be overcome by means of integrated airborne based LiDAR and very high resolution digital image datasets. This study presented a semi-automated approach for extracting urban trees from integrated airborne based LIDAR and multispectral digital image datasets over Istanbul city of Turkey. The above scheme includes detection and extraction of shadow free vegetation features based on spectral properties of digital images using shadow index and NDVI techniques and automated extraction of 3D information about vegetation features from the integrated processing of shadow free vegetation image and LiDAR point cloud datasets. The ability of the developed algorithms shows a promising result as an automated and cost effective approach to estimating and delineated 3D information of urban trees. The research also proved that integrated datasets is a suitable technology and a viable source of information for city managers to be used in urban trees management.

Three-dimensional sensor system using multistripe laser and stereo camera for environment recognition of mobile robots

NASA Astrophysics Data System (ADS)

Kim, Min Young; Cho, Hyung Suck; Kim, Jae H.

2002-10-01

In recent years, intelligent autonomous mobile robots have drawn tremendous interests as service robots for serving human or industrial robots for replacing human. To carry out the task, robots must be able to sense and recognize 3D space that they live or work. In this paper, we deal with the topic related to 3D sensing system for the environment recognition of mobile robots. For this, the structured lighting is basically utilized for a 3D visual sensor system because of the robustness on the nature of the navigation environment and the easy extraction of feature information of interest. The proposed sensing system is classified into a trinocular vision system, which is composed of the flexible multi-stripe laser projector, and two cameras. The principle of extracting the 3D information is based on the optical triangulation method. With modeling the projector as another camera and using the epipolar constraints which the whole cameras makes, the point-to-point correspondence between the line feature points in each image is established. In this work, the principle of this sensor is described in detail, and a series of experimental tests is performed to show the simplicity and efficiency and accuracy of this sensor system for 3D the environment sensing and recognition.

Spectral-spatial classification of hyperspectral image using three-dimensional convolution network

NASA Astrophysics Data System (ADS)

Liu, Bing; Yu, Xuchu; Zhang, Pengqiang; Tan, Xiong; Wang, Ruirui; Zhi, Lu

2018-01-01

Recently, hyperspectral image (HSI) classification has become a focus of research. However, the complex structure of an HSI makes feature extraction difficult to achieve. Most current methods build classifiers based on complex handcrafted features computed from the raw inputs. The design of an improved 3-D convolutional neural network (3D-CNN) model for HSI classification is described. This model extracts features from both the spectral and spatial dimensions through the application of 3-D convolutions, thereby capturing the important discrimination information encoded in multiple adjacent bands. The designed model views the HSI cube data altogether without relying on any pre- or postprocessing. In addition, the model is trained in an end-to-end fashion without any handcrafted features. The designed model was applied to three widely used HSI datasets. The experimental results demonstrate that the 3D-CNN-based method outperforms conventional methods even with limited labeled training samples.

Synergistic effect of apple extracts and quercetin 3-beta-d-glucoside combination on antiproliferative activity in MCF-7 human breast cancer cells in vitro.

PubMed

Yang, Jun; Liu, Rui Hai

2009-09-23

Breast cancer is the most frequently diagnosed cancer in women. An alternative strategy to reduce the risk of cancer is through dietary modification. Although phytochemicals naturally occur as complex mixtures, little information is available regarding possible additive, synergistic, or antagonistic interactions among compounds. The antiproliferative activity of apple extracts and quercetin 3-beta-d-glucoside (Q3G) was assessed by measurement of the inhibition of MCF-7 human breast cancer cell proliferation. Cell cytotoxicity was determined by the methylene blue assay. The two-way combination of apple plus Q3G was conducted. In this two-way combination, the EC(50) values of apple extracts and Q3G were 2- and 4-fold lower, respectively, than those of apple extracts and Q3G alone. The combination index (CI) values at 50 and 95% inhibition rates were 0.76 +/- 0.16 and 0.42 +/- 0.10, respectively. The dose-reduction index (DRI) values of the apple extracts and Q3G to achieve a 50% inhibition effect were reduced by 2.03 +/- 0.55 and 4.28 +/- 0.39-fold, respectively. The results suggest that the apple extracts plus Q3G combination possesses a synergistic effect in MCF-7 cell proliferation.

LiDAR Vegetation Investigation and Signature Analysis System (LVISA)

NASA Astrophysics Data System (ADS)

Höfle, Bernhard; Koenig, Kristina; Griesbaum, Luisa; Kiefer, Andreas; Hämmerle, Martin; Eitel, Jan; Koma, Zsófia

2015-04-01

Our physical environment undergoes constant changes in space and time with strongly varying triggers, frequencies, and magnitudes. Monitoring these environmental changes is crucial to improve our scientific understanding of complex human-environmental interactions and helps us to respond to environmental change by adaptation or mitigation. The three-dimensional (3D) description of the Earth surface features and the detailed monitoring of surface processes using 3D spatial data have gained increasing attention within the last decades, such as in climate change research (e.g., glacier retreat), carbon sequestration (e.g., forest biomass monitoring), precision agriculture and natural hazard management. In all those areas, 3D data have helped to improve our process understanding by allowing quantifying the structural properties of earth surface features and their changes over time. This advancement has been fostered by technological developments and increased availability of 3D sensing systems. In particular, LiDAR (light detection and ranging) technology, also referred to as laser scanning, has made significant progress and has evolved into an operational tool in environmental research and geosciences. The main result of LiDAR measurements is a highly spatially resolved 3D point cloud. Each point within the LiDAR point cloud has a XYZ coordinate associated with it and often additional information such as the strength of the returned backscatter. The point cloud provided by LiDAR contains rich geospatial, structural, and potentially biochemical information about the surveyed objects. To deal with the inherently unorganized datasets and the large data volume (frequently millions of XYZ coordinates) of LiDAR datasets, a multitude of algorithms for automatic 3D object detection (e.g., of single trees) and physical surface description (e.g., biomass) have been developed. However, so far the exchange of datasets and approaches (i.e., extraction algorithms) among LiDAR users lacks behind. We propose a novel concept, the LiDAR Vegetation Investigation and Signature Analysis System (LVISA), which shall enhance sharing of i) reference datasets of single vegetation objects with rich reference data (e.g., plant species, basic plant morphometric information) and ii) approaches for information extraction (e.g., single tree detection, tree species classification based on waveform LiDAR features). We will build an extensive LiDAR data repository for supporting the development and benchmarking of LiDAR-based object information extraction. The LiDAR Vegetation Investigation and Signature Analysis System (LVISA) uses international web service standards (Open Geospatial Consortium, OGC) for geospatial data access and also analysis (e.g., OGC Web Processing Services). This will allow the research community identifying plant object specific vegetation features from LiDAR data, while accounting for differences in LiDAR systems (e.g., beam divergence), settings (e.g., point spacing), and calibration techniques. It is the goal of LVISA to develop generic 3D information extraction approaches, which can be seamlessly transferred to other datasets, timestamps and also extraction tasks. The current prototype of LVISA can be visited and tested online via http://uni-heidelberg.de/lvisa. Video tutorials provide a quick overview and entry into the functionality of LVISA. We will present the current advances of LVISA and we will highlight future research and extension of LVISA, such as integrating low-cost LiDAR data and datasets acquired by highly temporal scanning of vegetation (e.g., continuous measurements). Everybody is invited to join the LVISA development and share datasets and analysis approaches in an interoperable way via the web-based LVISA geoportal.

Target 3-D reconstruction of streak tube imaging lidar based on Gaussian fitting

NASA Astrophysics Data System (ADS)

Yuan, Qingyu; Niu, Lihong; Hu, Cuichun; Wu, Lei; Yang, Hongru; Yu, Bing

2018-02-01

Streak images obtained by the streak tube imaging lidar (STIL) contain the distance-azimuth-intensity information of a scanned target, and a 3-D reconstruction of the target can be carried out through extracting the characteristic data of multiple streak images. Significant errors will be caused in the reconstruction result by the peak detection method due to noise and other factors. So as to get a more precise 3-D reconstruction, a peak detection method based on Gaussian fitting of trust region is proposed in this work. Gaussian modeling is performed on the returned wave of single time channel of each frame, then the modeling result which can effectively reduce the noise interference and possesses a unique peak could be taken as the new returned waveform, lastly extracting its feature data through peak detection. The experimental data of aerial target is for verifying this method. This work shows that the peak detection method based on Gaussian fitting reduces the extraction error of the feature data to less than 10%; utilizing this method to extract the feature data and reconstruct the target make it possible to realize the spatial resolution with a minimum 30 cm in the depth direction, and improve the 3-D imaging accuracy of the STIL concurrently.

Automatic extraction of pavement markings on streets from point cloud data of mobile LiDAR

NASA Astrophysics Data System (ADS)

Gao, Yang; Zhong, Ruofei; Tang, Tao; Wang, Liuzhao; Liu, Xianlin

2017-08-01

Pavement markings provide an important foundation as they help to keep roads users safe. Accurate and comprehensive information about pavement markings assists the road regulators and is useful in developing driverless technology. Mobile light detection and ranging (LiDAR) systems offer new opportunities to collect and process accurate pavement markings’ information. Mobile LiDAR systems can directly obtain the three-dimensional (3D) coordinates of an object, thus defining spatial data and the intensity of (3D) objects in a fast and efficient way. The RGB attribute information of data points can be obtained based on the panoramic camera in the system. In this paper, we present a novel method process to automatically extract pavement markings using multiple attribute information of the laser scanning point cloud from the mobile LiDAR data. This method process utilizes a differential grayscale of RGB color, laser pulse reflection intensity, and the differential intensity to identify and extract pavement markings. We utilized point cloud density to remove the noise and used morphological operations to eliminate the errors. In the application, we tested our method process on different sections of roads in Beijing, China, and Buffalo, NY, USA. The results indicated that both correctness (p) and completeness (r) were higher than 90%. The method process of this research can be applied to extract pavement markings from huge point cloud data produced by mobile LiDAR.

Segmentation of brain volume based on 3D region growing by integrating intensity and edge for image-guided surgery

NASA Astrophysics Data System (ADS)

Tsagaan, Baigalmaa; Abe, Keiichi; Goto, Masahiro; Yamamoto, Seiji; Terakawa, Susumu

2006-03-01

This paper presents a segmentation method of brain tissues from MR images, invented for our image-guided neurosurgery system under development. Our goal is to segment brain tissues for creating biomechanical model. The proposed segmentation method is based on 3-D region growing and outperforms conventional approaches by stepwise usage of intensity similarities between voxels in conjunction with edge information. Since the intensity and the edge information are complementary to each other in the region-based segmentation, we use them twice by performing a coarse-to-fine extraction. First, the edge information in an appropriate neighborhood of the voxel being considered is examined to constrain the region growing. The expanded region of the first extraction result is then used as the domain for the next processing. The intensity and the edge information of the current voxel only are utilized in the final extraction. Before segmentation, the intensity parameters of the brain tissues as well as partial volume effect are estimated by using expectation-maximization (EM) algorithm in order to provide an accurate data interpretation into the extraction. We tested the proposed method on T1-weighted MR images of brain and evaluated the segmentation effectiveness comparing the results with ground truths. Also, the generated meshes from the segmented brain volume by using mesh generating software are shown in this paper.

Three-dimensional ghost imaging lidar via sparsity constraint

NASA Astrophysics Data System (ADS)

Gong, Wenlin; Zhao, Chengqiang; Yu, Hong; Chen, Mingliang; Xu, Wendong; Han, Shensheng

2016-05-01

Three-dimensional (3D) remote imaging attracts increasing attentions in capturing a target’s characteristics. Although great progress for 3D remote imaging has been made with methods such as scanning imaging lidar and pulsed floodlight-illumination imaging lidar, either the detection range or application mode are limited by present methods. Ghost imaging via sparsity constraint (GISC), enables the reconstruction of a two-dimensional N-pixel image from much fewer than N measurements. By GISC technique and the depth information of targets captured with time-resolved measurements, we report a 3D GISC lidar system and experimentally show that a 3D scene at about 1.0 km range can be stably reconstructed with global measurements even below the Nyquist limit. Compared with existing 3D optical imaging methods, 3D GISC has the capability of both high efficiency in information extraction and high sensitivity in detection. This approach can be generalized in nonvisible wavebands and applied to other 3D imaging areas.

Point Cloud Classification of Tesserae from Terrestrial Laser Data Combined with Dense Image Matching for Archaeological Information Extraction

NASA Astrophysics Data System (ADS)

Poux, F.; Neuville, R.; Billen, R.

2017-08-01

Reasoning from information extraction given by point cloud data mining allows contextual adaptation and fast decision making. However, to achieve this perceptive level, a point cloud must be semantically rich, retaining relevant information for the end user. This paper presents an automatic knowledge-based method for pre-processing multi-sensory data and classifying a hybrid point cloud from both terrestrial laser scanning and dense image matching. Using 18 features including sensor's biased data, each tessera in the high-density point cloud from the 3D captured complex mosaics of Germigny-des-prés (France) is segmented via a colour multi-scale abstraction-based featuring extracting connectivity. A 2D surface and outline polygon of each tessera is generated by a RANSAC plane extraction and convex hull fitting. Knowledge is then used to classify every tesserae based on their size, surface, shape, material properties and their neighbour's class. The detection and semantic enrichment method shows promising results of 94% correct semantization, a first step toward the creation of an archaeological smart point cloud.

Optical 3D watermark based digital image watermarking for telemedicine

NASA Astrophysics Data System (ADS)

Li, Xiao Wei; Kim, Seok Tae

2013-12-01

Region of interest (ROI) of a medical image is an area including important diagnostic information and must be stored without any distortion. This algorithm for application of watermarking technique for non-ROI of the medical image preserving ROI. The paper presents a 3D watermark based medical image watermarking scheme. In this paper, a 3D watermark object is first decomposed into 2D elemental image array (EIA) by a lenslet array, and then the 2D elemental image array data is embedded into the host image. The watermark extraction process is an inverse process of embedding. The extracted EIA through the computational integral imaging reconstruction (CIIR) technique, the 3D watermark can be reconstructed. Because the EIA is composed of a number of elemental images possesses their own perspectives of a 3D watermark object. Even though the embedded watermark data badly damaged, the 3D virtual watermark can be successfully reconstructed. Furthermore, using CAT with various rule number parameters, it is possible to get many channels for embedding. So our method can recover the weak point having only one transform plane in traditional watermarking methods. The effectiveness of the proposed watermarking scheme is demonstrated with the aid of experimental results.

3D Gravity Inversion using Tikhonov Regularization

NASA Astrophysics Data System (ADS)

Toushmalani, Reza; Saibi, Hakim

2015-08-01

Subsalt exploration for oil and gas is attractive in regions where 3D seismic depth-migration to recover the geometry of a salt base is difficult. Additional information to reduce the ambiguity in seismic images would be beneficial. Gravity data often serve these purposes in the petroleum industry. In this paper, the authors present an algorithm for a gravity inversion based on Tikhonov regularization and an automatically regularized solution process. They examined the 3D Euler deconvolution to extract the best anomaly source depth as a priori information to invert the gravity data and provided a synthetic example. Finally, they applied the gravity inversion to recently obtained gravity data from the Bandar Charak (Hormozgan, Iran) to identify its subsurface density structure. Their model showed the 3D shape of salt dome in this region.

Dimensionality-varied convolutional neural network for spectral-spatial classification of hyperspectral data

NASA Astrophysics Data System (ADS)

Liu, Wanjun; Liang, Xuejian; Qu, Haicheng

2017-11-01

Hyperspectral image (HSI) classification is one of the most popular topics in remote sensing community. Traditional and deep learning-based classification methods were proposed constantly in recent years. In order to improve the classification accuracy and robustness, a dimensionality-varied convolutional neural network (DVCNN) was proposed in this paper. DVCNN was a novel deep architecture based on convolutional neural network (CNN). The input of DVCNN was a set of 3D patches selected from HSI which contained spectral-spatial joint information. In the following feature extraction process, each patch was transformed into some different 1D vectors by 3D convolution kernels, which were able to extract features from spectral-spatial data. The rest of DVCNN was about the same as general CNN and processed 2D matrix which was constituted by by all 1D data. So that the DVCNN could not only extract more accurate and rich features than CNN, but also fused spectral-spatial information to improve classification accuracy. Moreover, the robustness of network on water-absorption bands was enhanced in the process of spectral-spatial fusion by 3D convolution, and the calculation was simplified by dimensionality varied convolution. Experiments were performed on both Indian Pines and Pavia University scene datasets, and the results showed that the classification accuracy of DVCNN improved by 32.87% on Indian Pines and 19.63% on Pavia University scene than spectral-only CNN. The maximum accuracy improvement of DVCNN achievement was 13.72% compared with other state-of-the-art HSI classification methods, and the robustness of DVCNN on water-absorption bands noise was demonstrated.

Frequency Representation: Visualization and Clustering of Acoustic Data Using Self-Organizing Maps.

PubMed

Guo, Xinhua; Sun, Song; Yu, Xiantao; Wang, Pan; Nakamura, Kentaro

2017-11-01

Extraction and display of frequency information in three-dimensional (3D) acoustic data are important steps to analyze object characteristics, because the characteristics, such as profiles, sizes, surface structures, and material properties, may show frequency dependence. In this study, frequency representation (FR) based on phase information in multispectral acoustic imaging (MSAI) is proposed to overcome the limit of intensity or amplitude information in image display. Experiments are performed on 3D acoustic data collected from a rigid surface engraved with five different letters. The results show that the proposed FR technique can not only identify the depth of the five letters by the colors representing frequency characteristics but also demonstrate the 3D image of the five letters, providing more detailed characteristics that are unavailable by conventional acoustic imaging.

MRI segmentation by active contours model, 3D reconstruction, and visualization

NASA Astrophysics Data System (ADS)

Lopez-Hernandez, Juan M.; Velasquez-Aguilar, J. Guadalupe

2005-02-01

The advances in 3D data modelling methods are becoming increasingly popular in the areas of biology, chemistry and medical applications. The Nuclear Magnetic Resonance Imaging (NMRI) technique has progressed at a spectacular rate over the past few years, its uses have been spread over many applications throughout the body in both anatomical and functional investigations. In this paper we present the application of Zernike polynomials for 3D mesh model of the head using the contour acquired of cross-sectional slices by active contour model extraction and we propose the visualization with OpenGL 3D Graphics of the 2D-3D (slice-surface) information for the diagnostic aid in medical applications.

Basic level scene understanding: categories, attributes and structures

PubMed Central

Xiao, Jianxiong; Hays, James; Russell, Bryan C.; Patterson, Genevieve; Ehinger, Krista A.; Torralba, Antonio; Oliva, Aude

2013-01-01

A longstanding goal of computer vision is to build a system that can automatically understand a 3D scene from a single image. This requires extracting semantic concepts and 3D information from 2D images which can depict an enormous variety of environments that comprise our visual world. This paper summarizes our recent efforts toward these goals. First, we describe the richly annotated SUN database which is a collection of annotated images spanning 908 different scene categories with object, attribute, and geometric labels for many scenes. This database allows us to systematically study the space of scenes and to establish a benchmark for scene and object recognition. We augment the categorical SUN database with 102 scene attributes for every image and explore attribute recognition. Finally, we present an integrated system to extract the 3D structure of the scene and objects depicted in an image. PMID:24009590

On the use of orientation filters for 3D reconstruction in event-driven stereo vision

PubMed Central

Camuñas-Mesa, Luis A.; Serrano-Gotarredona, Teresa; Ieng, Sio H.; Benosman, Ryad B.; Linares-Barranco, Bernabe

2014-01-01

The recently developed Dynamic Vision Sensors (DVS) sense visual information asynchronously and code it into trains of events with sub-micro second temporal resolution. This high temporal precision makes the output of these sensors especially suited for dynamic 3D visual reconstruction, by matching corresponding events generated by two different sensors in a stereo setup. This paper explores the use of Gabor filters to extract information about the orientation of the object edges that produce the events, therefore increasing the number of constraints applied to the matching algorithm. This strategy provides more reliably matched pairs of events, improving the final 3D reconstruction. PMID:24744694

Second Iteration of Photogrammetric Pipeline to Enhance the Accuracy of Image Pose Estimation

NASA Astrophysics Data System (ADS)

Nguyen, T. G.; Pierrot-Deseilligny, M.; Muller, J.-M.; Thom, C.

2017-05-01

In classical photogrammetric processing pipeline, the automatic tie point extraction plays a key role in the quality of achieved results. The image tie points are crucial to pose estimation and have a significant influence on the precision of calculated orientation parameters. Therefore, both relative and absolute orientations of the 3D model can be affected. By improving the precision of image tie point measurement, one can enhance the quality of image orientation. The quality of image tie points is under the influence of several factors such as the multiplicity, the measurement precision and the distribution in 2D images as well as in 3D scenes. In complex acquisition scenarios such as indoor applications and oblique aerial images, tie point extraction is limited while only image information can be exploited. Hence, we propose here a method which improves the precision of pose estimation in complex scenarios by adding a second iteration to the classical processing pipeline. The result of a first iteration is used as a priori information to guide the extraction of new tie points with better quality. Evaluated with multiple case studies, the proposed method shows its validity and its high potiential for precision improvement.

3D-model building of the jaw impression

NASA Astrophysics Data System (ADS)

Ahmed, Moumen T.; Yamany, Sameh M.; Hemayed, Elsayed E.; Farag, Aly A.

1997-03-01

A novel approach is proposed to obtain a record of the patient's occlusion using computer vision. Data acquisition is obtained using intra-oral video cameras. The technique utilizes shape from shading to extract 3D information from 2D views of the jaw, and a novel technique for 3D data registration using genetic algorithms. The resulting 3D model can be used for diagnosis, treatment planning, and implant purposes. The overall purpose of this research is to develop a model-based vision system for orthodontics to replace traditional approaches. This system will be flexible, accurate, and will reduce the cost of orthodontic treatments.

Walker Ranch 3D seismic images

DOE Data Explorer

Robert J. Mellors

2016-03-01

Amplitude images (both vertical and depth slices) extracted from 3D seismic reflection survey over area of Walker Ranch area (adjacent to Raft River). Crossline spacing of 660 feet and inline of 165 feet using a Vibroseis source. Processing included depth migration. Micro-earthquake hypocenters on images. Stratigraphic information and nearby well tracks added to images. Images are embedded in a Microsoft Word document with additional information. Exact location and depth restricted for proprietary reasons. Data collection and processing funded by Agua Caliente. Original data remains property of Agua Caliente.

3D imaging of translucent media with a plenoptic sensor based on phase space optics

NASA Astrophysics Data System (ADS)

Zhang, Xuanzhe; Shu, Bohong; Du, Shaojun

2015-05-01

Traditional stereo imaging technology is not working for dynamical translucent media, because there are no obvious characteristic patterns on it and it's not allowed using multi-cameras in most cases, while phase space optics can solve the problem, extracting depth information directly from "space-spatial frequency" distribution of the target obtained by plenoptic sensor with single lens. This paper discussed the presentation of depth information in phase space data, and calculating algorithms with different transparency. A 3D imaging example of waterfall was given at last.

3D palmprint data fast acquisition and recognition

NASA Astrophysics Data System (ADS)

Wang, Xiaoxu; Huang, Shujun; Gao, Nan; Zhang, Zonghua

2014-11-01

This paper presents a fast 3D (Three-Dimension) palmprint capturing system and develops an efficient 3D palmprint feature extraction and recognition method. In order to fast acquire accurate 3D shape and texture of palmprint, a DLP projector triggers a CCD camera to realize synchronization. By generating and projecting green fringe pattern images onto the measured palm surface, 3D palmprint data are calculated from the fringe pattern images. The periodic feature vector can be derived from the calculated 3D palmprint data, so undistorted 3D biometrics is obtained. Using the obtained 3D palmprint data, feature matching test have been carried out by Gabor filter, competition rules and the mean curvature. Experimental results on capturing 3D palmprint show that the proposed acquisition method can fast get 3D shape information of palmprint. Some initial experiments on recognition show the proposed method is efficient by using 3D palmprint data.

X-ray phase contrast tomography by tracking near field speckle

PubMed Central

Wang, Hongchang; Berujon, Sebastien; Herzen, Julia; Atwood, Robert; Laundy, David; Hipp, Alexander; Sawhney, Kawal

2015-01-01

X-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption radiography. However, the extraction of phase information is often more difficult than the extraction of absorption information and requires a more sophisticated experimental arrangement. We here report a method for three-dimensional (3D) X-ray phase contrast computed tomography (CT) which gives quantitative volumetric information on the real part of the refractive index. The method is based on the recently developed X-ray speckle tracking technique in which the displacement of near field speckle is tracked using a digital image correlation algorithm. In addition to differential phase contrast projection images, the method allows the dark-field images to be simultaneously extracted. After reconstruction, compared to conventional absorption CT images, the 3D phase CT images show greatly enhanced contrast. This new imaging method has advantages compared to other X-ray imaging methods in simplicity of experimental arrangement, speed of measurement and relative insensitivity to beam movements. These features make the technique an attractive candidate for material imaging such as in-vivo imaging of biological systems containing soft tissue. PMID:25735237

Airway extraction from 3D chest CT volumes based on iterative extension of VOI enhanced by cavity enhancement filter

NASA Astrophysics Data System (ADS)

Meng, Qier; Kitasaka, Takayuki; Oda, Masahiro; Mori, Kensaku

2017-03-01

Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining an integrated 3-D airway tree structure from a CT volume is a quite challenging task. This paper presents a novel airway segmentation method based on intensity structure analysis and bronchi shape structure analysis in volume of interest (VOI). This method segments the bronchial regions by applying the cavity enhancement filter (CEF) to trace the bronchial tree structure from the trachea. It uses the CEF in each VOI to segment each branch and to predict the positions of VOIs which envelope the bronchial regions in next level. At the same time, a leakage detection is performed to avoid the leakage by analysing the pixel information and the shape information of airway candidate regions extracted in the VOI. Bronchial regions are finally obtained by unifying the extracted airway regions. The experiments results showed that the proposed method can extract most of the bronchial region in each VOI and led good results of the airway segmentation.

Towards Robust Self-Calibration for Handheld 3d Line Laser Scanning

NASA Astrophysics Data System (ADS)

Bleier, M.; Nüchter, A.

2017-11-01

This paper studies self-calibration of a structured light system, which reconstructs 3D information using video from a static consumer camera and a handheld cross line laser projector. Intersections between the individual laser curves and geometric constraints on the relative position of the laser planes are exploited to achieve dense 3D reconstruction. This is possible without any prior knowledge of the movement of the projector. However, inaccurrately extracted laser lines introduce noise in the detected intersection positions and therefore distort the reconstruction result. Furthermore, when scanning objects with specular reflections, such as glossy painted or metalic surfaces, the reflections are often extracted from the camera image as erroneous laser curves. In this paper we investiagte how robust estimates of the parameters of the laser planes can be obtained despite of noisy detections.

Browsing Through Closed Books: Evaluation of Preprocessing Methods for Page Extraction of a 3-D CT Book Volume

NASA Astrophysics Data System (ADS)

Stromer, D.; Christlein, V.; Schön, T.; Holub, W.; Maier, A.

2017-09-01

It is often the case that a document can not be opened, page-turned or touched anymore due to damages caused by aging processes, moisture or fire. To counter this, special imaging systems can be used. One of our earlier work revealed that a common 3-D X-ray micro-CT scanner is well suited for imaging and reconstructing historical documents written with iron gall ink - an ink consisting of metallic particles. We acquired a volume of a self-made book without opening or page-turning with a single 3-D scan. However, when investigating the reconstructed volume, we faced the problem of a proper automatic extraction of single pages within the volume in an acceptable time without losing information of the writings. Within this work, we evaluate different appropriate pre-processing methods with respect to computation time and accuracy which are decisive for a proper extraction of book pages from the reconstructed X-ray volume and the subsequent ink identification. The different methods were tested for an extreme case with low resolution, noisy input data and wavy pages. Finally, we present results of the page extraction after applying the evaluated methods.

Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

NASA Astrophysics Data System (ADS)

Hosoi, F.

2014-12-01

Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of consecutive voxels that filled the outer surface and the interior of the stem and large branches. From the model, the woody material volume of any part of the target tree can be directly calculated easily by counting the number of corresponding voxels and multiplying the result by the per-voxel volume.

3D kinematic measurement of human movement using low cost fish-eye cameras

NASA Astrophysics Data System (ADS)

Islam, Atiqul; Asikuzzaman, Md.; Garratt, Matthew A.; Pickering, Mark R.

2017-02-01

3D motion capture is difficult when the capturing is performed in an outdoor environment without controlled surroundings. In this paper, we propose a new approach of using two ordinary cameras arranged in a special stereoscopic configuration and passive markers on a subject's body to reconstruct the motion of the subject. Firstly for each frame of the video, an adaptive thresholding algorithm is applied for extracting the markers on the subject's body. Once the markers are extracted, an algorithm for matching corresponding markers in each frame is applied. Zhang's planar calibration method is used to calibrate the two cameras. As the cameras use the fisheye lens, they cannot be well estimated using a pinhole camera model which makes it difficult to estimate the depth information. In this work, to restore the 3D coordinates we use a unique calibration method for fisheye lenses. The accuracy of the 3D coordinate reconstruction is evaluated by comparing with results from a commercially available Vicon motion capture system.

Lip boundary detection techniques using color and depth information

NASA Astrophysics Data System (ADS)

Kim, Gwang-Myung; Yoon, Sung H.; Kim, Jung H.; Hur, Gi Taek

2002-01-01

This paper presents our approach to using a stereo camera to obtain 3-D image data to be used to improve existing lip boundary detection techniques. We show that depth information as provided by our approach can be used to significantly improve boundary detection systems. Our system detects the face and mouth area in the image by using color, geometric location, and additional depth information for the face. Initially, color and depth information can be used to localize the face. Then we can determine the lip region from the intensity information and the detected eye locations. The system has successfully been used to extract approximate lip regions using RGB color information of the mouth area. Merely using color information is not robust because the quality of the results may vary depending on light conditions, background, and the human race. To overcome this problem, we used a stereo camera to obtain 3-D facial images. 3-D data constructed from the depth information along with color information can provide more accurate lip boundary detection results as compared to color only based techniques.

The future of structural fieldwork - UAV assisted aerial photogrammetry

NASA Astrophysics Data System (ADS)

Vollgger, Stefan; Cruden, Alexander

2015-04-01

Unmanned aerial vehicles (UAVs), commonly referred to as drones, are opening new and low cost possibilities to acquire high-resolution aerial images and digital surface models (DSM) for applications in structural geology. UAVs can be programmed to fly autonomously along a user defined grid to systematically capture high-resolution photographs, even in difficult to access areas. The photographs are subsequently processed using software that employ SIFT (scale invariant feature transform) and SFM (structure from motion) algorithms. These photogrammetric routines allow the extraction of spatial information (3D point clouds, digital elevation models, 3D meshes, orthophotos) from 2D images. Depending on flight altitude and camera setup, sub-centimeter spatial resolutions can be achieved. By "digitally mapping" georeferenced 3D models and images, orientation data can be extracted directly and used to analyse the structural framework of the mapped object or area. We present UAV assisted aerial mapping results from a coastal platform near Cape Liptrap (Victoria, Australia), where deformed metasediments of the Palaeozoic Lachlan Fold Belt are exposed. We also show how orientation and spatial information of brittle and ductile structures extracted from the photogrammetric model can be linked to the progressive development of folds and faults in the region. Even though there are both technical and legislative limitations, which might prohibit the use of UAVs without prior commercial licensing and training, the benefits that arise from the resulting high-resolution, photorealistic models can substantially contribute to the collection of new data and insights for applications in structural geology.

3D face analysis by using Mesh-LBP feature

NASA Astrophysics Data System (ADS)

Wang, Haoyu; Yang, Fumeng; Zhang, Yuming; Wu, Congzhong

2017-11-01

Objective: Face Recognition is one of the widely application of image processing. Corresponding two-dimensional limitations, such as the pose and illumination changes, to a certain extent restricted its accurate rate and further development. How to overcome the pose and illumination changes and the effects of self-occlusion is the research hotspot and difficulty, also attracting more and more domestic and foreign experts and scholars to study it. 3D face recognition fusing shape and texture descriptors has become a very promising research direction. Method: Our paper presents a 3D point cloud based on mesh local binary pattern grid (Mesh-LBP), then feature extraction for 3D face recognition by fusing shape and texture descriptors. 3D Mesh-LBP not only retains the integrity of the 3D geometry, is also reduces the need for recognition process of normalization steps, because the triangle Mesh-LBP descriptor is calculated on 3D grid. On the other hand, in view of multi-modal consistency in face recognition advantage, construction of LBP can fusing shape and texture information on Triangular Mesh. In this paper, some of the operators used to extract Mesh-LBP, Such as the normal vectors of the triangle each face and vertex, the gaussian curvature, the mean curvature, laplace operator and so on. Conclusion: First, Kinect devices obtain 3D point cloud face, after the pretreatment and normalization, then transform it into triangular grid, grid local binary pattern feature extraction from face key significant parts of face. For each local face, calculate its Mesh-LBP feature with Gaussian curvature, mean curvature laplace operator and so on. Experiments on the our research database, change the method is robust and high recognition accuracy.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds.

PubMed

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-06-17

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds†

PubMed Central

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-01-01

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data. PMID:27322279

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

2015-10-01

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110-120 kHz), 1H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1H-1H homonuclear dipolar couplings and narrow 1H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1H-1H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical information for a variety of solid systems that possess high proton density.

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2015-10-14

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which rendermore » it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical information for a variety of solid systems that possess high proton density.« less

Intermodulation Atomic Force Microscopy and Spectroscopy

NASA Astrophysics Data System (ADS)

Hutter, Carsten; Platz, Daniel; Tholen, Erik; Haviland, David; Hansson, Hans

2009-03-01

We present a powerful new method of dynamic AFM, which allows to gain far more information about the tip-surface interaction than standard amplitude or phase imaging, while scanning at comparable speed. Our method, called intermodulation atomic force microscopy (ImAFM), employs the manifestly nonlinear phenomenon of intermodulation to extract information about tip-surface forces. ImAFM uses one eigenmode of a mechanical resonator, the latter driven at two frequencies to produce many spectral peaks near its resonace, where sensitivity is highest [1]. We furthermore present a protocol for decoding the combined information encoded in the spectrum of intermodulation peaks. Our theoretical framework suggests methods to enhance the gained information by using a different parameter regime as compared to Ref. [1]. We also discuss strategies for solving the inverse problem, i.e., for extracting the nonlinear tip-surface interaction from the response, also naming limitations of our theoretical analysis. We will further report on latest progress to experimentally employ our new protocol.[3pt] [1] D. Platz, E. A. Tholen, D. Pesen, and D. B. Haviland, Appl. Phys. Lett. 92, 153106 (2008).

Automated Recognition of 3D Features in GPIR Images

NASA Technical Reports Server (NTRS)

Park, Han; Stough, Timothy; Fijany, Amir

2007-01-01

A method of automated recognition of three-dimensional (3D) features in images generated by ground-penetrating imaging radar (GPIR) is undergoing development. GPIR 3D images can be analyzed to detect and identify such subsurface features as pipes and other utility conduits. Until now, much of the analysis of GPIR images has been performed manually by expert operators who must visually identify and track each feature. The present method is intended to satisfy a need for more efficient and accurate analysis by means of algorithms that can automatically identify and track subsurface features, with minimal supervision by human operators. In this method, data from multiple sources (for example, data on different features extracted by different algorithms) are fused together for identifying subsurface objects. The algorithms of this method can be classified in several different ways. In one classification, the algorithms fall into three classes: (1) image-processing algorithms, (2) feature- extraction algorithms, and (3) a multiaxis data-fusion/pattern-recognition algorithm that includes a combination of machine-learning, pattern-recognition, and object-linking algorithms. The image-processing class includes preprocessing algorithms for reducing noise and enhancing target features for pattern recognition. The feature-extraction algorithms operate on preprocessed data to extract such specific features in images as two-dimensional (2D) slices of a pipe. Then the multiaxis data-fusion/ pattern-recognition algorithm identifies, classifies, and reconstructs 3D objects from the extracted features. In this process, multiple 2D features extracted by use of different algorithms and representing views along different directions are used to identify and reconstruct 3D objects. In object linking, which is an essential part of this process, features identified in successive 2D slices and located within a threshold radius of identical features in adjacent slices are linked in a directed-graph data structure. Relative to past approaches, this multiaxis approach offers the advantages of more reliable detections, better discrimination of objects, and provision of redundant information, which can be helpful in filling gaps in feature recognition by one of the component algorithms. The image-processing class also includes postprocessing algorithms that enhance identified features to prepare them for further scrutiny by human analysts (see figure). Enhancement of images as a postprocessing step is a significant departure from traditional practice, in which enhancement of images is a preprocessing step.

Anti-plasmodial activity of Norcaesalpin D and extracts of four medicinal plants used traditionally for treatment of malaria.

PubMed

Nondo, Ramadhani Selemani Omari; Moshi, Mainen Julius; Erasto, Paul; Masimba, Pax Jessey; Machumi, Francis; Kidukuli, Abdul Waziri; Heydenreich, Matthias; Zofou, Denis

2017-03-24

Malaria is an old life-threatening parasitic disease that is still affecting many people, mainly children living in sub-Saharan Africa. Availability of effective antimalarial drugs played a significant role in the treatment and control of malaria. However, recent information on the emergence of P. falciparum parasites resistant to one of the artemisinin-based combination therapies suggests the need for discovery of new drug molecules. Therefore, this study aimed to evaluate the antiplasmodial activity of extracts, fractions and isolated compound from medicinal plants traditionally used in the treatment of malaria in Tanzania. Dry powdered plant materials were extracted by cold macerations using different solvents. Norcaesalpin D was isolated by column chromatography from dichloromethane root extract of Caesalpinia bonducella and its structure was assigned based on the spectral data. Crude extracts, fractions and isolated compound were evaluated for antiplasmodial activity against chloroquine-sensitive P. falciparum (3D7), chloroquine-resistant P. falciparum (Dd2, K1) and artemisinin-resistant P. falciparum (IPC 5202 Battambang, IPC 4912 Mondolkiri) strains using the parasite lactate dehydrogenase assay. The results indicated that extracts of Erythrina schliebenii, Holarrhena pubescens, Dissotis melleri and C. bonducella exhibited antiplasmodial activity against Dd2 parasites. Ethanolic root extract of E. schliebenii had an IC 50 of 1.87 μg/mL while methanolic and ethanolic root extracts of H. pubescens exhibited an IC 50  = 2.05 μg/mL and IC 50  = 2.43 μg/mL, respectively. Fractions from H. pubescens and C. bonducella roots were found to be highly active against K1, Dd2 and artemisinin-resistant parasites. Norcaesalpin D from C. bonducella root extract was active with IC 50 of 0.98, 1.85 and 2.13 μg/mL against 3D7, Dd2 and IPC 4912-Mondolkiri parasites, respectively. Antiplasmodial activity of norcaesalpin D and extracts of E. schliebenii, H. pubescens, D. melleri and C. bonducella reported in this study requires further attention for the discovery of antimalarial lead compounds for future drug development.

3D micro-mapping: Towards assessing the quality of crowdsourcing to support 3D point cloud analysis

NASA Astrophysics Data System (ADS)

Herfort, Benjamin; Höfle, Bernhard; Klonner, Carolin

2018-03-01

In this paper, we propose a method to crowdsource the task of complex three-dimensional information extraction from 3D point clouds. We design web-based 3D micro tasks tailored to assess segmented LiDAR point clouds of urban trees and investigate the quality of the approach in an empirical user study. Our results for three different experiments with increasing complexity indicate that a single crowdsourcing task can be solved in a very short time of less than five seconds on average. Furthermore, the results of our empirical case study reveal that the accuracy, sensitivity and precision of 3D crowdsourcing are high for most information extraction problems. For our first experiment (binary classification with single answer) we obtain an accuracy of 91%, a sensitivity of 95% and a precision of 92%. For the more complex tasks of the second Experiment 2 (multiple answer classification) the accuracy ranges from 65% to 99% depending on the label class. Regarding the third experiment - the determination of the crown base height of individual trees - our study highlights that crowdsourcing can be a tool to obtain values with even higher accuracy in comparison to an automated computer-based approach. Finally, we found out that the accuracy of the crowdsourced results for all experiments is hardly influenced by characteristics of the input point cloud data and of the users. Importantly, the results' accuracy can be estimated using agreement among volunteers as an intrinsic indicator, which makes a broad application of 3D micro-mapping very promising.

Quantitative 3-D Imaging, Segmentation and Feature Extraction of the Respiratory System in Small Mammals for Computational Biophysics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trease, Lynn L.; Trease, Harold E.; Fowler, John

2007-03-15

One of the critical steps toward performing computational biology simulations, using mesh based integration methods, is in using topologically faithful geometry derived from experimental digital image data as the basis for generating the computational meshes. Digital image data representations contain both the topology of the geometric features and experimental field data distributions. The geometric features that need to be captured from the digital image data are three-dimensional, therefore the process and tools we have developed work with volumetric image data represented as data-cubes. This allows us to take advantage of 2D curvature information during the segmentation and feature extraction process.more » The process is basically: 1) segmenting to isolate and enhance the contrast of the features that we wish to extract and reconstruct, 2) extracting the geometry of the features in an isosurfacing technique, and 3) building the computational mesh using the extracted feature geometry. “Quantitative” image reconstruction and feature extraction is done for the purpose of generating computational meshes, not just for producing graphics "screen" quality images. For example, the surface geometry that we extract must represent a closed water-tight surface.« less

3D-printed upper limb prostheses: a review.

PubMed

Ten Kate, Jelle; Smit, Gerwin; Breedveld, Paul

2017-04-01

This paper aims to provide an overview with quantitative information of existing 3D-printed upper limb prostheses. We will identify the benefits and drawbacks of 3D-printed devices to enable improvement of current devices based on the demands of prostheses users. A review was performed using Scopus, Web of Science and websites related to 3D-printing. Quantitative information on the mechanical and kinematic specifications and 3D-printing technology used was extracted from the papers and websites. The overview (58 devices) provides the general specifications, the mechanical and kinematic specifications of the devices and information regarding the 3D-printing technology used for hands. The overview shows prostheses for all different upper limb amputation levels with different types of control and a maximum material cost of $500. A large range of various prostheses have been 3D-printed, of which the majority are used by children. Evidence with respect to the user acceptance, functionality and durability of the 3D-printed hands is lacking. Contrary to what is often claimed, 3D-printing is not necessarily cheap, e.g., injection moulding can be cheaper. Conversely, 3D-printing provides a promising possibility for individualization, e.g., personalized socket, colour, shape and size, without the need for adjusting the production machine. Implications for rehabilitation Upper limb deficiency is a condition in which a part of the upper limb is missing as a result of a congenital limb deficiency of as a result of an amputation. A prosthetic hand can restore some of the functions of a missing limb and help the user in performing activities of daily living. Using 3D-printing technology is one of the solutions to manufacture hand prostheses. This overview provides information about the general, mechanical and kinematic specifications of all the devices and it provides the information about the 3D-printing technology used to print the hands.

A high resolution and high speed 3D imaging system and its application on ATR

NASA Astrophysics Data System (ADS)

Lu, Thomas T.; Chao, Tien-Hsin

2006-04-01

The paper presents an advanced 3D imaging system based on a combination of stereo vision and light projection methods. A single digital camera is used to take only one shot of the object and reconstruct the 3D model of an object. The stereo vision is achieved by employing a prism and mirror setup to split the views and combine them side by side in the camera. The advantage of this setup is its simple system architecture, easy synchronization, fast 3D imaging speed and high accuracy. The 3D imaging algorithms and potential applications are discussed. For ATR applications, it is critically important to extract maximum information for the potential targets and to separate the targets from the background and clutter noise. The added dimension of a 3D model provides additional features of surface profile, range information of the target. It is capable of removing the false shadow from camouflage and reveal the 3D profile of the object. It also provides arbitrary viewing angles and distances for training the filter bank for invariant ATR. The system architecture can be scaled to take large objects and to perform area 3D modeling onboard a UAV.

Simultaneous reconstruction of 3D refractive index, temperature, and intensity distribution of combustion flame by double computed tomography technologies based on spatial phase-shifting method

NASA Astrophysics Data System (ADS)

Guo, Zhenyan; Song, Yang; Yuan, Qun; Wulan, Tuya; Chen, Lei

2017-06-01

In this paper, a transient multi-parameter three-dimensional (3D) reconstruction method is proposed to diagnose and visualize a combustion flow field. Emission and transmission tomography based on spatial phase-shifted technology are combined to reconstruct, simultaneously, the various physical parameter distributions of a propane flame. Two cameras triggered by the internal trigger mode capture the projection information of the emission and moiré tomography, respectively. A two-step spatial phase-shifting method is applied to extract the phase distribution in the moiré fringes. By using the filtered back-projection algorithm, we reconstruct the 3D refractive-index distribution of the combustion flow field. Finally, the 3D temperature distribution of the flame is obtained from the refractive index distribution using the Gladstone-Dale equation. Meanwhile, the 3D intensity distribution is reconstructed based on the radiation projections from the emission tomography. Therefore, the structure and edge information of the propane flame are well visualized.

Towards semi-automatic rock mass discontinuity orientation and set analysis from 3D point clouds

NASA Astrophysics Data System (ADS)

Guo, Jiateng; Liu, Shanjun; Zhang, Peina; Wu, Lixin; Zhou, Wenhui; Yu, Yinan

2017-06-01

Obtaining accurate information on rock mass discontinuities for deformation analysis and the evaluation of rock mass stability is important. Obtaining measurements for high and steep zones with the traditional compass method is difficult. Photogrammetry, three-dimensional (3D) laser scanning and other remote sensing methods have gradually become mainstream methods. In this study, a method that is based on a 3D point cloud is proposed to semi-automatically extract rock mass structural plane information. The original data are pre-treated prior to segmentation by removing outlier points. The next step is to segment the point cloud into different point subsets. Various parameters, such as the normal, dip/direction and dip, can be calculated for each point subset after obtaining the equation of the best fit plane for the relevant point subset. A cluster analysis (a point subset that satisfies some conditions and thus forms a cluster) is performed based on the normal vectors by introducing the firefly algorithm (FA) and the fuzzy c-means (FCM) algorithm. Finally, clusters that belong to the same discontinuity sets are merged and coloured for visualization purposes. A prototype system is developed based on this method to extract the points of the rock discontinuity from a 3D point cloud. A comparison with existing software shows that this method is feasible. This method can provide a reference for rock mechanics, 3D geological modelling and other related fields.

VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations

PubMed Central

Hägerling, René; Drees, Dominik; Scherzinger, Aaron; Dierkes, Cathrin; Martin-Almedina, Silvia; Butz, Stefan; Gordon, Kristiana; Schäfers, Michael; Hinrichs, Klaus; Vestweber, Dietmar; Goerge, Tobias; Mansour, Sahar; Mortimer, Peter S.

2017-01-01

BACKGROUND. Lack of investigatory and diagnostic tools has been a major contributing factor to the failure to mechanistically understand lymphedema and other lymphatic disorders in order to develop effective drug and surgical therapies. One difficulty has been understanding the true changes in lymph vessel pathology from standard 2D tissue sections. METHODS. VIPAR (volume information-based histopathological analysis by 3D reconstruction and data extraction), a light-sheet microscopy–based approach for the analysis of tissue biopsies, is based on digital reconstruction and visualization of microscopic image stacks. VIPAR allows semiautomated segmentation of the vasculature and subsequent nonbiased extraction of characteristic vessel shape and connectivity parameters. We applied VIPAR to analyze biopsies from healthy lymphedematous and lymphangiomatous skin. RESULTS. Digital 3D reconstruction provided a directly visually interpretable, comprehensive representation of the lymphatic and blood vessels in the analyzed tissue volumes. The most conspicuous features were disrupted lymphatic vessels in lymphedematous skin and a hyperplasia (4.36-fold lymphatic vessel volume increase) in the lymphangiomatous skin. Both abnormalities were detected by the connectivity analysis based on extracted vessel shape and structure data. The quantitative evaluation of extracted data revealed a significant reduction of lymphatic segment length (51.3% and 54.2%) and straightness (89.2% and 83.7%) for lymphedematous and lymphangiomatous skin, respectively. Blood vessel length was significantly increased in the lymphangiomatous sample (239.3%). CONCLUSION. VIPAR is a volume-based tissue reconstruction data extraction and analysis approach that successfully distinguished healthy from lymphedematous and lymphangiomatous skin. Its application is not limited to the vascular systems or skin. FUNDING. Max Planck Society, DFG (SFB 656), and Cells-in-Motion Cluster of Excellence EXC 1003. PMID:28814672

VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations.

PubMed

Hägerling, René; Drees, Dominik; Scherzinger, Aaron; Dierkes, Cathrin; Martin-Almedina, Silvia; Butz, Stefan; Gordon, Kristiana; Schäfers, Michael; Hinrichs, Klaus; Ostergaard, Pia; Vestweber, Dietmar; Goerge, Tobias; Mansour, Sahar; Jiang, Xiaoyi; Mortimer, Peter S; Kiefer, Friedemann

2017-08-17

Lack of investigatory and diagnostic tools has been a major contributing factor to the failure to mechanistically understand lymphedema and other lymphatic disorders in order to develop effective drug and surgical therapies. One difficulty has been understanding the true changes in lymph vessel pathology from standard 2D tissue sections. VIPAR (volume information-based histopathological analysis by 3D reconstruction and data extraction), a light-sheet microscopy-based approach for the analysis of tissue biopsies, is based on digital reconstruction and visualization of microscopic image stacks. VIPAR allows semiautomated segmentation of the vasculature and subsequent nonbiased extraction of characteristic vessel shape and connectivity parameters. We applied VIPAR to analyze biopsies from healthy lymphedematous and lymphangiomatous skin. Digital 3D reconstruction provided a directly visually interpretable, comprehensive representation of the lymphatic and blood vessels in the analyzed tissue volumes. The most conspicuous features were disrupted lymphatic vessels in lymphedematous skin and a hyperplasia (4.36-fold lymphatic vessel volume increase) in the lymphangiomatous skin. Both abnormalities were detected by the connectivity analysis based on extracted vessel shape and structure data. The quantitative evaluation of extracted data revealed a significant reduction of lymphatic segment length (51.3% and 54.2%) and straightness (89.2% and 83.7%) for lymphedematous and lymphangiomatous skin, respectively. Blood vessel length was significantly increased in the lymphangiomatous sample (239.3%). VIPAR is a volume-based tissue reconstruction data extraction and analysis approach that successfully distinguished healthy from lymphedematous and lymphangiomatous skin. Its application is not limited to the vascular systems or skin. Max Planck Society, DFG (SFB 656), and Cells-in-Motion Cluster of Excellence EXC 1003.

A web-based 3D geological information visualization system

NASA Astrophysics Data System (ADS)

Song, Renbo; Jiang, Nan

2013-03-01

Construction of 3D geological visualization system has attracted much more concern in GIS, computer modeling, simulation and visualization fields. It not only can effectively help geological interpretation and analysis work, but also can it can help leveling up geosciences professional education. In this paper, an applet-based method was introduced for developing a web-based 3D geological information visualization system. The main aims of this paper are to explore a rapid and low-cost development method for constructing a web-based 3D geological system. First, the borehole data stored in Excel spreadsheets was extracted and then stored in SQLSERVER database of a web server. Second, the JDBC data access component was utilized for providing the capability of access the database. Third, the user interface was implemented with applet component embedded in JSP page and the 3D viewing and querying functions were implemented with PickCanvas of Java3D. Last, the borehole data acquired from geological survey were used for test the system, and the test results has shown that related methods of this paper have a certain application values.

3D-information fusion from very high resolution satellite sensors

NASA Astrophysics Data System (ADS)

Krauss, T.; d'Angelo, P.; Kuschk, G.; Tian, J.; Partovi, T.

2015-04-01

In this paper we show the pre-processing and potential for environmental applications of very high resolution (VHR) satellite stereo imagery like these from WorldView-2 or Pl'eiades with ground sampling distances (GSD) of half a metre to a metre. To process such data first a dense digital surface model (DSM) has to be generated. Afterwards from this a digital terrain model (DTM) representing the ground and a so called normalized digital elevation model (nDEM) representing off-ground objects are derived. Combining these elevation based data with a spectral classification allows detection and extraction of objects from the satellite scenes. Beside the object extraction also the DSM and DTM can directly be used for simulation and monitoring of environmental issues. Examples are the simulation of floodings, building-volume and people estimation, simulation of noise from roads, wave-propagation for cellphones, wind and light for estimating renewable energy sources, 3D change detection, earthquake preparedness and crisis relief, urban development and sprawl of informal settlements and much more. Also outside of urban areas volume information brings literally a new dimension to earth oberservation tasks like the volume estimations of forests and illegal logging, volume of (illegal) open pit mining activities, estimation of flooding or tsunami risks, dike planning, etc. In this paper we present the preprocessing from the original level-1 satellite data to digital surface models (DSMs), corresponding VHR ortho images and derived digital terrain models (DTMs). From these components we present how a monitoring and decision fusion based 3D change detection can be realized by using different acquisitions. The results are analyzed and assessed to derive quality parameters for the presented method. Finally the usability of 3D information fusion from VHR satellite imagery is discussed and evaluated.

Evaluating the utility of 3D TRUS image information in guiding intra-procedure registration for motion compensation

NASA Astrophysics Data System (ADS)

De Silva, Tharindu; Cool, Derek W.; Romagnoli, Cesare; Fenster, Aaron; Ward, Aaron D.

2014-03-01

In targeted 3D transrectal ultrasound (TRUS)-guided biopsy, patient and prostate movement during the procedure can cause target misalignments that hinder accurate sampling of pre-planned suspicious tissue locations. Multiple solutions have been proposed for motion compensation via registration of intra-procedural TRUS images to a baseline 3D TRUS image acquired at the beginning of the biopsy procedure. While 2D TRUS images are widely used for intra-procedural guidance, some solutions utilize richer intra-procedural images such as bi- or multi-planar TRUS or 3D TRUS, acquired by specialized probes. In this work, we measured the impact of such richer intra-procedural imaging on motion compensation accuracy, to evaluate the tradeoff between cost and complexity of intra-procedural imaging versus improved motion compensation. We acquired baseline and intra-procedural 3D TRUS images from 29 patients at standard sextant-template biopsy locations. We used the planes extracted from the 3D intra-procedural scans to simulate 2D and 3D information available in different clinically relevant scenarios for registration. The registration accuracy was evaluated by calculating the target registration error (TRE) using manually identified homologous fiducial markers (micro-calcifications). Our results indicate that TRE improves gradually when the number of intra-procedural imaging planes used in registration is increased. Full 3D TRUS information helps the registration algorithm to robustly converge to more accurate solutions. These results can also inform the design of a fail-safe workflow during motion compensation in a system using a tracked 2D TRUS probe, by prescribing rotational acquisitions that can be performed quickly and easily by the physician immediately prior to needle targeting.

Critical analysis of 3-D organoid in vitro cell culture models for high-throughput drug candidate toxicity assessments.

PubMed

Astashkina, Anna; Grainger, David W

2014-04-01

Drug failure due to toxicity indicators remains among the primary reasons for staggering drug attrition rates during clinical studies and post-marketing surveillance. Broader validation and use of next-generation 3-D improved cell culture models are expected to improve predictive power and effectiveness of drug toxicological predictions. However, after decades of promising research significant gaps remain in our collective ability to extract quality human toxicity information from in vitro data using 3-D cell and tissue models. Issues, challenges and future directions for the field to improve drug assay predictive power and reliability of 3-D models are reviewed. Copyright © 2014 Elsevier B.V. All rights reserved.

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

PubMed

Karthikeyan, Muthukumarasamy; Vyas, Renu

2016-01-01

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

Analysis of 3D Prints by X-ray Computed Microtomography and Terahertz Pulsed Imaging.

PubMed

Markl, Daniel; Zeitler, J Axel; Rasch, Cecilie; Michaelsen, Maria Høtoft; Müllertz, Anette; Rantanen, Jukka; Rades, Thomas; Bøtker, Johan

2017-05-01

A 3D printer was used to realise compartmental dosage forms containing multiple active pharmaceutical ingredient (API) formulations. This work demonstrates the microstructural characterisation of 3D printed solid dosage forms using X-ray computed microtomography (XμCT) and terahertz pulsed imaging (TPI). Printing was performed with either polyvinyl alcohol (PVA) or polylactic acid (PLA). The structures were examined by XμCT and TPI. Liquid self-nanoemulsifying drug delivery system (SNEDDS) formulations containing saquinavir and halofantrine were incorporated into the 3D printed compartmentalised structures and in vitro drug release determined. A clear difference in terms of pore structure between PVA and PLA prints was observed by extracting the porosity (5.5% for PVA and 0.2% for PLA prints), pore length and pore volume from the XμCT data. The print resolution and accuracy was characterised by XμCT and TPI on the basis of the computer-aided design (CAD) models of the dosage form (compartmentalised PVA structures were 7.5 ± 0.75% larger than designed; n = 3). The 3D printer can reproduce specific structures very accurately, whereas the 3D prints can deviate from the designed model. The microstructural information extracted by XμCT and TPI will assist to gain a better understanding about the performance of 3D printed dosage forms.

An Efficient Method for Automatic Road Extraction Based on Multiple Features from LiDAR Data

NASA Astrophysics Data System (ADS)

Li, Y.; Hu, X.; Guan, H.; Liu, P.

2016-06-01

The road extraction in urban areas is difficult task due to the complicated patterns and many contextual objects. LiDAR data directly provides three dimensional (3D) points with less occlusions and smaller shadows. The elevation information and surface roughness are distinguishing features to separate roads. However, LiDAR data has some disadvantages are not beneficial to object extraction, such as the irregular distribution of point clouds and lack of clear edges of roads. For these problems, this paper proposes an automatic road centerlines extraction method which has three major steps: (1) road center point detection based on multiple feature spatial clustering for separating road points from ground points, (2) local principal component analysis with least squares fitting for extracting the primitives of road centerlines, and (3) hierarchical grouping for connecting primitives into complete roads network. Compared with MTH (consist of Mean shift algorithm, Tensor voting, and Hough transform) proposed in our previous article, this method greatly reduced the computational cost. To evaluate the proposed method, the Vaihingen data set, a benchmark testing data provided by ISPRS for "Urban Classification and 3D Building Reconstruction" project, was selected. The experimental results show that our method achieve the same performance by less time in road extraction using LiDAR data.

Neuronize: a tool for building realistic neuronal cell morphologies

PubMed Central

Brito, Juan P.; Mata, Susana; Bayona, Sofia; Pastor, Luis; DeFelipe, Javier; Benavides-Piccione, Ruth

2013-01-01

This study presents a tool, Neuronize, for building realistic three-dimensional models of neuronal cells from the morphological information extracted through computer-aided tracing applications. Neuronize consists of a set of methods designed to build 3D neural meshes that approximate the cell membrane at different resolution levels, allowing a balance to be reached between the complexity and the quality of the final model. The main contribution of the present study is the proposal of a novel approach to build a realistic and accurate 3D shape of the soma from the incomplete information stored in the digitally traced neuron, which usually consists of a 2D cell body contour. This technique is based on the deformation of an initial shape driven by the position and thickness of the first order dendrites. The addition of a set of spines along the dendrites completes the model, building a final 3D neuronal cell suitable for its visualization in a wide range of 3D environments. PMID:23761740

Neuronize: a tool for building realistic neuronal cell morphologies.

PubMed

Brito, Juan P; Mata, Susana; Bayona, Sofia; Pastor, Luis; Defelipe, Javier; Benavides-Piccione, Ruth

2013-01-01

This study presents a tool, Neuronize, for building realistic three-dimensional models of neuronal cells from the morphological information extracted through computer-aided tracing applications. Neuronize consists of a set of methods designed to build 3D neural meshes that approximate the cell membrane at different resolution levels, allowing a balance to be reached between the complexity and the quality of the final model. The main contribution of the present study is the proposal of a novel approach to build a realistic and accurate 3D shape of the soma from the incomplete information stored in the digitally traced neuron, which usually consists of a 2D cell body contour. This technique is based on the deformation of an initial shape driven by the position and thickness of the first order dendrites. The addition of a set of spines along the dendrites completes the model, building a final 3D neuronal cell suitable for its visualization in a wide range of 3D environments.

Extension of RCC Topological Relations for 3d Complex Objects Components Extracted from 3d LIDAR Point Clouds

NASA Astrophysics Data System (ADS)

Xing, Xu-Feng; Abolfazl Mostafavia, Mir; Wang, Chen

2016-06-01

Topological relations are fundamental for qualitative description, querying and analysis of a 3D scene. Although topological relations for 2D objects have been extensively studied and implemented in GIS applications, their direct extension to 3D is very challenging and they cannot be directly applied to represent relations between components of complex 3D objects represented by 3D B-Rep models in R3. Herein we present an extended Region Connection Calculus (RCC) model to express and formalize topological relations between planar regions for creating 3D model represented by Boundary Representation model in R3. We proposed a new dimension extended 9-Intersection model to represent the basic relations among components of a complex object, including disjoint, meet and intersect. The last element in 3*3 matrix records the details of connection through the common parts of two regions and the intersecting line of two planes. Additionally, this model can deal with the case of planar regions with holes. Finally, the geometric information is transformed into a list of strings consisting of topological relations between two planar regions and detailed connection information. The experiments show that the proposed approach helps to identify topological relations of planar segments of point cloud automatically.

The effect of canola meal tannins on the intestinal absorption capacity of broilers using a D-xylose test.

PubMed

Mansoori, B; Rogiewicz, A; Slominski, B A

2015-12-01

In three D-xylose absorption experiments, the effect of 1% HCl/methanol, 70% methanol or 70% acetone extracts of canola meal (CM) or 70% acetone extract of soybean meal (SBM) containing polyphenols, phenolic acids, tannins and phytic acid on intestinal absorption capacity of broilers was determined. In Exp. 1, the experimental groups received orally D-xylose solution alone or with methanol/HCl, methanol or acetone extracts of CM. In Exp. 2, the experimental groups received D-xylose alone or with acetone extracts of CM or SBM. In Exp. 3, the experimental groups received D-xylose plus sucrose solution or D-xylose plus acetone extracts of CM or SBM. In Exps. 2 and 3, the CM extracts contained 2.7 and 2.6, 2.4 and 2.3, 3.2 and 3.2, and 2.4 and 2.2 times higher polyphenols, phenolic acids, tannins and condensed tannins than the corresponding SBM extracts respectively. Blood samples were collected in 40-min intervals, and plasma D-xylose was measured. Compared to the Control, plasma D-xylose in Exp. 1 was lower (p < 0.001) by 81, 69 and 73% at 40-min, by 41, 44 and 37% at 80-min and by 22, 31, and 23% at 120-min post-ingestion of the HCl/methanol, methanol and acetone extracts respectively. In both Exps. 2 and 3, plasma D-xylose level was lower (p < 0.001) in groups dosed with CM extract or SBM extract at each time of blood collection, when compared to the respective Control group. However, in Exp. 3, birds dosed with SBM extract had higher plasma D-xylose than CM extract-dosed birds by 28, 8 and 21% at 40, 80 and 120 min respectively (p < 0.01). In conclusion, although CM extract caused a lower absorption of D-xylose, based on 5 to 10% of CM inclusion levels in practical broiler rations, the soluble bioactive components of CM will likely have minor impact on the absorption capacity of the chicken intestine. Journal of Animal Physiology and Animal Nutrition © 2015 Blackwell Verlag GmbH.

Extracting 3d Semantic Information from Video Surveillance System Using Deep Learning

NASA Astrophysics Data System (ADS)

Zhang, J. S.; Cao, J.; Mao, B.; Shen, D. Q.

2018-04-01

At present, intelligent video analysis technology has been widely used in various fields. Object tracking is one of the important part of intelligent video surveillance, but the traditional target tracking technology based on the pixel coordinate system in images still exists some unavoidable problems. Target tracking based on pixel can't reflect the real position information of targets, and it is difficult to track objects across scenes. Based on the analysis of Zhengyou Zhang's camera calibration method, this paper presents a method of target tracking based on the target's space coordinate system after converting the 2-D coordinate of the target into 3-D coordinate. It can be seen from the experimental results: Our method can restore the real position change information of targets well, and can also accurately get the trajectory of the target in space.

Estimation of 3D shape from image orientations.

PubMed

Fleming, Roland W; Holtmann-Rice, Daniel; Bülthoff, Heinrich H

2011-12-20

One of the main functions of vision is to estimate the 3D shape of objects in our environment. Many different visual cues, such as stereopsis, motion parallax, and shading, are thought to be involved. One important cue that remains poorly understood comes from surface texture markings. When a textured surface is slanted in 3D relative to the observer, the surface patterns appear compressed in the retinal image, providing potentially important information about 3D shape. What is not known, however, is how the brain actually measures this information from the retinal image. Here, we explain how the key information could be extracted by populations of cells tuned to different orientations and spatial frequencies, like those found in the primary visual cortex. To test this theory, we created stimuli that selectively stimulate such cell populations, by "smearing" (filtering) images of 2D random noise into specific oriented patterns. We find that the resulting patterns appear vividly 3D, and that increasing the strength of the orientation signals progressively increases the sense of 3D shape, even though the filtering we apply is physically inconsistent with what would occur with a real object. This finding suggests we have isolated key mechanisms used by the brain to estimate shape from texture. Crucially, we also find that adapting the visual system's orientation detectors to orthogonal patterns causes unoriented random noise to look like a specific 3D shape. Together these findings demonstrate a crucial role of orientation detectors in the perception of 3D shape.

Human machine interface by using stereo-based depth extraction

NASA Astrophysics Data System (ADS)

Liao, Chao-Kang; Wu, Chi-Hao; Lin, Hsueh-Yi; Chang, Ting-Ting; Lin, Tung-Yang; Huang, Po-Kuan

2014-03-01

The ongoing success of three-dimensional (3D) cinema fuels increasing efforts to spread the commercial success of 3D to new markets. The possibilities of a convincing 3D experience at home, such as three-dimensional television (3DTV), has generated a great deal of interest within the research and standardization community. A central issue for 3DTV is the creation and representation of 3D content. Acquiring scene depth information is a fundamental task in computer vision, yet complex and error-prone. Dedicated range sensors, such as the Time­ of-Flight camera (ToF), can simplify the scene depth capture process and overcome shortcomings of traditional solutions, such as active or passive stereo analysis. Admittedly, currently available ToF sensors deliver only a limited spatial resolution. However, sophisticated depth upscaling approaches use texture information to match depth and video resolution. At Electronic Imaging 2012 we proposed an upscaling routine based on error energy minimization, weighted with edge information from an accompanying video source. In this article we develop our algorithm further. By adding temporal consistency constraints to the upscaling process, we reduce disturbing depth jumps and flickering artifacts in the final 3DTV content. Temporal consistency in depth maps enhances the 3D experience, leading to a wider acceptance of 3D media content. More content in better quality can boost the commercial success of 3DTV.

Classification of Mls Point Clouds in Urban Scenes Using Detrended Geometric Features from Supervoxel-Based Local Contexts

NASA Astrophysics Data System (ADS)

Sun, Z.; Xu, Y.; Hoegner, L.; Stilla, U.

2018-05-01

In this work, we propose a classification method designed for the labeling of MLS point clouds, with detrended geometric features extracted from the points of the supervoxel-based local context. To achieve the analysis of complex 3D urban scenes, acquired points of the scene should be tagged with individual labels of different classes. Thus, assigning a unique label to the points of an object that belong to the same category plays an essential role in the entire 3D scene analysis workflow. Although plenty of studies in this field have been reported, this work is still a challenging task. Specifically, in this work: 1) A novel geometric feature extraction method, detrending the redundant and in-salient information in the local context, is proposed, which is proved to be effective for extracting local geometric features from the 3D scene. 2) Instead of using individual point as basic element, the supervoxel-based local context is designed to encapsulate geometric characteristics of points, providing a flexible and robust solution for feature extraction. 3) Experiments using complex urban scene with manually labeled ground truth are conducted, and the performance of proposed method with respect to different methods is analyzed. With the testing dataset, we have obtained a result of 0.92 for overall accuracy for assigning eight semantic classes.

3D numerical simulations of negative hydrogen ion extraction using realistic plasma parameters, geometry of the extraction aperture and full 3D magnetic field map

NASA Astrophysics Data System (ADS)

Mochalskyy, S.; Wünderlich, D.; Ruf, B.; Franzen, P.; Fantz, U.; Minea, T.

2014-02-01

Decreasing the co-extracted electron current while simultaneously keeping negative ion (NI) current sufficiently high is a crucial issue on the development plasma source system for ITER Neutral Beam Injector. To support finding the best extraction conditions the 3D Particle-in-Cell Monte Carlo Collision electrostatic code ONIX (Orsay Negative Ion eXtraction) has been developed. Close collaboration with experiments and other numerical models allows performing realistic simulations with relevant input parameters: plasma properties, geometry of the extraction aperture, full 3D magnetic field map, etc. For the first time ONIX has been benchmarked with commercial positive ions tracing code KOBRA3D. A very good agreement in terms of the meniscus position and depth has been found. Simulation of NI extraction with different e/NI ratio in bulk plasma shows high relevance of the direct negative ion extraction from the surface produced NI in order to obtain extracted NI current as in the experimental results from BATMAN testbed.

Depth extraction method with high accuracy in integral imaging based on moving array lenslet technique

NASA Astrophysics Data System (ADS)

Wang, Yao-yao; Zhang, Juan; Zhao, Xue-wei; Song, Li-pei; Zhang, Bo; Zhao, Xing

2018-03-01

In order to improve depth extraction accuracy, a method using moving array lenslet technique (MALT) in pickup stage is proposed, which can decrease the depth interval caused by pixelation. In this method, the lenslet array is moved along the horizontal and vertical directions simultaneously for N times in a pitch to get N sets of elemental images. Computational integral imaging reconstruction method for MALT is taken to obtain the slice images of the 3D scene, and the sum modulus (SMD) blur metric is taken on these slice images to achieve the depth information of the 3D scene. Simulation and optical experiments are carried out to verify the feasibility of this method.

Passive Polarimetric Information Processing for Target Classification

NASA Astrophysics Data System (ADS)

Sadjadi, Firooz; Sadjadi, Farzad

Polarimetric sensing is an area of active research in a variety of applications. In particular, the use of polarization diversity has been shown to improve performance in automatic target detection and recognition. Within the diverse scope of polarimetric sensing, the field of passive polarimetric sensing is of particular interest. This chapter presents several new methods for gathering in formation using such passive techniques. One method extracts three-dimensional (3D) information and surface properties using one or more sensors. Another method extracts scene-specific algebraic expressions that remain unchanged under polariza tion transformations (such as along the transmission path to the sensor).

Score-level fusion of two-dimensional and three-dimensional palmprint for personal recognition systems

NASA Astrophysics Data System (ADS)

Chaa, Mourad; Boukezzoula, Naceur-Eddine; Attia, Abdelouahab

2017-01-01

Two types of scores extracted from two-dimensional (2-D) and three-dimensional (3-D) palmprint for personal recognition systems are merged, introducing a local image descriptor for 2-D palmprint-based recognition systems, named bank of binarized statistical image features (B-BSIF). The main idea of B-BSIF is that the extracted histograms from the binarized statistical image features (BSIF) code images (the results of applying the different BSIF descriptor size with the length 12) are concatenated into one to produce a large feature vector. 3-D palmprint contains the depth information of the palm surface. The self-quotient image (SQI) algorithm is applied for reconstructing illumination-invariant 3-D palmprint images. To extract discriminative Gabor features from SQI images, Gabor wavelets are defined and used. Indeed, the dimensionality reduction methods have shown their ability in biometrics systems. Given this, a principal component analysis (PCA)+linear discriminant analysis (LDA) technique is employed. For the matching process, the cosine Mahalanobis distance is applied. Extensive experiments were conducted on a 2-D and 3-D palmprint database with 10,400 range images from 260 individuals. Then, a comparison was made between the proposed algorithm and other existing methods in the literature. Results clearly show that the proposed framework provides a higher correct recognition rate. Furthermore, the best results were obtained by merging the score of B-BSIF descriptor with the score of the SQI+Gabor wavelets+PCA+LDA method, yielding an equal error rate of 0.00% and a recognition rate of rank-1=100.00%.

Auto-Context Convolutional Neural Network (Auto-Net) for Brain Extraction in Magnetic Resonance Imaging.

PubMed

Mohseni Salehi, Seyed Sadegh; Erdogmus, Deniz; Gholipour, Ali

2017-11-01

Brain extraction or whole brain segmentation is an important first step in many of the neuroimage analysis pipelines. The accuracy and the robustness of brain extraction, therefore, are crucial for the accuracy of the entire brain analysis process. The state-of-the-art brain extraction techniques rely heavily on the accuracy of alignment or registration between brain atlases and query brain anatomy, and/or make assumptions about the image geometry, and therefore have limited success when these assumptions do not hold or image registration fails. With the aim of designing an accurate, learning-based, geometry-independent, and registration-free brain extraction tool, in this paper, we present a technique based on an auto-context convolutional neural network (CNN), in which intrinsic local and global image features are learned through 2-D patches of different window sizes. We consider two different architectures: 1) a voxelwise approach based on three parallel 2-D convolutional pathways for three different directions (axial, coronal, and sagittal) that implicitly learn 3-D image information without the need for computationally expensive 3-D convolutions and 2) a fully convolutional network based on the U-net architecture. Posterior probability maps generated by the networks are used iteratively as context information along with the original image patches to learn the local shape and connectedness of the brain to extract it from non-brain tissue. The brain extraction results we have obtained from our CNNs are superior to the recently reported results in the literature on two publicly available benchmark data sets, namely, LPBA40 and OASIS, in which we obtained the Dice overlap coefficients of 97.73% and 97.62%, respectively. Significant improvement was achieved via our auto-context algorithm. Furthermore, we evaluated the performance of our algorithm in the challenging problem of extracting arbitrarily oriented fetal brains in reconstructed fetal brain magnetic resonance imaging (MRI) data sets. In this application, our voxelwise auto-context CNN performed much better than the other methods (Dice coefficient: 95.97%), where the other methods performed poorly due to the non-standard orientation and geometry of the fetal brain in MRI. Through training, our method can provide accurate brain extraction in challenging applications. This, in turn, may reduce the problems associated with image registration in segmentation tasks.

[A method for rapid extracting three-dimensional root model of vivo tooth from cone beam computed tomography data based on the anatomical characteristics of periodontal ligament].

PubMed

Zhao, Y J; Wang, S W; Liu, Y; Wang, Y

2017-02-18

To explore a new method for rapid extracting and rebuilding three-dimensional (3D) digital root model of vivo tooth from cone beam computed tomography (CBCT) data based on the anatomical characteristics of periodontal ligament, and to evaluate the extraction accuracy of the method. In the study, 15 extracted teeth (11 with single root, 4 with double roots) were collected from oral clinic and 3D digital root models of each tooth were obtained by 3D dental scanner with a high accuracy 0.02 mm in STL format. CBCT data for each patient were acquired before tooth extraction, DICOM data with a voxel size 0.3 mm were input to Mimics 18.0 software. Segmentation, Morphology operations, Boolean operations and Smart expanded function in Mimics software were used to edit teeth, bone and periodontal ligament threshold mask, and root threshold mask were automatically acquired after a series of mask operations. 3D digital root models were extracted in STL format finally. 3D morphology deviation between the extracted root models and corresponding vivo root models were compared in Geomagic Studio 2012 software. The 3D size errors in long axis, bucco-lingual direction and mesio-distal direction were also calculated. The average value of the 3D morphology deviation for 15 roots by calculating Root Mean Square (RMS) value was 0.22 mm, the average size errors in the mesio-distal direction, the bucco-lingual direction and the long axis were 0.46 mm, 0.36 mm and -0.68 mm separately. The average time of this new method for extracting single root was about 2-3 min. It could meet the accuracy requirement of the root 3D reconstruction fororal clinical use. This study established a new method for rapid extracting 3D root model of vivo tooth from CBCT data. It could simplify the traditional manual operation and improve the efficiency and automation of single root extraction. The strategy of this method for complete dentition extraction needs further research.

Fine-Scale Population Estimation by 3D Reconstruction of Urban Residential Buildings

PubMed Central

Wang, Shixin; Tian, Ye; Zhou, Yi; Liu, Wenliang; Lin, Chenxi

2016-01-01

Fine-scale population estimation is essential in emergency response and epidemiological applications as well as urban planning and management. However, representing populations in heterogeneous urban regions with a finer resolution is a challenge. This study aims to obtain fine-scale population distribution based on 3D reconstruction of urban residential buildings with morphological operations using optical high-resolution (HR) images from the Chinese No. 3 Resources Satellite (ZY-3). Specifically, the research area was first divided into three categories when dasymetric mapping was taken into consideration. The results demonstrate that the morphological building index (MBI) yielded better results than built-up presence index (PanTex) in building detection, and the morphological shadow index (MSI) outperformed color invariant indices (CIIT) in shadow extraction and height retrieval. Building extraction and height retrieval were then combined to reconstruct 3D models and to estimate population. Final results show that this approach is effective in fine-scale population estimation, with a mean relative error of 16.46% and an overall Relative Total Absolute Error (RATE) of 0.158. This study gives significant insights into fine-scale population estimation in complicated urban landscapes, when detailed 3D information of buildings is unavailable. PMID:27775670

Fringe-projection profilometry based on two-dimensional empirical mode decomposition.

PubMed

Zheng, Suzhen; Cao, Yiping

2013-11-01

In 3D shape measurement, because deformed fringes often contain low-frequency information degraded with random noise and background intensity information, a new fringe-projection profilometry is proposed based on 2D empirical mode decomposition (2D-EMD). The fringe pattern is first decomposed into numbers of intrinsic mode functions by 2D-EMD. Because the method has partial noise reduction, the background components can be removed to obtain the fundamental components needed to perform Hilbert transformation to retrieve the phase information. The 2D-EMD can effectively extract the modulation phase of a single direction fringe and an inclined fringe pattern because it is a full 2D analysis method and considers the relationship between adjacent lines of a fringe patterns. In addition, as the method does not add noise repeatedly, as does ensemble EMD, the data processing time is shortened. Computer simulations and experiments prove the feasibility of this method.

Smooth 2D manifold extraction from 3D image stack

PubMed Central

Shihavuddin, Asm; Basu, Sreetama; Rexhepaj, Elton; Delestro, Felipe; Menezes, Nikita; Sigoillot, Séverine M; Del Nery, Elaine; Selimi, Fekrije; Spassky, Nathalie; Genovesio, Auguste

2017-01-01

Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy. PMID:28561033

Building continental-scale 3D subsurface layers in the Digital Crust project: constrained interpolation and uncertainty estimation.

NASA Astrophysics Data System (ADS)

Yulaeva, E.; Fan, Y.; Moosdorf, N.; Richard, S. M.; Bristol, S.; Peters, S. E.; Zaslavsky, I.; Ingebritsen, S.

2015-12-01

The Digital Crust EarthCube building block creates a framework for integrating disparate 3D/4D information from multiple sources into a comprehensive model of the structure and composition of the Earth's upper crust, and to demonstrate the utility of this model in several research scenarios. One of such scenarios is estimation of various crustal properties related to fluid dynamics (e.g. permeability and porosity) at each node of any arbitrary unstructured 3D grid to support continental-scale numerical models of fluid flow and transport. Starting from Macrostrat, an existing 4D database of 33,903 chronostratigraphic units, and employing GeoDeepDive, a software system for extracting structured information from unstructured documents, we construct 3D gridded fields of sediment/rock porosity, permeability and geochemistry for large sedimentary basins of North America, which will be used to improve our understanding of large-scale fluid flow, chemical weathering rates, and geochemical fluxes into the ocean. In this talk, we discuss the methods, data gaps (particularly in geologically complex terrain), and various physical and geological constraints on interpolation and uncertainty estimation.

Two-dimensional wavelet analysis based classification of gas chromatogram differential mobility spectrometry signals.

PubMed

Zhao, Weixiang; Sankaran, Shankar; Ibáñez, Ana M; Dandekar, Abhaya M; Davis, Cristina E

2009-08-04

This study introduces two-dimensional (2-D) wavelet analysis to the classification of gas chromatogram differential mobility spectrometry (GC/DMS) data which are composed of retention time, compensation voltage, and corresponding intensities. One reported method to process such large data sets is to convert 2-D signals to 1-D signals by summing intensities either across retention time or compensation voltage, but it can lose important signal information in one data dimension. A 2-D wavelet analysis approach keeps the 2-D structure of original signals, while significantly reducing data size. We applied this feature extraction method to 2-D GC/DMS signals measured from control and disordered fruit and then employed two typical classification algorithms to testify the effects of the resultant features on chemical pattern recognition. Yielding a 93.3% accuracy of separating data from control and disordered fruit samples, 2-D wavelet analysis not only proves its feasibility to extract feature from original 2-D signals but also shows its superiority over the conventional feature extraction methods including converting 2-D to 1-D and selecting distinguishable pixels from training set. Furthermore, this process does not require coupling with specific pattern recognition methods, which may help ensure wide applications of this method to 2-D spectrometry data.

Three dimensional global modeling of atmospheric CO2

NASA Technical Reports Server (NTRS)

Fung, I.; Hansen, J.; Rind, D.

1983-01-01

A model was developed to study the prospects of extracting information on carbon dioxide sources and sinks from observed CO2 variations. The approach uses a three dimensional global transport model, based on winds from a 3-D general circulation model (GCM), to advect CO2 noninteractively, i.e., as a tracer, with specified sources and sinks of CO2 at the surface. The 3-D model employed is identified and biosphere, ocean and fossil fuel sources and sinks are discussed. Some preliminary model results are presented.

Augmented reality three-dimensional object visualization and recognition with axially distributed sensing.

PubMed

Markman, Adam; Shen, Xin; Hua, Hong; Javidi, Bahram

2016-01-15

An augmented reality (AR) smartglass display combines real-world scenes with digital information enabling the rapid growth of AR-based applications. We present an augmented reality-based approach for three-dimensional (3D) optical visualization and object recognition using axially distributed sensing (ADS). For object recognition, the 3D scene is reconstructed, and feature extraction is performed by calculating the histogram of oriented gradients (HOG) of a sliding window. A support vector machine (SVM) is then used for classification. Once an object has been identified, the 3D reconstructed scene with the detected object is optically displayed in the smartglasses allowing the user to see the object, remove partial occlusions of the object, and provide critical information about the object such as 3D coordinates, which are not possible with conventional AR devices. To the best of our knowledge, this is the first report on combining axially distributed sensing with 3D object visualization and recognition for applications to augmented reality. The proposed approach can have benefits for many applications, including medical, military, transportation, and manufacturing.

D Central Line Extraction of Fossil Oyster Shells

NASA Astrophysics Data System (ADS)

Djuricic, A.; Puttonen, E.; Harzhauser, M.; Mandic, O.; Székely, B.; Pfeifer, N.

2016-06-01

Photogrammetry provides a powerful tool to digitally document protected, inaccessible, and rare fossils. This saves manpower in relation to current documentation practice and makes the fragile specimens more available for paleontological analysis and public education. In this study, high resolution orthophoto (0.5 mm) and digital surface models (1 mm) are used to define fossil boundaries that are then used as an input to automatically extract fossil length information via central lines. In general, central lines are widely used in geosciences as they ease observation, monitoring and evaluation of object dimensions. Here, the 3D central lines are used in a novel paleontological context to study fossilized oyster shells with photogrammetric and LiDAR-obtained 3D point cloud data. 3D central lines of 1121 Crassostrea gryphoides oysters of various shapes and sizes were computed in the study. Central line calculation included: i) Delaunay triangulation between the fossil shell boundary points and formation of the Voronoi diagram; ii) extraction of Voronoi vertices and construction of a connected graph tree from them; iii) reduction of the graph to the longest possible central line via Dijkstra's algorithm; iv) extension of longest central line to the shell boundary and smoothing by an adjustment of cubic spline curve; and v) integration of the central line into the corresponding 3D point cloud. The resulting longest path estimate for the 3D central line is a size parameter that can be applied in oyster shell age determination both in paleontological and biological applications. Our investigation evaluates ability and performance of the central line method to measure shell sizes accurately by comparing automatically extracted central lines with manually collected reference data used in paleontological analysis. Our results show that the automatically obtained central line length overestimated the manually collected reference by 1.5% in the test set, which is deemed sufficient for the selected paleontological application, namely shell age determination.

Using Openstreetmap Data to Generate Building Models with Their Inner Structures for 3d Maps

NASA Astrophysics Data System (ADS)

Wang, Z.; Zipf, A.

2017-09-01

With the development of Web 2.0, more and more data related to indoor environments has been collected within the volunteered geographic information (VGI) framework, which creates a need for construction of indoor environments from VGI. In this study, we focus on generating 3D building models from OpenStreetMap (OSM) data, and provide an approach to support construction and visualization of indoor environments on 3D maps. In this paper, we present an algorithm which can extract building information from OSM data, and can construct building structures as well as inner building components (e.g., doors, rooms, and windows). A web application is built to support the processing and visualization of the building models on a 3D map. We test our approach with an indoor dataset collected from the field. The results show the feasibility of our approach and its potentials to provide support for a wide range of applications, such as indoor and outdoor navigation, urban planning, and incident management.

Modulation of the multidrug efflux pump EmrD-3 from Vibrio cholerae by Allium sativum extract and the bioactive agent allyl sulfide plus synergistic enhancement of antimicrobial susceptibility by A. sativum extract.

PubMed

Bruns, Merissa M; Kakarla, Prathusha; Floyd, Jared T; Mukherjee, Mun Mun; Ponce, Robert C; Garcia, John A; Ranaweera, Indrika; Sanford, Leslie M; Hernandez, Alberto J; Willmon, T Mark; Tolson, Grace L; Varela, Manuel F

2017-10-01

The causative agent of cholera, Vibrio cholerae, is a public health concern. Multidrug-resistant V. cholerae variants may reduce chemotherapeutic efficacies of severe cholera. We previously reported that the multidrug efflux pump EmrD-3 from V. cholerae confers resistance to multiple structurally distinct antimicrobials. Medicinal plant compounds are potential candidates for EmrD-3 efflux pump modulation. The antibacterial activities of garlic Allium sativum, although poorly understood, predicts that a main bioactive component, allyl sulfide, modulates EmrD-3 efflux. Thus, we tested whether A. sativum extract acts in synergy with antimicrobials and that a main bioactive component allyl sulfide inhibits EmrD-3 efflux. We found that A. sativum extract and allyl sulfide inhibited ethidium bromide efflux in cells harboring EmrD-3 and that A. sativum lowered the MICs of multiple antibacterials. We conclude that A. sativum and allyl sulfide inhibit EmrD-3 and that A. sativum extract synergistically enhances antibacterial agents.

Hdr Imaging for Feature Detection on Detailed Architectural Scenes

NASA Astrophysics Data System (ADS)

Kontogianni, G.; Stathopoulou, E. K.; Georgopoulos, A.; Doulamis, A.

2015-02-01

3D reconstruction relies on accurate detection, extraction, description and matching of image features. This is even truer for complex architectural scenes that pose needs for 3D models of high quality, without any loss of detail in geometry or color. Illumination conditions influence the radiometric quality of images, as standard sensors cannot depict properly a wide range of intensities in the same scene. Indeed, overexposed or underexposed pixels cause irreplaceable information loss and degrade digital representation. Images taken under extreme lighting environments may be thus prohibitive for feature detection/extraction and consequently for matching and 3D reconstruction. High Dynamic Range (HDR) images could be helpful for these operators because they broaden the limits of illumination range that Standard or Low Dynamic Range (SDR/LDR) images can capture and increase in this way the amount of details contained in the image. Experimental results of this study prove this assumption as they examine state of the art feature detectors applied both on standard dynamic range and HDR images.

Automatic three-dimensional rib centerline extraction from CT scans for enhanced visualization and anatomical context

NASA Astrophysics Data System (ADS)

Ramakrishnan, Sowmya; Alvino, Christopher; Grady, Leo; Kiraly, Atilla

2011-03-01

We present a complete automatic system to extract 3D centerlines of ribs from thoracic CT scans. Our rib centerline system determines the positional information for the rib cage consisting of extracted rib centerlines, spinal canal centerline, pairing and labeling of ribs. We show an application of this output to produce an enhanced visualization of the rib cage by the method of Kiraly et al., in which the ribs are digitally unfolded along their centerlines. The centerline extraction consists of three stages: (a) pre-trace processing for rib localization, (b) rib centerline tracing, and (c) post-trace processing to merge the rib traces. Then we classify ribs from non-ribs and determine anatomical rib labeling. Our novel centerline tracing technique uses the Random Walker algorithm to segment the structural boundary of the rib in successive 2D cross sections orthogonal to the longitudinal direction of the ribs. Then the rib centerline is progressively traced along the rib using a 3D Kalman filter. The rib centerline extraction framework was evaluated on 149 CT datasets with varying slice spacing, dose, and under a variety of reconstruction kernels. The results of the evaluation are presented. The extraction takes approximately 20 seconds on a modern radiology workstation and performs robustly even in the presence of partial volume effects or rib pathologies such as bone metastases or fractures, making the system suitable for assisting clinicians in expediting routine rib reading for oncology and trauma applications.

Automatic Rooftop Extraction in Stereo Imagery Using Distance and Building Shape Regularized Level Set Evolution

NASA Astrophysics Data System (ADS)

Tian, J.; Krauß, T.; d'Angelo, P.

2017-05-01

Automatic rooftop extraction is one of the most challenging problems in remote sensing image analysis. Classical 2D image processing techniques are expensive due to the high amount of features required to locate buildings. This problem can be avoided when 3D information is available. In this paper, we show how to fuse the spectral and height information of stereo imagery to achieve an efficient and robust rooftop extraction. In the first step, the digital terrain model (DTM) and in turn the normalized digital surface model (nDSM) is generated by using a newly step-edge approach. In the second step, the initial building locations and rooftop boundaries are derived by removing the low-level pixels and high-level pixels with higher probability to be trees and shadows. This boundary is then served as the initial level set function, which is further refined to fit the best possible boundaries through distance regularized level-set curve evolution. During the fitting procedure, the edge-based active contour model is adopted and implemented by using the edges indicators extracted from panchromatic image. The performance of the proposed approach is tested by using the WorldView-2 satellite data captured over Munich.

Whisking mechanics and active sensing

PubMed Central

Bush, Nicholas E; Solla, Sara A

2017-01-01

We describe recent advances in quantifying the three-dimensional (3D) geometry and mechanics of whisking. Careful delineation of relevant 3D reference frames reveals important geometric and mechanical distinctions between the localization problem (‘where’ is an object) and the feature extraction problem (‘what’ is an object). Head-centered and resting-whisker reference frames lend themselves to quantifying temporal and kinematic cues used for object localization. The whisking-centered reference frame lends itself to quantifying the contact mechanics likely associated with feature extraction. We offer the ‘windowed sampling’ hypothesis for active sensing: that rats can estimate an object’s spatial features by integrating mechanical information across whiskers during brief (25–60 ms) windows of ‘haptic enclosure’ with the whiskers, a motion that resembles a hand grasp. PMID:27632212

Whisking mechanics and active sensing.

PubMed

Bush, Nicholas E; Solla, Sara A; Hartmann, Mitra Jz

2016-10-01

We describe recent advances in quantifying the three-dimensional (3D) geometry and mechanics of whisking. Careful delineation of relevant 3D reference frames reveals important geometric and mechanical distinctions between the localization problem ('where' is an object) and the feature extraction problem ('what' is an object). Head-centered and resting-whisker reference frames lend themselves to quantifying temporal and kinematic cues used for object localization. The whisking-centered reference frame lends itself to quantifying the contact mechanics likely associated with feature extraction. We offer the 'windowed sampling' hypothesis for active sensing: that rats can estimate an object's spatial features by integrating mechanical information across whiskers during brief (25-60ms) windows of 'haptic enclosure' with the whiskers, a motion that resembles a hand grasp. Copyright © 2016. Published by Elsevier Ltd.

A practical salient region feature based 3D multi-modality registration method for medical images

NASA Astrophysics Data System (ADS)

Hahn, Dieter A.; Wolz, Gabriele; Sun, Yiyong; Hornegger, Joachim; Sauer, Frank; Kuwert, Torsten; Xu, Chenyang

2006-03-01

We present a novel representation of 3D salient region features and its integration into a hybrid rigid-body registration framework. We adopt scale, translation and rotation invariance properties of those intrinsic 3D features to estimate a transform between underlying mono- or multi-modal 3D medical images. Our method combines advantageous aspects of both feature- and intensity-based approaches and consists of three steps: an automatic extraction of a set of 3D salient region features on each image, a robust estimation of correspondences and their sub-pixel accurate refinement with outliers elimination. We propose a region-growing based approach for the extraction of 3D salient region features, a solution to the problem of feature clustering and a reduction of the correspondence search space complexity. Results of the developed algorithm are presented for both mono- and multi-modal intra-patient 3D image pairs (CT, PET and SPECT) that have been acquired for change detection, tumor localization, and time based intra-person studies. The accuracy of the method is clinically evaluated by a medical expert with an approach that measures the distance between a set of selected corresponding points consisting of both anatomical and functional structures or lesion sites. This demonstrates the robustness of the proposed method to image overlap, missing information and artefacts. We conclude by discussing potential medical applications and possibilities for integration into a non-rigid registration framework.

A Registration Method Based on Contour Point Cloud for 3D Whole-Body PET and CT Images

PubMed Central

Yang, Qiyao; Wang, Zhiguo; Zhang, Guoxu

2017-01-01

The PET and CT fusion image, combining the anatomical and functional information, has important clinical meaning. An effective registration of PET and CT images is the basis of image fusion. This paper presents a multithread registration method based on contour point cloud for 3D whole-body PET and CT images. Firstly, a geometric feature-based segmentation (GFS) method and a dynamic threshold denoising (DTD) method are creatively proposed to preprocess CT and PET images, respectively. Next, a new automated trunk slices extraction method is presented for extracting feature point clouds. Finally, the multithread Iterative Closet Point is adopted to drive an affine transform. We compare our method with a multiresolution registration method based on Mattes Mutual Information on 13 pairs (246~286 slices per pair) of 3D whole-body PET and CT data. Experimental results demonstrate the registration effectiveness of our method with lower negative normalization correlation (NC = −0.933) on feature images and less Euclidean distance error (ED = 2.826) on landmark points, outperforming the source data (NC = −0.496, ED = 25.847) and the compared method (NC = −0.614, ED = 16.085). Moreover, our method is about ten times faster than the compared one. PMID:28316979

A novel 3D shape descriptor for automatic retrieval of anatomical structures from medical images

NASA Astrophysics Data System (ADS)

Nunes, Fátima L. S.; Bergamasco, Leila C. C.; Delmondes, Pedro H.; Valverde, Miguel A. G.; Jackowski, Marcel P.

2017-03-01

Content-based image retrieval (CBIR) aims at retrieving from a database objects that are similar to an object provided by a query, by taking into consideration a set of extracted features. While CBIR has been widely applied in the two-dimensional image domain, the retrieval of3D objects from medical image datasets using CBIR remains to be explored. In this context, the development of descriptors that can capture information specific to organs or structures is desirable. In this work, we focus on the retrieval of two anatomical structures commonly imaged by Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) techniques, the left ventricle of the heart and blood vessels. Towards this aim, we developed the Area-Distance Local Descriptor (ADLD), a novel 3D local shape descriptor that employs mesh geometry information, namely facet area and distance from centroid to surface, to identify shape changes. Because ADLD only considers surface meshes extracted from volumetric medical images, it substantially diminishes the amount of data to be analyzed. A 90% precision rate was obtained when retrieving both convex (left ventricle) and non-convex structures (blood vessels), allowing for detection of abnormalities associated with changes in shape. Thus, ADLD has the potential to aid in the diagnosis of a wide range of vascular and cardiac diseases.

Analytical 3D views and virtual globes — scientific results in a familiar spatial context

NASA Astrophysics Data System (ADS)

Tiede, Dirk; Lang, Stefan

In this paper we introduce analytical three-dimensional (3D) views as a means for effective and comprehensible information delivery, using virtual globes and the third dimension as an additional information carrier. Four case studies are presented, in which information extraction results from very high spatial resolution (VHSR) satellite images were conditioned and aggregated or disaggregated to regular spatial units. The case studies were embedded in the context of: (1) urban life quality assessment (Salzburg/Austria); (2) post-disaster assessment (Harare/Zimbabwe); (3) emergency response (Lukole/Tanzania); and (4) contingency planning (faked crisis scenario/Germany). The results are made available in different virtual globe environments, using the implemented contextual data (such as satellite imagery, aerial photographs, and auxiliary geodata) as valuable additional context information. Both day-to-day users and high-level decision makers are addressees of this tailored information product. The degree of abstraction required for understanding a complex analytical content is balanced with the ease and appeal by which the context is conveyed.

Person identification by using 3D palmprint data

NASA Astrophysics Data System (ADS)

Bai, Xuefei; Huang, Shujun; Gao, Nan; Zhang, Zonghua

2016-11-01

Person identification based on biometrics is drawing more and more attentions in identity and information safety. This paper presents a biometric system to identify person using 3D palmprint data, including a non-contact system capturing 3D palmprint quickly and a method identifying 3D palmprint fast. In order to reduce the effect of slight shaking of palm on the data accuracy, a DLP (Digital Light Processing) projector is utilized to trigger a CCD camera based on structured-light and triangulation measurement and 3D palmprint data could be gathered within 1 second. Using the obtained database and the PolyU 3D palmprint database, feature extraction and matching method is presented based on MCI (Mean Curvature Image), Gabor filter and binary code list. Experimental results show that the proposed method can identify a person within 240 ms in the case of 4000 samples. Compared with the traditional 3D palmprint recognition methods, the proposed method has high accuracy, low EER (Equal Error Rate), small storage space, and fast identification speed.

A statistical shape modelling framework to extract 3D shape biomarkers from medical imaging data: assessing arch morphology of repaired coarctation of the aorta.

PubMed

Bruse, Jan L; McLeod, Kristin; Biglino, Giovanni; Ntsinjana, Hopewell N; Capelli, Claudio; Hsia, Tain-Yen; Sermesant, Maxime; Pennec, Xavier; Taylor, Andrew M; Schievano, Silvia

2016-05-31

Medical image analysis in clinical practice is commonly carried out on 2D image data, without fully exploiting the detailed 3D anatomical information that is provided by modern non-invasive medical imaging techniques. In this paper, a statistical shape analysis method is presented, which enables the extraction of 3D anatomical shape features from cardiovascular magnetic resonance (CMR) image data, with no need for manual landmarking. The method was applied to repaired aortic coarctation arches that present complex shapes, with the aim of capturing shape features as biomarkers of potential functional relevance. The method is presented from the user-perspective and is evaluated by comparing results with traditional morphometric measurements. Steps required to set up the statistical shape modelling analyses, from pre-processing of the CMR images to parameter setting and strategies to account for size differences and outliers, are described in detail. The anatomical mean shape of 20 aortic arches post-aortic coarctation repair (CoA) was computed based on surface models reconstructed from CMR data. By analysing transformations that deform the mean shape towards each of the individual patient's anatomy, shape patterns related to differences in body surface area (BSA) and ejection fraction (EF) were extracted. The resulting shape vectors, describing shape features in 3D, were compared with traditionally measured 2D and 3D morphometric parameters. The computed 3D mean shape was close to population mean values of geometric shape descriptors and visually integrated characteristic shape features associated with our population of CoA shapes. After removing size effects due to differences in body surface area (BSA) between patients, distinct 3D shape features of the aortic arch correlated significantly with EF (r = 0.521, p = .022) and were well in agreement with trends as shown by traditional shape descriptors. The suggested method has the potential to discover previously unknown 3D shape biomarkers from medical imaging data. Thus, it could contribute to improving diagnosis and risk stratification in complex cardiac disease.

The Extract of D. dasycarpus Ameliorates Oxazolone-Induced Skin Damage in Mice by Anti-Inflammatory and Antioxidant Mechanisms.

PubMed

Chang, Tsong-Min; Yang, Ting-Ya; Niu, Yu-Lin; Huang, Huey-Chun

2018-06-15

Dictamni dasycarpus is a type of Chinese medicine made from the root bark of D. dasycarpus . It has been reported to show a wide spectrum of biological and pharmacological effects, for example, it has been used widely for the treatment of rheumatism, nettle rash, itching, jaundice, chronic hepatitis and skin diseases. In the current study, D. dasycarpus extract was investigated for its antioxidant and anti-inflammatory effects, as well as its capability to alleviate oxazolone-induced skin damage in mice. The possible anti-inflammatory mechanism of D. dasycarpus extract against oxidative challenge was elucidated by measuring the levels of reactive oxygen species (ROS) production, interleukin-6, Tumor necrosis factor-α, NLRP3 (NACHT, LRR and PYD domains-containing protein 3 (NALP3)) inflammasome and interleukin-1β in HaCaT cells. D. dasycarpus extract did not affect cell viability in basal conditions. The extract significantly reduced oxazolone-induced epidermal swelling compared to untreated animal in the hairless albino mice (ICR mice) model. At the molecular level, Western blot assays indicated that the D. dasycarpus extract attenuated oxazolone-induced activation of apoptosis-associated speck-like protein containing CARD (ASC), procaspase-1, NF-κB and mitogen-activated protein kinase (MAPKs) such as c-Jun N-terminal protein kinase (JNK) and p38. This study demonstrates that D. dasycarpus extract could protect skin cells against oxidative and inflammatory insult by modulating the intracellular levels of ROS, TNF-α, interleukin-1, interleukin-6, NLR family pyrin domain containing 3 (NLRP3) inflammasome generation, antioxidant enzyme activity and cell signaling pathways. D. dasycarpus extract also attenuated the expression of NF-κB in HaCaT keratinocytes and thereby effectively downregulated inflammatory responses in the skin. Furthermore, D. dasycarpus extract alleviated oxazolone-induced damage in mice. Our results suggest the potential application of D. dasycarpus extract in preventing inflammatory processes in dermatitis.

Towards a 3d Based Platform for Cultural Heritage Site Survey and Virtual Exploration

NASA Astrophysics Data System (ADS)

Seinturier, J.; Riedinger, C.; Mahiddine, A.; Peloso, D.; Boï, J.-M.; Merad, D.; Drap, P.

2013-07-01

This paper present a 3D platform that enables to make both cultural heritage site survey and its virtual exploration. It provides a single and easy way to use framework for merging multi scaled 3D measurements based on photogrammetry, documentation produced by experts and the knowledge of involved domains leaving the experts able to extract and choose the relevant information to produce the final survey. Taking into account the interpretation of the real world during the process of archaeological surveys is in fact the main goal of a survey. New advances in photogrammetry and the capability to produce dense 3D point clouds do not solve the problem of surveys. New opportunities for 3D representation are now available and we must to use them and find new ways to link geometry and knowledge. The new platform is able to efficiently manage and process large 3D data (points set, meshes) thanks to the implementation of space partition methods coming from the state of the art such as octrees and kd-trees and thus can interact with dense point clouds (thousands to millions of points) in real time. The semantisation of raw 3D data relies on geometric algorithms such as geodetic path computation, surface extraction from dense points cloud and geometrical primitive optimization. The platform provide an interface that enables expert to describe geometric representations of interesting objects like ashlar blocs, stratigraphic units or generic items (contour, lines, … ) directly onto the 3D representation of the site and without explicit links to underlying algorithms. The platform provide two ways for describing geometric representation. If oriented photographs are available, the expert can draw geometry on a photograph and the system computes its 3D representation by projection on the underlying mesh or the points cloud. If photographs are not available or if the expert wants to only use the 3D representation then he can simply draw objects shape on it. When 3D representations of objects of a surveyed site are extracted from the mesh, the link with domain related documentation is done by means of a set of forms designed by experts. Information from these forms are linked with geometry such that documentation can be attached to the viewed objects. Additional semantisation methods related to specific domains have been added to the platform. Beyond realistic rendering of surveyed site, the platform embeds non photorealistic rendering (NPR) algorithms. These algorithms enable to dynamically illustrate objects of interest that are related to knowledge with specific styles. The whole platform is implemented with a Java framework and relies on an actual and effective 3D engine that make available latest rendering methods. We illustrate this work on various photogrammetric survey, in medieval archaeology with the Shawbak castle in Jordan and in underwater archaeology on different marine sites.

Integrated approach for quantification of fractured tight reservoir rocks: Porosity, permeability analyses and 3D fracture network characterisation on fractured dolomite samples

NASA Astrophysics Data System (ADS)

Voorn, Maarten; Barnhoorn, Auke; Exner, Ulrike; Baud, Patrick; Reuschlé, Thierry

2015-04-01

Fractured reservoir rocks make up an important part of the hydrocarbon reservoirs worldwide. A detailed analysis of fractures and fracture networks in reservoir rock samples is thus essential to determine the potential of these fractured reservoirs. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this study, we therefore explore the use of an additional method - non-destructive 3D X-ray micro-Computed Tomography (μCT) - to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna Basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. 3D μCT data is used to extract porosity, fracture aperture, fracture density and fracture orientations - in bulk as well as locally. The 3D analyses are complemented with thin sections made to provide some 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) of the µCT results towards more realistic reservoir conditions. Our results show that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other methods can therefore be a powerful approach in microstructural analysis of reservoir rocks, especially when applying the concepts that we present (on a small set of samples) in a larger study, in an automated and standardised manner.

Nanoscale Analysis of a Hierarchical Hybrid Solar Cell in 3D.

PubMed

Divitini, Giorgio; Stenzel, Ole; Ghadirzadeh, Ali; Guarnera, Simone; Russo, Valeria; Casari, Carlo S; Bassi, Andrea Li; Petrozza, Annamaria; Di Fonzo, Fabio; Schmidt, Volker; Ducati, Caterina

2014-05-01

A quantitative method for the characterization of nanoscale 3D morphology is applied to the investigation of a hybrid solar cell based on a novel hierarchical nanostructured photoanode. A cross section of the solar cell device is prepared by focused ion beam milling in a micropillar geometry, which allows a detailed 3D reconstruction of the titania photoanode by electron tomography. It is found that the hierarchical titania nanostructure facilitates polymer infiltration, thus favoring intermixing of the two semiconducting phases, essential for charge separation. The 3D nanoparticle network is analyzed with tools from stochastic geometry to extract information related to the charge transport in the hierarchical solar cell. In particular, the experimental dataset allows direct visualization of the percolation pathways that contribute to the photocurrent.

Nonrigid registration of 3D longitudinal optical coherence tomography volumes with choroidal neovascularization

NASA Astrophysics Data System (ADS)

Wei, Qiangding; Shi, Fei; Zhu, Weifang; Xiang, Dehui; Chen, Haoyu; Chen, Xinjian

2017-02-01

In this paper, we propose a 3D registration method for retinal optical coherence tomography (OCT) volumes. The proposed method consists of five main steps: First, a projection image of the 3D OCT scan is created. Second, the vessel enhancement filter is applied on the projection image to detect vessel shadow. Third, landmark points are extracted based on both vessel positions and layer information. Fourth, the coherent point drift method is used to align retinal OCT volumes. Finally, a nonrigid B-spline-based registration method is applied to find the optimal transform to match the data. We applied this registration method on 15 3D OCT scans of patients with Choroidal Neovascularization (CNV). The Dice coefficients (DSC) between layers are greatly improved after applying the nonrigid registration.

Nanoscale Analysis of a Hierarchical Hybrid Solar Cell in 3D

PubMed Central

Divitini, Giorgio; Stenzel, Ole; Ghadirzadeh, Ali; Guarnera, Simone; Russo, Valeria; Casari, Carlo S; Bassi, Andrea Li; Petrozza, Annamaria; Di Fonzo, Fabio; Schmidt, Volker; Ducati, Caterina

2014-01-01

A quantitative method for the characterization of nanoscale 3D morphology is applied to the investigation of a hybrid solar cell based on a novel hierarchical nanostructured photoanode. A cross section of the solar cell device is prepared by focused ion beam milling in a micropillar geometry, which allows a detailed 3D reconstruction of the titania photoanode by electron tomography. It is found that the hierarchical titania nanostructure facilitates polymer infiltration, thus favoring intermixing of the two semiconducting phases, essential for charge separation. The 3D nanoparticle network is analyzed with tools from stochastic geometry to extract information related to the charge transport in the hierarchical solar cell. In particular, the experimental dataset allows direct visualization of the percolation pathways that contribute to the photocurrent. PMID:25834481

A 3D Reconstruction Strategy of Vehicle Outline Based on Single-Pass Single-Polarization CSAR Data.

PubMed

Leping Chen; Daoxiang An; Xiaotao Huang; Zhimin Zhou

2017-11-01

In the last few years, interest in circular synthetic aperture radar (CSAR) acquisitions has arisen as a consequence of the potential achievement of 3D reconstructions over 360° azimuth angle variation. In real-world scenarios, full 3D reconstructions of arbitrary targets need multi-pass data, which makes the processing complex, money-consuming, and time expending. In this paper, we propose a processing strategy for the 3D reconstruction of vehicle, which can avoid using multi-pass data by introducing a priori information of vehicle's shape. Besides, the proposed strategy just needs the single-pass single-polarization CSAR data to perform vehicle's 3D reconstruction, which makes the processing much more economic and efficient. First, an analysis of the distribution of attributed scattering centers from vehicle facet model is presented. And the analysis results show that a smooth and continuous basic outline of vehicle could be extracted from the peak curve of a noncoherent processing image. Second, the 3D location of vehicle roofline is inferred from layover with empirical insets of the basic outline. At last, the basic line and roofline of the vehicle are used to estimate the vehicle's 3D information and constitute the vehicle's 3D outline. The simulated and measured data processing results prove the correctness and effectiveness of our proposed strategy.

A review on "A Novel Technique for Image Steganography Based on Block-DCT and Huffman Encoding"

NASA Astrophysics Data System (ADS)

Das, Rig; Tuithung, Themrichon

2013-03-01

This paper reviews the embedding and extraction algorithm proposed by "A. Nag, S. Biswas, D. Sarkar and P. P. Sarkar" on "A Novel Technique for Image Steganography based on Block-DCT and Huffman Encoding" in "International Journal of Computer Science and Information Technology, Volume 2, Number 3, June 2010" [3] and shows that the Extraction of Secret Image is Not Possible for the algorithm proposed in [3]. 8 bit Cover Image of size is divided into non joint blocks and a two dimensional Discrete Cosine Transformation (2-D DCT) is performed on each of the blocks. Huffman Encoding is performed on an 8 bit Secret Image of size and each bit of the Huffman Encoded Bit Stream is embedded in the frequency domain by altering the LSB of the DCT coefficients of Cover Image blocks. The Huffman Encoded Bit Stream and Huffman Table

The Tropical Brown Alga Lobophora variegata: A Source of Antiprotozoal Compounds

PubMed Central

Cantillo-Ciau, Zulema; Moo-Puc, Rosa; Quijano, Leovigildo; Freile-Pelegrín, Yolanda

2010-01-01

Lobophora variegata, a brown alga collected from the coast of the Yucatan peninsula, Mexico, was studied for antiprotozoal activity against Giardia intestinalis, Entamoeba histolytica and Trichomonas vaginalis. The whole extract showed the highest activity against T. vaginalis, with an IC50 value of 3.2 μg/mL. For the fractions, the best antiprotozoal activity was found in non-polar fractions. The chloroform fraction of the extract contained a major sulfoquinovosyldiacylglycerol (SQDG), identified as 1-O-palmitoyl-2-O-myristoyl-3-O-(6‴-sulfo-α-d-quinovopyranosyl)-glycerol (1), together with small amounts of 1,2-di-O-palmitoyl-3-O-(6‴-sulfo-α-d-quinovopyranosyl)-glycerol (2) and a new compound identified as 1-O-palmitoyl-2-O-oleoyl-3-O-(6‴-sulfo-α-d-quinovopyranosyl)-glycerol (3). Their structures were elucidated on the basis of chemical and enzymatic hydrolysis and careful analysis of FAB-MS and NMR spectroscopic data. This is the first report on the isolation of SQDGs from L. variegata. The mixture of 1–3 showed good activity against E. histolytica and moderate activity against T. vaginalis with IC50s of 3.9 and 8.0 μg/mL, respectively, however, the activity of 1–3 is not as effective as metronidazole. These results afford ground information for the potential use of the whole extract and fractions of this species in protozoal infections. PMID:20479979

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data.

PubMed

Suresh, Niraj; Stephens, Sean A; Adams, Lexor; Beck, Anthon N; McKinney, Adriana L; Varga, Tamas

2016-04-26

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and crop management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving plants. X-ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. We aimed to develop a costless and efficient tool that approximates the surface and volume of the root regardless of its shape from three-dimensional (3D) tomography data. The root structure of a Prairie dropseed (Sporobolus heterolepis) specimen was imaged using XCT. The root was reconstructed, and the primary root structure was extracted from the data using a combination of licensed and open-source software. An isosurface polygonal mesh was then created for ease of analysis. We have developed the standalone application imeshJ, generated in MATLAB(1), to calculate root volume and surface area from the mesh. The outputs of imeshJ are surface area (in mm(2)) and the volume (in mm(3)). The process, utilizing a unique combination of tools from imaging to quantitative root analysis, is described. A combination of XCT and open-source software proved to be a powerful combination to noninvasively image plant root samples, segment root data, and extract quantitative information from the 3D data. This methodology of processing 3D data should be applicable to other material/sample systems where there is connectivity between components of similar X-ray attenuation and difficulties arise with segmentation.

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Generalized Feature Extraction for Wrist Pulse Analysis: From 1-D Time Series to 2-D Matrix.

PubMed

Dimin Wang; Zhang, David; Guangming Lu

2017-07-01

Traditional Chinese pulse diagnosis, known as an empirical science, depends on the subjective experience. Inconsistent diagnostic results may be obtained among different practitioners. A scientific way of studying the pulse should be to analyze the objectified wrist pulse waveforms. In recent years, many pulse acquisition platforms have been developed with the advances in sensor and computer technology. And the pulse diagnosis using pattern recognition theories is also increasingly attracting attentions. Though many literatures on pulse feature extraction have been published, they just handle the pulse signals as simple 1-D time series and ignore the information within the class. This paper presents a generalized method of pulse feature extraction, extending the feature dimension from 1-D time series to 2-D matrix. The conventional wrist pulse features correspond to a particular case of the generalized models. The proposed method is validated through pattern classification on actual pulse records. Both quantitative and qualitative results relative to the 1-D pulse features are given through diabetes diagnosis. The experimental results show that the generalized 2-D matrix feature is effective in extracting both the periodic and nonperiodic information. And it is practical for wrist pulse analysis.

View-invariant gait recognition method by three-dimensional convolutional neural network

NASA Astrophysics Data System (ADS)

Xing, Weiwei; Li, Ying; Zhang, Shunli

2018-01-01

Gait as an important biometric feature can identify a human at a long distance. View change is one of the most challenging factors for gait recognition. To address the cross view issues in gait recognition, we propose a view-invariant gait recognition method by three-dimensional (3-D) convolutional neural network. First, 3-D convolutional neural network (3DCNN) is introduced to learn view-invariant feature, which can capture the spatial information and temporal information simultaneously on normalized silhouette sequences. Second, a network training method based on cross-domain transfer learning is proposed to solve the problem of the limited gait training samples. We choose the C3D as the basic model, which is pretrained on the Sports-1M and then fine-tune C3D model to adapt gait recognition. In the recognition stage, we use the fine-tuned model to extract gait features and use Euclidean distance to measure the similarity of gait sequences. Sufficient experiments are carried out on the CASIA-B dataset and the experimental results demonstrate that our method outperforms many other methods.

Plenoptic Imaging of a Three Dimensional Cold Atom Cloud

NASA Astrophysics Data System (ADS)

Lott, Gordon

2017-04-01

A plenoptic imaging system is capable of sampling the rays of light in a volume, both spatially and angularly, providing information about the three dimensional (3D) volume being imaged. The extraction of the 3D structure of a cold atom cloud is demonstrated, using a single plenoptic camera and a single image. The reconstruction is tested against a reference image and the results discussed along with the capabilities and limitations of the imaging system. This capability is useful when the 3D distribution of the atoms is desired, such as determining the shape of an atom trap, particularly when there is limited optical access. Gratefully acknowledge support from AFRL.

Fusion of Remote Sensing Methods, UAV Photogrammetry and LiDAR Scanning products for monitoring fluvial dynamics

NASA Astrophysics Data System (ADS)

Lendzioch, Theodora; Langhammer, Jakub; Hartvich, Filip

2015-04-01

Fusion of remote sensing data is a common and rapidly developing discipline, which combines data from multiple sources with different spatial and spectral resolution, from satellite sensors, aircraft and ground platforms. Fusion data contains more detailed information than each of the source and enhances the interpretation performance and accuracy of the source data and produces a high-quality visualisation of the final data. Especially, in fluvial geomorphology it is essential to get valuable images in sub-meter resolution to obtain high quality 2D and 3D information for a detailed identification, extraction and description of channel features of different river regimes and to perform a rapid mapping of changes in river topography. In order to design, test and evaluate a new approach for detection of river morphology, we combine different research techniques from remote sensing products to drone-based photogrammetry and LiDAR products (aerial LiDAR Scanner and TLS). Topographic information (e.g. changes in river channel morphology, surface roughness, evaluation of floodplain inundation, mapping gravel bars and slope characteristics) will be extracted either from one single layer or from combined layers in accordance to detect fluvial topographic changes before and after flood events. Besides statistical approaches for predictive geomorphological mapping and the determination of errors and uncertainties of the data, we will also provide 3D modelling of small fluvial features.

A 3D terrain reconstruction method of stereo vision based quadruped robot navigation system

NASA Astrophysics Data System (ADS)

Ge, Zhuo; Zhu, Ying; Liang, Guanhao

2017-01-01

To provide 3D environment information for the quadruped robot autonomous navigation system during walking through rough terrain, based on the stereo vision, a novel 3D terrain reconstruction method is presented. In order to solve the problem that images collected by stereo sensors have large regions with similar grayscale and the problem that image matching is poor at real-time performance, watershed algorithm and fuzzy c-means clustering algorithm are combined for contour extraction. Aiming at the problem of error matching, duel constraint with region matching and pixel matching is established for matching optimization. Using the stereo matching edge pixel pairs, the 3D coordinate algorithm is estimated according to the binocular stereo vision imaging model. Experimental results show that the proposed method can yield high stereo matching ratio and reconstruct 3D scene quickly and efficiently.

Extracting 3D Parametric Curves from 2D Images of Helical Objects.

PubMed

Willcocks, Chris G; Jackson, Philip T G; Nelson, Carl J; Obara, Boguslaw

2017-09-01

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively.

Fusion of 3D laser scanner and depth images for obstacle recognition in mobile applications

NASA Astrophysics Data System (ADS)

Budzan, Sebastian; Kasprzyk, Jerzy

2016-02-01

The problem of obstacle detection and recognition or, generally, scene mapping is one of the most investigated problems in computer vision, especially in mobile applications. In this paper a fused optical system using depth information with color images gathered from the Microsoft Kinect sensor and 3D laser range scanner data is proposed for obstacle detection and ground estimation in real-time mobile systems. The algorithm consists of feature extraction in the laser range images, processing of the depth information from the Kinect sensor, fusion of the sensor information, and classification of the data into two separate categories: road and obstacle. Exemplary results are presented and it is shown that fusion of information gathered from different sources increases the effectiveness of the obstacle detection in different scenarios, and it can be used successfully for road surface mapping.

Image-Based Airborne LiDAR Point Cloud Encoding for 3d Building Model Retrieval

NASA Astrophysics Data System (ADS)

Chen, Yi-Chen; Lin, Chao-Hung

2016-06-01

With the development of Web 2.0 and cyber city modeling, an increasing number of 3D models have been available on web-based model-sharing platforms with many applications such as navigation, urban planning, and virtual reality. Based on the concept of data reuse, a 3D model retrieval system is proposed to retrieve building models similar to a user-specified query. The basic idea behind this system is to reuse these existing 3D building models instead of reconstruction from point clouds. To efficiently retrieve models, the models in databases are compactly encoded by using a shape descriptor generally. However, most of the geometric descriptors in related works are applied to polygonal models. In this study, the input query of the model retrieval system is a point cloud acquired by Light Detection and Ranging (LiDAR) systems because of the efficient scene scanning and spatial information collection. Using Point clouds with sparse, noisy, and incomplete sampling as input queries is more difficult than that by using 3D models. Because that the building roof is more informative than other parts in the airborne LiDAR point cloud, an image-based approach is proposed to encode both point clouds from input queries and 3D models in databases. The main goal of data encoding is that the models in the database and input point clouds can be consistently encoded. Firstly, top-view depth images of buildings are generated to represent the geometry surface of a building roof. Secondly, geometric features are extracted from depth images based on height, edge and plane of building. Finally, descriptors can be extracted by spatial histograms and used in 3D model retrieval system. For data retrieval, the models are retrieved by matching the encoding coefficients of point clouds and building models. In experiments, a database including about 900,000 3D models collected from the Internet is used for evaluation of data retrieval. The results of the proposed method show a clear superiority over related methods.

Digital relief generation from 3D models

NASA Astrophysics Data System (ADS)

Wang, Meili; Sun, Yu; Zhang, Hongming; Qian, Kun; Chang, Jian; He, Dongjian

2016-09-01

It is difficult to extend image-based relief generation to high-relief generation, as the images contain insufficient height information. To generate reliefs from three-dimensional (3D) models, it is necessary to extract the height fields from the model, but this can only generate bas-reliefs. To overcome this problem, an efficient method is proposed to generate bas-reliefs and high-reliefs directly from 3D meshes. To produce relief features that are visually appropriate, the 3D meshes are first scaled. 3D unsharp masking is used to enhance the visual features in the 3D mesh, and average smoothing and Laplacian smoothing are implemented to achieve better smoothing results. A nonlinear variable scaling scheme is then employed to generate the final bas-reliefs and high-reliefs. Using the proposed method, relief models can be generated from arbitrary viewing positions with different gestures and combinations of multiple 3D models. The generated relief models can be printed by 3D printers. The proposed method provides a means of generating both high-reliefs and bas-reliefs in an efficient and effective way under the appropriate scaling factors.

Extracting, Tracking, and Visualizing Magnetic Flux Vortices in 3D Complex-Valued Superconductor Simulation Data.

PubMed

Guo, Hanqi; Phillips, Carolyn L; Peterka, Tom; Karpeyev, Dmitry; Glatz, Andreas

2016-01-01

We propose a method for the vortex extraction and tracking of superconducting magnetic flux vortices for both structured and unstructured mesh data. In the Ginzburg-Landau theory, magnetic flux vortices are well-defined features in a complex-valued order parameter field, and their dynamics determine electromagnetic properties in type-II superconductors. Our method represents each vortex line (a 1D curve embedded in 3D space) as a connected graph extracted from the discretized field in both space and time. For a time-varying discrete dataset, our vortex extraction and tracking method is as accurate as the data discretization. We then apply 3D visualization and 2D event diagrams to the extraction and tracking results to help scientists understand vortex dynamics and macroscale superconductor behavior in greater detail than previously possible.

A framework for automatic feature extraction from airborne light detection and ranging data

NASA Astrophysics Data System (ADS)

Yan, Jianhua

Recent advances in airborne Light Detection and Ranging (LIDAR) technology allow rapid and inexpensive measurements of topography over large areas. Airborne LIDAR systems usually return a 3-dimensional cloud of point measurements from reflective objects scanned by the laser beneath the flight path. This technology is becoming a primary method for extracting information of different kinds of geometrical objects, such as high-resolution digital terrain models (DTMs), buildings and trees, etc. In the past decade, LIDAR gets more and more interest from researchers in the field of remote sensing and GIS. Compared to the traditional data sources, such as aerial photography and satellite images, LIDAR measurements are not influenced by sun shadow and relief displacement. However, voluminous data pose a new challenge for automated extraction the geometrical information from LIDAR measurements because many raster image processing techniques cannot be directly applied to irregularly spaced LIDAR points. In this dissertation, a framework is proposed to filter out information about different kinds of geometrical objects, such as terrain and buildings from LIDAR automatically. They are essential to numerous applications such as flood modeling, landslide prediction and hurricane animation. The framework consists of several intuitive algorithms. Firstly, a progressive morphological filter was developed to detect non-ground LIDAR measurements. By gradually increasing the window size and elevation difference threshold of the filter, the measurements of vehicles, vegetation, and buildings are removed, while ground data are preserved. Then, building measurements are identified from no-ground measurements using a region growing algorithm based on the plane-fitting technique. Raw footprints for segmented building measurements are derived by connecting boundary points and are further simplified and adjusted by several proposed operations to remove noise, which is caused by irregularly spaced LIDAR measurements. To reconstruct 3D building models, the raw 2D topology of each building is first extracted and then further adjusted. Since the adjusting operations for simple building models do not work well on 2D topology, 2D snake algorithm is proposed to adjust 2D topology. The 2D snake algorithm consists of newly defined energy functions for topology adjusting and a linear algorithm to find the minimal energy value of 2D snake problems. Data sets from urbanized areas including large institutional, commercial, and small residential buildings were employed to test the proposed framework. The results demonstrated that the proposed framework achieves a very good performance.

A Workstation for Interactive Display and Quantitative Analysis of 3-D and 4-D Biomedical Images

PubMed Central

Robb, R.A.; Heffeman, P.B.; Camp, J.J.; Hanson, D.P.

1986-01-01

The capability to extract objective and quantitatively accurate information from 3-D radiographic biomedical images has not kept pace with the capabilities to produce the images themselves. This is rather an ironic paradox, since on the one hand the new 3-D and 4-D imaging capabilities promise significant potential for providing greater specificity and sensitivity (i.e., precise objective discrimination and accurate quantitative measurement of body tissue characteristics and function) in clinical diagnostic and basic investigative imaging procedures than ever possible before, but on the other hand, the momentous advances in computer and associated electronic imaging technology which have made these 3-D imaging capabilities possible have not been concomitantly developed for full exploitation of these capabilities. Therefore, we have developed a powerful new microcomputer-based system which permits detailed investigations and evaluation of 3-D and 4-D (dynamic 3-D) biomedical images. The system comprises a special workstation to which all the information in a large 3-D image data base is accessible for rapid display, manipulation, and measurement. The system provides important capabilities for simultaneously representing and analyzing both structural and functional data and their relationships in various organs of the body. This paper provides a detailed description of this system, as well as some of the rationale, background, theoretical concepts, and practical considerations related to system implementation. ImagesFigure 5Figure 7Figure 8Figure 9Figure 10Figure 11Figure 12Figure 13Figure 14Figure 15Figure 16

3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

PubMed Central

Cho, Nam-Hoon; Choi, Heung-Kook

2014-01-01

One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system. PMID:25371701

Multimodal-3D imaging based on μMRI and μCT techniques bridges the gap with histology in visualization of the bone regeneration process.

PubMed

Sinibaldi, R; Conti, A; Sinjari, B; Spadone, S; Pecci, R; Palombo, M; Komlev, V S; Ortore, M G; Tromba, G; Capuani, S; Guidotti, R; De Luca, F; Caputi, S; Traini, T; Della Penna, S

2018-03-01

Bone repair/regeneration is usually investigated through X-ray computed microtomography (μCT) supported by histology of extracted samples, to analyse biomaterial structure and new bone formation processes. Magnetic resonance imaging (μMRI) shows a richer tissue contrast than μCT, despite at lower resolution, and could be combined with μCT in the perspective of conducting non-destructive 3D investigations of bone. A pipeline designed to combine μMRI and μCT images of bone samples is here described and applied on samples of extracted human jawbone core following bone graft. We optimized the coregistration procedure between μCT and μMRI images to avoid bias due to the different resolutions and contrasts. Furthermore, we used an Adaptive Multivariate Clustering, grouping homologous voxels in the coregistered images, to visualize different tissue types within a fused 3D metastructure. The tissue grouping matched the 2D histology applied only on 1 slice, thus extending the histology labelling in 3D. Specifically, in all samples, we could separate and map 2 types of regenerated bone, calcified tissue, soft tissues, and/or fat and marrow space. Remarkably, μMRI and μCT alone were not able to separate the 2 types of regenerated bone. Finally, we computed volumes of each tissue in the 3D metastructures, which might be exploited by quantitative simulation. The 3D metastructure obtained through our pipeline represents a first step to bridge the gap between the quality of information obtained from 2D optical microscopy and the 3D mapping of the bone tissue heterogeneity and could allow researchers and clinicians to non-destructively characterize and follow-up bone regeneration. Copyright © 2017 John Wiley & Sons, Ltd.

iGRaND: an invariant frame for RGBD sensor feature detection and descriptor extraction with applications

NASA Astrophysics Data System (ADS)

Willis, Andrew R.; Brink, Kevin M.

2016-06-01

This article describes a new 3D RGBD image feature, referred to as iGRaND, for use in real-time systems that use these sensors for tracking, motion capture, or robotic vision applications. iGRaND features use a novel local reference frame derived from the image gradient and depth normal (hence iGRaND) that is invariant to scale and viewpoint for Lambertian surfaces. Using this reference frame, Euclidean invariant feature components are computed at keypoints which fuse local geometric shape information with surface appearance information. The performance of the feature for real-time odometry is analyzed and its computational complexity and accuracy is compared with leading alternative 3D features.

Highway 3D model from image and lidar data

NASA Astrophysics Data System (ADS)

Chen, Jinfeng; Chu, Henry; Sun, Xiaoduan

2014-05-01

We present a new method of highway 3-D model construction developed based on feature extraction in highway images and LIDAR data. We describe the processing road coordinate data that connect the image frames to the coordinates of the elevation data. Image processing methods are used to extract sky, road, and ground regions as well as significant objects (such as signs and building fronts) in the roadside for the 3D model. LIDAR data are interpolated and processed to extract the road lanes as well as other features such as trees, ditches, and elevated objects to form the 3D model. 3D geometry reasoning is used to match the image features to the 3D model. Results from successive frames are integrated to improve the final model.

Automated Ontology Generation Using Spatial Reasoning

NASA Astrophysics Data System (ADS)

Coalter, Alton; Leopold, Jennifer L.

Recently there has been much interest in using ontologies to facilitate knowledge representation, integration, and reasoning. Correspondingly, the extent of the information embodied by an ontology is increasing beyond the conventional is_a and part_of relationships. To address these requirements, a vast amount of digitally available information may need to be considered when building ontologies, prompting a desire for software tools to automate at least part of the process. The main efforts in this direction have involved textual information retrieval and extraction methods. For some domains extension of the basic relationships could be enhanced further by the analysis of 2D and/or 3D images. For this type of media, image processing algorithms are more appropriate than textual analysis methods. Herein we present an algorithm that, given a collection of 3D image files, utilizes Qualitative Spatial Reasoning (QSR) to automate the creation of an ontology for the objects represented by the images, relating the objects in terms of is_a and part_of relationships and also through unambiguous Relational Connection Calculus (RCC) relations.

Hybrid Automatic Building Interpretation System

NASA Astrophysics Data System (ADS)

Pakzad, K.; Klink, A.; Müterthies, A.; Gröger, G.; Stroh, V.; Plümer, L.

2011-09-01

HABIS (Hybrid Automatic Building Interpretation System) is a system for an automatic reconstruction of building roofs used in virtual 3D building models. Unlike most of the commercially available systems, HABIS is able to work to a high degree automatically. The hybrid method uses different sources intending to exploit the advantages of the particular sources. 3D point clouds usually provide good height and surface data, whereas spatial high resolution aerial images provide important information for edges and detail information for roof objects like dormers or chimneys. The cadastral data provide important basis information about the building ground plans. The approach used in HABIS works with a multi-stage-process, which starts with a coarse roof classification based on 3D point clouds. After that it continues with an image based verification of these predicted roofs. In a further step a final classification and adjustment of the roofs is done. In addition some roof objects like dormers and chimneys are also extracted based on aerial images and added to the models. In this paper the used methods are described and some results are presented.

Three-dimensional kinematics of the lumbar spine during gait using marker-based systems: a systematic review.

PubMed

Needham, Robert; Stebbins, Julie; Chockalingam, Nachiappan

2016-01-01

To review the current scientific literature on the assessment of three-dimensional movement of the lumbar spine with a focus on the utilisation of a 3D cluster. Electronic databases PubMed, OVID, CINAHL, The Cochrance Library, ScienceDirect, ProQuest and Web of Knowledge were searched between 1966 and March 2015. The reference lists of the articles that met the inclusion criteria were also searched. From the 1530 articles identified through an initial search, 16 articles met the inclusion criteria. All information relating to methodology and kinematic modelling of the lumbar segment along with the outcome measures were extracted from the studies identified for synthesis. Guidelines detailing 3D cluster construction were limited in the identified articles and the lack of information presented makes it difficult to assess the external validity of this technique. Scarce information was presented detailing time-series angle data of the lumbar spine during gait. Further developments of the 3D cluster technique are required and it is essential that the authors provide clear instruction, definitions and standards in their manuscript to improve clarity and reproducibility.

Progress in building a cognitive vision system

NASA Astrophysics Data System (ADS)

Benjamin, D. Paul; Lyons, Damian; Yue, Hong

2016-05-01

We are building a cognitive vision system for mobile robots that works in a manner similar to the human vision system, using saccadic, vergence and pursuit movements to extract information from visual input. At each fixation, the system builds a 3D model of a small region, combining information about distance, shape, texture and motion to create a local dynamic spatial model. These local 3D models are composed to create an overall 3D model of the robot and its environment. This approach turns the computer vision problem into a search problem whose goal is the acquisition of sufficient spatial understanding for the robot to succeed at its tasks. The research hypothesis of this work is that the movements of the robot's cameras are only those that are necessary to build a sufficiently accurate world model for the robot's current goals. For example, if the goal is to navigate through a room, the model needs to contain any obstacles that would be encountered, giving their approximate positions and sizes. Other information does not need to be rendered into the virtual world, so this approach trades model accuracy for speed.

Multilevel Contextual 3-D CNNs for False Positive Reduction in Pulmonary Nodule Detection.

PubMed

Dou, Qi; Chen, Hao; Yu, Lequan; Qin, Jing; Heng, Pheng-Ann

2017-07-01

False positive reduction is one of the most crucial components in an automated pulmonary nodule detection system, which plays an important role in lung cancer diagnosis and early treatment. The objective of this paper is to effectively address the challenges in this task and therefore to accurately discriminate the true nodules from a large number of candidates. We propose a novel method employing three-dimensional (3-D) convolutional neural networks (CNNs) for false positive reduction in automated pulmonary nodule detection from volumetric computed tomography (CT) scans. Compared with its 2-D counterparts, the 3-D CNNs can encode richer spatial information and extract more representative features via their hierarchical architecture trained with 3-D samples. More importantly, we further propose a simple yet effective strategy to encode multilevel contextual information to meet the challenges coming with the large variations and hard mimics of pulmonary nodules. The proposed framework has been extensively validated in the LUNA16 challenge held in conjunction with ISBI 2016, where we achieved the highest competition performance metric (CPM) score in the false positive reduction track. Experimental results demonstrated the importance and effectiveness of integrating multilevel contextual information into 3-D CNN framework for automated pulmonary nodule detection in volumetric CT data. While our method is tailored for pulmonary nodule detection, the proposed framework is general and can be easily extended to many other 3-D object detection tasks from volumetric medical images, where the targeting objects have large variations and are accompanied by a number of hard mimics.

Phytochemical Composition and Antioxidant Activities of Dianthus Thunbergii Hooper and Hypoxis Argentea Harv Ex Baker: Plants Used for the Management of Diabetes Mellitus in Eastern Cape, South Africa.

PubMed

Akinrinde, Akinleye Stephen; Afolayan, Anthony Jide; Bradley, Graeme

2018-01-01

Inhabitants of the Eastern Cape Province of South Africa use the roots of Dianthus thunbergii and corms of Hypoxis argentea to treat diabetes mellitus and other ailments. The objective of this study was to analyze the phytochemical composition and antioxidant activities of the aqueous and ethanol extracts of the roots and corms of two plants. Total phenolics, flavonoids, flavonols, proanthocyanidins, tannins, and alkaloids were determined by standard methods. The scavenging activities of the extracts against 1,1 diphenyl-2-picrylhydrazyl (DPPH), 2'-azino-bis (3-ethylbenthiazoline-6-sulfonic acid (ABTS), nitric oxide (NO), hydrogen peroxide (H 2 O 2 ), and their ferric-reducing antioxidant potentials (FRAPs) were measured. The ethanol extract of H. argentea had the highest content of phenolics (66.71 ± 2.71 mg gallic acid equivalent/g) and tannins (1.18 ± 0.07 mg TAE/g), while the ethanol extract of D. thunbergii gave higher contents of flavonoids and proanthocyanidins (62.21 ± 1.75 mg Qe/g and 432.62 ± 2.43 mg Ca/g, respectively). Flavonols were the most predominant in the aqueous extract of H. argentea (25.51 ± 1.92 mg Qe/g). We observed a concentration-dependent response in the ABTS- and H 2 O 2 -scavenging activities and FRAP values of the extracts and standards (Vitamin C, butylated hydroxytoluene, and rutin). The ethanol extracts of both plants generally demonstrated better antioxidant activities against H 2 O 2 , NO, and ABTS while also possessing better reducing power than the aqueous extracts. The aqueous extract of D. thunbergii , however, showed the best DPPH scavenging activity. The higher content of phytochemicals and antioxidant capacity obtained for the ethanol extracts of D. thunbergii and H. argentea may prove to be valuable information in selecting suitable extraction solvents for the medicinal applications of both plants. Ethanol extracts of Hypoxis argentea had the highest levels of phenolics and tanninsEthanol extracts of Dianthus thunbergii had the highest levels of flavonoids and proanthocyanidinsEthanol extracts of both plants possess better antioxidant activityagainst hydrogen peroxide, nitric oxide, and ABTS as well as higher reducingpower than the aqueous extractsAqueous extract of Dianthus thunbergii had the highest free radical scavenging activity as measured with DPPH. Abbreviations used: ABTS: 2'-azino-bis (3-ethylbenthiazoline-6-sulfonic acid); BHT: Butylated hydroxytoluene; DPPH: 1,1 diphenyl-2-picrylhydrazyl; DTA: Dianthus thunbergii aqueous extract (16.6%); DTE: Dianthus thunbergii ethanol extract (2.4%); Fe 3+ -TPTZ: Ferric tripyridyltriazine; FRAP: Ferric-reducing antioxidant potentials; GAE: Gallic acid equivalent; HAA: Hypoxis argentea aqueous extract (3.2%); HAE: Hypoxis argentea ethanol extract (1.8%); Qe: Quercetin equivalence; ROS: Reactive oxygen species; TBA: Thiobarbituric acid;TCA: Trichloroacetic acid.

Ear recognition from one sample per person.

PubMed

Chen, Long; Mu, Zhichun; Zhang, Baoqing; Zhang, Yi

2015-01-01

Biometrics has the advantages of efficiency and convenience in identity authentication. As one of the most promising biometric-based methods, ear recognition has received broad attention and research. Previous studies have achieved remarkable performance with multiple samples per person (MSPP) in the gallery. However, most conventional methods are insufficient when there is only one sample per person (OSPP) available in the gallery. To solve the OSPP problem by maximizing the use of a single sample, this paper proposes a hybrid multi-keypoint descriptor sparse representation-based classification (MKD-SRC) ear recognition approach based on 2D and 3D information. Because most 3D sensors capture 3D data accessorizing the corresponding 2D data, it is sensible to use both types of information. First, the ear region is extracted from the profile. Second, keypoints are detected and described for both the 2D texture image and 3D range image. Then, the hybrid MKD-SRC algorithm is used to complete the recognition with only OSPP in the gallery. Experimental results on a benchmark dataset have demonstrated the feasibility and effectiveness of the proposed method in resolving the OSPP problem. A Rank-one recognition rate of 96.4% is achieved for a gallery of 415 subjects, and the time involved in the computation is satisfactory compared to conventional methods.

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

A 3D Model Based Imdoor Navigation System for Hubei Provincial Museum

NASA Astrophysics Data System (ADS)

Xu, W.; Kruminaite, M.; Onrust, B.; Liu, H.; Xiong, Q.; Zlatanova, S.

2013-11-01

3D models are more powerful than 2D maps for indoor navigation in a complicate space like Hubei Provincial Museum because they can provide accurate descriptions of locations of indoor objects (e.g., doors, windows, tables) and context information of these objects. In addition, the 3D model is the preferred navigation environment by the user according to the survey. Therefore a 3D model based indoor navigation system is developed for Hubei Provincial Museum to guide the visitors of museum. The system consists of three layers: application, web service and navigation, which is built to support localization, navigation and visualization functions of the system. There are three main strengths of this system: it stores all data needed in one database and processes most calculations on the webserver which make the mobile client very lightweight, the network used for navigation is extracted semi-automatically and renewable, the graphic user interface (GUI), which is based on a game engine, has high performance of visualizing 3D model on a mobile display.

A strategy for efficient discovery of new natural compounds by integrating orthogonal column chromatography and liquid chromatography/mass spectrometry analysis: Its application in Panax ginseng, Panax quinquefolium and Panax notoginseng to characterize 437 potential new ginsenosides.

PubMed

Yang, Wen-zhi; Ye, Min; Qiao, Xue; Liu, Chun-fang; Miao, Wen-juan; Bo, Tao; Tao, Hai-yan; Guo, De-an

2012-08-20

To discover new natural compounds from herbal medicines tends to be more and more difficult. In this paper, a strategy integrating orthogonal column chromatography and liquid chromatography/mass spectrometry (LC/MS) analysis was proposed, and was applied for rapid discovery of new ginsenosides from Panax ginseng (PG), Panax quinquefolium (PQ), and Panax notoginseng (PN). The ginsenosides extracts were fractionated by MCI gel×silica gel orthogonal column chromatography. The fractions were then separated on a C(18) HPLC column, eluted with a three-component mobile phase (CH(3)CN/CH(3)OH/3mM CH(3)COONH(4)H(2)O), and detected by electrospray ionization tandem mass spectrometry. The structures of unknown ginsenosides were elucidated by analyzing negative and positive ion mass spectra, which provided complementary information on the sapogenins and oligosaccharide chains, respectively. A total of 623 comprising 437 potential new ginsenosides were characterized from the ethanol extracts of PG, PQ and PN. New acylations, diversified saccharide chains and C-17 side chains constituted novelty of the newly identified ginsenosides. An interpretation guideline was proposed for structural characterization of unknown ginsenosides by LC/MS. To confirm reliability of this strategy, two targeted unknown trace ginsenosides were obtained in pure form by LC/MS-guided isolation. Based on extensive NMR spectroscopic analysis and other techniques, they were identified as 3-O-[6-O-(E)-butenoyl-β-D-glucopyranosyl(1,2)-β-D-glucopyranosyl]-20(S)-protopanaxadiol-20-O-β-D-glucopyranosyl(1,6)-β-D-glucopyranoside (named ginsenoside IV) and 3-O-β-D-glucopyranosyl(1,2)-β-D-glucopyranosyl-3β,12β,20(S),24(R)-tetra hydroxy-dammar-25-ene-20-O-β-D-glucopyranosyl(1,6)-β-D-glucopyranoside (ginsenoside V), respectively. The fully established structures were consistent with the MS-oriented structural elucidation. This study expanded our understanding on ginsenosides of Panax species, and the proposed strategy was proved efficient and reliable in the discovery of new minor compounds from herbal extracts. Copyright © 2012 Elsevier B.V. All rights reserved.

Plenoptic layer-based modeling for image based rendering.

PubMed

Pearson, James; Brookes, Mike; Dragotti, Pier Luigi

2013-09-01

Image based rendering is an attractive alternative to model based rendering for generating novel views because of its lower complexity and potential for photo-realistic results. To reduce the number of images necessary for alias-free rendering, some geometric information for the 3D scene is normally necessary. In this paper, we present a fast automatic layer-based method for synthesizing an arbitrary new view of a scene from a set of existing views. Our algorithm takes advantage of the knowledge of the typical structure of multiview data to perform occlusion-aware layer extraction. In addition, the number of depth layers used to approximate the geometry of the scene is chosen based on plenoptic sampling theory with the layers placed non-uniformly to account for the scene distribution. The rendering is achieved using a probabilistic interpolation approach and by extracting the depth layer information on a small number of key images. Numerical results demonstrate that the algorithm is fast and yet is only 0.25 dB away from the ideal performance achieved with the ground-truth knowledge of the 3D geometry of the scene of interest. This indicates that there are measurable benefits from following the predictions of plenoptic theory and that they remain true when translated into a practical system for real world data.

Solid object visualization of 3D ultrasound data

NASA Astrophysics Data System (ADS)

Nelson, Thomas R.; Bailey, Michael J.

2000-04-01

Visualization of volumetric medical data is challenging. Rapid-prototyping (RP) equipment producing solid object prototype models of computer generated structures is directly applicable to visualization of medical anatomic data. The purpose of this study was to develop methods for transferring 3D Ultrasound (3DUS) data to RP equipment for visualization of patient anatomy. 3DUS data were acquired using research and clinical scanning systems. Scaling information was preserved and the data were segmented using threshold and local operators to extract features of interest, converted from voxel raster coordinate format to a set of polygons representing an iso-surface and transferred to the RP machine to create a solid 3D object. Fabrication required 30 to 60 minutes depending on object size and complexity. After creation the model could be touched and viewed. A '3D visualization hardcopy device' has advantages for conveying spatial relations compared to visualization using computer display systems. The hardcopy model may be used for teaching or therapy planning. Objects may be produced at the exact dimension of the original object or scaled up (or down) to facilitate matching the viewers reference frame more optimally. RP models represent a useful means of communicating important information in a tangible fashion to patients and physicians.

Low-Rank Tensor Subspace Learning for RGB-D Action Recognition.

PubMed

Jia, Chengcheng; Fu, Yun

2016-07-09

Since RGB-D action data inherently equip with extra depth information compared with RGB data, recently many works employ RGB-D data in a third-order tensor representation containing spatio-temporal structure to find a subspace for action recognition. However, there are two main challenges of these methods. First, the dimension of subspace is usually fixed manually. Second, preserving local information by finding intraclass and inter-class neighbors from a manifold is highly timeconsuming. In this paper, we learn a tensor subspace, whose dimension is learned automatically by low-rank learning, for RGB-D action recognition. Particularly, the tensor samples are factorized to obtain three Projection Matrices (PMs) by Tucker Decomposition, where all the PMs are performed by nuclear norm in a close-form to obtain the tensor ranks which are used as tensor subspace dimension. Additionally, we extract the discriminant and local information from a manifold using a graph constraint. This graph preserves the local knowledge inherently, which is faster than the previous way by calculating both the intra-class and inter-class neighbors of each sample. We evaluate the proposed method on four widely used RGB-D action datasets including MSRDailyActivity3D, MSRActionPairs, MSRActionPairs skeleton and UTKinect-Action3D datasets, and the experimental results show higher accuracy and efficiency of the proposed method.

D Modeling of Components of a Garden by Using Point Cloud Data

NASA Astrophysics Data System (ADS)

Kumazakia, R.; Kunii, Y.

2016-06-01

Laser measurement is currently applied to several tasks such as plumbing management, road investigation through mobile mapping systems, and elevation model utilization through airborne LiDAR. Effective laser measurement methods have been well-documented in civil engineering, but few attempts have been made to establish equally effective methods in landscape engineering. By using point cloud data acquired through laser measurement, the aesthetic landscaping of Japanese gardens can be enhanced. This study focuses on simple landscape simulations for pruning and rearranging trees as well as rearranging rocks, lanterns, and other garden features by using point cloud data. However, such simulations lack concreteness. Therefore, this study considers the construction of a library of garden features extracted from point cloud data. The library would serve as a resource for creating new gardens and simulating gardens prior to conducting repairs. Extracted garden features are imported as 3ds Max objects, and realistic 3D models are generated by using a material editor system. As further work toward the publication of a 3D model library, file formats for tree crowns and trunks should be adjusted. Moreover, reducing the size of created models is necessary. Models created using point cloud data are informative because simply shaped garden features such as trees are often seen in the 3D industry.

Document Exploration and Automatic Knowledge Extraction for Unstructured Biomedical Text

NASA Astrophysics Data System (ADS)

Chu, S.; Totaro, G.; Doshi, N.; Thapar, S.; Mattmann, C. A.; Ramirez, P.

2015-12-01

We describe our work on building a web-browser based document reader with built-in exploration tool and automatic concept extraction of medical entities for biomedical text. Vast amounts of biomedical information are offered in unstructured text form through scientific publications and R&D reports. Utilizing text mining can help us to mine information and extract relevant knowledge from a plethora of biomedical text. The ability to employ such technologies to aid researchers in coping with information overload is greatly desirable. In recent years, there has been an increased interest in automatic biomedical concept extraction [1, 2] and intelligent PDF reader tools with the ability to search on content and find related articles [3]. Such reader tools are typically desktop applications and are limited to specific platforms. Our goal is to provide researchers with a simple tool to aid them in finding, reading, and exploring documents. Thus, we propose a web-based document explorer, which we called Shangri-Docs, which combines a document reader with automatic concept extraction and highlighting of relevant terms. Shangri-Docsalso provides the ability to evaluate a wide variety of document formats (e.g. PDF, Words, PPT, text, etc.) and to exploit the linked nature of the Web and personal content by performing searches on content from public sites (e.g. Wikipedia, PubMed) and private cataloged databases simultaneously. Shangri-Docsutilizes Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) [4] and Unified Medical Language System (UMLS) to automatically identify and highlight terms and concepts, such as specific symptoms, diseases, drugs, and anatomical sites, mentioned in the text. cTAKES was originally designed specially to extract information from clinical medical records. Our investigation leads us to extend the automatic knowledge extraction process of cTAKES for biomedical research domain by improving the ontology guided information extraction process. We will describe our experience and implementation of our system and share lessons learned from our development. We will also discuss ways in which this could be adapted to other science fields. [1] Funk et al., 2014. [2] Kang et al., 2014. [3] Utopia Documents, http://utopiadocs.com [4] Apache cTAKES, http://ctakes.apache.org

Research on three-dimensional reconstruction method based on binocular vision

NASA Astrophysics Data System (ADS)

Li, Jinlin; Wang, Zhihui; Wang, Minjun

2018-03-01

As the hot and difficult issue in computer vision, binocular stereo vision is an important form of computer vision,which has a broad application prospects in many computer vision fields,such as aerial mapping,vision navigation,motion analysis and industrial inspection etc.In this paper, a research is done into binocular stereo camera calibration, image feature extraction and stereo matching. In the binocular stereo camera calibration module, the internal parameters of a single camera are obtained by using the checkerboard lattice of zhang zhengyou the field of image feature extraction and stereo matching, adopted the SURF operator in the local feature operator and the SGBM algorithm in the global matching algorithm are used respectively, and the performance are compared. After completed the feature points matching, we can build the corresponding between matching points and the 3D object points using the camera parameters which are calibrated, which means the 3D information.

Speckle-interferometric measurement system of 3D deformation to obtain thickness changes of thin specimen under tensile loads

NASA Astrophysics Data System (ADS)

Kowarsch, Robert; Zhang, Jiajun; Sguazzo, Carmen; Hartmann, Stefan; Rembe, Christian

2017-06-01

The analysis of materials and geometries in tensile tests and the extraction of mechanic parameters is an important field in solid mechanics. Especially the measurement of thickness changes is important to obtain accurate strain information of specimens under tensile loads. Current optical measurement methods comprising 3D digital image correlation enable thickness-change measurement only with nm-resolution. We present a phase-shifting electronic speckle-pattern interferometer in combination with speckle-correlation technique to measure the 3D deformation. The phase-shift for the interferometer is introduced by fast wavelength tuning of a visible diode laser by injection current. In a post-processing step, both measurements can be combined to reconstruct the 3D deformation. In this contribution, results of a 3Ddeformation measurement for a polymer membrane are presented. These measurements show sufficient resolution for the detection of 3D deformations of thin specimen in tensile test. In future work we address the thickness changes of thin specimen under tensile loads.

No-Reference Video Quality Assessment Based on Statistical Analysis in 3D-DCT Domain.

PubMed

Li, Xuelong; Guo, Qun; Lu, Xiaoqiang

2016-05-13

It is an important task to design models for universal no-reference video quality assessment (NR-VQA) in multiple video processing and computer vision applications. However, most existing NR-VQA metrics are designed for specific distortion types which are not often aware in practical applications. A further deficiency is that the spatial and temporal information of videos is hardly considered simultaneously. In this paper, we propose a new NR-VQA metric based on the spatiotemporal natural video statistics (NVS) in 3D discrete cosine transform (3D-DCT) domain. In the proposed method, a set of features are firstly extracted based on the statistical analysis of 3D-DCT coefficients to characterize the spatiotemporal statistics of videos in different views. These features are used to predict the perceived video quality via the efficient linear support vector regression (SVR) model afterwards. The contributions of this paper are: 1) we explore the spatiotemporal statistics of videos in 3DDCT domain which has the inherent spatiotemporal encoding advantage over other widely used 2D transformations; 2) we extract a small set of simple but effective statistical features for video visual quality prediction; 3) the proposed method is universal for multiple types of distortions and robust to different databases. The proposed method is tested on four widely used video databases. Extensive experimental results demonstrate that the proposed method is competitive with the state-of-art NR-VQA metrics and the top-performing FR-VQA and RR-VQA metrics.

Bim-Based Indoor Path Planning Considering Obstacles

NASA Astrophysics Data System (ADS)

Xu, M.; Wei, S.; Zlatanova, S.; Zhang, R.

2017-09-01

At present, 87 % of people's activities are in indoor environment; indoor navigation has become a research issue. As the building structures for people's daily life are more and more complex, many obstacles influence humans' moving. Therefore it is essential to provide an accurate and efficient indoor path planning. Nowadays there are many challenges and problems in indoor navigation. Most existing path planning approaches are based on 2D plans, pay more attention to the geometric configuration of indoor space, often ignore rich semantic information of building components, and mostly consider simple indoor layout without taking into account the furniture. Addressing the above shortcomings, this paper uses BIM (IFC) as the input data and concentrates on indoor navigation considering obstacles in the multi-floor buildings. After geometric and semantic information are extracted, 2D and 3D space subdivision methods are adopted to build the indoor navigation network and to realize a path planning that avoids obstacles. The 3D space subdivision is based on triangular prism. The two approaches are verified by the experiments.

Porosity, permeability and 3D fracture network characterisation of dolomite reservoir rock samples

PubMed Central

Voorn, Maarten; Exner, Ulrike; Barnhoorn, Auke; Baud, Patrick; Reuschlé, Thierry

2015-01-01

With fractured rocks making up an important part of hydrocarbon reservoirs worldwide, detailed analysis of fractures and fracture networks is essential. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) however suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this paper, we therefore explore the use of an additional method – non-destructive 3D X-ray micro-Computed Tomography (μCT) – to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. We process the 3D μCT data in this study by a Hessian-based fracture filtering routine and can successfully extract porosity, fracture aperture, fracture density and fracture orientations – in bulk as well as locally. Additionally, thin sections made from selected plug samples provide 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) towards more realistic reservoir conditions. This study shows that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that although there are limitations, several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other methods can therefore be a powerful approach in microstructural analysis of reservoir rocks, especially when applying the concepts that we present (on a small set of samples) in a larger study, in an automated and standardised manner. PMID:26549935

Porosity, permeability and 3D fracture network characterisation of dolomite reservoir rock samples.

PubMed

Voorn, Maarten; Exner, Ulrike; Barnhoorn, Auke; Baud, Patrick; Reuschlé, Thierry

2015-03-01

With fractured rocks making up an important part of hydrocarbon reservoirs worldwide, detailed analysis of fractures and fracture networks is essential. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) however suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this paper, we therefore explore the use of an additional method - non-destructive 3D X-ray micro-Computed Tomography (μCT) - to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. We process the 3D μCT data in this study by a Hessian-based fracture filtering routine and can successfully extract porosity, fracture aperture, fracture density and fracture orientations - in bulk as well as locally. Additionally, thin sections made from selected plug samples provide 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) towards more realistic reservoir conditions. This study shows that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that although there are limitations, several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other methods can therefore be a powerful approach in microstructural analysis of reservoir rocks, especially when applying the concepts that we present (on a small set of samples) in a larger study, in an automated and standardised manner.

Antibacterial, antioxidant, anti-cholinesterase potential and flavonol glycosides of Biscutella raphanifolia (Brassicaceae).

PubMed

Boudouda, Houria Berhail; Zeghib, Assia; Karioti, Anastazia; Bilia, Anna Rita; Öztürk, Mehmet; Aouni, Mahjoub; Kabouche, Ahmed; Kabouche, Zahia

2015-01-01

Different extracts of the aerial parts of Biscutella raphanifolia (Brassicaceae), which has not been the subject of any study, were screened for the phytochemical content, anti-microbial, antioxidant and anti-cholinesterase activities. We used four methods to identify the antioxidant activity namely, ABTS(•+), DPPH• scavenging, CUPRAC and ferrous-ions chelating methods. Since there is a relationship between antioxidants and cholinesterase enzyme inhibitors, we used two methods to determine the in vitro anti-cholinesterase activity by the use of the basic enzymes that occur in causing Alzheimer's disease: acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The extracts were also tested in vitro antimicrobial activity against various bacteria. The phytochemical study of B. raphanifolia afforded four flavonol glycosides; namely, quercetin-3-O-β-D-g1ucoside, quercetin-3-O-[β-D-glucosyl(1→2)-O-β-D-glucoside], quercetin-3-O-[β-D-glucosyl(1→3)-O-β-D-glucoside] and kaempferol-3-O-[β-D-glucosyl(1→2)-[(6'''p-coumaroyl)- β-D-glucoside], being isolated here for the first time from Biscutella raphanifolia and the genus. The ethyl acetate extract showed the highest activity in ABTS(•+), DPPH• and CUPRAC assays, while the petroleum ether extract demonstrated optimum efficiency metal chelating activity. The dicloromethane and petroleum ether extracts showed a mild inhibition against AChE and BChE. However, the petroleum ether extract showed a good antibacterial activity against the pathovars Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC) and Enterococcus feacalis, whereas the Enterohemorrhagic E. coli (EHEC) strain was more sensitive to dichloromethane and n-butanol extracts.

An automatic rat brain extraction method based on a deformable surface model.

PubMed

Li, Jiehua; Liu, Xiaofeng; Zhuo, Jiachen; Gullapalli, Rao P; Zara, Jason M

2013-08-15

The extraction of the brain from the skull in medical images is a necessary first step before image registration or segmentation. While pre-clinical MR imaging studies on small animals, such as rats, are increasing, fully automatic imaging processing techniques specific to small animal studies remain lacking. In this paper, we present an automatic rat brain extraction method, the Rat Brain Deformable model method (RBD), which adapts the popular human brain extraction tool (BET) through the incorporation of information on the brain geometry and MR image characteristics of the rat brain. The robustness of the method was demonstrated on T2-weighted MR images of 64 rats and compared with other brain extraction methods (BET, PCNN, PCNN-3D). The results demonstrate that RBD reliably extracts the rat brain with high accuracy (>92% volume overlap) and is robust against signal inhomogeneity in the images. Copyright © 2013 Elsevier B.V. All rights reserved.

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

DOE PAGES

Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan; ...

2017-05-04

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere. X-ray Computed Tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and in-house developed code was used to non-invasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure, and extract quantitative information from the 3D data, respectively. Based on the explicitly-resolved root structure, pore-scale computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soilmore » hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. Furthermore, the coupled imaging-modeling approach demonstrates a realistic platform to investigate rhizosphere flow processes and would be feasible to provide useful information linked to upscaled models.« less

A hybrid approach for fusing 4D-MRI temporal information with 3D-CT for the study of lung and lung tumor motion.

PubMed

Yang, Y X; Teo, S-K; Van Reeth, E; Tan, C H; Tham, I W K; Poh, C L

2015-08-01

Accurate visualization of lung motion is important in many clinical applications, such as radiotherapy of lung cancer. Advancement in imaging modalities [e.g., computed tomography (CT) and MRI] has allowed dynamic imaging of lung and lung tumor motion. However, each imaging modality has its advantages and disadvantages. The study presented in this paper aims at generating synthetic 4D-CT dataset for lung cancer patients by combining both continuous three-dimensional (3D) motion captured by 4D-MRI and the high spatial resolution captured by CT using the authors' proposed approach. A novel hybrid approach based on deformable image registration (DIR) and finite element method simulation was developed to fuse a static 3D-CT volume (acquired under breath-hold) and the 3D motion information extracted from 4D-MRI dataset, creating a synthetic 4D-CT dataset. The study focuses on imaging of lung and lung tumor. Comparing the synthetic 4D-CT dataset with the acquired 4D-CT dataset of six lung cancer patients based on 420 landmarks, accurate results (average error <2 mm) were achieved using the authors' proposed approach. Their hybrid approach achieved a 40% error reduction (based on landmarks assessment) over using only DIR techniques. The synthetic 4D-CT dataset generated has high spatial resolution, has excellent lung details, and is able to show movement of lung and lung tumor over multiple breathing cycles.

Enhanced visualization of the retinal vasculature using depth information in OCT.

PubMed

de Moura, Joaquim; Novo, Jorge; Charlón, Pablo; Barreira, Noelia; Ortega, Marcos

2017-12-01

Retinal vessel tree extraction is a crucial step for analyzing the microcirculation, a frequently needed process in the study of relevant diseases. To date, this has normally been done by using 2D image capture paradigms, offering a restricted visualization of the real layout of the retinal vasculature. In this work, we propose a new approach that automatically segments and reconstructs the 3D retinal vessel tree by combining near-infrared reflectance retinography information with Optical Coherence Tomography (OCT) sections. Our proposal identifies the vessels, estimates their calibers, and obtains the depth at all the positions of the entire vessel tree, thereby enabling the reconstruction of the 3D layout of the complete arteriovenous tree for subsequent analysis. The method was tested using 991 OCT images combined with their corresponding near-infrared reflectance retinography. The different stages of the methodology were validated using the opinion of an expert as a reference. The tests offered accurate results, showing coherent reconstructions of the 3D vasculature that can be analyzed in the diagnosis of relevant diseases affecting the retinal microcirculation, such as hypertension or diabetes, among others.

Fabric pilling measurement using three-dimensional image

NASA Astrophysics Data System (ADS)

Ouyang, Wenbin; Wang, Rongwu; Xu, Bugao

2013-10-01

We introduce a stereovision system and the three-dimensional (3-D) image analysis algorithms for fabric pilling measurement. Based on the depth information available in the 3-D image, the pilling detection process starts from the seed searching at local depth maxima to the region growing around the selected seeds using both depth and distance criteria. After the pilling detection, the density, height, and area of individual pills in the image can be extracted to describe the pilling appearance. According to the multivariate regression analysis on the 3-D images of 30 cotton fabrics treated by the random-tumble and home-laundering machines, the pilling grade is highly correlated with the pilling density (R=0.923) but does not consistently change with the pilling height and area. The pilling densities measured from the 3-D images also correlate well with those counted manually from the samples (R=0.985).

Three-dimensional shape perception from chromatic orientation flows

PubMed Central

Zaidi, Qasim; Li, Andrea

2010-01-01

The role of chromatic information in 3-D shape perception is controversial. We resolve this controversy by showing that chromatic orientation flows are sufficient for accurate perception of 3-D shape. Chromatic flows required less cone contrast to convey shape than did achromatic flows, thus ruling out luminance artifacts as a problem. Luminance artifacts were also ruled out by a protanope’s inability to see 3-D shape from chromatic flows. Since chromatic orientation flows can only be extracted from retinal images by neurons that are responsive to color modulations and selective for orientation, the psychophysical results also resolve the controversy over the existence of such neurons. In addition, we show that identification of 3-D shapes from chromatic flows can be masked by luminance modulations, indicating that it is subserved by orientation-tuned neurons sensitive to both chromatic and luminance modulations. PMID:16961963

Joint inversions of two VTEM surveys using quasi-3D TDEM and 3D magnetic inversion algorithms

NASA Astrophysics Data System (ADS)

Kaminski, Vlad; Di Massa, Domenico; Viezzoli, Andrea

2016-05-01

In the current paper, we present results of a joint quasi-three-dimensional (quasi-3D) inversion of two versatile time domain electromagnetic (VTEM) datasets, as well as a joint 3D inversion of associated aeromagnetic datasets, from two surveys flown six years apart from one another (2007 and 2013) over a volcanogenic massive sulphide gold (VMS-Au) prospect in northern Ontario, Canada. The time domain electromagnetic (TDEM) data were inverted jointly using the spatially constrained inversion (SCI) approach. In order to increase the coherency in the model space, a calibration parameter was added. This was followed by a joint inversion of the total magnetic intensity (TMI) data extracted from the two surveys. The results of the inversions have been studied and matched with the known geology, adding some new valuable information to the ongoing mineral exploration initiative.

Crustal structure of Australia from ambient seismic noise tomography

NASA Astrophysics Data System (ADS)

Saygin, Erdinc; Kennett, B. L. N.

2012-01-01

Surface wave tomography for Australian crustal structure has been carried out using group velocity measurements in the period range 1-32 s extracted from stacked correlations of ambient noise between station pairs. Both Rayleigh wave and Love wave group velocity maps are constructed for each period using the vertical and transverse component of the Green's function estimates from the ambient noise. The full suite of portable broadband deployments and permanent stations on the continent have been used with over 250 stations in all and up to 7500 paths. The permanent stations provide a useful link between the various shorter-term portable deployments. At each period the group velocity maps are constructed with a fully nonlinear tomographic inversion exploiting a subspace technique and the Fast Marching Method for wavefront tracking. For Rayleigh waves the continental coverage is good enough to allow the construction of a 3D shear wavespeed model in a two stage approach. Local group dispersion information is collated for a distribution of points across the continent and inverted for a 1D SV wavespeed profile using a Neighbourhood Algorithm method. The resulting set of 1D models are then interpolated to produce the final 3D wavespeed model. The group velocity maps show the strong influence of thick sediments at shorter periods, and distinct fast zones associated with cratonic regions. Below the sediments the 3D shear wavespeed model displays significant heterogeneity with only moderate correlation with surface tectonic features. For example, there is no evident expression of the Tasman Line marking the eastern edge of Precambrian outcrop. The large number of available inter-station paths extracted from the ambient noise analysis provide detailed shear wavespeed information for crustal structure across the Australian continent for the first time, including regions where there was no prior sampling because of difficult logistics.

Spatiotemporal Features of the Three-Dimensional Architectural Landscape in Qingdao, China.

PubMed

Zhang, Peifeng

2015-01-01

The evolution and development of the three-dimensional (3D) architectural landscape is the basis of proper urban planning, eco-environment construction and the improvement of environmental quality. This paper presents the spatiotemporal characteristics of the 3D architectural landscape of the Shinan and Shibei districts in Qingdao, China, based on buildings' 3D information extracted from Quickbird images from 2003 to 2012, supported by Barista, landscape metrics and GIS. The results demonstrated that: (1) Shinan and Shibei districts expanded vertically and urban land use intensity increased noticeably from year to year. (2) Significant differences in the 3D architectural landscape existed among the western, central and eastern regions, and among the 26 sub-districts over the study period. The differentiation was consistent with the diverse development history, function and planning of the two districts. Finally, we found that population correlates positively with the variation in the 3D architectural landscape. This research provides an important reference for related studies, urban planning and eco-city construction.

Spatiotemporal Features of the Three-Dimensional Architectural Landscape in Qingdao, China

PubMed Central

Zhang, Peifeng

2015-01-01

The evolution and development of the three-dimensional (3D) architectural landscape is the basis of proper urban planning, eco-environment construction and the improvement of environmental quality. This paper presents the spatiotemporal characteristics of the 3D architectural landscape of the Shinan and Shibei districts in Qingdao, China, based on buildings’ 3D information extracted from Quickbird images from 2003 to 2012, supported by Barista, landscape metrics and GIS. The results demonstrated that: (1) Shinan and Shibei districts expanded vertically and urban land use intensity increased noticeably from year to year. (2) Significant differences in the 3D architectural landscape existed among the western, central and eastern regions, and among the 26 sub-districts over the study period. The differentiation was consistent with the diverse development history, function and planning of the two districts. Finally, we found that population correlates positively with the variation in the 3D architectural landscape. This research provides an important reference for related studies, urban planning and eco-city construction. PMID:26361016

Biologically Inspired Model for Inference of 3D Shape from Texture

PubMed Central

Gomez, Olman; Neumann, Heiko

2016-01-01

A biologically inspired model architecture for inferring 3D shape from texture is proposed. The model is hierarchically organized into modules roughly corresponding to visual cortical areas in the ventral stream. Initial orientation selective filtering decomposes the input into low-level orientation and spatial frequency representations. Grouping of spatially anisotropic orientation responses builds sketch-like representations of surface shape. Gradients in orientation fields and subsequent integration infers local surface geometry and globally consistent 3D depth. From the distributions in orientation responses summed in frequency, an estimate of the tilt and slant of the local surface can be obtained. The model suggests how 3D shape can be inferred from texture patterns and their image appearance in a hierarchically organized processing cascade along the cortical ventral stream. The proposed model integrates oriented texture gradient information that is encoded in distributed maps of orientation-frequency representations. The texture energy gradient information is defined by changes in the grouped summed normalized orientation-frequency response activity extracted from the textured object image. This activity is integrated by directed fields to generate a 3D shape representation of a complex object with depth ordering proportional to the fields output, with higher activity denoting larger distance in relative depth away from the viewer. PMID:27649387

Transferring of speech movements from video to 3D face space.

PubMed

Pei, Yuru; Zha, Hongbin

2007-01-01

We present a novel method for transferring speech animation recorded in low quality videos to high resolution 3D face models. The basic idea is to synthesize the animated faces by an interpolation based on a small set of 3D key face shapes which span a 3D face space. The 3D key shapes are extracted by an unsupervised learning process in 2D video space to form a set of 2D visemes which are then mapped to the 3D face space. The learning process consists of two main phases: 1) Isomap-based nonlinear dimensionality reduction to embed the video speech movements into a low-dimensional manifold and 2) K-means clustering in the low-dimensional space to extract 2D key viseme frames. Our main contribution is that we use the Isomap-based learning method to extract intrinsic geometry of the speech video space and thus to make it possible to define the 3D key viseme shapes. To do so, we need only to capture a limited number of 3D key face models by using a general 3D scanner. Moreover, we also develop a skull movement recovery method based on simple anatomical structures to enhance 3D realism in local mouth movements. Experimental results show that our method can achieve realistic 3D animation effects with a small number of 3D key face models.

GIS prospectivity mapping and 3D modeling validation for potential uranium deposit targets in Shangnan district, China

NASA Astrophysics Data System (ADS)

Xie, Jiayu; Wang, Gongwen; Sha, Yazhou; Liu, Jiajun; Wen, Botao; Nie, Ming; Zhang, Shuai

2017-04-01

Integrating multi-source geoscience information (such as geology, geophysics, geochemistry, and remote sensing) using GIS mapping is one of the key topics and frontiers in quantitative geosciences for mineral exploration. GIS prospective mapping and three-dimensional (3D) modeling can be used not only to extract exploration criteria and delineate metallogenetic targets but also to provide important information for the quantitative assessment of mineral resources. This paper uses the Shangnan district of Shaanxi province (China) as a case study area. GIS mapping and potential granite-hydrothermal uranium targeting were conducted in the study area combining weights of evidence (WofE) and concentration-area (C-A) fractal methods with multi-source geoscience information. 3D deposit-scale modeling using GOCAD software was performed to validate the shapes and features of the potential targets at the subsurface. The research results show that: (1) the known deposits have potential zones at depth, and the 3D geological models can delineate surface or subsurface ore-forming features, which can be used to analyze the uncertainty of the shape and feature of prospectivity mapping at the subsurface; (2) single geochemistry anomalies or remote sensing anomalies at the surface require combining the depth exploration criteria of geophysics to identify potential targets; and (3) the single or sparse exploration criteria zone with few mineralization spots at the surface has high uncertainty in terms of the exploration target.

Modeling and Inversion of three-dimensional crustal structures beneath the Pyrenees and their foreland basins based upon geological, gravimetric and seismological data

NASA Astrophysics Data System (ADS)

Spangenberg, Hannah; Chevrot, Sébastien; Courrioux, Gabriel; Guillen, Antonio

2017-04-01

Our goal is to obtain a three-dimensional (3D) model of mass density and seismic velocities beneath the Pyrenees and their foreland basins (Aquitaine and Ebro basins), which accounts for all the geological and geophysical information available for that region. This model covers the whole mountain range going from the Atlantic Ocean to the Mediterranean Sea, and from the Iberian range to the Massif Central. The model is described by different units: the lower, middle, and upper crusts, the accretionary prism, and the consolidated and unconsolidated sediment layers. Furthermore, a sub-continental, serpentinized European mantle is introduced to describe the exhumed mantle bodies which are responsible for the positive Bouguer gravity anomalies in the western Pyrenees. We build a first 3D model using all the geological information: drill-hole surveys, seismic sections, and the geological map. We use the potential field method implemented in Geomodeler to interpolate these geological data. However, these data are too sparse to build a model that explains seismic travel times or gravimetric data, especially the Labourd and the St. Gaudens Bouguer gravity anomalies. In addition, inconsistencies between the different data sets exist. We thus add by trial and error additional data points, comparing modeled and observed Bouguer gravimetric anomalies. The result of this procedure is a 3D geological model that respects the geological data and explains the measured Bouguer gravimetric anomalies. In a second step, we use this model to determine the average density and seismic velocities inside each geological unit assuming uniform layers. To constrain the seismic velocities we use travel time picks extracted from the bulletin of the Pyrenean seismicity released by the Observatoire Midi Pyrenées. In a third step, we use this 3D a priori model in a Monte Carlo inversion to invert jointly gravimetric data and seismic travel times from the bulletin. This probabilistic approach yields detailed information about the sedimentary foreland basins and the crustal structures beneath the Pyrenees. We will present and discuss different key steps of the construction of the 3D model of the Pyrenees. We will also compare selected cross-sections extracted from this model to the ECORS profiles, as well as CCP stacks of receiver functions along several PYROPE transects. Keywords: Pyrenees, 3D modeling, gravity, seismic tomography, joint inversion

An ROI multi-resolution compression method for 3D-HEVC

NASA Astrophysics Data System (ADS)

Ti, Chunli; Guan, Yudong; Xu, Guodong; Teng, Yidan; Miao, Xinyuan

2017-09-01

3D High Efficiency Video Coding (3D-HEVC) provides a significant potential on increasing the compression ratio of multi-view RGB-D videos. However, the bit rate still rises dramatically with the improvement of the video resolution, which will bring challenges to the transmission network, especially the mobile network. This paper propose an ROI multi-resolution compression method for 3D-HEVC to better preserve the information in ROI on condition of limited bandwidth. This is realized primarily through ROI extraction and compression multi-resolution preprocessed video as alternative data according to the network conditions. At first, the semantic contours are detected by the modified structured forests to restrain the color textures inside objects. The ROI is then determined utilizing the contour neighborhood along with the face region and foreground area of the scene. Secondly, the RGB-D videos are divided into slices and compressed via 3D-HEVC under different resolutions for selection by the audiences and applications. Afterwards, the reconstructed low-resolution videos from 3D-HEVC encoder are directly up-sampled via Laplace transformation and used to replace the non-ROI areas of the high-resolution videos. Finally, the ROI multi-resolution compressed slices are obtained by compressing the ROI preprocessed videos with 3D-HEVC. The temporal and special details of non-ROI are reduced in the low-resolution videos, so the ROI will be better preserved by the encoder automatically. Experiments indicate that the proposed method can keep the key high-frequency information with subjective significance while the bit rate is reduced.

Active surface model improvement by energy function optimization for 3D segmentation.

PubMed

Azimifar, Zohreh; Mohaddesi, Mahsa

2015-04-01

This paper proposes an optimized and efficient active surface model by improving the energy functions, searching method, neighborhood definition and resampling criterion. Extracting an accurate surface of the desired object from a number of 3D images using active surface and deformable models plays an important role in computer vision especially medical image processing. Different powerful segmentation algorithms have been suggested to address the limitations associated with the model initialization, poor convergence to surface concavities and slow convergence rate. This paper proposes a method to improve one of the strongest and recent segmentation algorithms, namely the Decoupled Active Surface (DAS) method. We consider a gradient of wavelet edge extracted image and local phase coherence as external energy to extract more information from images and we use curvature integral as internal energy to focus on high curvature region extraction. Similarly, we use resampling of points and a line search for point selection to improve the accuracy of the algorithm. We further employ an estimation of the desired object as an initialization for the active surface model. A number of tests and experiments have been done and the results show the improvements with regards to the extracted surface accuracy and computational time of the presented algorithm compared with the best and recent active surface models. Copyright © 2015 Elsevier Ltd. All rights reserved.

3D Face Modeling Using the Multi-Deformable Method

PubMed Central

Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

2012-01-01

In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper. PMID:23201976

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

DAVIS: A direct algorithm for velocity-map imaging system

NASA Astrophysics Data System (ADS)

Harrison, G. R.; Vaughan, J. C.; Hidle, B.; Laurent, G. M.

2018-05-01

In this work, we report a direct (non-iterative) algorithm to reconstruct the three-dimensional (3D) momentum-space picture of any charged particles collected with a velocity-map imaging system from the two-dimensional (2D) projected image captured by a position-sensitive detector. The method consists of fitting the measured image with the 2D projection of a model 3D velocity distribution defined by the physics of the light-matter interaction. The meaningful angle-correlated information is first extracted from the raw data by expanding the image with a complete set of Legendre polynomials. Both the particle's angular and energy distributions are then directly retrieved from the expansion coefficients. The algorithm is simple, easy to implement, fast, and explicitly takes into account the pixelization effect in the measurement.

Ultrasonically extracted β-d-glucan from artificially cultivated mushroom, characteristic properties and antioxidant activity.

PubMed

Alzorqi, Ibrahim; Sudheer, Surya; Lu, Ting-Jang; Manickam, Sivakumar

2017-03-01

Ganoderma mushroom cultivated recently in Malaysia to produce chemically different nutritional fibers has attracted the attention of the local market. The extraction methods, molecular weight and degree of branching of (1-3; 1-6)-β-d-glucan polysaccharides is of prime importance to determine its antioxidant bioactivity. Therefore three extraction methods i.e. hot water extraction (HWE), soxhlet extraction (SE) and ultrasound assisted extraction (US) were employed to study the total content of (1-3; 1-6)-β-d-glucans, degree of branching, structural characteristics, monosaccharides composition, as well as the total yield of polysaccharides that could be obtained from the artificially cultivated Ganoderma. The physical characteristics by HPAEC-PAD, HPGPC and FTIR, as well as the antioxidant in vitro assays of DPPH scavenging activity and ferric reducing power (FRAP) indicated that (1-3; 1-6)-β-d-glucans of Malaysian mushroom have better antioxidant activity, higher molecular weight and optimal degree of branching when extracted by US in comparison with conventional methods. Copyright © 2016 Elsevier B.V. All rights reserved.

Non-rigid registration of 3D ultrasound for neurosurgery using automatic feature detection and matching.

PubMed

Machado, Inês; Toews, Matthew; Luo, Jie; Unadkat, Prashin; Essayed, Walid; George, Elizabeth; Teodoro, Pedro; Carvalho, Herculano; Martins, Jorge; Golland, Polina; Pieper, Steve; Frisken, Sarah; Golby, Alexandra; Wells, William

2018-06-04

The brain undergoes significant structural change over the course of neurosurgery, including highly nonlinear deformation and resection. It can be informative to recover the spatial mapping between structures identified in preoperative surgical planning and the intraoperative state of the brain. We present a novel feature-based method for achieving robust, fully automatic deformable registration of intraoperative neurosurgical ultrasound images. A sparse set of local image feature correspondences is first estimated between ultrasound image pairs, after which rigid, affine and thin-plate spline models are used to estimate dense mappings throughout the image. Correspondences are derived from 3D features, distinctive generic image patterns that are automatically extracted from 3D ultrasound images and characterized in terms of their geometry (i.e., location, scale, and orientation) and a descriptor of local image appearance. Feature correspondences between ultrasound images are achieved based on a nearest-neighbor descriptor matching and probabilistic voting model similar to the Hough transform. Experiments demonstrate our method on intraoperative ultrasound images acquired before and after opening of the dura mater, during resection and after resection in nine clinical cases. A total of 1620 automatically extracted 3D feature correspondences were manually validated by eleven experts and used to guide the registration. Then, using manually labeled corresponding landmarks in the pre- and post-resection ultrasound images, we show that our feature-based registration reduces the mean target registration error from an initial value of 3.3 to 1.5 mm. This result demonstrates that the 3D features promise to offer a robust and accurate solution for 3D ultrasound registration and to correct for brain shift in image-guided neurosurgery.

Algorithm of pulmonary emphysema extraction using thoracic 3D CT images

NASA Astrophysics Data System (ADS)

Saita, Shinsuke; Kubo, Mitsuru; Kawata, Yoshiki; Niki, Noboru; Nakano, Yasutaka; Ohmatsu, Hironobu; Tominaga, Keigo; Eguchi, Kenji; Moriyama, Noriyuki

2007-03-01

Recently, due to aging and smoking, emphysema patients are increasing. The restoration of alveolus which was destroyed by emphysema is not possible, thus early detection of emphysema is desired. We describe a quantitative algorithm for extracting emphysematous lesions and quantitatively evaluate their distribution patterns using low dose thoracic 3-D CT images. The algorithm identified lung anatomies, and extracted low attenuation area (LAA) as emphysematous lesion candidates. Applying the algorithm to thoracic 3-D CT images and then by follow-up 3-D CT images, we demonstrate its potential effectiveness to assist radiologists and physicians to quantitatively evaluate the emphysematous lesions distribution and their evolution in time interval changes.

Algorithm of pulmonary emphysema extraction using low dose thoracic 3D CT images

NASA Astrophysics Data System (ADS)

Saita, S.; Kubo, M.; Kawata, Y.; Niki, N.; Nakano, Y.; Omatsu, H.; Tominaga, K.; Eguchi, K.; Moriyama, N.

2006-03-01

Recently, due to aging and smoking, emphysema patients are increasing. The restoration of alveolus which was destroyed by emphysema is not possible, thus early detection of emphysema is desired. We describe a quantitative algorithm for extracting emphysematous lesions and quantitatively evaluate their distribution patterns using low dose thoracic 3-D CT images. The algorithm identified lung anatomies, and extracted low attenuation area (LAA) as emphysematous lesion candidates. Applying the algorithm to 100 thoracic 3-D CT images and then by follow-up 3-D CT images, we demonstrate its potential effectiveness to assist radiologists and physicians to quantitatively evaluate the emphysematous lesions distribution and their evolution in time interval changes.

Inhibitory effects of 1alpha, 25dihydroxyvitamin D3 and Ajuga iva extract on oxidative stress, toxicity and hypo-fertility in diabetic rat testes.

PubMed

Hamden, K; Carreau, S; Jamoussi, K; Ayadi, F; Garmazi, F; Mezgenni, N; Elfeki, A

2008-09-01

The aim of the current study is to investigate the therapeutic and preventive effects of 1alpha, 25dihydroxyvitaminD3 (1,25 (OH)2 D3) and Afuga iva (AI) extract on diabetes toxicity in rats testes. Thus diabetic rats were treated with 1alpha, 25dihydroxyvitaminD3 or Ajuga iva extract as both therapeutic and preventive treatments on diabetes toxicity in rats testes. Our results showed that diabetes induced a decrease in testosterone and 17beta-estradiol levels in testes and plasma. Besides, a fall in testicular antioxidant capacity appeared by a decrease in both antioxidant (superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx) activities) and nonenzymatic antioxidant (copper (Cu), magnesium (Mg) and iron (Fe) levels). All theses changes enhanced testicular toxicity (increase in testicular aspartate amino transaminase (AST), alanine amino transaminase (ALT), lactate dehydrogenase (LDH) activities and the lipid peroxidation and triglyceride (TG) levels). In addition, a decrease in testicular total cholesterol (TCh) level was observed in diabetic rats testes. All the changes lead to a decrease in the total number and mobility of epididymal spermatozoa. The administration of 1alpha,25dihydroxyvitaminD3 and Ajuga iva extract three weeks before and after diabetes induction interfered and prevented diabetes toxicity in the reproductive system. 1,25 (OH)2 D3 and Ajuga iva extract blunted all changes observed in diabetic rats. To sum up, the data suggested that 1,25 (OH)2 D3 and Ajuga iva extract have a protective effect on alloxan-induced damage in reproductive system by enhancing the testosterone and 17beta-estradiol levels, consequently protecting from oxidative stress, cellular toxicity and maintaining the number and motility of spermatozoids.

Bayesian depth estimation from monocular natural images.

PubMed

Su, Che-Chun; Cormack, Lawrence K; Bovik, Alan C

2017-05-01

Estimating an accurate and naturalistic dense depth map from a single monocular photographic image is a difficult problem. Nevertheless, human observers have little difficulty understanding the depth structure implied by photographs. Two-dimensional (2D) images of the real-world environment contain significant statistical information regarding the three-dimensional (3D) structure of the world that the vision system likely exploits to compute perceived depth, monocularly as well as binocularly. Toward understanding how this might be accomplished, we propose a Bayesian model of monocular depth computation that recovers detailed 3D scene structures by extracting reliable, robust, depth-sensitive statistical features from single natural images. These features are derived using well-accepted univariate natural scene statistics (NSS) models and recent bivariate/correlation NSS models that describe the relationships between 2D photographic images and their associated depth maps. This is accomplished by building a dictionary of canonical local depth patterns from which NSS features are extracted as prior information. The dictionary is used to create a multivariate Gaussian mixture (MGM) likelihood model that associates local image features with depth patterns. A simple Bayesian predictor is then used to form spatial depth estimates. The depth results produced by the model, despite its simplicity, correlate well with ground-truth depths measured by a current-generation terrestrial light detection and ranging (LIDAR) scanner. Such a strong form of statistical depth information could be used by the visual system when creating overall estimated depth maps incorporating stereopsis, accommodation, and other conditions. Indeed, even in isolation, the Bayesian predictor delivers depth estimates that are competitive with state-of-the-art "computer vision" methods that utilize highly engineered image features and sophisticated machine learning algorithms.

Decoding 2D-PAGE complex maps: relevance to proteomics.

PubMed

Pietrogrande, Maria Chiara; Marchetti, Nicola; Dondi, Francesco; Righetti, Pier Giorgio

2006-03-20

This review describes two mathematical approaches useful for decoding the complex signal of 2D-PAGE maps of protein mixtures. These methods are helpful for interpreting the large amount of data of each 2D-PAGE map by extracting all the analytical information hidden therein by spot overlapping. Here the basic theory and application to 2D-PAGE maps are reviewed: the means for extracting information from the experimental data and their relevance to proteomics are discussed. One method is based on the quantitative theory of statistical model of peak overlapping (SMO) using the spot experimental data (intensity and spatial coordinates). The second method is based on the study of the 2D-autocovariance function (2D-ACVF) computed on the experimental digitised map. They are two independent methods that are able to extract equal and complementary information from the 2D-PAGE map. Both methods permit to obtain fundamental information on the sample complexity and the separation performance and to single out ordered patterns present in spot positions: the availability of two independent procedures to compute the same separation parameters is a powerful tool to estimate the reliability of the obtained results. The SMO procedure is an unique tool to quantitatively estimate the degree of spot overlapping present in the map, while the 2D-ACVF method is particularly powerful in simply singling out the presence of order in the spot position from the complexity of the whole 2D map, i.e., spot trains. The procedures were validated by extensive numerical computation on computer-generated maps describing experimental 2D-PAGE gels of protein mixtures. Their applicability to real samples was tested on reference maps obtained from literature sources. The review describes the most relevant information for proteomics: sample complexity, separation performance, overlapping extent, identification of spot trains related to post-translational modifications (PTMs).

Phytochemical Composition and Antioxidant Activities of Dianthus Thunbergii Hooper and Hypoxis Argentea Harv Ex Baker: Plants Used for the Management of Diabetes Mellitus in Eastern Cape, South Africa

PubMed Central

Akinrinde, Akinleye Stephen; Afolayan, Anthony Jide; Bradley, Graeme

2018-01-01

Background: Inhabitants of the Eastern Cape Province of South Africa use the roots of Dianthus thunbergii and corms of Hypoxis argentea to treat diabetes mellitus and other ailments. Objective: The objective of this study was to analyze the phytochemical composition and antioxidant activities of the aqueous and ethanol extracts of the roots and corms of two plants. Materials and Methods: Total phenolics, flavonoids, flavonols, proanthocyanidins, tannins, and alkaloids were determined by standard methods. The scavenging activities of the extracts against 1,1 diphenyl-2-picrylhydrazyl (DPPH), 2'-azino-bis (3-ethylbenthiazoline-6-sulfonic acid (ABTS), nitric oxide (NO), hydrogen peroxide (H2O2), and their ferric-reducing antioxidant potentials (FRAPs) were measured. Results: The ethanol extract of H. argentea had the highest content of phenolics (66.71 ± 2.71 mg gallic acid equivalent/g) and tannins (1.18 ± 0.07 mg TAE/g), while the ethanol extract of D. thunbergii gave higher contents of flavonoids and proanthocyanidins (62.21 ± 1.75 mg Qe/g and 432.62 ± 2.43 mg Ca/g, respectively). Flavonols were the most predominant in the aqueous extract of H. argentea (25.51 ± 1.92 mg Qe/g). We observed a concentration-dependent response in the ABTS- and H2O2-scavenging activities and FRAP values of the extracts and standards (Vitamin C, butylated hydroxytoluene, and rutin). The ethanol extracts of both plants generally demonstrated better antioxidant activities against H2O2, NO, and ABTS while also possessing better reducing power than the aqueous extracts. The aqueous extract of D. thunbergii, however, showed the best DPPH scavenging activity. Conclusion: The higher content of phytochemicals and antioxidant capacity obtained for the ethanol extracts of D. thunbergii and H. argentea may prove to be valuable information in selecting suitable extraction solvents for the medicinal applications of both plants. SUMMARY Ethanol extracts of Hypoxis argentea had the highest levels of phenolics and tanninsEthanol extracts of Dianthus thunbergii had the highest levels of flavonoids and proanthocyanidinsEthanol extracts of both plants possess better antioxidant activityagainst hydrogen peroxide, nitric oxide, and ABTS as well as higher reducingpower than the aqueous extractsAqueous extract of Dianthus thunbergii had the highest free radical scavenging activity as measured with DPPH. Abbreviations used: ABTS: 2'-azino-bis (3-ethylbenthiazoline-6-sulfonic acid); BHT: Butylated hydroxytoluene; DPPH: 1,1 diphenyl-2-picrylhydrazyl; DTA: Dianthus thunbergii aqueous extract (16.6%); DTE: Dianthus thunbergii ethanol extract (2.4%); Fe3+-TPTZ: Ferric tripyridyltriazine; FRAP: Ferric-reducing antioxidant potentials; GAE: Gallic acid equivalent; HAA: Hypoxis argentea aqueous extract (3.2%); HAE: Hypoxis argentea ethanol extract (1.8%); Qe: Quercetin equivalence; ROS: Reactive oxygen species; TBA: Thiobarbituric acid;TCA: Trichloroacetic acid. PMID:29720831

Model for Semantically Rich Point Cloud Data

NASA Astrophysics Data System (ADS)

Poux, F.; Neuville, R.; Hallot, P.; Billen, R.

2017-10-01

This paper proposes an interoperable model for managing high dimensional point clouds while integrating semantics. Point clouds from sensors are a direct source of information physically describing a 3D state of the recorded environment. As such, they are an exhaustive representation of the real world at every scale: 3D reality-based spatial data. Their generation is increasingly fast but processing routines and data models lack of knowledge to reason from information extraction rather than interpretation. The enhanced smart point cloud developed model allows to bring intelligence to point clouds via 3 connected meta-models while linking available knowledge and classification procedures that permits semantic injection. Interoperability drives the model adaptation to potentially many applications through specialized domain ontologies. A first prototype is implemented in Python and PostgreSQL database and allows to combine semantic and spatial concepts for basic hybrid queries on different point clouds.

Action Recognition Using 3D Histograms of Texture and A Multi-Class Boosting Classifier.

PubMed

Zhang, Baochang; Yang, Yun; Chen, Chen; Yang, Linlin; Han, Jungong; Shao, Ling

2017-10-01

Human action recognition is an important yet challenging task. This paper presents a low-cost descriptor called 3D histograms of texture (3DHoTs) to extract discriminant features from a sequence of depth maps. 3DHoTs are derived from projecting depth frames onto three orthogonal Cartesian planes, i.e., the frontal, side, and top planes, and thus compactly characterize the salient information of a specific action, on which texture features are calculated to represent the action. Besides this fast feature descriptor, a new multi-class boosting classifier (MBC) is also proposed to efficiently exploit different kinds of features in a unified framework for action classification. Compared with the existing boosting frameworks, we add a new multi-class constraint into the objective function, which helps to maintain a better margin distribution by maximizing the mean of margin, whereas still minimizing the variance of margin. Experiments on the MSRAction3D, MSRGesture3D, MSRActivity3D, and UTD-MHAD data sets demonstrate that the proposed system combining 3DHoTs and MBC is superior to the state of the art.

The Pore3D library package for the textural analysis of X-ray computed microtomographic images of rocks

NASA Astrophysics Data System (ADS)

Zandomeneghi, Daria; Mancini, Lucia; Voltolini, Marco; Brun, Francesco; Polacci, Margherita

2010-05-01

Many research fields in Geosciences require the knowledge of the three-dimensional (3D) texture of rocks. X-ray computed microtomography (μCT) supplies an effective method to directly acquire 3D information. Transmission X-ray μCT is a non-destructive technique based on the mapping of the linear attenuation coefficient of X-rays crossing the investigated sample. The 3D distribution of constituents and the contrast based on the different absorption properties of the components can be enhanced by phase-contrast imaging. On an X-ray tomographic dataset, if spatial resolution at the micron scale and proper software are available, a complete textural and morphological quantitative analysis can be carried out and a number of parameters can be extracted, including geometry and organization of discrete rock components (such as crystals, vesicles, fractures, alteration-compositional zones). In the case of volcanic rocks, μCT can be used to image and quantify the textural and morphological characteristics of the rock constituents, such as vesicles (gas bubbles in solidified, erupted products), crystals and glass fibers. For pyroclastic rocks, investigated parameters to characterize the vesicle portion are the size distribution, geometry and orientation of the pores, the pore-throat size and organization, the pore-surface roughness and the topology of the overall pore and pore-throat network. In this work we present several procedures able to extract quantitative information from CT images of volcanic rocks. The imaging experiments have been carried out at the Elettra Synchrotron Light Laboratory in Trieste (Italy) using both the synchrotron radiation at the SYRMEP beamline and a custom-developed μCT system, named TOMOLAB, equipped with a microfocus X-ray tube and based on a cone-beam geometry. The reconstructed 3D images (or volumes) have been elaborated with a software library, named Pore3D, custom-developed by the SYRMEP group at Elettra. The Pore3D software library allows a quantitative description of the morphology and topology of the sample components and it operates directly in the 3D domain, without inferring about the 3D behavior from stacked 2D information. The library has been elaborated to merge together in a common environment some of the features already available in previous research and commercial software, customizing in some cases their applications, adding new tools for the artifact reduction in the tomographic images and enhancing state-of-the-art methods for the quantitative analysis, as based on the specific know-how acquired by the SYRMEP group. The microtomographic experiments on selected pumices and scoriae have given us the opportunity to reconstruct and study the 3D internal structure of very different samples, originated at volcanoes with unique eruptive behavior and hazard potential. In particular, the analysis of vesicle size, shape, distribution, orientation and degree of interconnectivity, quantifies aspects that are directly related to the magma nature and dynamics. In fact, magma near the Earth's surface exists as a multiphase system, including gas bubbles and solid crystals in a liquid medium. The rheology of the magma and the processes that govern the transition between effusive and explosive eruptions can be fully understood if the gas permeability and flow through the bubble networks are quantified. As pyroclasts are natural records of the magma state, in terms of texture and composition, during the last phases of the conduit ascent, the textural 3D information can be coupled to physical, rheological and chemical properties of the parent magma.

Rapid, semi-automatic fracture and contact mapping for point clouds, images and geophysical data

NASA Astrophysics Data System (ADS)

Thiele, Samuel T.; Grose, Lachlan; Samsu, Anindita; Micklethwaite, Steven; Vollgger, Stefan A.; Cruden, Alexander R.

2017-12-01

The advent of large digital datasets from unmanned aerial vehicle (UAV) and satellite platforms now challenges our ability to extract information across multiple scales in a timely manner, often meaning that the full value of the data is not realised. Here we adapt a least-cost-path solver and specially tailored cost functions to rapidly interpolate structural features between manually defined control points in point cloud and raster datasets. We implement the method in the geographic information system QGIS and the point cloud and mesh processing software CloudCompare. Using these implementations, the method can be applied to a variety of three-dimensional (3-D) and two-dimensional (2-D) datasets, including high-resolution aerial imagery, digital outcrop models, digital elevation models (DEMs) and geophysical grids. We demonstrate the algorithm with four diverse applications in which we extract (1) joint and contact patterns in high-resolution orthophotographs, (2) fracture patterns in a dense 3-D point cloud, (3) earthquake surface ruptures of the Greendale Fault associated with the Mw7.1 Darfield earthquake (New Zealand) from high-resolution light detection and ranging (lidar) data, and (4) oceanic fracture zones from bathymetric data of the North Atlantic. The approach improves the consistency of the interpretation process while retaining expert guidance and achieves significant improvements (35-65 %) in digitisation time compared to traditional methods. Furthermore, it opens up new possibilities for data synthesis and can quantify the agreement between datasets and an interpretation.

Root extractive from Daphne genkwa benefits in wound healing of anal fistula through up-regulation of collagen genes in human skin fibroblasts.

PubMed

Yang, Dong; Xu, Jun-Hua; Shi, Ren-Jie

2017-04-30

Wound healing is the main problem in the therapy of anal fistula (AF). Daphne genkwa root has been traditionally used as an agent to soak sutures in operation of AF patients, but its function in wound healing remains largely unclear. The aim of the present study was to illuminate mechanisms of D. genkwa root treatment on AF. In the present study, 60 AF patients after surgery were randomly divided into two groups, external applied with or without the D. genkwa extractive. Wound healing times were compared and granulation tissues were collected. In vitro , we constructed damaged human skin fibroblasts (HSFs) with the treatment of TNF-α (10 μg/ml). Cell Count Kit-8 (CCK-8) and flow cytometry analysis were used to determine the effects of D. genkwa root extractive on cell viability, cell cycle and apoptosis of damaged HSFs. Furthermore, protein levels of TGF-β, COL1A1, COL3A1, Timp-1 , matrix metalloproteinase (MMP)-3 ( MMP-3 ) and MEK/ERK signalling pathways were investigated both in vivo and in vitro Results showed that D. genkwa root extractive greatly shortens the wound healing time in AF patients. In granulation tissues and HSFs, treatment with the extractive significantly elevated the expressions of COL1A1, COL3A1, Timp-1, c-fos and Cyclin D1 , while reduced the expression of MMP-3 Further detection presented that MEK/ERK signalling was activated after the stimulation of extractive in HSFs. Our study demonstrated that extractive from D. genkwa root could effectively improve wound healing in patients with AF via the up-regulation of fibroblast proliferation and expressions of COL1A1 and COL3A1 . © 2017 The Author(s).

DOE Office of Scientific and Technical Information (OSTI.GOV)

An, Ho-Myoung; Kim, Hee-Dong; Kim, Tae Geun, E-mail: tgkim1@korea.ac.kr

Graphical abstract: The degradation tendency extracted by CP technique was almost the same in both the bulk-type and TFT-type cells. - Highlights: • D{sub it} is directly investigated from bulk-type and TFT-type CTF memory. • Charge pumping technique was employed to analyze the D{sub it} information. • To apply the CP technique to monitor the reliability of the 3D NAND flash. - Abstract: The energy distribution and density of interface traps (D{sub it}) are directly investigated from bulk-type and thin-film transistor (TFT)-type charge trap flash memory cells with tunnel oxide degradation, under program/erase (P/E) cycling using a charge pumping (CP)more » technique, in view of application in a 3-demension stackable NAND flash memory cell. After P/E cycling in bulk-type devices, the interface trap density gradually increased from 1.55 × 10{sup 12} cm{sup −2} eV{sup −1} to 3.66 × 10{sup 13} cm{sup −2} eV{sup −1} due to tunnel oxide damage, which was consistent with the subthreshold swing and transconductance degradation after P/E cycling. Its distribution moved toward shallow energy levels with increasing cycling numbers, which coincided with the decay rate degradation with short-term retention time. The tendency extracted with the CP technique for D{sub it} of the TFT-type cells was similar to those of bulk-type cells.« less

Extraction and visualization of the central chest lymph-node stations

NASA Astrophysics Data System (ADS)

Lu, Kongkuo; Merritt, Scott A.; Higgins, William E.

2008-03-01

Lung cancer remains the leading cause of cancer death in the United States and is expected to account for nearly 30% of all cancer deaths in 2007. Central to the lung-cancer diagnosis and staging process is the assessment of the central chest lymph nodes. This assessment typically requires two major stages: (1) location of the lymph nodes in a three-dimensional (3D) high-resolution volumetric multi-detector computed-tomography (MDCT) image of the chest; (2) subsequent nodal sampling using transbronchial needle aspiration (TBNA). We describe a computer-based system for automatically locating the central chest lymph-node stations in a 3D MDCT image. Automated analysis methods are first run that extract the airway tree, airway-tree centerlines, aorta, pulmonary artery, lungs, key skeletal structures, and major-airway labels. This information provides geometrical and anatomical cues for localizing the major nodal stations. Our system demarcates these stations, conforming to criteria outlined for the Mountain and Wang standard classification systems. Visualization tools within the system then enable the user to interact with these stations to locate visible lymph nodes. Results derived from a set of human 3D MDCT chest images illustrate the usage and efficacy of the system.

Sculpting 3D worlds with music: advanced texturing techniques

NASA Astrophysics Data System (ADS)

Greuel, Christian; Bolas, Mark T.; Bolas, Niko; McDowall, Ian E.

1996-04-01

Sound within the virtual environment is often considered to be secondary to the graphics. In a typical scenario, either audio cues are locally associated with specific 3D objects or a general aural ambiance is supplied in order to alleviate the sterility of an artificial experience. This paper discusses a completely different approach, in which cues are extracted from live or recorded music in order to create geometry and control object behaviors within a computer- generated environment. Advanced texturing techniques used to generate complex stereoscopic images are also discussed. By analyzing music for standard audio characteristics such as rhythm and frequency, information is extracted and repackaged for processing. With the Soundsculpt Toolkit, this data is mapped onto individual objects within the virtual environment, along with one or more predetermined behaviors. Mapping decisions are implemented with a user definable schedule and are based on the aesthetic requirements of directors and designers. This provides for visually active, immersive environments in which virtual objects behave in real-time correlation with the music. The resulting music-driven virtual reality opens up several possibilities for new types of artistic and entertainment experiences, such as fully immersive 3D `music videos' and interactive landscapes for live performance.

Medical image retrieval system using multiple features from 3D ROIs

NASA Astrophysics Data System (ADS)

Lu, Hongbing; Wang, Weiwei; Liao, Qimei; Zhang, Guopeng; Zhou, Zhiming

2012-02-01

Compared to a retrieval using global image features, features extracted from regions of interest (ROIs) that reflect distribution patterns of abnormalities would benefit more for content-based medical image retrieval (CBMIR) systems. Currently, most CBMIR systems have been designed for 2D ROIs, which cannot reflect 3D anatomical features and region distribution of lesions comprehensively. To further improve the accuracy of image retrieval, we proposed a retrieval method with 3D features including both geometric features such as Shape Index (SI) and Curvedness (CV) and texture features derived from 3D Gray Level Co-occurrence Matrix, which were extracted from 3D ROIs, based on our previous 2D medical images retrieval system. The system was evaluated with 20 volume CT datasets for colon polyp detection. Preliminary experiments indicated that the integration of morphological features with texture features could improve retrieval performance greatly. The retrieval result using features extracted from 3D ROIs accorded better with the diagnosis from optical colonoscopy than that based on features from 2D ROIs. With the test database of images, the average accuracy rate for 3D retrieval method was 76.6%, indicating its potential value in clinical application.

Synthesis of image sequences for Korean sign language using 3D shape model

NASA Astrophysics Data System (ADS)

Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

1995-05-01

This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

System for definition of the central-chest vasculature

NASA Astrophysics Data System (ADS)

Taeprasartsit, Pinyo; Higgins, William E.

2009-02-01

Accurate definition of the central-chest vasculature from three-dimensional (3D) multi-detector CT (MDCT) images is important for pulmonary applications. For instance, the aorta and pulmonary artery help in automatic definition of the Mountain lymph-node stations for lung-cancer staging. This work presents a system for defining major vascular structures in the central chest. The system provides automatic methods for extracting the aorta and pulmonary artery and semi-automatic methods for extracting the other major central chest arteries/veins, such as the superior vena cava and azygos vein. Automatic aorta and pulmonary artery extraction are performed by model fitting and selection. The system also extracts certain vascular structure information to validate outputs. A semi-automatic method extracts vasculature by finding the medial axes between provided important sites. Results of the system are applied to lymph-node station definition and guidance of bronchoscopic biopsy.

Digital disaster evaluation and its application to 2015 Ms 8.1 Nepal Earthquake

NASA Astrophysics Data System (ADS)

WANG, Xiaoqing; LV, Jinxia; DING, Xiang; DOU, Aixia

2016-11-01

The purpose of the article is to probe the technique resolution of disaster information extraction and evaluation from the digital RS images based on the internet environment and aided by the social and geographic information. The solution is composed with such methods that the fast post-disaster assessment system will assess automatically the disaster area and grade, the multi-phase satellite and airborne high resolution digital RS images will provide the basis to extract the disaster areas or spots, assisted by the fast position of potential serious damage risk targets according to the geographic, administrative, population, buildings and other information in the estimated disaster region, the 2D digital map system or 3D digital earth system will provide platforms to interpret cooperatively the damage information in the internet environment, and further to estimate the spatial distribution of damage index or intensity, casualties or economic losses, which are very useful for the decision-making of emergency rescue and disaster relief, resettlement and reconstruction. The spatial seismic damage distribution of 2015 Ms 8.1 Nepal earthquake, as an example of the above solution, is evaluated by using the high resolution digital RS images, auxiliary geographic information and ground survey. The results are compared with the statistical disaster information issued by the ground truth by field surveying, and show good consistency.

3D texture analysis for classification of second harmonic generation images of human ovarian cancer

NASA Astrophysics Data System (ADS)

Wen, Bruce; Campbell, Kirby R.; Tilbury, Karissa; Nadiarnykh, Oleg; Brewer, Molly A.; Patankar, Manish; Singh, Vikas; Eliceiri, Kevin. W.; Campagnola, Paul J.

2016-10-01

Remodeling of the collagen architecture in the extracellular matrix (ECM) has been implicated in ovarian cancer. To quantify these alterations we implemented a form of 3D texture analysis to delineate the fibrillar morphology observed in 3D Second Harmonic Generation (SHG) microscopy image data of normal (1) and high risk (2) ovarian stroma, benign ovarian tumors (3), low grade (4) and high grade (5) serous tumors, and endometrioid tumors (6). We developed a tailored set of 3D filters which extract textural features in the 3D image sets to build (or learn) statistical models of each tissue class. By applying k-nearest neighbor classification using these learned models, we achieved 83-91% accuracies for the six classes. The 3D method outperformed the analogous 2D classification on the same tissues, where we suggest this is due the increased information content. This classification based on ECM structural changes will complement conventional classification based on genetic profiles and can serve as an additional biomarker. Moreover, the texture analysis algorithm is quite general, as it does not rely on single morphological metrics such as fiber alignment, length, and width but their combined convolution with a customizable basis set.

Common-path biodynamic imaging for dynamic fluctuation spectroscopy of 3D living tissue

NASA Astrophysics Data System (ADS)

Li, Zhe; Turek, John; Nolte, David D.

2017-03-01

Biodynamic imaging is a novel 3D optical imaging technology based on short-coherence digital holography that measures intracellular motions of cells inside their natural microenvironments. Here both common-path and Mach-Zehnder designs are presented. Biological tissues such as tumor spheroids and ex vivo biopsies are used as targets, and backscattered light is collected as signal. Drugs are applied to samples, and their effects are evaluated by identifying biomarkers that capture intracellular dynamics from the reconstructed holograms. Through digital holography and coherence gating, information from different depths of the samples can be extracted, enabling the deep-tissue measurement of the responses to drugs.

Visual information for judging temporal range

NASA Technical Reports Server (NTRS)

Kaiser, Mary K.; Mowafy, Lyn

1993-01-01

Work in our laboratory suggests that pilots can extract temporal range information (i.e., the time to pass a given waypoint) directly from out-the-window motion information. This extraction does not require the use of velocity or distance, but rather operates solely on a 2-D motion cue. In this paper, we present the mathematical derivation of this information, psychophysical evidence of human observers' sensitivity, and possible advantages and limitations of basing vehicle control on this parameter.

Efficient local representations for three-dimensional palmprint recognition

NASA Astrophysics Data System (ADS)

Yang, Bing; Wang, Xiaohua; Yao, Jinliang; Yang, Xin; Zhu, Wenhua

2013-10-01

Palmprints have been broadly used for personal authentication because they are highly accurate and incur low cost. Most previous works have focused on two-dimensional (2-D) palmprint recognition in the past decade. Unfortunately, 2-D palmprint recognition systems lose the shape information when capturing palmprint images. Moreover, such 2-D palmprint images can be easily forged or affected by noise. Hence, three-dimensional (3-D) palmprint recognition has been regarded as a promising way to further improve the performance of palmprint recognition systems. We have developed a simple, but efficient method for 3-D palmprint recognition by using local features. We first utilize shape index representation to describe the geometry of local regions in 3-D palmprint data. Then, we extract local binary pattern and Gabor wavelet features from the shape index image. The two types of complementary features are finally fused at a score level for further improvements. The experimental results on the Hong Kong Polytechnic 3-D palmprint database, which contains 8000 samples from 400 palms, illustrate the effectiveness of the proposed method.

Coupled X-ray computed tomography and grey level co-occurrence matrices as a method for quantification of mineralogy and texture in 3D

NASA Astrophysics Data System (ADS)

Jardine, M. A.; Miller, J. A.; Becker, M.

2018-02-01

Texture is one of the most basic descriptors used in the geological sciences. The value derived from textural characterisation extends into engineering applications associated with mining, mineral processing and metal extraction where quantitative textural information is required for models predicting the response of the ore through a particular process. This study extends the well-known 2D grey level co-occurrence matrices methodology into 3D as a method for image analysis of 3D x-ray computed tomography grey scale volumes of drill core. Subsequent interrogation of the information embedded within the grey level occurrence matrices (GLCM) indicates they are sensitive to changes in mineralogy and texture of samples derived from a magmatic nickel sulfide ore. The position of the peaks in the GLCM is an indication of the relative density (specific gravity, SG) of the minerals and when interpreted using a working knowledge of the mineralogy of the ore presented a means to determine the relative abundance of the sulfide minerals (SG > 4), dense silicate minerals (SG > 3), and lighter silicate minerals (SG < 3). The spread of the peaks in the GLCM away from the diagonal is an indication of the degree of grain boundary interaction with wide peaks representing fine grain sizes and narrow peaks representing coarse grain sizes. The method lends itself to application as part of a generic methodology for routine use on large XCT volumes providing quantitative, timely, meaningful and automated information on mineralogy and texture in 3D.

Extraction and characterization of beta-D-glucan from oat for industrial utilization.

PubMed

Ahmad, Asif; Anjum, Faqir Muhammad; Zahoor, Tahir; Nawaz, Haq; Ahmed, Zaheer

2010-04-01

Oat beta-D-glucan is a valuable functional ingredient having numerous industrial, nutritional and health benefits. Its extraction needs careful attention as extraction process may affect the physiochemical and functional properties of extracted beta-D-glucan. The present study aimed at analyzing the effect of extraction of beta-D-glucan gum pellets from oat cultivar followed by detailed chemical and functional analysis. Enzymatic extraction process resulted in highest yield and recovery. Chemical analysis revealed protein as a dominating impurity. The water binding capacity of the beta-D-glucan ranged between 3.14 and 4.52 g g(-1) of sample. beta-D-Glucan exhibited ideal foaming stability when appropriate extraction technique was used. The viscosity of beta-D-glucan gum ranged between 35.6 and 56.16 cp. The color analysis showed L* value of beta-D-glucan gum pellet ranged between 72.18 and 83.54. Phosphorus, potassium and calcium appeared as major minerals in beta-D-glucan gum whereas iron, manganese and copper appeared as minor minerals. FTIR spectroscopy also confirms the presence of beta-D-glucan, protein and other components in extracted beta-D-glucan gum pellets. Overall, extracted beta-D-glucan showed a good potential for industrial usage. Copyright 2010 Elsevier B.V. All rights reserved.

Change detection on LOD 2 building models with very high resolution spaceborne stereo imagery

NASA Astrophysics Data System (ADS)

Qin, Rongjun

2014-10-01

Due to the fast development of the urban environment, the need for efficient maintenance and updating of 3D building models is ever increasing. Change detection is an essential step to spot the changed area for data (map/3D models) updating and urban monitoring. Traditional methods based on 2D images are no longer suitable for change detection in building scale, owing to the increased spectral variability of the building roofs and larger perspective distortion of the very high resolution (VHR) imagery. Change detection in 3D is increasingly being investigated using airborne laser scanning data or matched Digital Surface Models (DSM), but rare study has been conducted regarding to change detection on 3D city models with VHR images, which is more informative but meanwhile more complicated. This is due to the fact that the 3D models are abstracted geometric representation of the urban reality, while the VHR images record everything. In this paper, a novel method is proposed to detect changes directly on LOD (Level of Detail) 2 building models with VHR spaceborne stereo images from a different date, with particular focus on addressing the special characteristics of the 3D models. In the first step, the 3D building models are projected onto a raster grid, encoded with building object, terrain object, and planar faces. The DSM is extracted from the stereo imagery by hierarchical semi-global matching (SGM). In the second step, a multi-channel change indicator is extracted between the 3D models and stereo images, considering the inherent geometric consistency (IGC), height difference, and texture similarity for each planar face. Each channel of the indicator is then clustered with the Self-organizing Map (SOM), with "change", "non-change" and "uncertain change" status labeled through a voting strategy. The "uncertain changes" are then determined with a Markov Random Field (MRF) analysis considering the geometric relationship between faces. In the third step, buildings are extracted combining the multispectral images and the DSM by morphological operators, and the new buildings are determined by excluding the verified unchanged buildings from the second step. Both the synthetic experiment with Worldview-2 stereo imagery and the real experiment with IKONOS stereo imagery are carried out to demonstrate the effectiveness of the proposed method. It is shown that the proposed method can be applied as an effective way to monitoring the building changes, as well as updating 3D models from one epoch to the other.

Quantifying hydrogen-deuterium exchange of meteoritic dicarboxylic acids during aqueous extraction

NASA Astrophysics Data System (ADS)

Fuller, M.; Huang, Y.

2003-03-01

Hydrogen isotope ratios of organic compounds in carbonaceous chondrites provide critical information about their origins and evolutionary history. However, because many of these compounds are obtained by aqueous extraction, the degree of hydrogen-deuterium (H/D) exchange that occurs during the process needs to be quantitatively evaluated. This study uses compound- specific hydrogen isotopic analysis to quantify the H/D exchange during aqueous extraction. Three common meteoritic dicarboxylic acids (succinic, glutaric, and 2-methyl glutaric acids) were refluxed under conditions simulating the extraction process. Changes in D values of the dicarboxylic acids were measured following the reflux experiments. A pseudo-first order rate law was used to model the H/D exchange rates which were then used to calculate the isotope exchange resulting from aqueous extraction. The degree of H/D exchange varies as a result of differences in molecular structure, the alkalinity of the extraction solution and presence/absence of meteorite powder. However, our model indicates that succinic, glutaric, and 2-methyl glutaric acids with a D of 1800 would experience isotope changes of 38, 10, and 6, respectively during the extraction process. Therefore, the overall change in D values of the dicarboxylic acids during the aqueous extraction process is negligible. We also demonstrate that H/D exchange occurs on the chiral -carbon in 2-methyl glutaric acid. The results suggest that the racemic mixture of 2-methyl glutaric acid in the Tagish Lake meteorite could result from post-synthesis aqueous alteration. The approach employed in this study can also be used to quantify H/D exchange for other important meteoritic compounds such as amino acids.

A hybrid approach for fusing 4D-MRI temporal information with 3D-CT for the study of lung and lung tumor motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Y. X.; Van Reeth, E.; Poh, C. L., E-mail: clpoh@ntu.edu.sg

2015-08-15

Purpose: Accurate visualization of lung motion is important in many clinical applications, such as radiotherapy of lung cancer. Advancement in imaging modalities [e.g., computed tomography (CT) and MRI] has allowed dynamic imaging of lung and lung tumor motion. However, each imaging modality has its advantages and disadvantages. The study presented in this paper aims at generating synthetic 4D-CT dataset for lung cancer patients by combining both continuous three-dimensional (3D) motion captured by 4D-MRI and the high spatial resolution captured by CT using the authors’ proposed approach. Methods: A novel hybrid approach based on deformable image registration (DIR) and finite elementmore » method simulation was developed to fuse a static 3D-CT volume (acquired under breath-hold) and the 3D motion information extracted from 4D-MRI dataset, creating a synthetic 4D-CT dataset. Results: The study focuses on imaging of lung and lung tumor. Comparing the synthetic 4D-CT dataset with the acquired 4D-CT dataset of six lung cancer patients based on 420 landmarks, accurate results (average error <2 mm) were achieved using the authors’ proposed approach. Their hybrid approach achieved a 40% error reduction (based on landmarks assessment) over using only DIR techniques. Conclusions: The synthetic 4D-CT dataset generated has high spatial resolution, has excellent lung details, and is able to show movement of lung and lung tumor over multiple breathing cycles.« less

RGB-D SLAM Combining Visual Odometry and Extended Information Filter

PubMed Central

Zhang, Heng; Liu, Yanli; Tan, Jindong; Xiong, Naixue

2015-01-01

In this paper, we present a novel RGB-D SLAM system based on visual odometry and an extended information filter, which does not require any other sensors or odometry. In contrast to the graph optimization approaches, this is more suitable for online applications. A visual dead reckoning algorithm based on visual residuals is devised, which is used to estimate motion control input. In addition, we use a novel descriptor called binary robust appearance and normals descriptor (BRAND) to extract features from the RGB-D frame and use them as landmarks. Furthermore, considering both the 3D positions and the BRAND descriptors of the landmarks, our observation model avoids explicit data association between the observations and the map by marginalizing the observation likelihood over all possible associations. Experimental validation is provided, which compares the proposed RGB-D SLAM algorithm with just RGB-D visual odometry and a graph-based RGB-D SLAM algorithm using the publicly-available RGB-D dataset. The results of the experiments demonstrate that our system is quicker than the graph-based RGB-D SLAM algorithm. PMID:26263990

Three-dimensional contour edge detection algorithm

NASA Astrophysics Data System (ADS)

Wang, Yizhou; Ong, Sim Heng; Kassim, Ashraf A.; Foong, Kelvin W. C.

2000-06-01

This paper presents a novel algorithm for automatically extracting 3D contour edges, which are points of maximum surface curvature in a surface range image. The 3D image data are represented as a surface polygon mesh. The algorithm transforms the range data, obtained by scanning a dental plaster cast, into a 2D gray scale image by linearly converting the z-value of each vertex to a gray value. The Canny operator is applied to the median-filtered image to obtain the edge pixels and their orientations. A vertex in the 3D object corresponding to the detected edge pixel and its neighbors in the direction of the edge gradient are further analyzed with respect to their n-curvatures to extract the real 3D contour edges. This algorithm provides a fast method of reducing and sorting the unwieldy data inherent in the surface mesh representation. It employs powerful 2D algorithms to extract features from the transformed 3D models and refers to the 3D model for further analysis of selected data. This approach substantially reduces the computational burden without losing accuracy. It is also easily extended to detect 3D landmarks and other geometrical features, thus making it applicable to a wide range of applications.

Forensic print extraction using 3D technology and its processing

NASA Astrophysics Data System (ADS)

Rajeev, Srijith; Shreyas, Kamath K. M.; Panetta, Karen; Agaian, Sos S.

2017-05-01

Biometric evidence plays a crucial role in criminal scene analysis. Forensic prints can be extracted from any solid surface such as firearms, doorknobs, carpets and mugs. Prints such as fingerprints, palm prints, footprints and lip-prints can be classified into patent, latent, and three-dimensional plastic prints. Traditionally, law enforcement officers capture these forensic traits using an electronic device or extract them manually, and save the data electronically using special scanners. The reliability and accuracy of the method depends on the ability of the officer or the electronic device to extract and analyze the data. Furthermore, the 2-D acquisition and processing system is laborious and cumbersome. This can lead to the increase in false positive and true negative rates in print matching. In this paper, a method and system to extract forensic prints from any surface, irrespective of its shape, is presented. First, a suitable 3-D camera is used to capture images of the forensic print, and then the 3-D image is processed and unwrapped to obtain 2-D equivalent biometric prints. Computer simulations demonstrate the effectiveness of using 3-D technology for biometric matching of fingerprints, palm prints, and lip-prints. This system can be further extended to other biometric and non-biometric modalities.

In vitro antiplasmodial activity of plants used in Benin in traditional medicine to treat malaria.

PubMed

Bero, Joanne; Ganfon, Habib; Jonville, Marie-Caroline; Frédérich, Michel; Gbaguidi, Fernand; DeMol, Patrick; Moudachirou, Mansourou; Quetin-Leclercq, Joëlle

2009-04-21

The aim of the study was to evaluate the in vitro antiplasmodial activity of crude extracts of 12 plant species traditionally used in Benin for the treatment of malaria in order to validate their use. For each species, dichloromethane, methanol and total aqueous extracts were tested. The antiplasmodial activity of extracts was evaluated using the measurement of the plasmodial lactate dehydrogenase activity on chloroquine-sensitive (3D7) and resistant (W2) strains of Plasmodium falciparum. The selectivity of the different extracts was evaluated using the MTT test on J774 macrophage-like murine cells and WI38 human normal fibroblasts. The best growth inhibition of both strains of Plasmodium falciparum was observed with the dichloromethane extracts of Acanthospermum hispidum DC. (Asteraceae) (IC(50)=7.5 microg/ml on 3D7 and 4.8 microg/ml on W2), Keetia leucantha (K. Krause) Bridson (syn. Plectronia leucantha Krause) (Rubiaceae) leaves and twigs (IC(50)=13.8 and 11.3 microg/ml on 3D7 and IC(50)=26.5 and 15.8 microg/ml on W2, respectively), Carpolobia lutea G.Don. (Polygalaceae) (IC(50)=19.4 microg/ml on 3D7 and 8.1 microg/ml on W2) and Strychnos spinosa Lam. (Loganiaceae) leaves (IC(50)=15.6 microg/ml on 3D7 and 8.9 microg/ml on W2). All these extracts had a low cytotoxicity. Our study gives some justifications for the traditional uses of some investigated plants.

Personalized 3D printed model of kidney and tumor anatomy: a useful tool for patient education.

PubMed

Bernhard, Jean-Christophe; Isotani, Shuji; Matsugasumi, Toru; Duddalwar, Vinay; Hung, Andrew J; Suer, Evren; Baco, Eduard; Satkunasivam, Raj; Djaladat, Hooman; Metcalfe, Charles; Hu, Brian; Wong, Kelvin; Park, Daniel; Nguyen, Mike; Hwang, Darryl; Bazargani, Soroush T; de Castro Abreu, Andre Luis; Aron, Monish; Ukimura, Osamu; Gill, Inderbir S

2016-03-01

To assess the impact of 3D printed models of renal tumor on patient's understanding of their conditions. Patient understanding of their medical condition and treatment satisfaction has gained increasing attention in medicine. Novel technologies such as additive manufacturing [also termed three-dimensional (3D) printing] may play a role in patient education. A prospective pilot study was conducted, and seven patients with a primary diagnosis of kidney tumor who were being considered for partial nephrectomy were included after informed consent. All patients underwent four-phase multi-detector computerized tomography (MDCT) scanning from which renal volume data were extracted to create life-size patient-specific 3D printed models. Patient knowledge and understanding were evaluated before and after 3D model presentation. Patients' satisfaction with their specific 3D printed model was also assessed through a visual scale. After viewing their personal 3D kidney model, patients demonstrated an improvement in understanding of basic kidney physiology by 16.7 % (p = 0.018), kidney anatomy by 50 % (p = 0.026), tumor characteristics by 39.3 % (p = 0.068) and the planned surgical procedure by 44.6 % (p = 0.026). Presented herein is the initial clinical experience with 3D printing to facilitate patient's pre-surgical understanding of their kidney tumor and surgery.

Geoinformation techniques for the 3D visualisation of historic buildings and representation of a building's pathology

NASA Astrophysics Data System (ADS)

Tsilimantou, Elisavet; Delegou, Ekaterini; Ioannidis, Charalabos; Moropoulou, Antonia

2016-08-01

In this paper, the documentation of an historic building registered as Cultural Heritage asset is presented. The aim of the survey is to create a 3D geometric representation of a historic building and in accordance with multidisciplinary study extract useful information regarding the extent of degradation, constructions' durability etc. For the implementation of the survey, a combination of different types of acquisition technologies is used. The project focuses on the study of Villa Klonaridi, in Athens, Greece. For the complete documentation of the building, conventional topography, photogrammetric and laser scanning techniques is combined. Close range photogrammetric techniques are used for the acquisition of the façades and architectural details. One of the main objectives is the development of an accurate 3D model, where the photorealistic representation of the building is achieved, along with the decay pathology, historical phases and architectural components. In order to achieve a suitable graphical representation for the study of the material and decay patterns beyond the 2D representation, 3D modelling and additional information modelling is performed for comparative analysis. The study provides various conclusions regarding the scale of deterioration obtained by the 2D and 3D analysis respectively. Considering the variation in material and decay patterns, comparative results are obtained regarding the degradation of the building. Overall, the paper describes a process performed on a Historic Building, where the 3D digital acquisition of the monuments' structure is realized with the combination of close range surveying and laser scanning methods.

Applications of 3D-EDGE Detection for ALS Point Cloud

NASA Astrophysics Data System (ADS)

Ni, H.; Lin, X. G.; Zhang, J. X.

2017-09-01

Edge detection has been one of the major issues in the field of remote sensing and photogrammetry. With the fast development of sensor technology of laser scanning system, dense point clouds have become increasingly common. Precious 3D-edges are able to be detected from these point clouds and a great deal of edge or feature line extraction methods have been proposed. Among these methods, an easy-to-use 3D-edge detection method, AGPN (Analyzing Geometric Properties of Neighborhoods), has been proposed. The AGPN method detects edges based on the analysis of geometric properties of a query point's neighbourhood. The AGPN method detects two kinds of 3D-edges, including boundary elements and fold edges, and it has many applications. This paper presents three applications of AGPN, i.e., 3D line segment extraction, ground points filtering, and ground breakline extraction. Experiments show that the utilization of AGPN method gives a straightforward solution to these applications.

Methods from Information Extraction from LIDAR Intensity Data and Multispectral LIDAR Technology

NASA Astrophysics Data System (ADS)

Scaioni, M.; Höfle, B.; Baungarten Kersting, A. P.; Barazzetti, L.; Previtali, M.; Wujanz, D.

2018-04-01

LiDAR is a consolidated technology for topographic mapping and 3D reconstruction, which is implemented in several platforms On the other hand, the exploitation of the geometric information has been coupled by the use of laser intensity, which may provide additional data for multiple purposes. This option has been emphasized by the availability of sensors working on different wavelength, thus able to provide additional information for classification of surfaces and objects. Several applications ofmonochromatic and multi-spectral LiDAR data have been already developed in different fields: geosciences, agriculture, forestry, building and cultural heritage. The use of intensity data to extract measures of point cloud quality has been also developed. The paper would like to give an overview on the state-of-the-art of these techniques, and to present the modern technologies for the acquisition of multispectral LiDAR data. In addition, the ISPRS WG III/5 on `Information Extraction from LiDAR Intensity Data' has collected and made available a few open data sets to support scholars to do research on this field. This service is presented and data sets delivered so far as are described.

3D object retrieval using salient views

PubMed Central

Shapiro, Linda G.

2013-01-01

This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223–232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223–232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

Computer-based synthetic data to assess the tree delineation algorithm from airborne LiDAR survey

Treesearch

Lei Wang; Andrew G. Birt; Charles W. Lafon; David M. Cairns; Robert N. Coulson; Maria D. Tchakerian; Weimin Xi; Sorin C. Popescu; James M. Guldin

2013-01-01

Small Footprint LiDAR (Light Detection And Ranging) has been proposed as an effective tool for measuring detailed biophysical characteristics of forests over broad spatial scales. However, by itself LiDAR yields only a sample of the true 3D structure of a forest. In order to extract useful forestry relevant information, this data must be interpreted using mathematical...

Biomedical sensing and imaging for the anterior segment of the eye

NASA Astrophysics Data System (ADS)

Eom, Tae Joong; Yoo, Young-Sik; Lee, Yong-Eun; Kim, Beop-Min; Joo, Choun-Ki

2015-07-01

Eye is an optical system composed briefly of cornea, lens, and retina. Ophthalmologists can diagnose status of patient's eye from information provided by optical sensors or images as well as from history taking or physical examinations. Recently, we developed a prototype of optical coherence tomography (OCT) image guided femtosecond laser cataract surgery system. The system combined a swept-source OCT and a femtosecond (fs) laser and afford the 2D and 3D structure information to increase the efficiency and safety of the cataract procedure. The OCT imaging range was extended to achieve the 3D image from the cornea to lens posterior. A prototype of OCT image guided fs laser cataract surgery system. The surgeons can plan the laser illumination range for the nuclear division and segmentation, and monitor the whole cataract surgery procedure using the real time OCT. The surgery system was demonstrated with an extracted pig eye and in vivo rabbit eye to verify the system performance and stability.

Comparison of MRI techniques and modelling with R-SWMS for determining solute distribution patterns and root water uptake of a white lupine plant (Lupinus Albus L.).

NASA Astrophysics Data System (ADS)

Koch, Axelle; Schröder, Natalie; Pohlmeier, Andreas; Garré, Sarah; Vanderborght, Jan; Javaux, Mathieu

2017-04-01

Measuring water extraction by plant would allow us to better understand root water uptake processes and how soil and plant properties affect them. Yet, direct measurement of root water uptake is still challenging and determining its distribution requires coupling experimentation and modelling. In this study, we investigated how the 3D monitoring of a tracer movement in a sand container with a lupine plant could inform us about root water uptake process. A sand column (10 cm height, 5 cm inner diameter) planted with an 18-day-old white lupine was subject to a tracer experiment with a chemically inert tracer (1 mmol/L Gd-DTPA2-) applied for 6 days. Then the tracer and water fluxes were stopped. The plume was monitored in 3-D for 7 days by Magnetic Resonance Imaging (Haber-Pohlmeier et al, unp). In addition the breakthrough curve at the outlet was also measured. We used a biophysical 3-D soil-plant model: R-SWMS (Javaux et al, 2008) to extract information from this experiment. First, we ran a virtual experiment to check the assumption that Gd concentration increase around roots is proportional to the extracted soil water during the same period. We also investigated whether this type of experiment helps discriminate different root hydraulic properties with a sensitivity analysis. Then, we compared the experimental and simulated Gd concentration patterns. A preliminary (qualitative) assessment showed that measured Gd distribution patterns were better represented by the model at day 7, where the main driver of the concentration distribution was root and not soil heterogeneity (which is not taken into account in the model). The main spatial and temporal features of the transport where adequately reproduced by the model in particular during the last day. The distribution of the tracer was shown to be sensitive to the root hydraulic properties. To conclude, information about root water uptake distributions and so about root hydraulic properties could be deduced from Gd concentration maps. Keywords: R-SWMS; Modelling; MRI; Root Water Uptake; Gadolinium

Multisensor Fusion for Change Detection

NASA Astrophysics Data System (ADS)

Schenk, T.; Csatho, B.

2005-12-01

Combining sensors that record different properties of a 3-D scene leads to complementary and redundant information. If fused properly, a more robust and complete scene description becomes available. Moreover, fusion facilitates automatic procedures for object reconstruction and modeling. For example, aerial imaging sensors, hyperspectral scanning systems, and airborne laser scanning systems generate complementary data. We describe how data from these sensors can be fused for such diverse applications as mapping surface erosion and landslides, reconstructing urban scenes, monitoring urban land use and urban sprawl, and deriving velocities and surface changes of glaciers and ice sheets. An absolute prerequisite for successful fusion is a rigorous co-registration of the sensors involved. We establish a common 3-D reference frame by using sensor invariant features. Such features are caused by the same object space phenomena and are extracted in multiple steps from the individual sensors. After extracting, segmenting and grouping the features into more abstract entities, we discuss ways on how to automatically establish correspondences. This is followed by a brief description of rigorous mathematical models suitable to deal with linear and area features. In contrast to traditional, point-based registration methods, lineal and areal features lend themselves to a more robust and more accurate registration. More important, the chances to automate the registration process increases significantly. The result of the co-registration of the sensors is a unique transformation between the individual sensors and the object space. This makes spatial reasoning of extracted information more versatile; reasoning can be performed in sensor space or in 3-D space where domain knowledge about features and objects constrains reasoning processes, reduces the search space, and helps to make the problem well-posed. We demonstrate the feasibility of the proposed multisensor fusion approach with detecting surface elevation changes on the Byrd Glacier, Antarctica, with aerial imagery from 1980s and ICESat laser altimetry data from 2003-05. Change detection from such disparate data sets is an intricate fusion problem, beginning with sensor alignment, and on to reasoning with spatial information as to where changes occurred and to what extent.

a Method for the Registration of Hemispherical Photographs and Tls Intensity Images

NASA Astrophysics Data System (ADS)

Schmidt, A.; Schilling, A.; Maas, H.-G.

2012-07-01

Terrestrial laser scanners generate dense and accurate 3D point clouds with minimal effort, which represent the geometry of real objects, while image data contains texture information of object surfaces. Based on the complementary characteristics of both data sets, a combination is very appealing for many applications, including forest-related tasks. In the scope of our research project, independent data sets of a plain birch stand have been taken by a full-spherical laser scanner and a hemispherical digital camera. Previously, both kinds of data sets have been considered separately: Individual trees were successfully extracted from large 3D point clouds, and so-called forest inventory parameters could be determined. Additionally, a simplified tree topology representation was retrieved. From hemispherical images, leaf area index (LAI) values, as a very relevant parameter for describing a stand, have been computed. The objective of our approach is to merge a 3D point cloud with image data in a way that RGB values are assigned to each 3D point. So far, segmentation and classification of TLS point clouds in forestry applications was mainly based on geometrical aspects of the data set. However, a 3D point cloud with colour information provides valuable cues exceeding simple statistical evaluation of geometrical object features and thus may facilitate the analysis of the scan data significantly.

Quantitative IR microscopy and spectromics open the way to 3D digital pathology.

PubMed

Bobroff, Vladimir; Chen, Hsiang-Hsin; Delugin, Maylis; Javerzat, Sophie; Petibois, Cyril

2017-04-01

Currently, only mass-spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro-microscopy is reported. An automated curve-fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR-absorption spectrum into a IR-band spectrum; (3) the reconstruction of an 3D IR-band matrix (x, y, z for voxel position and a 4 th dimension with all IR-band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessing similarity analysis of chromatographic fingerprints of Cyclopia subternata extracts as potential screening tool for in vitro glucose utilisation.

PubMed

Schulze, Alexandra E; De Beer, Dalene; Mazibuko, Sithandiwe E; Muller, Christo J F; Roux, Candice; Willenburg, Elize L; Nyunaï, Nyemb; Louw, Johan; Manley, Marena; Joubert, Elizabeth

2016-01-01

Similarity analysis of the phenolic fingerprints of a large number of aqueous extracts of Cyclopia subternata, obtained by high-performance liquid chromatography (HPLC), was evaluated as a potential tool to screen extracts for relative bioactivity. The assessment was based on the (dis)similarity of their fingerprints to that of a reference active extract of C. subternata, proven to enhance glucose uptake in vitro and in vivo. In vitro testing of extracts, selected as being most similar (n = 5; r ≥ 0.962) and most dissimilar (n = 5; r ≤ 0.688) to the reference active extract, showed that no clear pattern in terms of relative glucose uptake efficacy in C2C12 myocytes emerged, irrespective of the dose. Some of the most dissimilar extracts had higher glucose-lowering activity than the reference active extract. Principal component analysis revealed the major compounds responsible for the most variation within the chromatographic fingerprints, as mangiferin, isomangiferin, iriflophenone-3-C-β-D-glucoside-4-O-β-D-glucoside, iriflophenone-3-C-β-D-glucoside, scolymoside, and phloretin-3',5'-di-C-β-D-glucoside. Quantitative analysis of the selected extracts showed that the most dissimilar extracts contained the highest mangiferin and isomangiferin levels, whilst the most similar extracts had the highest scolymoside content. These compounds demonstrated similar glucose uptake efficacy in C2C12 myocytes. It can be concluded that (dis)similarity of chromatographic fingerprints of extracts of unknown activity to that of a proven bioactive extract does not necessarily translate to lower or higher bioactivity.

Membrane Interaction of Antimicrobial Peptides Using E. coli Lipid Extract as Model Bacterial Cell Membranes and SFG Spectroscopy

PubMed Central

Soblosky, Lauren; Ramamoorthy, Ayyalusamy; Chen, Zhan

2015-01-01

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/E. coli polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties. PMID:25707312

The Use of IMMUs in a Water Environment: Instrument Validation and Application of 3D Multi-Body Kinematic Analysis in Medicine and Sport

PubMed Central

Mangia, Anna Lisa; Cortesi, Matteo; Fantozzi, Silvia; Giovanardi, Andrea; Borra, Davide; Gatta, Giorgio

2017-01-01

The aims of the present study were the instrumental validation of inertial-magnetic measurements units (IMMUs) in water, and the description of their use in clinical and sports aquatic applications applying customized 3D multi-body models. Firstly, several tests were performed to map the magnetic field in the swimming pool and to identify the best volume for experimental test acquisition with a mean dynamic orientation error lower than 5°. Successively, the gait and the swimming analyses were explored in terms of spatiotemporal and joint kinematics variables. The extraction of only spatiotemporal parameters highlighted several critical issues and the joint kinematic information has shown to be an added value for both rehabilitative and sport training purposes. Furthermore, 3D joint kinematics applied using the IMMUs provided similar quantitative information than that of more expensive and bulky systems but with a simpler and faster setup preparation, a lower time consuming processing phase, as well as the possibility to record and analyze a higher number of strides/strokes without limitations imposed by the cameras. PMID:28441739

Metrological analysis of the human foot: 3D multisensor exploration

NASA Astrophysics Data System (ADS)

Muñoz Potosi, A.; Meneses Fonseca, J.; León Téllez, J.

2011-08-01

In the podiatry field, many of the foot dysfunctions are mainly generated due to: Congenital malformations, accidents or misuse of footwear. For the treatment or prevention of foot disorders, the podiatrist diagnoses prosthesis or specific adapted footwear, according to the real dimension of foot. Therefore, it is necessary to acquire 3D information of foot with 360 degrees of observation. As alternative solution, it was developed and implemented an optical system of threedimensional reconstruction based in the principle of laser triangulation. The system is constituted by an illumination unit that project a laser plane into the foot surface, an acquisition unit with 4 CCD cameras placed around of axial foot axis, an axial moving unit that displaces the illumination and acquisition units in the axial axis direction and a processing and exploration unit. The exploration software allows the extraction of distances on three-dimensional image, taking into account the topography of foot. The optical system was tested and their metrological performances were evaluated in experimental conditions. The optical system was developed to acquire 3D information in order to design and make more appropriate footwear.

The Use of IMMUs in a Water Environment: Instrument Validation and Application of 3D Multi-Body Kinematic Analysis in Medicine and Sport.

PubMed

Mangia, Anna Lisa; Cortesi, Matteo; Fantozzi, Silvia; Giovanardi, Andrea; Borra, Davide; Gatta, Giorgio

2017-04-22

The aims of the present study were the instrumental validation of inertial-magnetic measurements units (IMMUs) in water, and the description of their use in clinical and sports aquatic applications applying customized 3D multi-body models. Firstly, several tests were performed to map the magnetic field in the swimming pool and to identify the best volume for experimental test acquisition with a mean dynamic orientation error lower than 5°. Successively, the gait and the swimming analyses were explored in terms of spatiotemporal and joint kinematics variables. The extraction of only spatiotemporal parameters highlighted several critical issues and the joint kinematic information has shown to be an added value for both rehabilitative and sport training purposes. Furthermore, 3D joint kinematics applied using the IMMUs provided similar quantitative information than that of more expensive and bulky systems but with a simpler and faster setup preparation, a lower time consuming processing phase, as well as the possibility to record and analyze a higher number of strides/strokes without limitations imposed by the cameras.

Robust space-time extraction of ventricular surface evolution using multiphase level sets

NASA Astrophysics Data System (ADS)

Drapaca, Corina S.; Cardenas, Valerie; Studholme, Colin

2004-05-01

This paper focuses on the problem of accurately extracting the CSF-tissue boundary, particularly around the ventricular surface, from serial structural MRI of the brain acquired in imaging studies of aging and dementia. This is a challenging problem because of the common occurrence of peri-ventricular lesions which locally alter the appearance of white matter. We examine a level set approach which evolves a four dimensional description of the ventricular surface over time. This has the advantage of allowing constraints on the contour in the temporal dimension, improving the consistency of the extracted object over time. We follow the approach proposed by Chan and Vese which is based on the Mumford and Shah model and implemented using the Osher and Sethian level set method. We have extended this to the 4 dimensional case to propagate a 4D contour toward the tissue boundaries through the evolution of a 5D implicit function. For convergence we use region-based information provided by the image rather than the gradient of the image. This is adapted to allow intensity contrast changes between time frames in the MRI sequence. Results on time sequences of 3D brain MR images are presented and discussed.

Classification of building infrastructure and automatic building footprint delineation using airborne laser swath mapping data

NASA Astrophysics Data System (ADS)

Caceres, Jhon

Three-dimensional (3D) models of urban infrastructure comprise critical data for planners working on problems in wireless communications, environmental monitoring, civil engineering, and urban planning, among other tasks. Photogrammetric methods have been the most common approach to date to extract building models. However, Airborne Laser Swath Mapping (ALSM) observations offer a competitive alternative because they overcome some of the ambiguities that arise when trying to extract 3D information from 2D images. Regardless of the source data, the building extraction process requires segmentation and classification of the data and building identification. In this work, approaches for classifying ALSM data, separating building and tree points, and delineating ALSM footprints from the classified data are described. Digital aerial photographs are used in some cases to verify results, but the objective of this work is to develop methods that can work on ALSM data alone. A robust approach for separating tree and building points in ALSM data is presented. The method is based on supervised learning of the classes (tree vs. building) in a high dimensional feature space that yields good class separability. Features used for classification are based on the generation of local mappings, from three-dimensional space to two-dimensional space, known as "spin images" for each ALSM point to be classified. The method discriminates ALSM returns in compact spaces and even where the classes are very close together or overlapping spatially. A modified algorithm of the Hough Transform is used to orient the spin images, and the spin image parameters are specified such that the mutual information between the spin image pixel values and class labels is maximized. This new approach to ALSM classification allows us to fully exploit the 3D point information in the ALSM data while still achieving good class separability, which has been a difficult trade-off in the past. Supported by the spin image analysis for obtaining an initial classification, an automatic approach for delineating accurate building footprints is presented. The physical fact that laser pulses that happen to strike building edges can produce very different 1st and last return elevations has been long recognized. However, in older generation ALSM systems (<50 kHz pulse rates) such points were too few and far between to delineate building footprints precisely. Furthermore, without the robust separation of nearby trees and vegetation from the buildings, simply extracting ALSM shots where the elevation of the first return was much higher than the elevation of the last return, was not a reliable means of identifying building footprints. However, with the advent of ALSM systems with pulse rates in excess of 100 kHz, and by using spin-imaged based segmentation, it is now possible to extract building edges from the point cloud. A refined classification resulting from incorporating "on-edge" information is developed for obtaining quadrangular footprints. The footprint fitting process involves line generalization, least squares-based clustering and dominant points finding for segmenting individual building edges. In addition, an algorithm for fitting complex footprints using the segmented edges and data inside footprints is also proposed.

Feature extraction via KPCA for classification of gait patterns.

PubMed

Wu, Jianning; Wang, Jue; Liu, Li

2007-06-01

Automated recognition of gait pattern change is important in medical diagnostics as well as in the early identification of at-risk gait in the elderly. We evaluated the use of Kernel-based Principal Component Analysis (KPCA) to extract more gait features (i.e., to obtain more significant amounts of information about human movement) and thus to improve the classification of gait patterns. 3D gait data of 24 young and 24 elderly participants were acquired using an OPTOTRAK 3020 motion analysis system during normal walking, and a total of 36 gait spatio-temporal and kinematic variables were extracted from the recorded data. KPCA was used first for nonlinear feature extraction to then evaluate its effect on a subsequent classification in combination with learning algorithms such as support vector machines (SVMs). Cross-validation test results indicated that the proposed technique could allow spreading the information about the gait's kinematic structure into more nonlinear principal components, thus providing additional discriminatory information for the improvement of gait classification performance. The feature extraction ability of KPCA was affected slightly with different kernel functions as polynomial and radial basis function. The combination of KPCA and SVM could identify young-elderly gait patterns with 91% accuracy, resulting in a markedly improved performance compared to the combination of PCA and SVM. These results suggest that nonlinear feature extraction by KPCA improves the classification of young-elderly gait patterns, and holds considerable potential for future applications in direct dimensionality reduction and interpretation of multiple gait signals.

Three-dimensional tracking for efficient fire fighting in complex situations

NASA Astrophysics Data System (ADS)

Akhloufi, Moulay; Rossi, Lucile

2009-05-01

Each year, hundred millions hectares of forests burn causing human and economic losses. For efficient fire fighting, the personnel in the ground need tools permitting the prediction of fire front propagation. In this work, we present a new technique for automatically tracking fire spread in three-dimensional space. The proposed approach uses a stereo system to extract a 3D shape from fire images. A new segmentation technique is proposed and permits the extraction of fire regions in complex unstructured scenes. It works in the visible spectrum and combines information extracted from YUV and RGB color spaces. Unlike other techniques, our algorithm does not require previous knowledge about the scene. The resulting fire regions are classified into different homogenous zones using clustering techniques. Contours are then extracted and a feature detection algorithm is used to detect interest points like local maxima and corners. Extracted points from stereo images are then used to compute the 3D shape of the fire front. The resulting data permits to build the fire volume. The final model is used to compute important spatial and temporal fire characteristics like: spread dynamics, local orientation, heading direction, etc. Tests conducted on the ground show the efficiency of the proposed scheme. This scheme is being integrated with a fire spread mathematical model in order to predict and anticipate the fire behaviour during fire fighting. Also of interest to fire-fighters, is the proposed automatic segmentation technique that can be used in early detection of fire in complex scenes.

Serial sectioning methods for 3D investigations in materials science.

PubMed

Zankel, Armin; Wagner, Julian; Poelt, Peter

2014-07-01

A variety of methods for the investigation and 3D representation of the inner structure of materials has been developed. In this paper, techniques based on slice and view using scanning microscopy for imaging are presented and compared. Three different methods of serial sectioning combined with either scanning electron or scanning ion microscopy or atomic force microscopy (AFM) were placed under scrutiny: serial block-face scanning electron microscopy, which facilitates an ultramicrotome built into the chamber of a variable pressure scanning electron microscope; three-dimensional (3D) AFM, which combines an (cryo-) ultramicrotome with an atomic force microscope, and 3D FIB, which delivers results by slicing with a focused ion beam. These three methods complement one another in many respects, e.g., in the type of materials that can be investigated, the resolution that can be obtained and the information that can be extracted from 3D reconstructions. A detailed review is given about preparation, the slice and view process itself, and the limitations of the methods and possible artifacts. Applications for each technique are also provided. Copyright © 2014 Elsevier Ltd. All rights reserved.

Efficiency analysis for 3D filtering of multichannel images

NASA Astrophysics Data System (ADS)

Kozhemiakin, Ruslan A.; Rubel, Oleksii; Abramov, Sergey K.; Lukin, Vladimir V.; Vozel, Benoit; Chehdi, Kacem

2016-10-01

Modern remote sensing systems basically acquire images that are multichannel (dual- or multi-polarization, multi- and hyperspectral) where noise, usually with different characteristics, is present in all components. If noise is intensive, it is desirable to remove (suppress) it before applying methods of image classification, interpreting, and information extraction. This can be done using one of two approaches - by component-wise or by vectorial (3D) filtering. The second approach has shown itself to have higher efficiency if there is essential correlation between multichannel image components as this often happens for multichannel remote sensing data of different origin. Within the class of 3D filtering techniques, there are many possibilities and variations. In this paper, we consider filtering based on discrete cosine transform (DCT) and pay attention to two aspects of processing. First, we study in detail what changes in DCT coefficient statistics take place for 3D denoising compared to component-wise processing. Second, we analyze how selection of component images united into 3D data array influences efficiency of filtering and can the observed tendencies be exploited in processing of images with rather large number of channels.

A CNN Regression Approach for Real-Time 2D/3D Registration.

PubMed

Shun Miao; Wang, Z Jane; Rui Liao

2016-05-01

In this paper, we present a Convolutional Neural Network (CNN) regression approach to address the two major limitations of existing intensity-based 2-D/3-D registration technology: 1) slow computation and 2) small capture range. Different from optimization-based methods, which iteratively optimize the transformation parameters over a scalar-valued metric function representing the quality of the registration, the proposed method exploits the information embedded in the appearances of the digitally reconstructed radiograph and X-ray images, and employs CNN regressors to directly estimate the transformation parameters. An automatic feature extraction step is introduced to calculate 3-D pose-indexed features that are sensitive to the variables to be regressed while robust to other factors. The CNN regressors are then trained for local zones and applied in a hierarchical manner to break down the complex regression task into multiple simpler sub-tasks that can be learned separately. Weight sharing is furthermore employed in the CNN regression model to reduce the memory footprint. The proposed approach has been quantitatively evaluated on 3 potential clinical applications, demonstrating its significant advantage in providing highly accurate real-time 2-D/3-D registration with a significantly enlarged capture range when compared to intensity-based methods.

Disentangling the intragroup HI in Compact Groups of galaxies by means of X3D visualization

NASA Astrophysics Data System (ADS)

Verdes-Montenegro, Lourdes; Vogt, Frederic; Aubery, Claire; Duret, Laetitie; Garrido, Julián; Sánchez, Susana; Yun, Min S.; Borthakur, Sanchayeeta; Hess, Kelley; Cluver, Michelle; Del Olmo, Ascensión; Perea, Jaime

2017-03-01

As an extreme kind of environment, Hickson Compact groups (HCGs) have shown to be very complex systems. HI-VLA observations revealed an intrincated network of HI tails and bridges, tracing pre-processing through extreme tidal interactions. We found HCGs to show a large HI deficiency supporting an evolutionary sequence where gas-rich groups transform via tidal interactions and ISM (interstellar medium) stripping into gas-poor systems. We detected as well a diffuse HI component in the groups, increasing with evolutionary phase, although with uncertain distribution. The complex net of detected HI as observed with the VLA seems hence so puzzling as the missing one. In this talk we revisit the existing VLA information on the HI distribution and kinematics of HCGs by means of X3D visualization. X3D constitutes a powerful tool to extract the most from HI data cubes and a mean of simplifying and easing the access to data visualization and publication via three-dimensional (3-D) diagrams.

A novel approach to segmentation and measurement of medical image using level set methods.

PubMed

Chen, Yao-Tien

2017-06-01

The study proposes a novel approach for segmentation and visualization plus value-added surface area and volume measurements for brain medical image analysis. The proposed method contains edge detection and Bayesian based level set segmentation, surface and volume rendering, and surface area and volume measurements for 3D objects of interest (i.e., brain tumor, brain tissue, or whole brain). Two extensions based on edge detection and Bayesian level set are first used to segment 3D objects. Ray casting and a modified marching cubes algorithm are then adopted to facilitate volume and surface visualization of medical-image dataset. To provide physicians with more useful information for diagnosis, the surface area and volume of an examined 3D object are calculated by the techniques of linear algebra and surface integration. Experiment results are finally reported in terms of 3D object extraction, surface and volume rendering, and surface area and volume measurements for medical image analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis on Time-Lag Effect of Research and Development Investment in the Pharmaceutical Industry in Korea

PubMed Central

Lee, Munjae; Choi, Mankyu

2015-01-01

Objectives The aim of this study is to analyze the influence of the research and development (R&D) investment of pharmaceutical companies on enterprise value. Methods The period of the empirical analysis is from 2000 to 2012, considering the period after the influence of the financial crisis. Financial statements and comments in general and internal transactions were extracted from TS-2000 of the Korea Listed Company Association, and data related to stock price were extracted from KISVALUE-III of National Information and Credit Evaluation Information Service Co., Ltd. STATA 12.0 was used as the statistical package for panel analysis. Results In the pharmaceutical firms, the influence of the R&D intensity with regard to Tobin's q was found to be positive. However, only the R&D expenditure intensities of previous years 2 and 5 (t–2 and t–5, respectively) were statistically significant (p < 0.1), whereas those of previous years 1, 3, and 4 years (t–1, t–3, and t–4, respectively) were not statistically significant. Conclusion R&D investment not only affects the enterprise value but is also evaluated as an investment activity that raises the long-term enterprise value. The research findings will serve as valuable data to understand the enterprise value of the Korea pharmaceutical industry and to strengthen reform measures. Not only should new drug development be made, but also investment and support should be provided according to the specific factors suitable to improve the competitiveness of each company, such as generic, incrementally modified drugs, and biosimilar products. PMID:26473091

Analysis on Time-Lag Effect of Research and Development Investment in the Pharmaceutical Industry in Korea.

PubMed

Lee, Munjae; Choi, Mankyu

2015-08-01

The aim of this study is to analyze the influence of the research and development (R&D) investment of pharmaceutical companies on enterprise value. The period of the empirical analysis is from 2000 to 2012, considering the period after the influence of the financial crisis. Financial statements and comments in general and internal transactions were extracted from TS-2000 of the Korea Listed Company Association, and data related to stock price were extracted from KISVALUE-III of National Information and Credit Evaluation Information Service Co., Ltd. STATA 12.0 was used as the statistical package for panel analysis. In the pharmaceutical firms, the influence of the R&D intensity with regard to Tobin's q was found to be positive. However, only the R&D expenditure intensities of previous years 2 and 5 (t-2 and t-5, respectively) were statistically significant (p < 0.1), whereas those of previous years 1, 3, and 4 years (t-1, t-3, and t-4, respectively) were not statistically significant. R&D investment not only affects the enterprise value but is also evaluated as an investment activity that raises the long-term enterprise value. The research findings will serve as valuable data to understand the enterprise value of the Korea pharmaceutical industry and to strengthen reform measures. Not only should new drug development be made, but also investment and support should be provided according to the specific factors suitable to improve the competitiveness of each company, such as generic, incrementally modified drugs, and biosimilar products.

Automatic extraction and visualization of object-oriented software design metrics

NASA Astrophysics Data System (ADS)

Lakshminarayana, Anuradha; Newman, Timothy S.; Li, Wei; Talburt, John

2000-02-01

Software visualization is a graphical representation of software characteristics and behavior. Certain modes of software visualization can be useful in isolating problems and identifying unanticipated behavior. In this paper we present a new approach to aid understanding of object- oriented software through 3D visualization of software metrics that can be extracted from the design phase of software development. The focus of the paper is a metric extraction method and a new collection of glyphs for multi- dimensional metric visualization. Our approach utilize the extensibility interface of a popular CASE tool to access and automatically extract the metrics from Unified Modeling Language class diagrams. Following the extraction of the design metrics, 3D visualization of these metrics are generated for each class in the design, utilizing intuitively meaningful 3D glyphs that are representative of the ensemble of metrics. Extraction and visualization of design metrics can aid software developers in the early study and understanding of design complexity.

3D galaxy clustering with future wide-field surveys: Advantages of a spherical Fourier-Bessel analysis

NASA Astrophysics Data System (ADS)

Lanusse, F.; Rassat, A.; Starck, J.-L.

2015-06-01

Context. Upcoming spectroscopic galaxy surveys are extremely promising to help in addressing the major challenges of cosmology, in particular in understanding the nature of the dark universe. The strength of these surveys, naturally described in spherical geometry, comes from their unprecedented depth and width, but an optimal extraction of their three-dimensional information is of utmost importance to best constrain the properties of the dark universe. Aims: Although there is theoretical motivation and novel tools to explore these surveys using the 3D spherical Fourier-Bessel (SFB) power spectrum of galaxy number counts Cℓ(k,k'), most survey optimisations and forecasts are based on the tomographic spherical harmonics power spectrum C(ij)_ℓ. The goal of this paper is to perform a new investigation of the information that can be extracted from these two analyses in the context of planned stage IV wide-field galaxy surveys. Methods: We compared tomographic and 3D SFB techniques by comparing the forecast cosmological parameter constraints obtained from a Fisher analysis. The comparison was made possible by careful and coherent treatment of non-linear scales in the two analyses, which makes this study the first to compare 3D SFB and tomographic constraints on an equal footing. Nuisance parameters related to a scale- and redshift-dependent galaxy bias were also included in the computation of the 3D SFB and tomographic power spectra for the first time. Results: Tomographic and 3D SFB methods can recover similar constraints in the absence of systematics. This requires choosing an optimal number of redshift bins for the tomographic analysis, which we computed to be N = 26 for zmed ≃ 0.4, N = 30 for zmed ≃ 1.0, and N = 42 for zmed ≃ 1.7. When marginalising over nuisance parameters related to the galaxy bias, the forecast 3D SFB constraints are less affected by this source of systematics than the tomographic constraints. In addition, the rate of increase of the figure of merit as a function of median redshift is higher for the 3D SFB method than for the 2D tomographic method. Conclusions: Constraints from the 3D SFB analysis are less sensitive to unavoidable systematics stemming from a redshift- and scale-dependent galaxy bias. Even for surveys that are optimised with tomography in mind, a 3D SFB analysis is more powerful. In addition, for survey optimisation, the figure of merit for the 3D SFB method increases more rapidly with redshift, especially at higher redshifts, suggesting that the 3D SFB method should be preferred for designing and analysing future wide-field spectroscopic surveys. CosmicPy, the Python package developed for this paper, is freely available at https://cosmicpy.github.io. Appendices are available in electronic form at http://www.aanda.org

Large Scale EOF Analysis of Climate Data

NASA Astrophysics Data System (ADS)

Prabhat, M.; Gittens, A.; Kashinath, K.; Cavanaugh, N. R.; Mahoney, M.

2016-12-01

We present a distributed approach towards extracting EOFs from 3D climate data. We implement the method in Apache Spark, and process multi-TB sized datasets on O(1000-10,000) cores. We apply this method to latitude-weighted ocean temperature data from CSFR, a 2.2 terabyte-sized data set comprising ocean and subsurface reanalysis measurements collected at 41 levels in the ocean, at 6 hour intervals over 31 years. We extract the first 100 EOFs of this full data set and compare to the EOFs computed simply on the surface temperature field. Our analyses provide evidence of Kelvin and Rossy waves and components of large-scale modes of oscillation including the ENSO and PDO that are not visible in the usual SST EOFs. Further, they provide information on the the most influential parts of the ocean, such as the thermocline, that exist below the surface. Work is ongoing to understand the factors determining the depth-varying spatial patterns observed in the EOFs. We will experiment with weighting schemes to appropriately account for the differing depths of the observations. We also plan to apply the same distributed approach to analysis of analysis of 3D atmospheric climatic data sets, including multiple variables. Because the atmosphere changes on a quicker time-scale than the ocean, we expect that the results will demonstrate an even greater advantage to computing 3D EOFs in lieu of 2D EOFs.

Effect of Curcuma longa on CYP2D6- and CYP3A4-mediated metabolism of dextromethorphan in human liver microsomes and healthy human subjects.

PubMed

Al-Jenoobi, Fahad Ibrahim; Al-Thukair, Areej A; Alam, Mohd Aftab; Abbas, Fawkeya A; Al-Mohizea, Abdullah M; Alkharfy, Khalid M; Al-Suwayeh, Saleh A

2015-03-01

Effect of Curcuma longa rhizome powder and its ethanolic extract on CYP2D6 and CYP3A4 metabolic activity was investigated in vitro using human liver microsomes and clinically in healthy human subjects. Dextromethorphan (DEX) was used as common probe for CYP2D6 and CYP3A4 enzymes. Metabolic activity of CYP2D6 and CYP3A4 was evaluated through in vitro study; where microsomes were incubated with NADPH in presence and absence of Curcuma extract. In clinical study phase-I, six healthy human subjects received a single dose (30 mg) of DEX syrup, and in phase-II DEX syrup was administered with Curcuma powder. The enzyme CYP2D6 and CYP3A4 mediated O- and N-demethylation of dextromethorphan into dextrorphan (DOR) and 3-methoxymorphinan (3-MM), respectively. Curcuma extract significantly inhibited the formation of DOR and 3-MM, in a dose-dependent and linear fashion. The 100 μg/ml dose of curcuma extract produced highest inhibition, which was about 70 % for DOR and 80 % for 3-MM. Curcuma significantly increases the urine metabolic ratio of DEX/DOR but the change in DEX/3-MM ratio was statistically insignificant. Present findings suggested that curcuma significantly inhibits the activity of CYP2D6 in in vitro as well as in vivo; which indicates that curcuma has potential to interact with CYP2D6 substrates.

Wide field of view common-path lateral-shearing digital holographic interference microscope

NASA Astrophysics Data System (ADS)

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes.

Wide field of view common-path lateral-shearing digital holographic interference microscope.

PubMed

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Small incision lenticule extraction (SMILE) versus laser in-situ keratomileusis (LASIK): study protocol for a randomized, non-inferiority trial.

PubMed

Ang, Marcus; Tan, Donald; Mehta, Jodhbir S

2012-05-31

Small incision lenticule extraction or SMILE is a novel form of 'flapless' corneal refractive surgery that was adapted from refractive lenticule extraction (ReLEx). SMILE uses only one femtosecond laser to complete the refractive surgery, potentially reducing surgical time, side effects, and cost. If successful, SMILE could potentially replace the current, widely practiced laser in-situ keratomileusis or LASIK. The aim of this study is to evaluate whether SMILE is non-inferior to LASIK in terms of refractive outcomes at 3 months post-operatively. Single tertiary center, parallel group, single-masked, paired-eye design, non-inferiority, randomized controlled trial. Participants who are eligible for LASIK will be enrolled for study after informed consent. Each participant will be randomized to receive SMILE and LASIK in each eye. Our primary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> -3.00 diopter (D)) at a tertiary eye center in terms of refractive predictability at 3 months post-operatively. Our secondary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> -3.00 D) at a tertiary eye center in terms of other refractive outcomes (efficacy, safety, higher-order aberrations) at 3 months post-operatively. Our primary outcome is refractive predictability, which is one of several standard refractive outcomes, defined as the proportion of eyes achieving a postoperative spherical equivalent (SE) within ±0.50 D of the intended target. Randomization will be performed using random allocation sequence generated by a computer with no blocks or restrictions, and implemented by concealing the number-coded surgery within sealed envelopes until just before the procedure. In this single-masked trial, subjects and their caregivers will be masked to the assigned treatment in each eye. This novel trial will provide information on whether SMILE has comparable, if not superior, refractive outcomes compared to the established LASIK for myopia, thus providing evidence for translation into clinical practice. Clinicaltrials.gov NCT01216475.

Second-harmonic patterned polarization-analyzed reflection confocal microscope

NASA Astrophysics Data System (ADS)

Okoro, Chukwuemeka; Toussaint, Kimani C.

2017-08-01

We introduce the second-harmonic patterned polarization-analyzed reflection confocal (SPPARC) microscope-a multimodal imaging platform that integrates Mueller matrix polarimetry with reflection confocal and second-harmonic generation (SHG) microscopy. SPPARC microscopy provides label-free three-dimensional (3-D), SHG-patterned confocal images that lend themselves to spatially dependent, linear polarimetric analysis for extraction of rich polarization information based on the Mueller calculus. To demonstrate its capabilities, we use SPPARC microscopy to analyze both porcine tendon and ligament samples and find differences in both circular degree-of-polarization and depolarization parameters. Moreover, using the collagen-generated SHG signal as an endogenous counterstain, we show that the technique can be used to provide 3-D polarimetric information of the surrounding extrafibrillar matrix plus cells or EFMC region. The unique characteristics of SPPARC microscopy holds strong potential for it to more accurately and quantitatively describe microstructural changes in collagen-rich samples in three spatial dimensions.

Femtosecond pump-probe microscopy generates virtual cross-sections in historic artwork

PubMed Central

Villafana, Tana Elizabeth; Brown, William P.; Delaney, John K.; Palmer, Michael; Warren, Warren S.; Fischer, Martin C.

2014-01-01

The layering structure of a painting contains a wealth of information about the artist's choice of materials and working methods, but currently, no 3D noninvasive method exists to replace the taking of small paint samples in the study of the stratigraphy. Here, we adapt femtosecond pump-probe imaging, previously shown in tissue, to the case of the color palette in paintings, where chromophores have much greater variety. We show that combining the contrasts of multispectral and multidelay pump-probe spectroscopy permits nondestructive 3D imaging of paintings with molecular and structural contrast, even for pigments with linear absorption spectra that are broad and relatively featureless. We show virtual cross-sectioning capabilities in mockup paintings, with pigment separation and nondestructive imaging on an intact 14th century painting (The Crucifixion by Puccio Capanna). Our approach makes it possible to extract microscopic information for a broad range of applications to cultural heritage. PMID:24449855

On the Limitations of Breakthrough Curve Analysis in Fixed-Bed Adsorption

NASA Technical Reports Server (NTRS)

Knox, James C.; Ebner, Armin D.; LeVan, M. Douglas; Coker, Robert F.; Ritter, James A.

2016-01-01

This work examined in detail the a priori prediction of the axial dispersion coefficient from available correlations versus obtaining it and also mass transfer information from experimental breakthrough data and the consequences that may arise when doing so based on using a 1-D axially dispersed plug flow model and its associated Danckwerts outlet boundary condition. These consequences mainly included determining the potential for erroneous extraction of the axial dispersion coefficient and/or the LDF mass transfer coefficient from experimental data, especially when non-plug flow conditions prevailed in the bed. Two adsorbent/adsorbate cases were considered, i.e., carbon dioxide and water vapor in zeolite 5A, because they both experimentally exhibited significant non-plug flow behavior, and the water-zeolite 5A system exhibited unusual concentration front sharpening that destroyed the expected constant pattern behavior (CPB) when modeled with the 1-D axially dispersed plug flow model. Overall, this work showed that it was possible to extract accurate mass transfer and dispersion information from experimental breakthrough curves using a 1-D axial dispersed plug flow model when they were measured both inside and outside the bed. To ensure the extracted information was accurate, the inside the bed breakthrough curves and their derivatives from the model were plotted to confirm whether or not the adsorbate/adsorbent system was exhibiting CPB or any concentration front sharpening near the bed exit. Even when concentration front sharpening was occurring with the water-zeolite 5A system, it was still possible to use the experimental inside and outside the bed breakthrough curves to extract fundamental mass transfer and dispersion information from the 1-D axial dispersed plug flow model based on the systematic methodology developed in this work.

Tunable quantum interference in a 3D integrated circuit.

PubMed

Chaboyer, Zachary; Meany, Thomas; Helt, L G; Withford, Michael J; Steel, M J

2015-04-27

Integrated photonics promises solutions to questions of stability, complexity, and size in quantum optics. Advances in tunable and non-planar integrated platforms, such as laser-inscribed photonics, continue to bring the realisation of quantum advantages in computation and metrology ever closer, perhaps most easily seen in multi-path interferometry. Here we demonstrate control of two-photon interference in a chip-scale 3D multi-path interferometer, showing a reduced periodicity and enhanced visibility compared to single photon measurements. Observed non-classical visibilities are widely tunable, and explained well by theoretical predictions based on classical measurements. With these predictions we extract Fisher information approaching a theoretical maximum. Our results open a path to quantum enhanced phase measurements.

Security authentication with a three-dimensional optical phase code using random forest classifier: an overview

NASA Astrophysics Data System (ADS)

Markman, Adam; Carnicer, Artur; Javidi, Bahram

2017-05-01

We overview our recent work [1] on utilizing three-dimensional (3D) optical phase codes for object authentication using the random forest classifier. A simple 3D optical phase code (OPC) is generated by combining multiple diffusers and glass slides. This tag is then placed on a quick-response (QR) code, which is a barcode capable of storing information and can be scanned under non-uniform illumination conditions, rotation, and slight degradation. A coherent light source illuminates the OPC and the transmitted light is captured by a CCD to record the unique signature. Feature extraction on the signature is performed and inputted into a pre-trained random-forest classifier for authentication.

TH-EF-BRA-06: A Novel Retrospective 3D K-Space Sorting 4D-MRI Technique Using a Radial K-Space Acquisition MRI Sequence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Y; Subashi, E; Yin, F

Purpose: Current retrospective 4D-MRI provides superior tumor-to-tissue contrast and accurate respiratory motion information for radiotherapy motion management. The developed 4D-MRI techniques based on 2D-MRI image sorting require a high frame-rate of the MR sequences. However, several MRI sequences provide excellent image quality but have low frame-rate. This study aims at developing a novel retrospective 3D k-space sorting 4D-MRI technique using radial k-space acquisition MRI sequences to improve 4D-MRI image quality and temporal-resolution for imaging irregular organ/tumor respiratory motion. Methods: The method is based on a RF-spoiled, steady-state, gradient-recalled sequence with minimal echo time. A 3D radial k-space data acquisition trajectorymore » was used for sampling the datasets. Each radial spoke readout data line starts from the 3D center of Field-of-View. Respiratory signal can be extracted from the k-space center data point of each spoke. The spoke data was sorted based on its self-synchronized respiratory signal using phase sorting. Subsequently, 3D reconstruction was conducted to generate the time-resolved 4D-MRI images. As a feasibility study, this technique was implemented on a digital human phantom XCAT. The respiratory motion was controlled by an irregular motion profile. To validate using k-space center data as a respiratory surrogate, we compared it with the XCAT input controlling breathing profile. Tumor motion trajectories measured on reconstructed 4D-MRI were compared to the average input trajectory. The mean absolute amplitude difference (D) was calculated. Results: The signal extracted from k-space center data matches well with the input controlling respiratory profile of XCAT. The relative amplitude error was 8.6% and the relative phase error was 3.5%. XCAT 4D-MRI demonstrated a clear motion pattern with little serrated artifacts. D of tumor trajectories was 0.21mm, 0.23mm and 0.23mm in SI, AP and ML directions, respectively. Conclusion: A novel retrospective 3D k-space sorting 4D-MRI technique has been developed and evaluated on human digital phantom. NIH (1R21CA165384-01A1)« less

Fast and Easy 3D Reconstruction with the Help of Geometric Constraints and Genetic Algorithms

NASA Astrophysics Data System (ADS)

Annich, Afafe; El Abderrahmani, Abdellatif; Satori, Khalid

2017-09-01

The purpose of the work presented in this paper is to describe new method of 3D reconstruction from one or more uncalibrated images. This method is based on two important concepts: geometric constraints and genetic algorithms (GAs). At first, we are going to discuss the combination between bundle adjustment and GAs that we have proposed in order to improve 3D reconstruction efficiency and success. We used GAs in order to improve fitness quality of initial values that are used in the optimization problem. It will increase surely convergence rate. Extracted geometric constraints are used first to obtain an estimated value of focal length that helps us in the initialization step. Matching homologous points and constraints is used to estimate the 3D model. In fact, our new method gives us a lot of advantages: reducing the estimated parameter number in optimization step, decreasing used image number, winning time and stabilizing good quality of 3D results. At the end, without any prior information about our 3D scene, we obtain an accurate calibration of the cameras, and a realistic 3D model that strictly respects the geometric constraints defined before in an easy way. Various data and examples will be used to highlight the efficiency and competitiveness of our present approach.

Robust extraction of the aorta and pulmonary artery from 3D MDCT image data

NASA Astrophysics Data System (ADS)

Taeprasartsit, Pinyo; Higgins, William E.

2010-03-01

Accurate definition of the aorta and pulmonary artery from three-dimensional (3D) multi-detector CT (MDCT) images is important for pulmonary applications. This work presents robust methods for defining the aorta and pulmonary artery in the central chest. The methods work on both contrast enhanced and no-contrast 3D MDCT image data. The automatic methods use a common approach employing model fitting and selection and adaptive refinement. During the occasional event that more precise vascular extraction is desired or the method fails, we also have an alternate semi-automatic fail-safe method. The semi-automatic method extracts the vasculature by extending the medial axes into a user-guided direction. A ground-truth study over a series of 40 human 3D MDCT images demonstrates the efficacy, accuracy, robustness, and efficiency of the methods.

Quantitative evaluation for small surface damage based on iterative difference and triangulation of 3D point cloud

NASA Astrophysics Data System (ADS)

Zhang, Yuyan; Guo, Quanli; Wang, Zhenchun; Yang, Degong

2018-03-01

This paper proposes a non-contact, non-destructive evaluation method for the surface damage of high-speed sliding electrical contact rails. The proposed method establishes a model of damage identification and calculation. A laser scanning system is built to obtain the 3D point cloud data of the rail surface. In order to extract the damage region of the rail surface, the 3D point cloud data are processed using iterative difference, nearest neighbours search and a data registration algorithm. The curvature of the point cloud data in the damage region is mapped to RGB color information, which can directly reflect the change trend of the curvature of the point cloud data in the damage region. The extracted damage region is divided into three prism elements by a method of triangulation. The volume and mass of a single element are calculated by the method of geometric segmentation. Finally, the total volume and mass of the damage region are obtained by the principle of superposition. The proposed method is applied to several typical injuries and the results are discussed. The experimental results show that the algorithm can identify damage shapes and calculate damage mass with milligram precision, which are useful for evaluating the damage in a further research stage.

Using articulated scene models for dynamic 3d scene analysis in vista spaces

NASA Astrophysics Data System (ADS)

Beuter, Niklas; Swadzba, Agnes; Kummert, Franz; Wachsmuth, Sven

2010-09-01

In this paper we describe an efficient but detailed new approach to analyze complex dynamic scenes directly in 3D. The arising information is important for mobile robots to solve tasks in the area of household robotics. In our work a mobile robot builds an articulated scene model by observing the environment in the visual field or rather in the so-called vista space. The articulated scene model consists of essential knowledge about the static background, about autonomously moving entities like humans or robots and finally, in contrast to existing approaches, information about articulated parts. These parts describe movable objects like chairs, doors or other tangible entities, which could be moved by an agent. The combination of the static scene, the self-moving entities and the movable objects in one articulated scene model enhances the calculation of each single part. The reconstruction process for parts of the static scene benefits from removal of the dynamic parts and in turn, the moving parts can be extracted more easily through the knowledge about the background. In our experiments we show, that the system delivers simultaneously an accurate static background model, moving persons and movable objects. This information of the articulated scene model enables a mobile robot to detect and keep track of interaction partners, to navigate safely through the environment and finally, to strengthen the interaction with the user through the knowledge about the 3D articulated objects and 3D scene analysis. [Figure not available: see fulltext.

Image processing tools dedicated to quantification in 3D fluorescence microscopy

NASA Astrophysics Data System (ADS)

Dieterlen, A.; De Meyer, A.; Colicchio, B.; Le Calvez, S.; Haeberlé, O.; Jacquey, S.

2006-05-01

3-D optical fluorescent microscopy now becomes an efficient tool for the volume investigation of living biological samples. Developments in instrumentation have permitted to beat off the conventional Abbe limit. In any case the recorded image can be described by the convolution equation between the original object and the Point Spread Function (PSF) of the acquisition system. Due to the finite resolution of the instrument, the original object is recorded with distortions and blurring, and contaminated by noise. This induces that relevant biological information cannot be extracted directly from raw data stacks. If the goal is 3-D quantitative analysis, then to assess optimal performance of the instrument and to ensure the data acquisition reproducibility, the system characterization is mandatory. The PSF represents the properties of the image acquisition system; we have proposed the use of statistical tools and Zernike moments to describe a 3-D PSF system and to quantify the variation of the PSF. This first step toward standardization is helpful to define an acquisition protocol optimizing exploitation of the microscope depending on the studied biological sample. Before the extraction of geometrical information and/or intensities quantification, the data restoration is mandatory. Reduction of out-of-focus light is carried out computationally by deconvolution process. But other phenomena occur during acquisition, like fluorescence photo degradation named "bleaching", inducing an alteration of information needed for restoration. Therefore, we have developed a protocol to pre-process data before the application of deconvolution algorithms. A large number of deconvolution methods have been described and are now available in commercial package. One major difficulty to use this software is the introduction by the user of the "best" regularization parameters. We have pointed out that automating the choice of the regularization level; also greatly improves the reliability of the measurements although it facilitates the use. Furthermore, to increase the quality and the repeatability of quantitative measurements a pre-filtering of images improves the stability of deconvolution process. In the same way, the PSF prefiltering stabilizes the deconvolution process. We have shown that Zemike polynomials can be used to reconstruct experimental PSF, preserving system characteristics and removing the noise contained in the PSF.

Forensic microradiology: micro-computed tomography (Micro-CT) and analysis of patterned injuries inside of bone.

PubMed

Thali, Michael J; Taubenreuther, Ulrike; Karolczak, Marek; Braun, Marcel; Brueschweiler, Walter; Kalender, Willi A; Dirnhofer, Richard

2003-11-01

When a knife is stabbed in bone, it leaves an impression in the bone. The characteristics (shape, size, etc.) may indicate the type of tool used to produce the patterned injury in bone. Until now it has been impossible in forensic sciences to document such damage precisely and non-destructively. Micro-computed tomography (Micro-CT) offers an opportunity to analyze patterned injuries of tool marks made in bone. Using high-resolution Micro-CT and computer software, detailed analysis of three-dimensional (3D) architecture has recently become feasible and allows microstructural 3D bone information to be collected. With adequate viewing software, data from 2D slice of an arbitrary plane can be extracted from 3D datasets. Using such software as a "digital virtual knife," the examiner can interactively section and analyze the 3D sample. Analysis of the bone injury revealed that Micro-CT provides an opportunity to correlate a bone injury to an injury-causing instrument. Even broken knife tips can be graphically and non-destructively assigned to a suspect weapon.

- and Graph-Based Point Cloud Segmentation of 3d Scenes Using Perceptual Grouping Laws

NASA Astrophysics Data System (ADS)

Xu, Y.; Hoegner, L.; Tuttas, S.; Stilla, U.

2017-05-01

Segmentation is the fundamental step for recognizing and extracting objects from point clouds of 3D scene. In this paper, we present a strategy for point cloud segmentation using voxel structure and graph-based clustering with perceptual grouping laws, which allows a learning-free and completely automatic but parametric solution for segmenting 3D point cloud. To speak precisely, two segmentation methods utilizing voxel and supervoxel structures are reported and tested. The voxel-based data structure can increase efficiency and robustness of the segmentation process, suppressing the negative effect of noise, outliers, and uneven points densities. The clustering of voxels and supervoxel is carried out using graph theory on the basis of the local contextual information, which commonly conducted utilizing merely pairwise information in conventional clustering algorithms. By the use of perceptual laws, our method conducts the segmentation in a pure geometric way avoiding the use of RGB color and intensity information, so that it can be applied to more general applications. Experiments using different datasets have demonstrated that our proposed methods can achieve good results, especially for complex scenes and nonplanar surfaces of objects. Quantitative comparisons between our methods and other representative segmentation methods also confirms the effectiveness and efficiency of our proposals.

Intracellular Doppler Signatures of Platinum Sensitivity Captured by Biodynamic Profiling in Ovarian Xenografts

NASA Astrophysics Data System (ADS)

Merrill, Daniel; An, Ran; Sun, Hao; Yakubov, Bakhtiyor; Matei, Daniela; Turek, John; Nolte, David

2016-01-01

Three-dimensional (3D) tissue cultures are replacing conventional two-dimensional (2D) cultures for applications in cancer drug development. However, direct comparisons of in vitro 3D models relative to in vivo models derived from the same cell lines have not been reported because of the lack of sensitive optical probes that can extract high-content information from deep inside living tissue. Here we report the use of biodynamic imaging (BDI) to measure response to platinum in 3D living tissue. BDI combines low-coherence digital holography with intracellular Doppler spectroscopy to study tumor drug response. Human ovarian cancer cell lines were grown either in vitro as 3D multicellular monoculture spheroids or as xenografts in nude mice. Fragments of xenografts grown in vivo in nude mice from a platinum-sensitive human ovarian cell line showed rapid and dramatic signatures of induced cell death when exposed to platinum ex vivo, while the corresponding 3D multicellular spheroids grown in vitro showed negligible response. The differences in drug response between in vivo and in vitro growth have important implications for predicting chemotherapeutic response using tumor biopsies from patients or patient-derived xenografts.

Crustal Structure of Australia from Ambient Seismic Noise Tomography

NASA Astrophysics Data System (ADS)

Saygin, E.; Kennett, B. L.

2011-12-01

We create surface wave tomography for Australian crustal structure by using the group velocity measurements in the period range 1-32 s extracted from the stacked transfer functions of ambient noise between station pairs. Both Rayleigh wave and Love wave group velocity maps are constructed for each period using the vertical and transverse component of the Green's function estimates from the ambient noise. The all of the portable broadband deployments and permanent stations on the continent have been used with over 250 stations in all and up to 7500 paths. The permanent stations fill the gap between the various shorter-term portable deployments. At each period the group velocity maps are constructed with a fully nonlinear tomographic inversion exploiting a subspace technique and the Fast Marching Method for wavefront tracking. For Rayleigh waves the continental coverage is good enough to allow the construction of a 3D shear wavespeed model in a two stage approach. Local group dispersion information is collated for a distribution of points across the continent and inverted for a 1D SV wavespeed profile using a Neighbourhood Algorithm method with weak constraints on the sedimentary thickness and Moho depth. The resulting set of 1D models are then interpolated to produce the final 3D wavespeed model. The group velocity maps show the strong influence of thick sediments at shorter periods, and distinct fast zones associated with cratonic regions. Below the sediments the 3D shear wavespeed model displays significant heterogeneity with only moderate correlation with surface tectonic features. For example, there is no evident expression of the Tasman Line marking the eastern edge of Precambrian outcrop. The large number of available interstation paths extracted from the ambient noise analysis provide detailed shear wavespeed information for crustal structure across the Australian continent for the first time, including regions where there was no prior sampling because of difficult logistics.

Computational Simulation of Thermal and Spattering Phenomena and Microstructure in Selective Laser Melting of Inconel 625

NASA Astrophysics Data System (ADS)

Özel, Tuğrul; Arısoy, Yiğit M.; Criales, Luis E.

Computational modelling of Laser Powder Bed Fusion (L-PBF) processes such as Selective laser Melting (SLM) can reveal information that is hard to obtain or unobtainable by in-situ experimental measurements. A 3D thermal field that is not visible by the thermal camera can be obtained by solving the 3D heat transfer problem. Furthermore, microstructural modelling can be used to predict the quality and mechanical properties of the product. In this paper, a nonlinear 3D Finite Element Method based computational code is developed to simulate the SLM process with different process parameters such as laser power and scan velocity. The code is further improved by utilizing an in-situ thermal camera recording to predict spattering which is in turn included as a stochastic heat loss. Then, thermal gradients extracted from the simulations applied to predict growth directions in the resulting microstructure.

Three-Dimensional Grain Shape-Fabric from Unconsolidated Pyroclastic Density Current Deposits: Implications for Extracting Flow Direction and Insights on Rheology

NASA Astrophysics Data System (ADS)

Hawkins, T. T.; Brand, B. D.; Sarrochi, D.; Pollock, N.

2016-12-01

One of the greatest challenges volcanologists face is the ability to extrapolate information about eruption dynamics and emplacement conditions from deposits. Pyroclastic density current (PDC) deposits are particularly challenging given the wide range of initial current conditions, (e.g., granular, fluidized, concentrated, dilute), and rapid flow transformations due to interaction with evolving topography. Analysis of particle shape-fabric can be used to determine flow direction, and may help to understand the rheological characteristics of the flows. However, extracting shape-fabric information from outcrop (2D) apparent fabric is limited, especially when outcrop exposure is incomplete or lacks context. To better understand and quantify the complex flow dynamics reflected in PDC deposits, we study the complete shape-fabric data in 3D using oriented samples. In the field, the prospective sample is carved from the unconsolidated deposit in blocks, the dimensions of which depend on the average clast size in the sample. The sample is saturated in situ with a water-based sodium silicate solution, then wrapped in plaster-soaked gauze to form a protective cast. The orientation of the sample is recorded on the block faces. The samples dry for five days and are then extracted in intact blocks. In the lab, the sample is vacuum impregnated with sodium silicate and cured in an oven. The fully lithified sample is first cut along the plan view to identify orientations of the long axes of the grains (flow direction), and then cut in the two plains perpendicular to grain elongation. 3D fabric analysis is performed using high resolution images of the cut-faces using computer assisted image analysis software devoted to shape-fabric analysis. Here we present the results of samples taken from the 18 May 1980 PDC deposit facies, including massive, diffuse-stratified and cross-stratified lapilli tuff. We show a relationship between the strength of iso-orientation of the elongated particles and different facies architectures, which is used to interpret rheological conditions of the flow. We chose the 18 May PDC deposits because their well-exposed and well-studied outcrops provide context, which allow us to test the method and extract information useful for interpreting ancient deposits that lack context.

Automatic detection of pelvic lymph nodes using multiple MR sequences

NASA Astrophysics Data System (ADS)

Yan, Michelle; Lu, Yue; Lu, Renzhi; Requardt, Martin; Moeller, Thomas; Takahashi, Satoru; Barentsz, Jelle

2007-03-01

A system for automatic detection of pelvic lymph nodes is developed by incorporating complementary information extracted from multiple MR sequences. A single MR sequence lacks sufficient diagnostic information for lymph node localization and staging. Correct diagnosis often requires input from multiple complementary sequences which makes manual detection of lymph nodes very labor intensive. Small lymph nodes are often missed even by highly-trained radiologists. The proposed system is aimed at assisting radiologists in finding lymph nodes faster and more accurately. To the best of our knowledge, this is the first such system reported in the literature. A 3-dimensional (3D) MR angiography (MRA) image is employed for extracting blood vessels that serve as a guide in searching for pelvic lymph nodes. Segmentation, shape and location analysis of potential lymph nodes are then performed using a high resolution 3D T1-weighted VIBE (T1-vibe) MR sequence acquired by Siemens 3T scanner. An optional contrast-agent enhanced MR image, such as post ferumoxtran-10 T2*-weighted MEDIC sequence, can also be incorporated to further improve detection accuracy of malignant nodes. The system outputs a list of potential lymph node locations that are overlaid onto the corresponding MR sequences and presents them to users with associated confidence levels as well as their sizes and lengths in each axis. Preliminary studies demonstrates the feasibility of automatic lymph node detection and scenarios in which this system may be used to assist radiologists in diagnosis and reporting.

PC software package to confront multimodality images and a stereotactic atlas in neurosurgery

NASA Astrophysics Data System (ADS)

Barillot, Christian; Lemoine, Didier; Gibaud, Bernard; Toulemont, P. J.; Scarabin, Jean-Marie

1990-07-01

The aim of this application is to interactively transfer information between CT, MRI or DSA data and a 3D stereotactic atlas digitized on a C. Based on a 3D organization of data, this system is devoted to assist a neurosurgeon in surgical planning by numerically cross-assigning information between heterogeneous data (in-vivo or atlas). All these images can be retrieved in digital form from the PACS central archive (SIRENE PACS system). The basic feature of this confrontation is the Talairach's proportional squaring which consists in dividing the 3D cerebral space in independently deformable sub-parts. This 3D model is based on anatomical structures such as the AC-PC line and its two associated vertical lines VAC and VPC. Based on this proportional squaring, the atlas has been digitized in order to get atlas plates along the three orthogonal directions of this geometrical reference (axial, coronal, sagittal). The registration of in-vivo data to the proportional squaring is done by extracting either external framework landmarks or anatomical reference structures (i.e. AC and PC structures on the MRI sagittal mid-plane image). Geometrical transformations and scaling are then recorded for each modality or acquisition according to the proportional squaring. These transformations make for instance possible the transfer of a 3D point of a MRI examination to its 3D location within the proportional squaring and furthermore to its 3D location within another data set (in-vivo or atlas). From that stage, the application gives the choice to the neurosurgeon to select any confrontation between input data (in-vivo images or atlas) and output data (id).

Medical image segmentation using 3D MRI data

NASA Astrophysics Data System (ADS)

Voronin, V.; Marchuk, V.; Semenishchev, E.; Cen, Yigang; Agaian, S.

2017-05-01

Precise segmentation of three-dimensional (3D) magnetic resonance imaging (MRI) image can be a very useful computer aided diagnosis (CAD) tool in clinical routines. Accurate automatic extraction a 3D component from images obtained by magnetic resonance imaging (MRI) is a challenging segmentation problem due to the small size objects of interest (e.g., blood vessels, bones) in each 2D MRA slice and complex surrounding anatomical structures. Our objective is to develop a specific segmentation scheme for accurately extracting parts of bones from MRI images. In this paper, we use a segmentation algorithm to extract the parts of bones from Magnetic Resonance Imaging (MRI) data sets based on modified active contour method. As a result, the proposed method demonstrates good accuracy in a comparison between the existing segmentation approaches on real MRI data.

Recovery correction technique for NMR spectroscopy of perchloric acid extracts using DL-valine-2,3-d2: validation and application to 5-fluorouracil-induced brain damage.

PubMed

Nakagami, Ryutaro; Yamaguchi, Masayuki; Ezawa, Kenji; Kimura, Sadaaki; Hamamichi, Shusei; Sekine, Norio; Furukawa, Akira; Niitsu, Mamoru; Fujii, Hirofumi

2014-01-01

We explored a recovery correction technique that can correct metabolite loss during perchloric acid (PCA) extraction and minimize inter-assay variance in quantitative (1)H nuclear magnetic resonance (NMR) spectroscopy of the brain and evaluated its efficacy in 5-fluorouracil (5-FU)- and saline-administered rats. We measured the recovery of creatine and dl-valine-2,3-d2 from PCA extract containing both compounds (0.5 to 8 mM). We intravenously administered either 5-FU for 4 days (total, 100 mg/kg body weight) or saline into 2 groups of 11 rats each. We subsequently performed PCA extraction of the whole brain on Day 9, externally adding 7 µmol of dl-valine-2,3-d2. We estimated metabolite concentrations using an NMR spectrometer with recovery correction, correcting metabolite concentrations based on the recovery factor of dl-valine-2,3-d2. For each metabolite concentration, we calculated the coefficient of variation (CEV) and compared differences between the 2 groups using unpaired t-test. Equivalent recoveries of dl-valine-2,3-d2 (89.4 ± 3.9%) and creatine (89.7 ± 3.9%) in the PCA extract of the mixed solution indicated the suitability of dl-valine-2,3-d2 as an internal reference. In the rat study, recovery of dl-valine-2,3-d2 was 90.6 ± 9.2%. Nine major metabolite concentrations adjusted by recovery of dl-valine-2,3-d2 in saline-administered rats were comparable to data in the literature. CEVs of these metabolites were reduced from 10 to 17% before to 7 to 16% after correction. The significance of differences in alanine and taurine between the 5-FU- and saline-administered groups was determined only after recovery correction (0.75 ± 0.12 versus 0.86 ± 0.07 for alanine; 5.17 ± 0.59 versus 5.66 ± 0.42 for taurine [µmol/g brain tissue]; P < 0.05). A new recovery correction technique corrected metabolite loss during PCA extraction, minimized inter-assay variance in quantitative (1)H NMR spectroscopy of brain tissue, and effectively detected inter-group differences in concentrations of brain metabolites between 5-FU- and saline-administered rats.

Historical Buildings Models and Their Handling via 3d Survey: from Points Clouds to User-Oriented Hbim

NASA Astrophysics Data System (ADS)

Chiabrando, F.; Sammartano, G.; Spanò, A.

2016-06-01

This paper retraces some research activities and application of 3D survey techniques and Building Information Modelling (BIM) in the environment of Cultural Heritage. It describes the diffusion of as-built BIM approach in the last years in Heritage Assets management, the so-called Built Heritage Information Modelling/Management (BHIMM or HBIM), that is nowadays an important and sustainable perspective in documentation and administration of historic buildings and structures. The work focuses the documentation derived from 3D survey techniques that can be understood like a significant and unavoidable knowledge base for the BIM conception and modelling, in the perspective of a coherent and complete management and valorisation of CH. It deepens potentialities, offered by 3D integrated survey techniques, to acquire productively and quite easilymany 3D information, not only geometrical but also radiometric attributes, helping the recognition, interpretation and characterization of state of conservation and degradation of architectural elements. From these data, they provide more and more high descriptive models corresponding to the geometrical complexity of buildings or aggregates in the well-known 5D (3D + time and cost dimensions). Points clouds derived from 3D survey acquisition (aerial and terrestrial photogrammetry, LiDAR and their integration) are reality-based models that can be use in a semi-automatic way to manage, interpret, and moderately simplify geometrical shapes of historical buildings that are examples, as is well known, of non-regular and complex geometry, instead of modern constructions with simple and regular ones. In the paper, some of these issues are addressed and analyzed through some experiences regarding the creation and the managing of HBIMprojects on historical heritage at different scales, using different platforms and various workflow. The paper focuses on LiDAR data handling with the aim to manage and extract geometrical information; on development and optimization of semi-automatic process of segmentation, recognition and modelling of historical shapes of complex structures; on communication of historical heritage by virtual and augmented reality (VR/AR) in a 3D reconstruction of buildings aggregates from a LiDAR and UAV survey. The HBIM model have been implemented and optimized to be managed and browse by mobile devices for not only touristic or informative scopes, but also to ensure that HBIM platforms will become more easy and valuable tools helping all professionals of AEC involved in the documentation and valorisation process, that nowadays more and more distinguish CH policies.

2D DOST based local phase pattern for face recognition

NASA Astrophysics Data System (ADS)

Moniruzzaman, Md.; Alam, Mohammad S.

2017-05-01

A new two dimensional (2-D) Discrete Orthogonal Stcokwell Transform (DOST) based Local Phase Pattern (LPP) technique has been proposed for efficient face recognition. The proposed technique uses 2-D DOST as preliminary preprocessing and local phase pattern to form robust feature signature which can effectively accommodate various 3D facial distortions and illumination variations. The S-transform, is an extension of the ideas of the continuous wavelet transform (CWT), is also known for its local spectral phase properties in time-frequency representation (TFR). It provides a frequency dependent resolution of the time-frequency space and absolutely referenced local phase information while maintaining a direct relationship with the Fourier spectrum which is unique in TFR. After utilizing 2-D Stransform as the preprocessing and build local phase pattern from extracted phase information yield fast and efficient technique for face recognition. The proposed technique shows better correlation discrimination compared to alternate pattern recognition techniques such as wavelet or Gabor based face recognition. The performance of the proposed method has been tested using the Yale and extended Yale facial database under different environments such as illumination variation and 3D changes in facial expressions. Test results show that the proposed technique yields better performance compared to alternate time-frequency representation (TFR) based face recognition techniques.

Pose estimation of teeth through crown-shape matching

NASA Astrophysics Data System (ADS)

Mok, Vevin; Ong, Sim Heng; Foong, Kelvin W. C.; Kondo, Toshiaki

2002-05-01

This paper presents a technique for determining a tooth's pose given a dental plaster cast and a set of generic tooth models. The ultimate goal of pose estimation is to obtain information about the sizes and positions of the roots, which lie hidden within the gums, without the use of X-rays, CT or MRI. In our approach, the tooth of interest is first extracted from the 3D dental cast image through segmentation. 2D views are then generated from the extracted tooth and are matched against a target view generated from the generic model with known pose. Additional views are generated in the vicinity of the best view and the entire process is repeated until convergence. Upon convergence, the generic tooth is superimposed onto the dental cast to show the position of the root. The results of applying the technique to canines demonstrate the excellent potential of the algorithm for generic tooth fitting.

Data for free--can an electronic medical record provide outcome data for incontinence/prolapse repair procedures?

PubMed

Steidl, Matthew; Zimmern, Philippe

2013-01-01

We determined whether a custom computer program can improve the extraction and accuracy of key outcome measures from progress notes in an electronic medical record compared to a traditional data recording system for incontinence and prolapse repair procedures. Following institutional review board approval, progress notes were exported from the Epic electronic medical record system for outcome measure extraction by a custom computer program. The extracted data (D1) were compared against a manually maintained outcome measures database (D2). This work took place in 2 phases. During the first phase, volatile data such as questionnaires and standardized physical examination findings using the POP-Q (pelvic organ prolapse quantification) system were extracted from existing progress notes. The second phase used a progress note template incorporating key outcome measures to evaluate improvement in data accuracy and extraction rates. Phase 1 compared 6,625 individual outcome measures from 316 patients in D2 to 3,534 outcome measures extracted from progress notes in D1, resulting in an extraction rate of 53.3%. A subset of 3,763 outcome measures from D1 was created by excluding data that did not exist in the extraction, yielding an accuracy rate of 93.9%. With the use of the template in phase 2, the extraction rate improved to 91.9% (273 of 297) and the accuracy rate improved to 100% (273 of 273). In the field of incontinence and prolapse, the disciplined use of an electronic medical record template containing a preestablished set of key outcome measures can provide the ideal interface between required documentation and clinical research. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

A simple, rapid atmospheric pressure chemical ionization liquid chromatography tandem mass spectrometry method for the determination of 25-hydroxyvitamin D2 and D3.

PubMed

Garg, Uttam; Munar, Ada; Frazee, Clinton; Scott, David

2012-09-01

Vitamin D plays a vital role not only in bone health but also in pathophysiology of many other body functions. In recent years, there has been significant increase in testing of 25-hydroxyvitamin D (25-OH vitamin D), a marker of vitamin D deficiency. The most commonly used methods for the measurement of 25-OH vitamin D are immunoassays and liquid chromatography tandem mass spectrometry (LC-MS-MS). Since immunoassays suffer from inaccuracies and interferences, LC-MS-MS is a preferred method. In LC-MS-MS methods, 25-OH vitamin D is extracted from serum or plasma by solid-phase or liquid-phase extraction. Because these extraction methods are time consuming, we developed an easy method that uses simple protein precipitation followed by injection of the supernatant to LC-MS-MS. Several mass-to-charge (m/z) ratio transitions, including commonly used transitions based on water loss, were evaluated and several tube types were tested. The optimal transitions for 25-OH vitamin D2 and D3 were 395.5 > 269.5 and 383.4 > 257.3, respectively. The reportable range of the method was 1-100 ng/mL, and repeatability (within-run) and within-laboratory imprecision were <4% and <6%, respectively. The method agreed well with the solid-phase extraction methods. © 2012 Wiley Periodicals, Inc.

Cytotoxicity and anti-inflammatory effects of zinc ions and eugenol during setting of ZOE in immortalized human oral keratinocytes grown as three-dimensional spheroids.

PubMed

Lee, Jung-Hwan; Lee, Hae-Hyoung; Kim, Kyoung-Nam; Kim, Kwang-Mahn

2016-05-01

The objective of this study is to assess the cytotoxic and anti-inflammatory effects of ZOE cement during setting in two-dimensional (2D) or three-dimensional (3D) cultures of immortalized human oral keratinocytes (IHOKs) with determining the extract components responsible for these effects. Extracts of mixed ZOE at different stages of setting were analyzed by a digital pH meter, ICP-MS, and GC-MS. Serial concentrations of extract and their mixture of ZnCl2, ZnSO4·H2O, and eugenol liquid were added to the 2D and 3D IHOK cultures to determine the half maximal effective concentration in investigating the cause of cytotoxicity by means of WST assay and to investigate mRNA expression levels of inflammatory cytokines by RT-PCR. Zn(2+) and eugenol (4-19 ppm) were detected in the extracts. In the early setting stage, significant cytotoxicity was observed in the 2D and 3D IHOK cultures (P<0.05). The EC50 of Zn(2+) from ZnCl2 was 5-44 ppm in both cultures, whereas the EC50 of eugenol was not detectable under 100 ppm. Along with the lower levels of inflammatory cytokine gene expressions in the extract, treatment of the 2D IHOKs with Zn(2+) alone and treatment of the 3D IHOKs with Zn(2+) plus eugenol resulted in significantly lower expression levels of IL-1β, IL-6, and IL-8 (P<0.05). The cytotoxic effect of ZOE on IHOKs was greater during the setting stage owing to the presence of Zn(2+). The anti-inflammatory response to ZOE was induced by a combination of Zn(2+) and eugenol. Cytotoxic and anti-inflammatory effects differed between the 2D and 3D IHOK cultures. Copyright © 2016. Published by Elsevier Ltd.

From Specific Information Extraction to Inferences: A Hierarchical Framework of Graph Comprehension

DTIC Science & Technology

2004-09-01

The skill to interpret the information displayed in graphs is so important to have, the National Council of Teachers of Mathematics has created...guidelines to ensure that students learn these skills ( NCTM : Standards for Mathematics , 2003). These guidelines are based primarily on the extraction of...graphical perception. Human Computer Interaction, 8, 353-388. NCTM : Standards for Mathematics . (2003, 2003). Peebles, D., & Cheng, P. C.-H. (2002

Shape based segmentation of MRIs of the bones in the knee using phase and intensity information

NASA Astrophysics Data System (ADS)

Fripp, Jurgen; Bourgeat, Pierrick; Crozier, Stuart; Ourselin, Sébastien

2007-03-01

The segmentation of the bones from MR images is useful for performing subsequent segmentation and quantitative measurements of cartilage tissue. In this paper, we present a shape based segmentation scheme for the bones that uses texture features derived from the phase and intensity information in the complex MR image. The phase can provide additional information about the tissue interfaces, but due to the phase unwrapping problem, this information is usually discarded. By using a Gabor filter bank on the complex MR image, texture features (including phase) can be extracted without requiring phase unwrapping. These texture features are then analyzed using a support vector machine classifier to obtain probability tissue matches. The segmentation of the bone is fully automatic and performed using a 3D active shape model based approach driven using gradient and texture information. The 3D active shape model is automatically initialized using a robust affine registration. The approach is validated using a database of 18 FLASH MR images that are manually segmented, with an average segmentation overlap (Dice similarity coefficient) of 0.92 compared to 0.9 obtained using the classifier only.

Mom's shadow: structure-from-motion in newly hatched chicks as revealed by an imprinting procedure.

PubMed

Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio

2009-03-01

The ability to recognize three-dimensional objects from two-dimensional (2-D) displays was investigated in domestic chicks, focusing on the role of the object's motion. In Experiment 1 newly hatched chicks, imprinted on a three-dimensional (3-D) object, were allowed to choose between the shadows of the familiar object and of an object never seen before. In Experiments 2 and 3 random-dot displays were used to produce the perception of a solid shape only when set in motion. Overall, the results showed that domestic chicks were able to recognize familiar shapes from 2-D motion stimuli. It is likely that similar general mechanisms underlying the perception of structure-from-motion and the extraction of 3-D information are shared by humans and animals. The present data shows that they occur similarly in birds as known for mammals, two separate vertebrate classes; this possibly indicates a common phylogenetic origin of these processes.

Indoor Navigation from Point Clouds: 3d Modelling and Obstacle Detection

NASA Astrophysics Data System (ADS)

Díaz-Vilariño, L.; Boguslawski, P.; Khoshelham, K.; Lorenzo, H.; Mahdjoubi, L.

2016-06-01

In the recent years, indoor modelling and navigation has become a research of interest because many stakeholders require navigation assistance in various application scenarios. The navigational assistance for blind or wheelchair people, building crisis management such as fire protection, augmented reality for gaming, tourism or training emergency assistance units are just some of the direct applications of indoor modelling and navigation. Navigational information is traditionally extracted from 2D drawings or layouts. Real state of indoors, including opening position and geometry for both windows and doors, and the presence of obstacles is commonly ignored. In this work, a real indoor-path planning methodology based on 3D point clouds is developed. The value and originality of the approach consist on considering point clouds not only for reconstructing semantically-rich 3D indoor models, but also for detecting potential obstacles in the route planning and using these for readapting the routes according to the real state of the indoor depictured by the laser scanner.

Accurate load prediction by BEM with airfoil data from 3D RANS simulations

NASA Astrophysics Data System (ADS)

Schneider, Marc S.; Nitzsche, Jens; Hennings, Holger

2016-09-01

In this paper, two methods for the extraction of airfoil coefficients from 3D CFD simulations of a wind turbine rotor are investigated, and these coefficients are used to improve the load prediction of a BEM code. The coefficients are extracted from a number of steady RANS simulations, using either averaging of velocities in annular sections, or an inverse BEM approach for determination of the induction factors in the rotor plane. It is shown that these 3D rotor polars are able to capture the rotational augmentation at the inner part of the blade as well as the load reduction by 3D effects close to the blade tip. They are used as input to a simple BEM code and the results of this BEM with 3D rotor polars are compared to the predictions of BEM with 2D airfoil coefficients plus common empirical corrections for stall delay and tip loss. While BEM with 2D airfoil coefficients produces a very different radial distribution of loads than the RANS simulation, the BEM with 3D rotor polars manages to reproduce the loads from RANS very accurately for a variety of load cases, as long as the blade pitch angle is not too different from the cases from which the polars were extracted.

A Fischer rat substrain deficient in dipeptidyl peptidase IV activity makes normal steady-state RNA levels and an altered protein. Use as a liver-cell transplantation model.

PubMed Central

Thompson, N L; Hixson, D C; Callanan, H; Panzica, M; Flanagan, D; Faris, R A; Hong, W J; Hartel-Schenk, S; Doyle, D

1991-01-01

Dipeptidyl peptidase IV (DPPIV) is a serine exoproteinase expressed at high levels in epithelial cells of kidney, liver and small intestine. Recently Watanabe, Kohima & Fujimoto [(1987) Experientia 43, 400-401] and Gossrau et al. [(1990) Histochem. J. 22, 172-173] reported that Fischer 344 rats are deficient in this enzyme. We have examined DPPIV expression in Fischer 344 rats available from U.S. and German suppliers and find that livers of the U.S. Fischer rats, in contrast with their German counterparts, express active DPPIV (D+). Northern analysis of liver RNA showed comparable levels of 3.4 kb and 5.6 kb DPPIV transcripts in both D+ rats from the U.S. and German (D-) rats. Monoclonal antibody (MAb) 236.3 to DPPIV immunoprecipitated at 150 kDa enzymically active (105 kDa, denatured) protein from surface-labelled D+ hepatocytes and reacted with canalicular and sinusoidal membranes (as shown by immunofluorescence microscopy). MAb 236.3 failed to immunoprecipitate a labelled peptide from D- cell extract or to stain D- liver sections. Polyclonal antibody (PAb) specific for DPPIV immunoprecipitated an enzymically active peptide from D+ hepatocyte extracts and a smaller, inactive peptide from D- hepatocyte extracts. Peptide maps of DPPIV immunoprecipitated from D+ extracts with MAb 236.3 and PAb were identical, but differed from that of the D- hepatocyte component recognized by PAb. The molecular basis of the DPPIV deficiency in the D- rats thus appears to be the translation of an enzymically inactive protein missing the epitope recognized by MAb 236.3. We have exploited these D- rats as hosts for syngeneic transplantation of liver cells from D+ Fischer rats. DPPIV expression is stable in the transplanted cells and allows them to be readily distinguished from the surrounding D- tissue. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:1705112

Integration of aerial remote sensing imaging data in a 3D-GIS environment

NASA Astrophysics Data System (ADS)

Moeller, Matthias S.

2003-03-01

For some years sensor systems have been available providing digital images of a new quality. Especially aerial stereo scanners acquire digital multispectral images with an extremely high ground resolution of about 0.10 - 0.15m and provide in addition a Digital Surface Models (DSM). These imaging products both can be used for a detailed monitoring at scales up to 1:500. The processed georeferenced multispectral orthoimages can be readily integrated into GIS making them useful for a number of applications. The DSM, derived from forward and backward facing sensors of an aerial imaging system provides a ground resolution of 0.5 m and can be used for 3D visualization purposes. In some cases it is essential, to store the ground elevation as a Digital Terrain Model (DTM) and also the height of 3-dimensional objects in a separated database. Existing automated algorithms do not work precise for the extraction of DTM from aerial scanner DSM. This paper presents a new approach which combines the visible image data and the DSM data for the generation of DTM with a reliable geometric accuracy. Already existing cadastral data can be used as a knowledge base for the extraction of building heights in cities. These elevation data is the essential source for a GIS based urban information system with a 3D visualization component.

3D Segmentation with an application of level set-method using MRI volumes for image guided surgery.

PubMed

Bosnjak, A; Montilla, G; Villegas, R; Jara, I

2007-01-01

This paper proposes an innovation in the application for image guided surgery using a comparative study of three different method of segmentation. This segmentation method is faster than the manual segmentation of images, with the advantage that it allows to use the same patient as anatomical reference, which has more precision than a generic atlas. This new methodology for 3D information extraction is based on a processing chain structured of the following modules: 1) 3D Filtering: the purpose is to preserve the contours of the structures and to smooth the homogeneous areas; several filters were tested and finally an anisotropic diffusion filter was used. 2) 3D Segmentation. This module compares three different methods: Region growing Algorithm, Cubic spline hand assisted, and Level Set Method. It then proposes a Level Set-based on the front propagation method that allows the making of the reconstruction of the internal walls of the anatomical structures of the brain. 3) 3D visualization. The new contribution of this work consists on the visualization of the segmented model and its use in the pre-surgery planning.

Detection and 3D reconstruction of traffic signs from multiple view color images

NASA Astrophysics Data System (ADS)

Soheilian, Bahman; Paparoditis, Nicolas; Vallet, Bruno

2013-03-01

3D reconstruction of traffic signs is of great interest in many applications such as image-based localization and navigation. In order to reflect the reality, the reconstruction process should meet both accuracy and precision. In order to reach such a valid reconstruction from calibrated multi-view images, accurate and precise extraction of signs in every individual view is a must. This paper presents first an automatic pipeline for identifying and extracting the silhouette of signs in every individual image. Then, a multi-view constrained 3D reconstruction algorithm provides an optimum 3D silhouette for the detected signs. The first step called detection, tackles with a color-based segmentation to generate ROIs (Region of Interests) in image. The shape of every ROI is estimated by fitting an ellipse, a quadrilateral or a triangle to edge points. A ROI is rejected if none of the three shapes can be fitted sufficiently precisely. Thanks to the estimated shape the remained candidates ROIs are rectified to remove the perspective distortion and then matched with a set of reference signs using textural information. Poor matches are rejected and the types of remained ones are identified. The output of the detection algorithm is a set of identified road signs whose silhouette in image plane is represented by and ellipse, a quadrilateral or a triangle. The 3D reconstruction process is based on a hypothesis generation and verification. Hypotheses are generated by a stereo matching approach taking into account epipolar geometry and also the similarity of the categories. The hypotheses that are plausibly correspond to the same 3D road sign are identified and grouped during this process. Finally, all the hypotheses of the same group are merged to generate a unique 3D road sign by a multi-view algorithm integrating a priori knowledges about 3D shape of road signs as constraints. The algorithm is assessed on real and synthetic images and reached and average accuracy of 3.5cm for position and 4.5° for orientation.

In vitro antimalarial activity of medicinal plant extracts against Plasmodium falciparum.

PubMed

Bagavan, Asokan; Rahuman, Abdul Abdul; Kaushik, Naveen Kumar; Sahal, Dinkar

2011-01-01

Malaria is a major global public health problem, and the alarming spread of drug resistance and limited number of effective drugs now available underline how important it is to discover new antimalarial compounds. In the present study, ten plants were extracted with ethyl acetate and methanol and tested for their antimalarial activity against chloroquine (CQ)-sensitive (3D7) and CQ-resistant (Dd2 and INDO) strains of Plasmodium falciparum in culture using the fluorescence-based SYBR Green assay. Plant extracts showed moderate to good antiparasitic effects. Promising antiplasmodial activity was found in the extracts from two plants, Phyllanthus emblica leaf 50% inhibitory concentration (IC₅₀) 3D7: 7.25 μg/mL (ethyl acetate extract), 3.125 μg/mL (methanol extract), and Syzygium aromaticum flower bud, IC₅₀ 3D7:13 μg/mL, (ethyl acetate extract) and 6.25 μg/mL (methanol extract). Moderate activity (30-75 μg/mL) was found in the ethyl acetate and methanol extracts of Abrus precatorius (seed) and Gloriosa superba (leaf); leaf ethyl acetate extracts of Annona squamosa and flower of Musa paradisiaca. The above mentioned plant extracts were also found to be active against CQ-resistant strains (Dd2 and INDO). Cytotoxicity study with P. emblica leaf and S. aromaticum flower bud, extracts showed good therapeutic indices. These results demonstrate that leaf ethyl acetate and methanol extracts of P. emblica and flower bud extract of S. aromaticum may serve as antimalarial agents even in their crude form. The isolation of compounds from P. emblica and S. aromaticum seems to be of special interest for further antimalarial studies.

Comparative evaluation of 12 immature citrus fruit extracts for the inhibition of cytochrome P450 isoform activities.

PubMed

Fujita, Tadashi; Kawase, Atsushi; Niwa, Toshiro; Tomohiro, Norimichi; Masuda, Megumi; Matsuda, Hideaki; Iwaki, Masahiro

2008-05-01

In a previous study we found that 50% ethanol extracts of immature fruits of Citrus unshiu (satsuma mandarin) have anti-allergic effects against the Type I, II and IV allergic reactions. However, many adverse interactions between citrus fruit, especially grapefruit juice, and drugs have been reported due to the inhibition of cytochrome P450 (CYP) activities. The purpose of this study was to examine the competitive inhibitory effects of extracts from immature citrus fruit on CYP activity. Extracts were prepared from 12 citrus species or cultivars, and were tested against three kinds of major CYPs, CYP2C9, CYP2D6 and CYP3A4, in human liver microsomes. We also estimated the amounts of flavonoids (narirutin, hesperidin, naringin and neohesperidin) and furanocoumarins (bergapten, 6',7'-dihydroxybergamottin and bergamottin) in each extract using HPLC. Citrus paradisi (grapefruit) showed the greatest inhibition of CYP activities, while Citrus unshiu which has an antiallergic effect, showed relatively weak inhibitory effects. Extracts having relatively strong inhibitory effects for CYP3A4 tended to contain higher amounts of naringin, bergamottin and 6',7'-dihydroxybergamottin. These results, providing comparative information on the inhibitory effects of citrus extracts on CYP isoforms, suggest that citrus extracts containing high levels of narirutin and hesperidin and lower levels of furanocoumarins such as C. unshiu are favorable as antiallergic functional ingredients.

Isolation and identification of sea buckthorn (Hippophae rhamnoides) phenolics with antioxidant activity and α-glucosidase inhibitory effect.

PubMed

Kim, Ju-Sung; Kwon, Yong-Soo; Sa, Yeo-Jin; Kim, Myong-Jo

2011-01-12

This study was performed to evaluate the antioxidant and α-glucosidase inhibitory effects from the extract, fractions, and isolated compounds of sea buckthorn leaves. Six compounds, kaempferol-3-O-β-D-(6''-O-coumaryl) glycoside, 1-feruloyl-β-D-glucopyranoside, isorhamnetin-3-O-glucoside, quercetin 3-O-β-D-glucopyranoside, quercetin 3-O-β-D-glucopyranosyl-7-O-α-L-rhamnopyranoside, and isorhamnetin-3-O-rutinoside, were isolated from sea buckthorn leaf extracts. The butanol fraction (EC(50) = 1.81 μg/mL) along with quercetin 3-O-β-D-glucopyranoside (EC(50) = 1.86 μg/mL) had a higher DPPH radical-scavenging activity and showed stronger reducing power (OD(700) = 1.83 and 1.78, respectively). The butanol fraction (477 mg GAE/g) contained the highest amount of phenolic compounds and also the most powerful α-glucosidase inhibitory effect (86%) at 5 μg/mL. The results indicate that sea buckthorn leaf extracts could potentially be used for food additives and the development of useful natural compounds.

Angular description for 3D scattering centers

NASA Astrophysics Data System (ADS)

Bhalla, Rajan; Raynal, Ann Marie; Ling, Hao; Moore, John; Velten, Vincent J.

2006-05-01

The electromagnetic scattered field from an electrically large target can often be well modeled as if it is emanating from a discrete set of scattering centers (see Fig. 1). In the scattering center extraction tool we developed previously based on the shooting and bouncing ray technique, no correspondence is maintained amongst the 3D scattering center extracted at adjacent angles. In this paper we present a multi-dimensional clustering algorithm to track the angular and spatial behaviors of 3D scattering centers and group them into features. The extracted features for the Slicy and backhoe targets are presented. We also describe two metrics for measuring the angular persistence and spatial mobility of the 3D scattering centers that make up these features in order to gather insights into target physics and feature stability. We find that features that are most persistent are also the most mobile and discuss implications for optimal SAR imaging.

Antioxidant Activities and Chemical Constituents of Flavonoids from the Flower of Paeonia ostii.

PubMed

Zhang, Huifang; Li, Xiaofang; Wu, Ke; Wang, Mengke; Liu, Pu; Wang, Xinsheng; Deng, Ruixue

2016-12-23

Paeonia ostii is a traditional medicinal plant popularly used in China. This study intended to evaluate the antioxidant properties and the chemical components of the flavonoid-rich extracts from the flowers of P. ostii . The results showed that the flavonoid-rich extracts from the flowers of P. ostii had strong scavenging capacities on 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS), hydroxyls, superoxide anions, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals in a dose-dependent manner. Five flavonoids, dihydrokaempferol ( 1 ), apigenin-7- O -β-d-glucoside ( 2 ), apigenin-7- O -β-d-neohesperidoside ( 3 ), kaempferol-7- O -β-d-glucopyranoside ( 4 ), and kaempferol-3- O -β-d-glucopyranosyl-7- O -β-d-glucopyranoside ( 5 ), were isolated from the flavonoid-rich extracts of the flowers of P. ostii . High-performance liquid chromatography (HPLC) analysis revealed that compounds 3 and 4 were abundant in the P. ostii flower and in flavonoid-rich extracts. The main components of the flower of P. ostii are flavonoids. The high antioxidant activity of the flavonoid-rich extracts may be attributed to the high content of flavonoids. The five isolated flavonoids were the primary antioxidant ingredients, and may play important roles in the strong antioxidant activities of this flower. Based on the obtained results, the flower of P. ostii could be a potential source of natural antioxidants in food and pharmaceutical applications.

View subspaces for indexing and retrieval of 3D models

NASA Astrophysics Data System (ADS)

Dutagaci, Helin; Godil, Afzal; Sankur, Bülent; Yemez, Yücel

2010-02-01

View-based indexing schemes for 3D object retrieval are gaining popularity since they provide good retrieval results. These schemes are coherent with the theory that humans recognize objects based on their 2D appearances. The viewbased techniques also allow users to search with various queries such as binary images, range images and even 2D sketches. The previous view-based techniques use classical 2D shape descriptors such as Fourier invariants, Zernike moments, Scale Invariant Feature Transform-based local features and 2D Digital Fourier Transform coefficients. These methods describe each object independent of others. In this work, we explore data driven subspace models, such as Principal Component Analysis, Independent Component Analysis and Nonnegative Matrix Factorization to describe the shape information of the views. We treat the depth images obtained from various points of the view sphere as 2D intensity images and train a subspace to extract the inherent structure of the views within a database. We also show the benefit of categorizing shapes according to their eigenvalue spread. Both the shape categorization and data-driven feature set conjectures are tested on the PSB database and compared with the competitor view-based 3D shape retrieval algorithms.

The relationship between nitrogen fixation and the production of HD from D2 by cell-free extracts of soya-bean nodule bacteroids

PubMed Central

Turner, G. L.; Bergersen, F. J.

1969-01-01

1. Cell-free extracts prepared from soya-bean nodule bacteroids produced HD from D2 in the presence of dithionite, an ATP-generating system and nitrogen. 2. Crude extracts of bacteroids or of Azotobacter vinelandii showed some background D2 exchange when any one of these was omitted. 3. Partial purification of bacteroid extracts diminished this background activity and gave increased D2 exchange and nitrogen fixation. 4. Although increasing pN2 stimulated both reactions, the apparent Km (N2) for nitrogen fixation was much higher than the apparent Km (N2) for D2 exchange when partially purified bacteroid extracts were used. 5. Carbon monoxide was a competitive inhibitor of nitrogen fixation by partially purified bacteroid extracts, but D2 exchange was inhibited in a non-competitive fashion. 6. These results are discussed in relation to the possible existence of enzyme-bound intermediates of nitrogen fixation. PMID:5353527

Protein-based stable isotope probing.

PubMed

Jehmlich, Nico; Schmidt, Frank; Taubert, Martin; Seifert, Jana; Bastida, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Vogt, Carsten

2010-12-01

We describe a stable isotope probing (SIP) technique that was developed to link microbe-specific metabolic function to phylogenetic information. Carbon ((13)C)- or nitrogen ((15)N)-labeled substrates (typically with >98% heavy label) were used in cultivation experiments and the heavy isotope incorporation into proteins (protein-SIP) on growth was determined. The amount of incorporation provides a measure for assimilation of a substrate, and the sequence information from peptide analysis obtained by mass spectrometry delivers phylogenetic information about the microorganisms responsible for the metabolism of the particular substrate. In this article, we provide guidelines for incubating microbial cultures with labeled substrates and a protocol for protein-SIP. The protocol guides readers through the proteomics pipeline, including protein extraction, gel-free and gel-based protein separation, the subsequent mass spectrometric analysis of peptides and the calculation of the incorporation of stable isotopes into peptides. Extraction of proteins and the mass fingerprint measurements of unlabeled and labeled fractions can be performed in 2-3 d.

Membrane interaction of antimicrobial peptides using E. coli lipid extract as model bacterial cell membranes and SFG spectroscopy.

PubMed

Soblosky, Lauren; Ramamoorthy, Ayyalusamy; Chen, Zhan

2015-04-01

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/Escherichia coli (E. coli) polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Massive parallel 3D PIC simulation of negative ion extraction

NASA Astrophysics Data System (ADS)

Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu

2017-09-01

The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.

On the utility of 3D hand cursors to explore medical volume datasets with a touchless interface.

PubMed

Lopes, Daniel Simões; Parreira, Pedro Duarte de Figueiredo; Paulo, Soraia Figueiredo; Nunes, Vitor; Rego, Paulo Amaral; Neves, Manuel Cassiano; Rodrigues, Pedro Silva; Jorge, Joaquim Armando

2017-08-01

Analyzing medical volume datasets requires interactive visualization so that users can extract anatomo-physiological information in real-time. Conventional volume rendering systems rely on 2D input devices, such as mice and keyboards, which are known to hamper 3D analysis as users often struggle to obtain the desired orientation that is only achieved after several attempts. In this paper, we address which 3D analysis tools are better performed with 3D hand cursors operating on a touchless interface comparatively to a 2D input devices running on a conventional WIMP interface. The main goals of this paper are to explore the capabilities of (simple) hand gestures to facilitate sterile manipulation of 3D medical data on a touchless interface, without resorting on wearables, and to evaluate the surgical feasibility of the proposed interface next to senior surgeons (N=5) and interns (N=2). To this end, we developed a touchless interface controlled via hand gestures and body postures to rapidly rotate and position medical volume images in three-dimensions, where each hand acts as an interactive 3D cursor. User studies were conducted with laypeople, while informal evaluation sessions were carried with senior surgeons, radiologists and professional biomedical engineers. Results demonstrate its usability as the proposed touchless interface improves spatial awareness and a more fluent interaction with the 3D volume than with traditional 2D input devices, as it requires lesser number of attempts to achieve the desired orientation by avoiding the composition of several cumulative rotations, which is typically necessary in WIMP interfaces. However, tasks requiring precision such as clipping plane visualization and tagging are best performed with mouse-based systems due to noise, incorrect gestures detection and problems in skeleton tracking that need to be addressed before tests in real medical environments might be performed. Copyright © 2017 Elsevier Inc. All rights reserved.

Multilevel depth and image fusion for human activity detection.

PubMed

Ni, Bingbing; Pei, Yong; Moulin, Pierre; Yan, Shuicheng

2013-10-01

Recognizing complex human activities usually requires the detection and modeling of individual visual features and the interactions between them. Current methods only rely on the visual features extracted from 2-D images, and therefore often lead to unreliable salient visual feature detection and inaccurate modeling of the interaction context between individual features. In this paper, we show that these problems can be addressed by combining data from a conventional camera and a depth sensor (e.g., Microsoft Kinect). We propose a novel complex activity recognition and localization framework that effectively fuses information from both grayscale and depth image channels at multiple levels of the video processing pipeline. In the individual visual feature detection level, depth-based filters are applied to the detected human/object rectangles to remove false detections. In the next level of interaction modeling, 3-D spatial and temporal contexts among human subjects or objects are extracted by integrating information from both grayscale and depth images. Depth information is also utilized to distinguish different types of indoor scenes. Finally, a latent structural model is developed to integrate the information from multiple levels of video processing for an activity detection. Extensive experiments on two activity recognition benchmarks (one with depth information) and a challenging grayscale + depth human activity database that contains complex interactions between human-human, human-object, and human-surroundings demonstrate the effectiveness of the proposed multilevel grayscale + depth fusion scheme. Higher recognition and localization accuracies are obtained relative to the previous methods.

Fast Localization in Large-Scale Environments Using Supervised Indexing of Binary Features.

PubMed

Youji Feng; Lixin Fan; Yihong Wu

2016-01-01

The essence of image-based localization lies in matching 2D key points in the query image and 3D points in the database. State-of-the-art methods mostly employ sophisticated key point detectors and feature descriptors, e.g., Difference of Gaussian (DoG) and Scale Invariant Feature Transform (SIFT), to ensure robust matching. While a high registration rate is attained, the registration speed is impeded by the expensive key point detection and the descriptor extraction. In this paper, we propose to use efficient key point detectors along with binary feature descriptors, since the extraction of such binary features is extremely fast. The naive usage of binary features, however, does not lend itself to significant speedup of localization, since existing indexing approaches, such as hierarchical clustering trees and locality sensitive hashing, are not efficient enough in indexing binary features and matching binary features turns out to be much slower than matching SIFT features. To overcome this, we propose a much more efficient indexing approach for approximate nearest neighbor search of binary features. This approach resorts to randomized trees that are constructed in a supervised training process by exploiting the label information derived from that multiple features correspond to a common 3D point. In the tree construction process, node tests are selected in a way such that trees have uniform leaf sizes and low error rates, which are two desired properties for efficient approximate nearest neighbor search. To further improve the search efficiency, a probabilistic priority search strategy is adopted. Apart from the label information, this strategy also uses non-binary pixel intensity differences available in descriptor extraction. By using the proposed indexing approach, matching binary features is no longer much slower but slightly faster than matching SIFT features. Consequently, the overall localization speed is significantly improved due to the much faster key point detection and descriptor extraction. It is empirically demonstrated that the localization speed is improved by an order of magnitude as compared with state-of-the-art methods, while comparable registration rate and localization accuracy are still maintained.

Visual Representations of DNA Replication: Middle Grades Students' Perceptions and Interpretations

NASA Astrophysics Data System (ADS)

Patrick, Michelle D.; Carter, Glenda; Wiebe, Eric N.

2005-09-01

Visual representations play a critical role in the communication of science concepts for scientists and students alike. However, recent research suggests that novice students experience difficulty extracting relevant information from representations. This study examined students' interpretations of visual representations of DNA replication. Each of the four steps of DNA replication included in the instructional presentation was represented as a text slide, a simple 2D graphic, and a rich 3D graphic. Participants were middle grade girls ( n = 21) attending a summer math and science program. Students' eye movements were measured as they viewed the representations. Participants were interviewed following instruction to assess their perceived salient features. Eye tracking fixation counts indicated that the same features (look zones) in the corresponding 2D and 3D graphics had different salience. The interviews revealed that students used different characteristics such as color, shape, and complexity to make sense of the graphics. The results of this study have implications for the design of instructional representations. Since many students have difficulty distinguishing between relevant and irrelevant information, cueing and directing student attention through the instructional representation could allow cognitive resources to be directed to the most relevant material.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

In vivo hypoglycemic effect of methanolic fruit extract of Momordica charantia L.

PubMed

Nkambo, W; Anyama, N G; Onegi, B

2013-12-01

Momordica charantia L. is a medicinal plant commonly used in the management of diabetes mellitus. We investigated the blood glucose lowering effect of the methanolic fruit extract of the Ugandan variety of M. charantia L. in alloxan-induced diabetic albino rats. 500g of M. charantia powder were macerated in methanol and the extract administered to two groups of alloxan-induced diabetic rats. The first group received 125mg/kg, the second 375mg/kg and a third group 7mg/kg of metformin. A fourth group received 1ml normal saline. Fasting blood glucose (FBG) levels were measured at 0.5,1,2,3,5,8 and 12 hours and compared using one-way ANOVA. There was an initial rise in FBG for 1 hour after administration of extracts followed by steep reductions. Significant reduction in FBG occurred at 2 hours for 125mg/kg of extract (-3.2%, 313±25.9 to 303±25.0mg/dL, p = 0.049), 375mg/kg of extract (-3.9%, 356±19.7 to 342±20.3mg/dL, p = 0.001), and metformin (-2.6%, 344±21.7 to 335±21.1mg/dL, p = 0.003) when compared to normal saline. The maximum percentage reduction in FBG by both extracts occurred between 3 and 12 hours post dose. The methanolic fruit extract of M. charantia exhibits dose dependent hypoglycaemic activity in vivo.

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

Full-field optical coherence tomography used for security and document identity

NASA Astrophysics Data System (ADS)

Chang, Shoude; Mao, Youxin; Sherif, Sherif; Flueraru, Costel

2006-09-01

The optical coherence tomography (OCT) is an emerging technology for high-resolution cross-sectional imaging of 3D structures. In the past years, OCT systems have been used mainly for medical, especially ophthalmological diagnostics. Concerning the nature of OCT system being capable to explore the internal features of an object, we apply the OCT technology to directly retrieve the 2D information pre-stored in a multiple-layer information carrier. The standard depth-resolution of an OCT system is at micrometer level. If a 20mm by 20mm sampling area with a 1024 x 1024 CCD array is used in the OCT system having 10 μm, an information carrier having a volume of 20mm x 20mm x 2mm could contain 200 Mega-pixel images. Because of its tiny size and large information volume, the information carrier, with its OCT retrieving system, will have potential applications in documents security and object identification. In addition, as the information carrier can be made by low-scattering transparent material, the signal/noise ratio will be improved dramatically. As a consequence, the specific hardware and complicated software can also be greatly simplified. Owing to non-scanning along X-Y axis, the full-field OCT could be the simplest and most economic imaging system for extracting information from such a multilayer information carrier. In this paper, deign and implementation of a full-field OCT system is described and the related algorithms are introduced. In our experiments, a four layers information carrier is used, which contains 4 layers of image pattern, two text images and two fingerprint images. The extracted tomography images of each layer are also provided.

Automated 3D Phenotype Analysis Using Data Mining

PubMed Central

Plyusnin, Ilya; Evans, Alistair R.; Karme, Aleksis; Gionis, Aristides; Jernvall, Jukka

2008-01-01

The ability to analyze and classify three-dimensional (3D) biological morphology has lagged behind the analysis of other biological data types such as gene sequences. Here, we introduce the techniques of data mining to the study of 3D biological shapes to bring the analyses of phenomes closer to the efficiency of studying genomes. We compiled five training sets of highly variable morphologies of mammalian teeth from the MorphoBrowser database. Samples were labeled either by dietary class or by conventional dental types (e.g. carnassial, selenodont). We automatically extracted a multitude of topological attributes using Geographic Information Systems (GIS)-like procedures that were then used in several combinations of feature selection schemes and probabilistic classification models to build and optimize classifiers for predicting the labels of the training sets. In terms of classification accuracy, computational time and size of the feature sets used, non-repeated best-first search combined with 1-nearest neighbor classifier was the best approach. However, several other classification models combined with the same searching scheme proved practical. The current study represents a first step in the automatic analysis of 3D phenotypes, which will be increasingly valuable with the future increase in 3D morphology and phenomics databases. PMID:18320060

Three-dimensional Hessian matrix-based quantitative vascular imaging of rat iris with optical-resolution photoacoustic microscopy in vivo

NASA Astrophysics Data System (ADS)

Zhao, Huangxuan; Wang, Guangsong; Lin, Riqiang; Gong, Xiaojing; Song, Liang; Li, Tan; Wang, Wenjia; Zhang, Kunya; Qian, Xiuqing; Zhang, Haixia; Li, Lin; Liu, Zhicheng; Liu, Chengbo

2018-04-01

For the diagnosis and evaluation of ophthalmic diseases, imaging and quantitative characterization of vasculature in the iris are very important. The recently developed photoacoustic imaging, which is ultrasensitive in imaging endogenous hemoglobin molecules, provides a highly efficient label-free method for imaging blood vasculature in the iris. However, the development of advanced vascular quantification algorithms is still needed to enable accurate characterization of the underlying vasculature. We have developed a vascular information quantification algorithm by adopting a three-dimensional (3-D) Hessian matrix and applied for processing iris vasculature images obtained with a custom-built optical-resolution photoacoustic imaging system (OR-PAM). For the first time, we demonstrate in vivo 3-D vascular structures of a rat iris with a the label-free imaging method and also accurately extract quantitative vascular information, such as vessel diameter, vascular density, and vascular tortuosity. Our results indicate that the developed algorithm is capable of quantifying the vasculature in the 3-D photoacoustic images of the iris in-vivo, thus enhancing the diagnostic capability of the OR-PAM system for vascular-related ophthalmic diseases in vivo.

3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.

PubMed

Ciesielski, Peter N; Matthews, James F; Tucker, Melvin P; Beckham, Gregg T; Crowley, Michael F; Himmel, Michael E; Donohoe, Bryon S

2013-09-24

Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils.

Acquiring a 2D rolled equivalent fingerprint image from a non-contact 3D finger scan

NASA Astrophysics Data System (ADS)

Fatehpuria, Abhishika; Lau, Daniel L.; Hassebrook, Laurence G.

2006-04-01

The use of fingerprints as a biometric is both the oldest mode of computer aided personal identification and the most relied-upon technology in use today. But current fingerprint scanning systems have some challenging and peculiar difficulties. Often skin conditions and imperfect acquisition circumstances cause the captured fingerprint image to be far from ideal. Also some of the acquisition techniques can be slow and cumbersome to use and may not provide the complete information required for reliable feature extraction and fingerprint matching. Most of the difficulties arise due to the contact of the fingerprint surface with the sensor platen. To attain a fast-capture, non-contact, fingerprint scanning technology, we are developing a scanning system that employs structured light illumination as a means for acquiring a 3-D scan of the finger with sufficiently high resolution to record ridge-level details. In this paper, we describe the postprocessing steps used for converting the acquired 3-D scan of the subject's finger into a 2-D rolled equivalent image.

Human silhouette matching based on moment invariants

NASA Astrophysics Data System (ADS)

Sun, Yong-Chao; Qiu, Xian-Jie; Xia, Shi-Hong; Wang, Zhao-Qi

2005-07-01

This paper aims to apply the method of silhouette matching based on moment invariants to infer the human motion parameters from video sequences of single monocular uncalibrated camera. Currently, there are two ways of tracking human motion: Marker and Markerless. While a hybrid framework is introduced in this paper to recover the input video contents. A standard 3D motion database is built up by marker technique in advance. Given a video sequences, human silhouettes are extracted as well as the viewpoint information of the camera which would be utilized to project the standard 3D motion database onto the 2D one. Therefore, the video recovery problem is formulated as a matching issue of finding the most similar body pose in standard 2D library with the one in video image. The framework is applied to the special trampoline sport where we can obtain the complicated human motion parameters in the single camera video sequences, and a lot of experiments are demonstrated that this approach is feasible in the field of monocular video-based 3D motion reconstruction.

Panoramic 3D Reconstruction by Fusing Color Intensity and Laser Range Data

NASA Astrophysics Data System (ADS)

Jiang, Wei; Lu, Jian

Technology for capturing panoramic (360 degrees) three-dimensional information in a real environment have many applications in fields: virtual and complex reality, security, robot navigation, and so forth. In this study, we examine an acquisition device constructed of a regular CCD camera and a 2D laser range scanner, along with a technique for panoramic 3D reconstruction using a data fusion algorithm based on an energy minimization framework. The acquisition device can capture two types of data of a panoramic scene without occlusion between two sensors: a dense spatio-temporal volume from a camera and distance information from a laser scanner. We resample the dense spatio-temporal volume for generating a dense multi-perspective panorama that has equal spatial resolution to that of the original images acquired using a regular camera, and also estimate a dense panoramic depth-map corresponding to the generated reference panorama by extracting trajectories from the dense spatio-temporal volume with a selecting camera. Moreover, for determining distance information robustly, we propose a data fusion algorithm that is embedded into an energy minimization framework that incorporates active depth measurements using a 2D laser range scanner and passive geometry reconstruction from an image sequence obtained using the CCD camera. Thereby, measurement precision and robustness can be improved beyond those available by conventional methods using either passive geometry reconstruction (stereo vision) or a laser range scanner. Experimental results using both synthetic and actual images show that our approach can produce high-quality panoramas and perform accurate 3D reconstruction in a panoramic environment.

Automated kidney detection for 3D ultrasound using scan line searching

NASA Astrophysics Data System (ADS)

Noll, Matthias; Nadolny, Anne; Wesarg, Stefan

2016-04-01

Ultrasound (U/S) is a fast and non-expensive imaging modality that is used for the examination of various anatomical structures, e.g. the kidneys. One important task for automatic organ tracking or computer-aided diagnosis is the identification of the organ region. During this process the exact information about the transducer location and orientation is usually unavailable. This renders the implementation of such automatic methods exceedingly challenging. In this work we like to introduce a new automatic method for the detection of the kidney in 3D U/S images. This novel technique analyses the U/S image data along virtual scan lines. Here, characteristic texture changes when entering and leaving the symmetric tissue regions of the renal cortex are searched for. A subsequent feature accumulation along a second scan direction produces a 2D heat map of renal cortex candidates, from which the kidney location is extracted in two steps. First, the strongest candidate as well as its counterpart are extracted by heat map intensity ranking and renal cortex size analysis. This process exploits the heat map gap caused by the renal pelvis region. Substituting the renal pelvis detection with this combined cortex tissue feature increases the detection robustness. In contrast to model based methods that generate characteristic pattern matches, our method is simpler and therefore faster. An evaluation performed on 61 3D U/S data sets showed, that in 55 cases showing none or minor shadowing the kidney location could be correctly identified.

Roof Type Selection Based on Patch-Based Classification Using Deep Learning for High Resolution Satellite Imagery

NASA Astrophysics Data System (ADS)

Partovi, T.; Fraundorfer, F.; Azimi, S.; Marmanis, D.; Reinartz, P.

2017-05-01

3D building reconstruction from remote sensing image data from satellites is still an active research topic and very valuable for 3D city modelling. The roof model is the most important component to reconstruct the Level of Details 2 (LoD2) for a building in 3D modelling. While the general solution for roof modelling relies on the detailed cues (such as lines, corners and planes) extracted from a Digital Surface Model (DSM), the correct detection of the roof type and its modelling can fail due to low quality of the DSM generated by dense stereo matching. To reduce dependencies of roof modelling on DSMs, the pansharpened satellite images as a rich resource of information are used in addition. In this paper, two strategies are employed for roof type classification. In the first one, building roof types are classified in a state-of-the-art supervised pre-trained convolutional neural network (CNN) framework. In the second strategy, deep features from deep layers of different pre-trained CNN model are extracted and then an RBF kernel using SVM is employed to classify the building roof type. Based on roof complexity of the scene, a roof library including seven types of roofs is defined. A new semi-automatic method is proposed to generate training and test patches of each roof type in the library. Using the pre-trained CNN model does not only decrease the computation time for training significantly but also increases the classification accuracy.

Ship Detection in Optical Satellite Image Based on RX Method and PCAnet

NASA Astrophysics Data System (ADS)

Shao, Xiu; Li, Huali; Lin, Hui; Kang, Xudong; Lu, Ting

2017-12-01

In this paper, we present a novel method for ship detection in optical satellite image based on the ReedXiaoli (RX) method and the principal component analysis network (PCAnet). The proposed method consists of the following three steps. First, the spatially adjacent pixels in optical image are arranged into a vector, transforming the optical image into a 3D cube image. By taking this process, the contextual information of the spatially adjacent pixels can be integrated to magnify the discrimination between ship and background. Second, the RX anomaly detection method is adopted to preliminarily extract ship candidates from the produced 3D cube image. Finally, real ships are further confirmed among ship candidates by applying the PCAnet and the support vector machine (SVM). Specifically, the PCAnet is a simple deep learning network which is exploited to perform feature extraction, and the SVM is applied to achieve feature pooling and decision making. Experimental results demonstrate that our approach is effective in discriminating between ships and false alarms, and has a good ship detection performance.

Two-stage Framework for a Topology-Based Projection and Visualization of Classified Document Collections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oesterling, Patrick; Scheuermann, Gerik; Teresniak, Sven

During the last decades, electronic textual information has become the world's largest and most important information source available. People have added a variety of daily newspapers, books, scientific and governmental publications, blogs and private messages to this wellspring of endless information and knowledge. Since neither the existing nor the new information can be read in its entirety, computers are used to extract and visualize meaningful or interesting topics and documents from this huge information clutter. In this paper, we extend, improve and combine existing individual approaches into an overall framework that supports topological analysis of high dimensional document point cloudsmore » given by the well-known tf-idf document-term weighting method. We show that traditional distance-based approaches fail in very high dimensional spaces, and we describe an improved two-stage method for topology-based projections from the original high dimensional information space to both two dimensional (2-D) and three dimensional (3-D) visualizations. To show the accuracy and usability of this framework, we compare it to methods introduced recently and apply it to complex document and patent collections.« less

Efficient generation of 3D hologram for American Sign Language using look-up table

NASA Astrophysics Data System (ADS)

Park, Joo-Sup; Kim, Seung-Cheol; Kim, Eun-Soo

2010-02-01

American Sign Language (ASL) is one of the languages giving the greatest help for communication of the hearing impaired person. Current 2-D broadcasting, 2-D movies are used the ASL to give some information, help understand the situation of the scene and translate the foreign language. These ASL will not be disappeared in future three-dimensional (3-D) broadcasting or 3-D movies because the usefulness of the ASL. On the other hands, some approaches for generation of CGH patterns have been suggested like the ray-tracing method and look-up table (LUT) method. However, these methods have some drawbacks that needs much time or needs huge memory size for look-up table. Recently, a novel LUT (N-LUT) method for fast generation of CGH patterns of 3-D objects with a dramatically reduced LUT without the loss of computational speed was proposed. Therefore, we proposed the method to efficiently generate the holographic ASL in holographic 3DTV or 3-D movies using look-up table method. The proposed method is largely consisted of five steps: construction of the LUT for each ASL images, extraction of characters in scripts or situation, call the fringe patterns for characters in the LUT for each ASL, composition of hologram pattern for 3-D video and hologram pattern for ASL and reconstruct the holographic 3D video with ASL. Some simulation results confirmed the feasibility of the proposed method in efficient generation of CGH patterns for ASL.

Decoding Mode-mixing in Black-hole Merger Ringdown

NASA Technical Reports Server (NTRS)

Kelly, Bernard J.; Baker, John G.

2013-01-01

Optimal extraction of information from gravitational-wave observations of binary black-hole coalescences requires detailed knowledge of the waveforms. Current approaches for representing waveform information are based on spin-weighted spherical harmonic decomposition. Higher-order harmonic modes carrying a few percent of the total power output near merger can supply information critical to determining intrinsic and extrinsic parameters of the binary. One obstacle to constructing a full multi-mode template of merger waveforms is the apparently complicated behavior of some of these modes; instead of settling down to a simple quasinormal frequency with decaying amplitude, some |m| = modes show periodic bumps characteristic of mode-mixing. We analyze the strongest of these modes the anomalous (3, 2) harmonic mode measured in a set of binary black-hole merger waveform simulations, and show that to leading order, they are due to a mismatch between the spherical harmonic basis used for extraction in 3D numerical relativity simulations, and the spheroidal harmonics adapted to the perturbation theory of Kerr black holes. Other causes of mode-mixing arising from gauge ambiguities and physical properties of the quasinormal ringdown modes are also considered and found to be small for the waveforms studied here.

Evaluation of Cholesterol-lowering Activity of Standardized Extract of Mangifera indica in Albino Wistar Rats.

PubMed

Gururaja, G M; Mundkinajeddu, Deepak; Kumar, A Senthil; Dethe, Shekhar Michael; Allan, J Joshua; Agarwal, Amit

2017-01-01

Cholesterol lowering activity of Mangifera indica L. has been determined by earlier researchers and kernel, leaf and bark have shown significant activity. However, the specific cholesterol lowering activity of leaf methanol extract has not been determined. The present study involved evaluation of cholesterol lowering potential of methanol extract of M. indica leaves using high cholesterol diet model in albino Wistar rats. The acute oral toxicity at a dose of 5000 mg/ kg body weight was also determined in female albino Wistar rats. Phytoconstituents Iriflophenone 3-C-β-D-glucoside and mangiferin were quantified in methanol extracts of different varieties of mango leaves using high performance liquid chromatography. Significant cholesterol lowering activity was observed with methanol extract of M. indica leaves, at dose of 90 mg/kg body weight in rats and it was also found to be safe at dose of 5000 mg/kg rat body. Iriflophenone 3-C-β-D-glucoside and mangiferin were found to be in the range of 1.2 to 2.8% w/w and 3.9 to 4.6% w/w, respectively which along with 3 β taraxerol and other sterols could be contributing to the cholesterol lowering activity of mango leaves extract. The phytosterols rich extract of Mangifera indica leaves is a good source of nutraceutical ingredient that have the potential to lower serum cholesterol levels. The Mangifera indica leaves methanolic extract showed significant cholesterol lowering activity in high cholesterol diet induced hypercholesterolaemia model in rats when evaluated at a dose of 90 mg/kg rat body weight. The extract was found to contain Iriflophenone 3-C-β-D-glucoside and mangiferin which along with 3 β taraxerol and other sterols could be contributing to the cholesterol lowering activity.

Pixel-based approach for building heights determination by SAR radargrammetry

NASA Astrophysics Data System (ADS)

Dubois, C.; Thiele, A.; Hinz, S.

2013-10-01

Numerous advances have been made recently in photogrammetry, laser scanning, and remote sensing for the creation of 3D city models. More and more cities are interested in getting 3D city models, be it for urban planning purposes or for supporting public utility companies. In areas often affected by natural disaster, rapid updating of the 3D information may also be useful for helping rescue forces. The high resolutions that can be achieved by the new spaceborne SAR sensor generation enables the analysis of city areas at building level and make those sensors attractive for the extraction of 3D information. Moreover, they present the advantage of weather and sunlight independency, which make them more practicable than optical data, in particular for tasks where rapid response is required. Furthermore, their short revisit time and the possibility of multi-sensor constellation enable providing several acquisitions within a few hours. This opens up the floor for new applications, especially radargrammetric applications, which consider acquisitions taken under different incidence angles. In this paper, we present a new approach for determining building heights, relying only on the radargrammetric analysis of building layover. By taking into account same-side acquisitions, we present the workflow of building height determination. Focus is set on some geometric considerations, pixel-based approach for disparity map calculation, and analysis of the building layover signature for different configurations in order to determine building height.

Combining 3D structure of real video and synthetic objects

NASA Astrophysics Data System (ADS)

Kim, Man-Bae; Song, Mun-Sup; Kim, Do-Kyoon

1998-04-01

This paper presents a new approach of combining real video and synthetic objects. The purpose of this work is to use the proposed technology in the fields of advanced animation, virtual reality, games, and so forth. Computer graphics has been used in the fields previously mentioned. Recently, some applications have added real video to graphic scenes for the purpose of augmenting the realism that the computer graphics lacks in. This approach called augmented or mixed reality can produce more realistic environment that the entire use of computer graphics. Our approach differs from the virtual reality and augmented reality in the manner that computer- generated graphic objects are combined to 3D structure extracted from monocular image sequences. The extraction of the 3D structure requires the estimation of 3D depth followed by the construction of a height map. Graphic objects are then combined to the height map. The realization of our proposed approach is carried out in the following steps: (1) We derive 3D structure from test image sequences. The extraction of the 3D structure requires the estimation of depth and the construction of a height map. Due to the contents of the test sequence, the height map represents the 3D structure. (2) The height map is modeled by Delaunay triangulation or Bezier surface and each planar surface is texture-mapped. (3) Finally, graphic objects are combined to the height map. Because 3D structure of the height map is already known, Step (3) is easily manipulated. Following this procedure, we produced an animation video demonstrating the combination of the 3D structure and graphic models. Users can navigate the realistic 3D world whose associated image is rendered on the display monitor.

An automated 3D reconstruction method of UAV images

NASA Astrophysics Data System (ADS)

Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

2015-10-01

In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

Automatic 3D high-fidelity traffic interchange modeling using 2D road GIS data

NASA Astrophysics Data System (ADS)

Wang, Jie; Shen, Yuzhong

2011-03-01

3D road models are widely used in many computer applications such as racing games and driving simulations. However, almost all high-fidelity 3D road models were generated manually by professional artists at the expense of intensive labor. There are very few existing methods for automatically generating 3D high-fidelity road networks, especially for those existing in the real world. Real road network contains various elements such as road segments, road intersections and traffic interchanges. Among them, traffic interchanges present the most challenges to model due to their complexity and the lack of height information (vertical position) of traffic interchanges in existing road GIS data. This paper proposes a novel approach that can automatically produce 3D high-fidelity road network models, including traffic interchange models, from real 2D road GIS data that mainly contain road centerline information. The proposed method consists of several steps. The raw road GIS data are first preprocessed to extract road network topology, merge redundant links, and classify road types. Then overlapped points in the interchanges are detected and their elevations are determined based on a set of level estimation rules. Parametric representations of the road centerlines are then generated through link segmentation and fitting, and they have the advantages of arbitrary levels of detail with reduced memory usage. Finally a set of civil engineering rules for road design (e.g., cross slope, superelevation) are selected and used to generate realistic road surfaces. In addition to traffic interchange modeling, the proposed method also applies to other more general road elements. Preliminary results show that the proposed method is highly effective and useful in many applications.

Development of a Novel Motor Imagery Control Technique and Application in a Gaming Environment.

PubMed

Li, Ting; Zhang, Jinhua; Xue, Tao; Wang, Baozeng

2017-01-01

We present a methodology for a hybrid brain-computer interface (BCI) system, with the recognition of motor imagery (MI) based on EEG and blink EOG signals. We tested the BCI system in a 3D Tetris and an analogous 2D game playing environment. To enhance player's BCI control ability, the study focused on feature extraction from EEG and control strategy supporting Game-BCI system operation. We compared the numerical differences between spatial features extracted with common spatial pattern (CSP) and the proposed multifeature extraction. To demonstrate the effectiveness of 3D game environment at enhancing player's event-related desynchronization (ERD) and event-related synchronization (ERS) production ability, we set the 2D Screen Game as the comparison experiment. According to a series of statistical results, the group performing MI in the 3D Tetris environment showed more significant improvements in generating MI-associated ERD/ERS. Analysis results of game-score indicated that the players' scores presented an obvious uptrend in 3D Tetris environment but did not show an obvious downward trend in 2D Screen Game. It suggested that the immersive and rich-control environment for MI would improve the associated mental imagery and enhance MI-based BCI skills.

Control of Salmonella on fresh chicken breasts by κ-carrageenan/chitosan-based coatings containing allyl isothiocyanate or deodorized Oriental mustard extract plus EDTA.

PubMed

Olaimat, Amin N; Holley, Richard A

2015-06-01

Control of Salmonella in poultry is a public health concern as salmonellosis is one of the most common foodborne diseases worldwide. This study aimed to screen the ability of 5 Salmonella serovars to degrade the mustard glucosinolate, sinigrin (by bacterial myrosinase) in Mueller-Hinton broth at 25 °C for 21 d and to reduce Salmonella on fresh chicken breasts by developing an edible 0.2% (w/v) κ-carrageenan/2% (w/v) chitosan-based coating containing Oriental mustard extract, allyl isothiocyanate (AITC), EDTA or their combinations. Individual Salmonella serovars degraded 50.2%-55.9% of the sinigrin present in 21 d. κ-Carrageenan/chitosan-based coatings containing 250 mg Oriental mustard extract/g or 50 μl AITC/g reduced the numbers of Salmonella on chicken breasts 2.3 log10 CFU/g at 21 d at 4 °C. However, when either mustard extract or AITC was combined with 15 mg/g EDTA in κ-carrageenan/chitosan-based coatings, Salmonella numbers were reduced 2.3 log10 CFU/g at 5 d and 3.0 log10 CFU/g at 21 d. Moreover, these treatments reduced numbers of lactic acid bacteria and aerobic bacteria by 2.5-3.3 log10 CFU/g at 21 d. κ-Carrageenan/chitosan coatings containing either 50 μl AITC/g or 250 mg Oriental mustard extract/g plus 15 mg EDTA/g have the potential to reduce Salmonella on raw chicken. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extraction of water and solutes from argillaceous rocks for geochemical characterisation: Methods, processes and current understanding

NASA Astrophysics Data System (ADS)

Sacchi, Elisa; Michelot, Jean-Luc; Pitsch, Helmut; Lalieux, Philippe; Aranyossy, Jean-François

2001-01-01

This paper summarises the results of a comprehensive critical review, initiated by the OECD/NEA "Clay Club," of the extraction techniques available to obtain water and solutes from argillaceous rocks. The paper focuses on the mechanisms involved in the extraction processes, the consequences on the isotopic and chemical composition of the extracted pore water and the attempts made to reconstruct its original composition. Finally, it provides some examples of reliable techniques and information, as a function of the purpose of the geochemical study. Résumé. Cet article résume les résultats d'une synthèse critique d'ensemble, lancée par le OECD/NEA "Clay Club", sur les techniques d'extraction disponibles pour obtenir l'eau et les solutés de roches argileuses. L'article est consacré aux mécanismes impliqués dans les processus d'extraction, aux conséquences sur la composition isotopique et chimique de l'eau porale extraite et aux tentatives faites pour reconstituer sa composition originelle. Finalement, il donne quelques exemples de techniques fiables et d'informations, en fonction du but de l'étude géochimique. Resúmen. Este artículo resume los resultados de una revisión crítica exhaustiva (iniciada por el "Clay Club" OECD/NEA) de las técnicas de extracción disponibles para obtener agua y solutos en rocas arcillosas. El artículo se centra en los mecanismos involucrados en los procesos extractivos, las consecuencias en la composición isotópica y química del agua intersticial extraída, y en los intentos realizados para reconstruir su composición original. Finalmente, se presentan algunos ejemplos de técnicas fiables e información, en función del propósito del estudio geoquímico.

Geographic Video 3d Data Model And Retrieval

NASA Astrophysics Data System (ADS)

Han, Z.; Cui, C.; Kong, Y.; Wu, H.

2014-04-01

Geographic video includes both spatial and temporal geographic features acquired through ground-based or non-ground-based cameras. With the popularity of video capture devices such as smartphones, the volume of user-generated geographic video clips has grown significantly and the trend of this growth is quickly accelerating. Such a massive and increasing volume poses a major challenge to efficient video management and query. Most of the today's video management and query techniques are based on signal level content extraction. They are not able to fully utilize the geographic information of the videos. This paper aimed to introduce a geographic video 3D data model based on spatial information. The main idea of the model is to utilize the location, trajectory and azimuth information acquired by sensors such as GPS receivers and 3D electronic compasses in conjunction with video contents. The raw spatial information is synthesized to point, line, polygon and solid according to the camcorder parameters such as focal length and angle of view. With the video segment and video frame, we defined the three categories geometry object using the geometry model of OGC Simple Features Specification for SQL. We can query video through computing the spatial relation between query objects and three categories geometry object such as VFLocation, VSTrajectory, VSFOView and VFFovCone etc. We designed the query methods using the structured query language (SQL) in detail. The experiment indicate that the model is a multiple objective, integration, loosely coupled, flexible and extensible data model for the management of geographic stereo video.

Seismic attribute analysis for reservoir and fluid prediction, Malay Basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mansor, M.N.; Rudolph, K.W.; Richards, F.B.

1994-07-01

The Malay Basin is characterized by excellent seismic data quality, but complex clastic reservoir architecture. With these characteristics, seismic attribute analysis is a very important tool in exploration and development geoscience and is routinely used for mapping fluids and reservoir, recognizing and risking traps, assessment, depth conversion, well placement, and field development planning. Attribute analysis can be successfully applied to both 2-D and 3-D data as demonstrated by comparisons of 2-D and 3-D amplitude maps of the same area. There are many different methods of extracting amplitude information from seismic data, including amplitude mapping, horizon slice, summed horizon slice, isochronmore » slice, and horizon slice from AVO (amplitude versus offset) cube. Within the Malay Basin, horizon/isochron slice techniques have several advantages over simply extracting amplitudes from a picked horizon: they are much faster, permit examination of the amplitude structure of the entire cube, yield better results for weak/variable signatures, and aid summation of amplitudes. Summation in itself often yields improved results because it incorporates the signature from the entire reservoir interval, reducing any effects due to noise, mispicking, or waveform variations. Dip and azimuth attributes have been widely applied by industry for fault identification. In addition, these attributes can also be used to map signature variations associated with hydrocarbon contacts or stratigraphic changes, and this must be considered when using these attributes for structural interpretation.« less

Adaptive Local Spatiotemporal Features from RGB-D Data for One-Shot Learning Gesture Recognition

PubMed Central

Lin, Jia; Ruan, Xiaogang; Yu, Naigong; Yang, Yee-Hong

2016-01-01

Noise and constant empirical motion constraints affect the extraction of distinctive spatiotemporal features from one or a few samples per gesture class. To tackle these problems, an adaptive local spatiotemporal feature (ALSTF) using fused RGB-D data is proposed. First, motion regions of interest (MRoIs) are adaptively extracted using grayscale and depth velocity variance information to greatly reduce the impact of noise. Then, corners are used as keypoints if their depth, and velocities of grayscale and of depth meet several adaptive local constraints in each MRoI. With further filtering of noise, an accurate and sufficient number of keypoints is obtained within the desired moving body parts (MBPs). Finally, four kinds of multiple descriptors are calculated and combined in extended gradient and motion spaces to represent the appearance and motion features of gestures. The experimental results on the ChaLearn gesture, CAD-60 and MSRDailyActivity3D datasets demonstrate that the proposed feature achieves higher performance compared with published state-of-the-art approaches under the one-shot learning setting and comparable accuracy under the leave-one-out cross validation. PMID:27999337

Adaptive Local Spatiotemporal Features from RGB-D Data for One-Shot Learning Gesture Recognition.

PubMed

Lin, Jia; Ruan, Xiaogang; Yu, Naigong; Yang, Yee-Hong

2016-12-17

Noise and constant empirical motion constraints affect the extraction of distinctive spatiotemporal features from one or a few samples per gesture class. To tackle these problems, an adaptive local spatiotemporal feature (ALSTF) using fused RGB-D data is proposed. First, motion regions of interest (MRoIs) are adaptively extracted using grayscale and depth velocity variance information to greatly reduce the impact of noise. Then, corners are used as keypoints if their depth, and velocities of grayscale and of depth meet several adaptive local constraints in each MRoI. With further filtering of noise, an accurate and sufficient number of keypoints is obtained within the desired moving body parts (MBPs). Finally, four kinds of multiple descriptors are calculated and combined in extended gradient and motion spaces to represent the appearance and motion features of gestures. The experimental results on the ChaLearn gesture, CAD-60 and MSRDailyActivity3D datasets demonstrate that the proposed feature achieves higher performance compared with published state-of-the-art approaches under the one-shot learning setting and comparable accuracy under the leave-one-out cross validation.

An innovative approach for characteristic analysis and state-of-health diagnosis for a Li-ion cell based on the discrete wavelet transform

NASA Astrophysics Data System (ADS)

Kim, Jonghoon; Cho, B. H.

2014-08-01

This paper introduces an innovative approach to analyze electrochemical characteristics and state-of-health (SOH) diagnosis of a Li-ion cell based on the discrete wavelet transform (DWT). In this approach, the DWT has been applied as a powerful tool in the analysis of the discharging/charging voltage signal (DCVS) with non-stationary and transient phenomena for a Li-ion cell. Specifically, DWT-based multi-resolution analysis (MRA) is used for extracting information on the electrochemical characteristics in both time and frequency domain simultaneously. Through using the MRA with implementation of the wavelet decomposition, the information on the electrochemical characteristics of a Li-ion cell can be extracted from the DCVS over a wide frequency range. Wavelet decomposition based on the selection of the order 3 Daubechies wavelet (dB3) and scale 5 as the best wavelet function and the optimal decomposition scale is implemented. In particular, this present approach develops these investigations one step further by showing low and high frequency components (approximation component An and detail component Dn, respectively) extracted from variable Li-ion cells with different electrochemical characteristics caused by aging effect. Experimental results show the clearness of the DWT-based approach for the reliable diagnosis of the SOH for a Li-ion cell.

CD-SEM real time bias correction using reference metrology based modeling

NASA Astrophysics Data System (ADS)

Ukraintsev, V.; Banke, W.; Zagorodnev, G.; Archie, C.; Rana, N.; Pavlovsky, V.; Smirnov, V.; Briginas, I.; Katnani, A.; Vaid, A.

2018-03-01

Accuracy of patterning impacts yield, IC performance and technology time to market. Accuracy of patterning relies on optical proximity correction (OPC) models built using CD-SEM inputs and intra die critical dimension (CD) control based on CD-SEM. Sub-nanometer measurement uncertainty (MU) of CD-SEM is required for current technologies. Reported design and process related bias variation of CD-SEM is in the range of several nanometers. Reference metrology and numerical modeling are used to correct SEM. Both methods are slow to be used for real time bias correction. We report on real time CD-SEM bias correction using empirical models based on reference metrology (RM) data. Significant amount of currently untapped information (sidewall angle, corner rounding, etc.) is obtainable from SEM waveforms. Using additional RM information provided for specific technology (design rules, materials, processes) CD extraction algorithms can be pre-built and then used in real time for accurate CD extraction from regular CD-SEM images. The art and challenge of SEM modeling is in finding robust correlation between SEM waveform features and bias of CD-SEM as well as in minimizing RM inputs needed to create accurate (within the design and process space) model. The new approach was applied to improve CD-SEM accuracy of 45 nm GATE and 32 nm MET1 OPC 1D models. In both cases MU of the state of the art CD-SEM has been improved by 3x and reduced to a nanometer level. Similar approach can be applied to 2D (end of line, contours, etc.) and 3D (sidewall angle, corner rounding, etc.) cases.

a Quadtree Organization Construction and Scheduling Method for Urban 3d Model Based on Weight

NASA Astrophysics Data System (ADS)

Yao, C.; Peng, G.; Song, Y.; Duan, M.

2017-09-01

The increasement of Urban 3D model precision and data quantity puts forward higher requirements for real-time rendering of digital city model. Improving the organization, management and scheduling of 3D model data in 3D digital city can improve the rendering effect and efficiency. This paper takes the complexity of urban models into account, proposes a Quadtree construction and scheduling rendering method for Urban 3D model based on weight. Divide Urban 3D model into different rendering weights according to certain rules, perform Quadtree construction and schedule rendering according to different rendering weights. Also proposed an algorithm for extracting bounding box extraction based on model drawing primitives to generate LOD model automatically. Using the algorithm proposed in this paper, developed a 3D urban planning&management software, the practice has showed the algorithm is efficient and feasible, the render frame rate of big scene and small scene are both stable at around 25 frames.

Identification of epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3''Me) and amino acid profiles in various tea (Camellia sinensis L.) cultivars.

PubMed

Ji, Hyang-Gi; Lee, Yeong-Ran; Lee, Min-Seuk; Hwang, Kyeng Hwan; Kim, Eun-Hee; Park, Jun Seong; Hong, Young-Shick

2017-10-01

This article includes experimental data on the identification of epigallocatechin-3-O-(3-O-methyl)-gallate (EGCG3''Me) by 2-dimensional (2D) proton ( 1 H) NMR analysis and on the information of amino acid and catechin compound profiles by HPLC analysis in leaf extracts of various tea cultivars. These data are related to the research article " Metabolic phenotyping of various tea (Camellia sinensis L.) cultivars and understanding of their intrinsic metabolism " (Ji et al., 2017) [1]. The assignment for EGCG3x''Me by 1 H NMR analysis was also confirmed with spiking experiment of its pure chemical.

Magnetic resonance studies of dissolving particulate solids.

PubMed

Johns, M L; Gladden, L F

2003-01-01

Magnetic resonance methods have been used to elucidate the internal pore structure of particulate solids, in particular detergent tablets. Such information is essential to a comprehensive understanding of the dissolution characteristics of these materials and how this property is related to processing conditions during tablet formation. In particular 3-D images of porosity are produced and 2-D self-diffusion maps are acquired as a function of observation time, which enables pore size to be quantified as a function of position via the extracted surface-to-volume ratio of the pore space. These properties are determined as a function of processing parameters, in particular the compression force used in tablet formation.

3D tumor measurement in cone-beam CT breast imaging

NASA Astrophysics Data System (ADS)

Chen, Zikuan; Ning, Ruola

2004-05-01

Cone-beam CT breast imaging provides a digital volume representation of a breast. With a digital breast volume, the immediate task is to extract the breast tissue information, especially for suspicious tumors, preferably in an automatic manner or with minimal user interaction. This paper reports a program for three-dimensional breast tissue analysis. It consists of volumetric segmentation (by globally thresholding), subsegmentation (connection-based separation), and volumetric component measurement (volume, surface, shape, and other geometrical specifications). A combination scheme of multi-thresholding and binary volume morphology is proposed to fast determine the surface gradients, which may be interpreted as the surface evolution (outward growth or inward shrinkage) for a tumor volume. This scheme is also used to optimize the volumetric segmentation. With a binary volume, we decompose the foreground into components according to spatial connectedness. Since this decomposition procedure is performed after volumetric segmentation, it is called subsegmentation. The subsegmentation brings the convenience for component visualization and measurement, in the whole support space, without interference from others. Upon the tumor component identification, we measure the following specifications: volume, surface area, roundness, elongation, aspect, star-shapedness, and location (centroid). A 3D morphological operation is used to extract the cluster shell and, by delineating the corresponding volume from the grayscale volume, to measure the shell stiffness. This 3D tissue measurement is demonstrated with a tumor-borne breast specimen (a surgical part).

Use of condensed tannin extract from quebracho trees to reduce methane emissions from cattle.

PubMed

Beauchemin, K A; McGinn, S M; Martinez, T F; McAllister, T A

2007-08-01

Our objective was to determine if condensed tannin extract from quebracho trees (Schinopsis quebracho-colorado; red quebracho) could be used to reduce enteric methane emissions from cattle. The experiment was designed as a repeated 3 x 3 Latin square (4 squares) with 3 treatments (0, 1, and 2% of dietary DM as quebracho tannin extract) and 3 28-d periods. Six spayed Angus heifers (238 +/- 13.3 kg of initial BW) and 6 Angus steers (207 +/- 8.2 kg of initial BW) were each assigned to 2 squares. The measured condensed tannin content of the extract was 91%, and the basal diet contained 70% forage (DM basis). Feeding quebracho tannin extract had no effect on BW, ADG, or nutrient intakes. Furthermore, it had no effect on DM, energy, or fiber (ADF and NDF) digestibility, but apparent digestibility of CP decreased linearly (P < 0.001) by 5 and 15% with 1 and 2% quebracho tannin extract, respectively. There were no effects of quebracho tannin extract on methane emissions (g/d, g/kg of DM, % of GE intake, or % of DE intake). Feeding up to 2% of the dietary DM as quebracho tannin extract failed to reduce enteric methane emissions from growing cattle, although the protein-binding effect of the quebracho tannin extract was evident.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, M; Suh, T; Cho, W

Purpose: A potential validation tool for compensating patient positioning error was developed using 2D/3D and 3D/3D image registration. Methods: For 2D/3D registration, digitally reconstructed radiography (DRR) and three-dimensional computed tomography (3D-CT) images were applied. The ray-casting algorithm is the most straightforward method for generating DRR. We adopted the traditional ray-casting method, which finds the intersections of a ray with all objects, voxels of the 3D-CT volume in the scene. The similarity between the extracted DRR and orthogonal image was measured by using a normalized mutual information method. Two orthogonal images were acquired from a Cyber-Knife system from the anterior-posterior (AP)more » and right lateral (RL) views. The 3D-CT and two orthogonal images of an anthropomorphic phantom and head and neck cancer patient were used in this study. For 3D/3D registration, planning CT and in-room CT image were applied. After registration, the translation and rotation factors were calculated to position a couch to be movable in six dimensions. Results: Registration accuracies and average errors of 2.12 mm ± 0.50 mm for transformations and 1.23° ± 0.40° for rotations were acquired by 2D/3D registration using an anthropomorphic Alderson-Rando phantom. In addition, registration accuracies and average errors of 0.90 mm ± 0.30 mm for transformations and 1.00° ± 0.2° for rotations were acquired using CT image sets. Conclusion: We demonstrated that this validation tool could compensate for patient positioning error. In addition, this research could be the fundamental step for compensating patient positioning error at the first Korea heavy-ion medical accelerator treatment center.« less

Cross-Domain Multi-View Object Retrieval via Multi-Scale Topic Models.

PubMed

Hong, Richang; Hu, Zhenzhen; Wang, Ruxin; Wang, Meng; Tao, Dacheng

2016-09-27

The increasing number of 3D objects in various applications has increased the requirement for effective and efficient 3D object retrieval methods, which attracted extensive research efforts in recent years. Existing works mainly focus on how to extract features and conduct object matching. With the increasing applications, 3D objects come from different areas. In such circumstances, how to conduct object retrieval becomes more important. To address this issue, we propose a multi-view object retrieval method using multi-scale topic models in this paper. In our method, multiple views are first extracted from each object, and then the dense visual features are extracted to represent each view. To represent the 3D object, multi-scale topic models are employed to extract the hidden relationship among these features with respected to varied topic numbers in the topic model. In this way, each object can be represented by a set of bag of topics. To compare the objects, we first conduct topic clustering for the basic topics from two datasets, and then generate the common topic dictionary for new representation. Then, the two objects can be aligned to the same common feature space for comparison. To evaluate the performance of the proposed method, experiments are conducted on two datasets. The 3D object retrieval experimental results and comparison with existing methods demonstrate the effectiveness of the proposed method.

Vertical Corner Feature Based Precise Vehicle Localization Using 3D LIDAR in Urban Area

PubMed Central

Im, Jun-Hyuck; Im, Sung-Hyuck; Jee, Gyu-In

2016-01-01

Tall buildings are concentrated in urban areas. The outer walls of buildings are vertically erected to the ground and almost flat. Therefore, the vertical corners that meet the vertical planes are present everywhere in urban areas. These corners act as convenient landmarks, which can be extracted by using the light detection and ranging (LIDAR) sensor. A vertical corner feature based precise vehicle localization method is proposed in this paper and implemented using 3D LIDAR (Velodyne HDL-32E). The vehicle motion is predicted by accumulating the pose increment output from the iterative closest point (ICP) algorithm based on the geometric relations between the scan data of the 3D LIDAR. The vertical corner is extracted using the proposed corner extraction method. The vehicle position is then corrected by matching the prebuilt corner map with the extracted corner. The experiment was carried out in the Gangnam area of Seoul, South Korea. In the experimental results, the maximum horizontal position error is about 0.46 m and the 2D Root Mean Square (RMS) horizontal error is about 0.138 m. PMID:27517936

Image Segmentation, Registration, Compression, and Matching

NASA Technical Reports Server (NTRS)

Yadegar, Jacob; Wei, Hai; Yadegar, Joseph; Ray, Nilanjan; Zabuawala, Sakina

2011-01-01

A novel computational framework was developed of a 2D affine invariant matching exploiting a parameter space. Named as affine invariant parameter space (AIPS), the technique can be applied to many image-processing and computer-vision problems, including image registration, template matching, and object tracking from image sequence. The AIPS is formed by the parameters in an affine combination of a set of feature points in the image plane. In cases where the entire image can be assumed to have undergone a single affine transformation, the new AIPS match metric and matching framework becomes very effective (compared with the state-of-the-art methods at the time of this reporting). No knowledge about scaling or any other transformation parameters need to be known a priori to apply the AIPS framework. An automated suite of software tools has been created to provide accurate image segmentation (for data cleaning) and high-quality 2D image and 3D surface registration (for fusing multi-resolution terrain, image, and map data). These tools are capable of supporting existing GIS toolkits already in the marketplace, and will also be usable in a stand-alone fashion. The toolkit applies novel algorithmic approaches for image segmentation, feature extraction, and registration of 2D imagery and 3D surface data, which supports first-pass, batched, fully automatic feature extraction (for segmentation), and registration. A hierarchical and adaptive approach is taken for achieving automatic feature extraction, segmentation, and registration. Surface registration is the process of aligning two (or more) data sets to a common coordinate system, during which the transformation between their different coordinate systems is determined. Also developed here are a novel, volumetric surface modeling and compression technique that provide both quality-guaranteed mesh surface approximations and compaction of the model sizes by efficiently coding the geometry and connectivity/topology components of the generated models. The highly efficient triangular mesh compression compacts the connectivity information at the rate of 1.5-4 bits per vertex (on average for triangle meshes), while reducing the 3D geometry by 40-50 percent. Finally, taking into consideration the characteristics of 3D terrain data, and using the innovative, regularized binary decomposition mesh modeling, a multistage, pattern-drive modeling, and compression technique has been developed to provide an effective framework for compressing digital elevation model (DEM) surfaces, high-resolution aerial imagery, and other types of NASA data.

Improving the extraction of crisis information in the context of flood, fire, and landslide rapid mapping using SAR and optical remote sensing data

NASA Astrophysics Data System (ADS)

Martinis, Sandro; Clandillon, Stephen; Twele, André; Huber, Claire; Plank, Simon; Maxant, Jérôme; Cao, Wenxi; Caspard, Mathilde; May, Stéphane

2016-04-01

Optical and radar satellite remote sensing have proven to provide essential crisis information in case of natural disasters, humanitarian relief activities and civil security issues in a growing number of cases through mechanisms such as the Copernicus Emergency Management Service (EMS) of the European Commission or the International Charter 'Space and Major Disasters'. The aforementioned programs and initiatives make use of satellite-based rapid mapping services aimed at delivering reliable and accurate crisis information after natural hazards. Although these services are increasingly operational, they need to be continuously updated and improved through research and development (R&D) activities. The principal objective of ASAPTERRA (Advancing SAR and Optical Methods for Rapid Mapping), the ESA-funded R&D project being described here, is to improve, automate and, hence, speed-up geo-information extraction procedures in the context of natural hazards response. This is performed through the development, implementation, testing and validation of novel image processing methods using optical and Synthetic Aperture Radar (SAR) data. The methods are mainly developed based on data of the German radar satellites TerraSAR-X and TanDEM-X, the French satellite missions Pléiades-1A/1B as well as the ESA missions Sentinel-1/2 with the aim to better characterize the potential and limitations of these sensors and their synergy. The resulting algorithms and techniques are evaluated in real case applications during rapid mapping activities. The project is focussed on three types of natural hazards: floods, landslides and fires. Within this presentation an overview of the main methodological developments in each topic is given and demonstrated in selected test areas. The following developments are presented in the context of flood mapping: a fully automated Sentinel-1 based processing chain for detecting open flood surfaces, a method for the improved detection of flooded vegetation in Sentinel-1data using Entropy/Alpha decomposition, unsupervised Wishart Classification, and object-based post-classification as well as semi-automatic approaches for extracting inundated areas and flood traces in rural and urban areas from VHR and HR optical imagery using machine learning techniques. Methodological developments related to fires are the implementation of fast and robust methods for mapping burnt scars using change detection procedures using SAR (Sentinel-1, TerraSAR-X) and HR optical (e.g. SPOT, Sentinel-2) data as well as the extraction of 3D surface and volume change information from Pléiades stereo-pairs. In the context of landslides, fast and transferable change detection procedures based on SAR (TerraSAR-X) and optical (SPOT) data as well methods for extracting the extent of landslides only based on polarimetric VHR SAR (TerraSAR-X) data are presented.

Antioxidant activity and chemical composition of Juniperus excelsa ssp. polycarpos wood extracts.

PubMed

Hosseinihashemi, S K; Dadpour, A; Lashgari, A

2017-03-01

Extracts from the wood of Juniperus excelsa ssp. polycarpos were analysed for their antioxidant activity using the DPPH method and compared with ascorbic acid and butylated hydroxytoluene. The most active extracts were analysed for their chemical composition using gas chromatography-mass spectrometry. Acetone extract was found to be moderately active as an antioxidant agent at 58.38%, which was lower than the value of vitamin C (98.56%) at the concentration of 14.20 mg/mL. The major components identified in the acetone extract as trimethylsilyl (TMS) derivatives were pimaric acid TMS (24.56%), followed by α-d-glucopyranoside,1,3,4,6-tetrakis-O-(TMS)-β-d-fructofuranosyl 2,3,4,6-tetrakis-O-(TMS) (21.39%), triflouromethyl-bis-(TMS)methyl ketone (9.32%), and cedrol (0.72%). The dissolved water:methanol (1:1 v/v) partitioned from acetone extract afforded 12 fractions; among them, the F9 fraction was found to have good antioxidant activity (88.49%) at the concentration of 14.20 mg/mL. The major compounds identified in F9 fraction were α-d-glucopyranoside, 1,3,4,6-tetrakis-O-(TMS) (20.22%) and trifluoromethyl-bis-(TMS)methyl ketone (5.10%).

Automatic 3D Extraction of Buildings, Vegetation and Roads from LIDAR Data

NASA Astrophysics Data System (ADS)

Bellakaout, A.; Cherkaoui, M.; Ettarid, M.; Touzani, A.

2016-06-01

Aerial topographic surveys using Light Detection and Ranging (LiDAR) technology collect dense and accurate information from the surface or terrain; it is becoming one of the important tools in the geosciences for studying objects and earth surface. Classification of Lidar data for extracting ground, vegetation, and buildings is a very important step needed in numerous applications such as 3D city modelling, extraction of different derived data for geographical information systems (GIS), mapping, navigation, etc... Regardless of what the scan data will be used for, an automatic process is greatly required to handle the large amount of data collected because the manual process is time consuming and very expensive. This paper is presenting an approach for automatic classification of aerial Lidar data into five groups of items: buildings, trees, roads, linear object and soil using single return Lidar and processing the point cloud without generating DEM. Topological relationship and height variation analysis is adopted to segment, preliminary, the entire point cloud preliminarily into upper and lower contours, uniform and non-uniform surface, non-uniform surfaces, linear objects, and others. This primary classification is used on the one hand to know the upper and lower part of each building in an urban scene, needed to model buildings façades; and on the other hand to extract point cloud of uniform surfaces which contain roofs, roads and ground used in the second phase of classification. A second algorithm is developed to segment the uniform surface into buildings roofs, roads and ground, the second phase of classification based on the topological relationship and height variation analysis, The proposed approach has been tested using two areas : the first is a housing complex and the second is a primary school. The proposed approach led to successful classification results of buildings, vegetation and road classes.

Valeriana officinalis extract and its main component, valerenic acid, ameliorate D-galactose-induced reductions in memory, cell proliferation, and neuroblast differentiation by reducing corticosterone levels and lipid peroxidation.

PubMed

Nam, Sung Min; Choi, Jung Hoon; Yoo, Dae Young; Kim, Woosuk; Jung, Hyo Young; Kim, Jong Whi; Kang, Soo-Yong; Park, Jaeil; Kim, Dong-Woo; Kim, Wan Jae; Yoon, Yeo Sung; Hwang, In Koo

2013-11-01

Valeriana officinalis is used in herbal medicine of many cultures as mild sedatives and tranquilizers. In this study, we investigated the effects of extract from valerian root extracts and its major component, valerenic acid on memory function, cell proliferation, neuroblast differentiation, serum corticosterone, and lipid peroxidation in adult and aged mice. For the aging model, D-galactose (100 mg/kg) was administered subcutaneously to 6-week-old male mice for 10 weeks. At 13 weeks of age, valerian root extracts (100 mg/kg) or valerenic acid (340 μg/kg) was administered orally to control and D-galactose-treated mice for 3 weeks. The dosage of valerenic acid (340 μg/kg), which is the active ingredient of valerian root extract, was determined by the content of valerenic acid in valerian root extract (3.401±0.066 mg/g) measured by HPLC. The administration of valerian root extract and valerenic acid significantly improved the preferential exploration of new objects in novel object recognition test and the escape latency, swimming speeds, platform crossings, and spatial preference for the target quadrant in Morris water maze test compared to the D-galactose-treated mice. Cell proliferation and neuroblast differentiation were significantly decreased, while serum corticosterone level and lipid peroxidation in hippocampus were significantly increased in the D-galactose-treated group compared to that in the control group. The administration of valerian root extract significantly ameliorated these changes in the dentate gyrus of both control and D-galactose-treated groups. In addition, valerenic acid also mitigated the D-galactose-induced reduction of these changes. These results indicate that valerian root extract and valerenic acid enhance cognitive function, promote cell proliferation and neuroblast differentiation, and reduce serum corticosterone and lipid peroxidation in aged mice. © 2013.

3D Forest: An application for descriptions of three-dimensional forest structures using terrestrial LiDAR

PubMed Central

Krůček, Martin; Vrška, Tomáš; Král, Kamil

2017-01-01

Terrestrial laser scanning is a powerful technology for capturing the three-dimensional structure of forests with a high level of detail and accuracy. Over the last decade, many algorithms have been developed to extract various tree parameters from terrestrial laser scanning data. Here we present 3D Forest, an open-source non-platform-specific software application with an easy-to-use graphical user interface with the compilation of algorithms focused on the forest environment and extraction of tree parameters. The current version (0.42) extracts important parameters of forest structure from the terrestrial laser scanning data, such as stem positions (X, Y, Z), tree heights, diameters at breast height (DBH), as well as more advanced parameters such as tree planar projections, stem profiles or detailed crown parameters including convex and concave crown surface and volume. Moreover, 3D Forest provides quantitative measures of between-crown interactions and their real arrangement in 3D space. 3D Forest also includes an original algorithm of automatic tree segmentation and crown segmentation. Comparison with field data measurements showed no significant difference in measuring DBH or tree height using 3D Forest, although for DBH only the Randomized Hough Transform algorithm proved to be sufficiently resistant to noise and provided results comparable to traditional field measurements. PMID:28472167

Automatic extraction of three-dimensional thoracic aorta geometric model from phase contrast MRI for morphometric and hemodynamic characterization.

PubMed

Volonghi, Paola; Tresoldi, Daniele; Cadioli, Marcello; Usuelli, Antonio M; Ponzini, Raffaele; Morbiducci, Umberto; Esposito, Antonio; Rizzo, Giovanna

2016-02-01

To propose and assess a new method that automatically extracts a three-dimensional (3D) geometric model of the thoracic aorta (TA) from 3D cine phase contrast MRI (PCMRI) acquisitions. The proposed method is composed of two steps: segmentation of the TA and creation of the 3D geometric model. The segmentation algorithm, based on Level Set, was set and applied to healthy subjects acquired in three different modalities (with and without SENSE reduction factors). Accuracy was evaluated using standard quality indices. The 3D model is characterized by the vessel surface mesh and its centerline; the comparison of models obtained from the three different datasets was also carried out in terms of radius of curvature (RC) and average tortuosity (AT). In all datasets, the segmentation quality indices confirmed very good agreement between manual and automatic contours (average symmetric distance < 1.44 mm, DICE Similarity Coefficient > 0.88). The 3D models extracted from the three datasets were found to be comparable, with differences of less than 10% for RC and 11% for AT. Our method was found effective on PCMRI data to provide a 3D geometric model of the TA, to support morphometric and hemodynamic characterization of the aorta. © 2015 Wiley Periodicals, Inc.

Three-dimensional Imaging Methods for Quantitative Analysis of Facial Soft Tissues and Skeletal Morphology in Patients with Orofacial Clefts: A Systematic Review

PubMed Central

Kuijpers, Mette A. R.; Chiu, Yu-Ting; Nada, Rania M.; Carels, Carine E. L.; Fudalej, Piotr S.

2014-01-01

Background Current guidelines for evaluating cleft palate treatments are mostly based on two-dimensional (2D) evaluation, but three-dimensional (3D) imaging methods to assess treatment outcome are steadily rising. Objective To identify 3D imaging methods for quantitative assessment of soft tissue and skeletal morphology in patients with cleft lip and palate. Data sources Literature was searched using PubMed (1948–2012), EMBASE (1980–2012), Scopus (2004–2012), Web of Science (1945–2012), and the Cochrane Library. The last search was performed September 30, 2012. Reference lists were hand searched for potentially eligible studies. There was no language restriction. Study selection We included publications using 3D imaging techniques to assess facial soft tissue or skeletal morphology in patients older than 5 years with a cleft lip with/or without cleft palate. We reviewed studies involving the facial region when at least 10 subjects in the sample size had at least one cleft type. Only primary publications were included. Data extraction Independent extraction of data and quality assessments were performed by two observers. Results Five hundred full text publications were retrieved, 144 met the inclusion criteria, with 63 high quality studies. There were differences in study designs, topics studied, patient characteristics, and success measurements; therefore, only a systematic review could be conducted. Main 3D-techniques that are used in cleft lip and palate patients are CT, CBCT, MRI, stereophotogrammetry, and laser surface scanning. These techniques are mainly used for soft tissue analysis, evaluation of bone grafting, and changes in the craniofacial skeleton. Digital dental casts are used to evaluate treatment and changes over time. Conclusion Available evidence implies that 3D imaging methods can be used for documentation of CLP patients. No data are available yet showing that 3D methods are more informative than conventional 2D methods. Further research is warranted to elucidate it. Systematic review registration International Prospective Register of Systematic Reviews, PROSPERO CRD42012002041 PMID:24710215

Preparation of 2D sequences of corneal images for 3D model building.

PubMed

Elbita, Abdulhakim; Qahwaji, Rami; Ipson, Stanley; Sharif, Mhd Saeed; Ghanchi, Faruque

2014-04-01

A confocal microscope provides a sequence of images, at incremental depths, of the various corneal layers and structures. From these, medical practioners can extract clinical information on the state of health of the patient's cornea. In this work we are addressing problems associated with capturing and processing these images including blurring, non-uniform illumination and noise, as well as the displacement of images laterally and in the anterior-posterior direction caused by subject movement. The latter may cause some of the captured images to be out of sequence in terms of depth. In this paper we introduce automated algorithms for classification, reordering, registration and segmentation to solve these problems. The successful implementation of these algorithms could open the door for another interesting development, which is the 3D modelling of these sequences. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A new derivatization approach with D-cysteine for the sensitive and simple analysis of acrylamide in foods by liquid chromatography-tandem mass spectrometry.

PubMed

Lim, Hyun-Hee; Shin, Ho-Sang

2014-09-26

A liquid chromatography-tandem mass spectrometry method (LC-MS/MS) was developed in order to determine the amount of acrylamide in foods after derivatization with d-cysteine. The sulfhydryl group of d-cysteine was added at the β-site double bond of acrylamide to form 2-amino-3-(3-amino-3-oxo-propyl)sulfanyl-propanoic acid. Deuterated acrylamide (acrylamide-d3) was chosen as the internal standard (IS) for analyzing the food samples. Acrylamide was extracted from 2.0 g of food sample with 6 mL of methylene chloride, and the organic extract was diluted with 3 mL of hexane, and then the analyte was back-extracted with 0.5 mL of pure water. The derivatization of acrylamide was performed in the water extract. The best reaction conditions (3.0mg of d-cysteine, a pH 6.5, a reaction temperature of 90°C, and a heating time of 50 min) were established by the variation of parameters. The formed derivative was injected into the LC-MS/MS without further extraction or purification procedures. Separation and detection were improved with the use of an ion-pairing reagent of perfluorooctanoic acid. Under the established conditions, the limits of detection and the limits of quantification were 0.04 μg/kg and 0.14 μg/kg, respectively, and the inter-day relative standard deviation was less than 8% at concentrations of 20 and 100 μg/kg. The method was successfully applied to determine the amount of acrylamide in potato chips, French fries, and coffee. Copyright © 2014 Elsevier B.V. All rights reserved.

D Tracking Based Augmented Reality for Cultural Heritage Data Management

NASA Astrophysics Data System (ADS)

Battini, C.; Landi, G.

2015-02-01

The development of contactless documentation techniques is allowing researchers to collect high volumes of three-dimensional data in a short time but with high levels of accuracy. The digitalisation of cultural heritage opens up the possibility of using image processing and analysis, and computer graphics techniques, to preserve this heritage for future generations; augmenting it with additional information or with new possibilities for its enjoyment and use. The collection of precise datasets about cultural heritage status is crucial for its interpretation, its conservation and during the restoration processes. The application of digital-imaging solutions for various feature extraction, image data-analysis techniques, and three-dimensional reconstruction of ancient artworks, allows the creation of multidimensional models that can incorporate information coming from heterogeneous data sets, research results and historical sources. Real objects can be scanned and reconstructed virtually, with high levels of data accuracy and resolution. Real-time visualisation software and hardware is rapidly evolving and complex three-dimensional models can be interactively visualised and explored on applications developed for mobile devices. This paper will show how a 3D reconstruction of an object, with multiple layers of information, can be stored and visualised through a mobile application that will allow interaction with a physical object for its study and analysis, using 3D Tracking based Augmented Reality techniques.

Fully 3D-Printed Preconcentrator for Selective Extraction of Trace Elements in Seawater.

PubMed

Su, Cheng-Kuan; Peng, Pei-Jin; Sun, Yuh-Chang

2015-07-07

In this study, we used a stereolithographic 3D printing technique and polyacrylate polymers to manufacture a solid phase extraction preconcentrator for the selective extraction of trace elements and the removal of unwanted salt matrices, enabling accurate and rapid analyses of trace elements in seawater samples when combined with a quadrupole-based inductively coupled plasma mass spectrometer. To maximize the extraction efficiency, we evaluated the effect of filling the extraction channel with ordered cuboids to improve liquid mixing. Upon automation of the system and optimization of the method, the device allowed highly sensitive and interference-free determination of Mn, Ni, Zn, Cu, Cd, and Pb, with detection limits comparable with those of most conventional methods. The system's analytical reliability was further confirmed through analyses of reference materials and spike analyses of real seawater samples. This study suggests that 3D printing can be a powerful tool for building multilayer fluidic manipulation devices, simplifying the construction of complex experimental components, and facilitating the operation of sophisticated analytical procedures for most sample pretreatment applications.

On-chip concentration of bacteria using a 3D dielectrophoretic chip and subsequent laser-based DNA extraction in the same chip

NASA Astrophysics Data System (ADS)

Cho, Yoon-Kyoung; Kim, Tae-hyeong; Lee, Jeong-Gun

2010-06-01

We report the on-chip concentration of bacteria using a dielectrophoretic (DEP) chip with 3D electrodes and subsequent laser-based DNA extraction in the same chip. The DEP chip has a set of interdigitated Au post electrodes with 50 µm height to generate a network of non-uniform electric fields for the efficient trapping by DEP. The metal post array was fabricated by photolithography and subsequent Ni and Au electroplating. Three model bacteria samples (Escherichia coli, Staphylococcus epidermidis, Streptococcus mutans) were tested and over 80-fold concentrations were achieved within 2 min. Subsequently, on-chip DNA extraction from the concentrated bacteria in the 3D DEP chip was performed by laser irradiation using the laser-irradiated magnetic bead system (LIMBS) in the same chip. The extracted DNA was analyzed with silicon chip-based real-time polymerase chain reaction (PCR). The total process of on-chip bacteria concentration and the subsequent DNA extraction can be completed within 10 min including the manual operation time.

The topology of geology 1: Topological analysis

NASA Astrophysics Data System (ADS)

Thiele, Samuel T.; Jessell, Mark W.; Lindsay, Mark; Ogarko, Vitaliy; Wellmann, J. Florian; Pakyuz-Charrier, Evren

2016-10-01

Topology has been used to characterise and quantify the properties of complex systems in a diverse range of scientific domains. This study explores the concept and applications of topological analysis in geology. We have developed an automatic system for extracting first order 2D topological information from geological maps, and 3D topological information from models built with the Noddy kinematic modelling system, and equivalent analyses should be possible for other implicit modelling systems. A method is presented for describing the spatial and temporal topology of geological models using a set of adjacency relationships that can be expressed as a topology network, thematic adjacency matrix or hive diagram. We define three types of spatial topology (cellular, structural and lithological) that allow us to analyse different aspects of the geology, and then apply them to investigate the geology of the Hamersley Basin, Western Australia.

Melanoma Is Skin Deep: A 3D Reconstruction Technique for Computerized Dermoscopic Skin Lesion Classification

PubMed Central

Satheesha, T. Y.; Prasad, M. N. Giri; Dhruve, Kashyap D.

2017-01-01

Melanoma mortality rates are the highest amongst skin cancer patients. Melanoma is life threating when it grows beyond the dermis of the skin. Hence, depth is an important factor to diagnose melanoma. This paper introduces a non-invasive computerized dermoscopy system that considers the estimated depth of skin lesions for diagnosis. A 3-D skin lesion reconstruction technique using the estimated depth obtained from regular dermoscopic images is presented. On basis of the 3-D reconstruction, depth and 3-D shape features are extracted. In addition to 3-D features, regular color, texture, and 2-D shape features are also extracted. Feature extraction is critical to achieve accurate results. Apart from melanoma, in-situ melanoma the proposed system is designed to diagnose basal cell carcinoma, blue nevus, dermatofibroma, haemangioma, seborrhoeic keratosis, and normal mole lesions. For experimental evaluations, the PH2, ISIC: Melanoma Project, and ATLAS dermoscopy data sets is considered. Different feature set combinations is considered and performance is evaluated. Significant performance improvement is reported the post inclusion of estimated depth and 3-D features. The good classification scores of sensitivity = 96%, specificity = 97% on PH2 data set and sensitivity = 98%, specificity = 99% on the ATLAS data set is achieved. Experiments conducted to estimate tumor depth from 3-D lesion reconstruction is presented. Experimental results achieved prove that the proposed computerized dermoscopy system is efficient and can be used to diagnose varied skin lesion dermoscopy images. PMID:28512610

Ultra-high-speed variable focus optics for novel applications in advanced imaging

NASA Astrophysics Data System (ADS)

Kang, S.; Dotsenko, E.; Amrhein, D.; Theriault, C.; Arnold, C. B.

2018-02-01

With the advancement of ultra-fast manufacturing technologies, high speed imaging with high 3D resolution has become increasingly important. Here we show the use of an ultra-high-speed variable focus optical element, the TAG Lens, to enable new ways to acquire 3D information from an object. The TAG Lens uses sound to adjust the index of refraction profile in a liquid and thereby can achieve focal scanning rates greater than 100 kHz. When combined with a high-speed pulsed LED and a high-speed camera, we can exploit this phenomenon to achieve high-resolution imaging through large depths. By combining the image acquisition with digital image processing, we can extract relevant parameters such as tilt and angle information from objects in the image. Due to the high speeds at which images can be collected and processed, we believe this technique can be used as an efficient method of industrial inspection and metrology for high throughput applications.

Automatic Recognition of Indoor Navigation Elements from Kinect Point Clouds

NASA Astrophysics Data System (ADS)

Zeng, L.; Kang, Z.

2017-09-01

This paper realizes automatically the navigating elements defined by indoorGML data standard - door, stairway and wall. The data used is indoor 3D point cloud collected by Kinect v2 launched in 2011 through the means of ORB-SLAM. By contrast, it is cheaper and more convenient than lidar, but the point clouds also have the problem of noise, registration error and large data volume. Hence, we adopt a shape descriptor - histogram of distances between two randomly chosen points, proposed by Osada and merges with other descriptor - in conjunction with random forest classifier to recognize the navigation elements (door, stairway and wall) from Kinect point clouds. This research acquires navigation elements and their 3-d location information from each single data frame through segmentation of point clouds, boundary extraction, feature calculation and classification. Finally, this paper utilizes the acquired navigation elements and their information to generate the state data of the indoor navigation module automatically. The experimental results demonstrate a high recognition accuracy of the proposed method.

The effects of flow on schooling Devario aequipinnatus: school structure, startle response and information transmission

PubMed Central

Chicoli, A.; Butail, S.; Lun, Y.; Bak-Coleman, J.; Coombs, S.; Paley, D.A.

2014-01-01

To assess how flow affects school structure and threat detection, startle response rates of solitary and small groups of giant danio Devario aequipinnatus were compared to visual looming stimuli in flow and no-flow conditions. The instantaneous position and heading of each D. aequipinnatus were extracted from high-speed videos. Behavioural results indicate that (1) school structure is altered in flow such that D. aequipinnatus orient upstream while spanning out in a crosswise direction, (2) the probability of at least one D. aequipinnatus detecting the visual looming stimulus is higher in flow than no flow for both solitary D. aequipinnatus and groups of eight D. aequipinnatus, however, (3) the probability of three or more individuals responding is higher in no flow than flow. Taken together, these results indicate a higher probability of stimulus detection in flow but a higher probability of internal transmission of information in no flow. Finally, results were well predicted by a computational model of collective fright response that included the probability of direct detection (based on signal detection theory) and indirect detection (i.e. via interactions between group members) of threatening stimuli. This model provides a new theoretical framework for analysing the collective transfer of information among groups of fishes and other organisms. PMID:24773538

Characterization of cogon grass (Imperata cylindrica) pollen extract and preliminary analysis of grass group 1, 4 and 5 homologues using monoclonal antibodies to Phleum pratense.

PubMed

Kumar, L; Sridhara, S; Singh, B P; Gangal, S V

1998-11-01

Previous studies have established the role of Imperata cylindrica (Ic) pollen in type I allergic disorders. However, no systematic information is available on the allergen composition of Ic pollen extract. To characterize the IgE-binding proteins of Ic pollen extract and to detect the presence of grass group 1, 4 and 5 allergen homologues, if any. Pollen extract of Ic was analyzed by in vivo and in vitro procedures such as intradermal tests (ID), enzyme-linked immunosorbent assay (ELISA), ELISA-inhibition, thin-layer isoelectric focusing (TLIEF), sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Dot blot assay was carried out to check the presence of well-known group 1, 4, and 5 allergen homologues in Ic pollen extract. Out of 303 respiratory allergies patients skin-tested, 27 showed sensitivity to Ic pollen extract. Specific IgE levels were elevated in all 15 serum samples tested. The extract prepared for this study was found to be highly potent since it required only 400 ng of homologous proteins for 50% inhibition of binding in ELISA inhibition assays. TLIEF of Ic pollen extract showed 44 silver-stained bands (pI 3.5-7.0) while SDS-PAGE resolved it into 24 Coomassie-Brilliant-Blue-stained bands (MW 100-10 kD). Immunoblotting with individual patient sera recognized 7 major IgE-binding bands (MW 85, 62, 57, 43, 40, 28 and 16 kD) in Ic pollen extract. A panel of monoclonal antibodies, specific to group 1, 4 and 5 allergens from Phleum pratense pollen extract identified group 5 and group 4 homologues in Ic pollen extract. Ic pollen extract was characterized for the protein profile by TLIEF and SDS-PAGE. IgE reactivity was determined by ELISA and immunoblot. Monoclonal antibodies to group 5 and group 4 allergens reacted weakly showing that this pollen contains group 5 and group 4 homologous allergens.

High-resolution structural and functional assessments of cerebral microvasculature using 3D Gas ΔR2*-mMRA.

PubMed

Huang, Chien-Hsiang; Chen, Chiao-Chi V; Siow, Tiing-Yee; Hsu, Sheng-Hsiou S; Hsu, Yi-Hua; Jaw, Fu-Shan; Chang, Chen

2013-01-01

The ability to evaluate the cerebral microvascular structure and function is crucial for investigating pathological processes in brain disorders. Previous angiographic methods based on blood oxygen level-dependent (BOLD) contrast offer appropriate visualization of the cerebral vasculature, but these methods remain to be optimized in order to extract more comprehensive information. This study aimed to integrate the advantages of BOLD MRI in both structural and functional vascular assessments. The BOLD contrast was manipulated by a carbogen challenge, and signal changes in gradient-echo images were computed to generate ΔR2* maps. Simultaneously, a functional index representing the regional cerebral blood volume was derived by normalizing the ΔR2* values of a given region to those of vein-filled voxels of the sinus. This method is named 3D gas ΔR2*-mMRA (microscopic MRA). The advantages of using 3D gas ΔR2*-mMRA to observe the microvasculature include the ability to distinguish air-tissue interfaces, a high vessel-to-tissue contrast, and not being affected by damage to the blood-brain barrier. A stroke model was used to demonstrate the ability of 3D gas ΔR2*-mMRA to provide information about poststroke revascularization at 3 days after reperfusion. However, this technique has some limitations that cannot be overcome and hence should be considered when it is applied, such as magnifying vessel sizes and predominantly revealing venous vessels.

Determination of the Three-Dimensional Morphology of ALH84001 and Biogenic MV-1 Magnetite: Comparison of Results from Electron Tomography and Classical Transmission Electron Microscopy

NASA Technical Reports Server (NTRS)

Thomas-Keprta, Kathie L.; Clemett, Simon J.; Schwartz, Cindy; Morphew, Mary; McIntosh, J. Richard; Bazylinski, Dennis A.; Kirschvink, Joseph L.; Wentworth, Susan J.; McKay, David S.; Vali, Hojatollah

2004-01-01

Dated at approximately 3.9 billion years of age, carbonate disks, found within fractures of the host rock of Martian meteorite ALH84001, have been interpreted as secondary minerals that formed at low temperature in an aqueous medium. Heterogeneously distributed within these disks are magnetite nanocrystals that are of Martian origin. Approximately one quarter of these magnetites have morphological and chemical similarities to magnetite particles produced by magnetotactic bacteria strain MV-1, which are ubiquitous in aquatic habitats on Earth. Moreover, these types of magnetite particles are not known or expected to be produced by abiotic means either through geological processes or synthetically in the laboratory. The remaining three quarters of the ALH84001 magnetites are likely products of multiple processes including, but not limited to, precipitation from a hydrothermal fluid, thermal decomposition of the carbonate matrix in which they are embedded, and extracellular formation by dissimilatory Fe-reducing bacteria. We have proposed that the origins of magnetites in ALH84001 can be best explained as the products of multiple processes, one of which is biological. Recently the three-dimensional (3-D) external morphology of the purported biogenic fraction of the ALH84001 magnetites has been the subject of considerable debate. We report here the 3-D geometry of biogenic magnetite crystals extracted from MV-1 and of those extracted from ALH84001 carbonate disks using a combination of high resolution classical and tomographic transmission electron microscopy (TEM). We focus on answering the following questions: (1) which technique provides adequate information to deduce the 3-D external crystal morphology?; and, (2) what is the precise 3-D geometry of the ALH84001 and MV-1 magnetites?

Characterizing Urban Volumetry Using LIDAR Data

NASA Astrophysics Data System (ADS)

Santos, T.; Rodrigues, A. M.; Tenedório, J. A.

2013-05-01

Urban indicators are efficient tools designed to simplify, quantify and communicate relevant information for land planners. Since urban data has a strong spatial representation, one can use geographical data as the basis for constructing information regarding urban environments. One important source of information about the land status is imagery collected through remote sensing. Afterwards, using digital image processing techniques, thematic detail can be extracted from those images and used to build urban indicators. Most common metrics are based on area (2D) measurements. These include indicators like impervious area per capita or surface occupied by green areas, having usually as primary source a spectral image obtained through a satellite or airborne camera. More recently, laser scanning data has become available for large-scale applications. Such sensors acquire altimetric information and are used to produce Digital Surface Models (DSM). In this context, LiDAR data available for the city is explored along with demographic information, and a framework to produce volumetric (3D) urban indexes is proposed, and measures like Built Volume per capita, Volumetric Density and Volumetric Homogeneity are computed.

Small incision lenticule extraction (SMILE) versus laser in-situ keratomileusis (LASIK): study protocol for a randomized, non-inferiority trial

PubMed Central

2012-01-01

Background Small incision lenticule extraction or SMILE is a novel form of ‘flapless’ corneal refractive surgery that was adapted from refractive lenticule extraction (ReLEx). SMILE uses only one femtosecond laser to complete the refractive surgery, potentially reducing surgical time, side effects, and cost. If successful, SMILE could potentially replace the current, widely practiced laser in-situ keratomileusis or LASIK. The aim of this study is to evaluate whether SMILE is non-inferior to LASIK in terms of refractive outcomes at 3 months post-operatively. Methods/Design Single tertiary center, parallel group, single-masked, paired-eye design, non-inferiority, randomized controlled trial. Participants who are eligible for LASIK will be enrolled for study after informed consent. Each participant will be randomized to receive SMILE and LASIK in each eye. Our primary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> −3.00 diopter (D)) at a tertiary eye center in terms of refractive predictability at 3 months post-operatively. Our secondary hypothesis (stated as null) in this non-inferiority trial would be that SMILE differs from LASIK in adults (>21 years old) with myopia (> −3.00 D) at a tertiary eye center in terms of other refractive outcomes (efficacy, safety, higher-order aberrations) at 3 months post-operatively. Our primary outcome is refractive predictability, which is one of several standard refractive outcomes, defined as the proportion of eyes achieving a postoperative spherical equivalent (SE) within ±0.50 D of the intended target. Randomization will be performed using random allocation sequence generated by a computer with no blocks or restrictions, and implemented by concealing the number-coded surgery within sealed envelopes until just before the procedure. In this single-masked trial, subjects and their caregivers will be masked to the assigned treatment in each eye. Discussion This novel trial will provide information on whether SMILE has comparable, if not superior, refractive outcomes compared to the established LASIK for myopia, thus providing evidence for translation into clinical practice. Trial registration Clinicaltrials.gov NCT01216475. PMID:22647480

Classification of CT brain images based on deep learning networks.

PubMed

Gao, Xiaohong W; Hui, Rui; Tian, Zengmin

2017-01-01

While computerised tomography (CT) may have been the first imaging tool to study human brain, it has not yet been implemented into clinical decision making process for diagnosis of Alzheimer's disease (AD). On the other hand, with the nature of being prevalent, inexpensive and non-invasive, CT does present diagnostic features of AD to a great extent. This study explores the significance and impact on the application of the burgeoning deep learning techniques to the task of classification of CT brain images, in particular utilising convolutional neural network (CNN), aiming at providing supplementary information for the early diagnosis of Alzheimer's disease. Towards this end, three categories of CT images (N = 285) are clustered into three groups, which are AD, lesion (e.g. tumour) and normal ageing. In addition, considering the characteristics of this collection with larger thickness along the direction of depth (z) (~3-5 mm), an advanced CNN architecture is established integrating both 2D and 3D CNN networks. The fusion of the two CNN networks is subsequently coordinated based on the average of Softmax scores obtained from both networks consolidating 2D images along spatial axial directions and 3D segmented blocks respectively. As a result, the classification accuracy rates rendered by this elaborated CNN architecture are 85.2%, 80% and 95.3% for classes of AD, lesion and normal respectively with an average of 87.6%. Additionally, this improved CNN network appears to outperform the others when in comparison with 2D version only of CNN network as well as a number of state of the art hand-crafted approaches. As a result, these approaches deliver accuracy rates in percentage of 86.3, 85.6 ± 1.10, 86.3 ± 1.04, 85.2 ± 1.60, 83.1 ± 0.35 for 2D CNN, 2D SIFT, 2D KAZE, 3D SIFT and 3D KAZE respectively. The two major contributions of the paper constitute a new 3-D approach while applying deep learning technique to extract signature information rooted in both 2D slices and 3D blocks of CT images and an elaborated hand-crated approach of 3D KAZE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Feature extraction from high resolution satellite imagery as an input to the development and rapid update of a METRANS geographic information system (GIS).

DOT National Transportation Integrated Search

2011-06-01

This report describes an accuracy assessment of extracted features derived from three : subsets of Quickbird pan-sharpened high resolution satellite image for the area of the : Port of Los Angeles, CA. Visual Learning Systems Feature Analyst and D...

Outcomes of small incision lenticule extraction (SMILE) in low myopia.

PubMed

Reinstein, Dan Z; Carp, Glenn I; Archer, Timothy J; Gobbe, Marine

2014-12-01

To report the visual and refractive outcomes of small incision lenticule extraction for low myopia using the VisuMax femtosecond laser (Carl Zeiss Meditec, Jena, Germany). A retrospective analysis of 120 consecutive small incision lenticule extraction procedures was performed for low myopia. Inclusion criteria were preoperative spherical equivalent refraction up to -3.50 diopters (D), cylinder up to 1.50 D, and corrected distance visual acuity of 20/20 or better. Outcomes analysis was performed for all eyes with 1-year follow-up according to the Standard Graphs for Reporting Refractive Surgery, and also including mesopic contrast sensitivity. One-year data were available for 110 eyes (92%). Preoperatively, mean spherical equivalent refraction was -2.61 ± 0.54 D (range: -1.03 to -3.50 D) and mean cylinder was 0.55 ± 0.38 D (range: 0.00 to 1.50 D). Postoperatively, mean spherical equivalent refraction was -0.05 ± 0.36 D (range: -0.94 to +1.25 D) and mean cylinder was ± 0.50 D in 84% and ± 1.00 D in 99% of eyes. Uncorrected distance visual acuity was 20/20 or better in 96% of eyes and 20/25 or better in 100% of eyes. One line of corrected distance visual acuity was lost in 9%, but no eyes lost two or more lines. There was an initial overcorrection in mean spherical equivalent refraction on day 1 (+0.37 D) as expected, which regressed to +0.10 D at 1 month and -0.05 D at 3 months, after which stability was reached (mean spherical equivalent refraction was -0.05 D at 1 year). Contrast sensitivity at 1 year was slightly increased at 3, 6, 12, and 18 cycles per degree (P < .05). Small incision lenticule extraction for low myopia was found to be safe and effective with outcomes similar to those previously reported for LASIK. Copyright 2014, SLACK Incorporated.

Almost but not quite 2D, Non-linear Bayesian Inversion of CSEM Data

NASA Astrophysics Data System (ADS)

Ray, A.; Key, K.; Bodin, T.

2013-12-01

The geophysical inverse problem can be elegantly stated in a Bayesian framework where a probability distribution can be viewed as a statement of information regarding a random variable. After all, the goal of geophysical inversion is to provide information on the random variables of interest - physical properties of the earth's subsurface. However, though it may be simple to postulate, a practical difficulty of fully non-linear Bayesian inversion is the computer time required to adequately sample the model space and extract the information we seek. As a consequence, in geophysical problems where evaluation of a full 2D/3D forward model is computationally expensive, such as marine controlled source electromagnetic (CSEM) mapping of the resistivity of seafloor oil and gas reservoirs, Bayesian studies have largely been conducted with 1D forward models. While the 1D approximation is indeed appropriate for exploration targets with planar geometry and geological stratification, it only provides a limited, site-specific idea of uncertainty in resistivity with depth. In this work, we extend our fully non-linear 1D Bayesian inversion to a 2D model framework, without requiring the usual regularization of model resistivities in the horizontal or vertical directions used to stabilize quasi-2D inversions. In our approach, we use the reversible jump Markov-chain Monte-Carlo (RJ-MCMC) or trans-dimensional method and parameterize the subsurface in a 2D plane with Voronoi cells. The method is trans-dimensional in that the number of cells required to parameterize the subsurface is variable, and the cells dynamically move around and multiply or combine as demanded by the data being inverted. This approach allows us to expand our uncertainty analysis of resistivity at depth to more than a single site location, allowing for interactions between model resistivities at different horizontal locations along a traverse over an exploration target. While the model is parameterized in 2D, we efficiently evaluate the forward response using 1D profiles extracted from the model at the common-midpoints of the EM source-receiver pairs. Since the 1D approximation is locally valid at different midpoint locations, the computation time is far lower than is required by a full 2D or 3D simulation. We have applied this method to both synthetic and real CSEM survey data from the Scarborough gas field on the Northwest shelf of Australia, resulting in a spatially variable quantification of resistivity and its uncertainty in 2D. This Bayesian approach results in a large database of 2D models that comprise a posterior probability distribution, which we can subset to test various hypotheses about the range of model structures compatible with the data. For example, we can subset the model distributions to examine the hypothesis that a resistive reservoir extends overs a certain spatial extent. Depending on how this conditions other parts of the model space, light can be shed on the geological viability of the hypothesis. Since tackling spatially variable uncertainty and trade-offs in 2D and 3D is a challenging research problem, the insights gained from this work may prove valuable for subsequent full 2D and 3D Bayesian inversions.

Identification and determination of fat-soluble vitamins and metabolites in human serum by liquid chromatography/triple quadrupole mass spectrometry with multiple reaction monitoring.

PubMed

Priego Capote, Feliciano; Jiménez, José Ruiz; Granados, José María Mata; de Castro, María Dolores Luque

2007-01-01

A method for determination of fat-soluble vitamins K(1), K(3), A, D(2), D(3) and E (as alpha- and delta-tocopherol) and metabolites 25-hydroxyvitamin D(2) and D(3) and 1,25-dihydroxyvitamin D(3) in human serum by liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in positive mode is proposed. Highly selective identification of the target compounds in serum was confirmed by the most representative transitions from precursor ion to product ion. Quantitative MS/MS analysis was carried out by multiple reaction monitoring optimizing the most sensitive transition for each analyte in order to achieve low detection limits (from 0.012 to 0.3 ng/mL estimated with serum). The analysis was performed with 1 mL of serum, which was subjected to protein precipitation, liquid-liquid extraction to an organic phase, evaporation to dryness and reconstitution with methanol. The precision of the overall method ranged from 3.17-6.76% as intra-day variability and from 5.07-11.53% as inter-day variability. The method, validated by the standard addition method, provides complete information on the fat-soluble vitamins profile, which is of interest in clinical and metabolomics studies.

Three-dimensional intraoperative ultrasound of vascular malformations and supratentorial tumors.

PubMed

Woydt, Michael; Horowski, Anja; Krauss, Juergen; Krone, Andreas; Soerensen, Niels; Roosen, Klaus

2002-01-01

The benefits and limits of a magnetic sensor-based 3-dimensional (3D) intraoperative ultrasound technique during surgery of vascular malformations and supratentorial tumors were evaluated. Twenty patients with 11 vascular malformations and 9 supratentorial tumors undergoing microsurgical resection or clipping were investigated with an interactive magnetic sensor data acquisition system allowing freehand scanning. An ultrasound probe with a mounted sensor was used after craniotomies to localize lesions, outline tumors or malformation margins, and identify supplying vessels. A 3D data set was obtained allowing reformation of multiple slices in all 3 planes and comparison to 2-dimensional (2D) intraoperative ultrasound images. Off-line gray-scale segmentation analysis allowed differentiation between tissue with different echogenicities. Color-coded information about blood flow was extracted from the images with a reconstruction algorithm. This allowed photorealistic surface displays of perfused tissue, tumor, and surrounding vessels. Three-dimensional intraoperative ultrasound data acquisition was obtained within 5 minutes. Off-line analysis and reconstruction time depends on the type of imaging display and can take up to 30 minutes. The spatial relation between aneurysm sac and surrounding vessels or the skull base could be enhanced in 3 out of 6 aneurysms with 3D intraoperative ultrasound. Perforating arteries were visible in 3 cases only by using 3D imaging. 3D ultrasound provides a promising imaging technique, offering the neurosurgeon an intraoperative spatial orientation of the lesion and its vascular relationships. Thereby, it may improve safety of surgery and understanding of 2D ultrasound images.

[Chemical constituents of Swertia angustifolia].

PubMed

He, Kang; Cao, Tuan-wu; Wang, Hong-ling; Geng, Chang-an; Zhang, Xue-mei; Chen, Ji-jun

2015-09-01

This present work is to study the chemical constituents of Swertia angustifolia. The whole plants of air-dried Swertia angustifolia was extracted with 90% EtOH. The water extract was suspended in H2O and extracted with petroleum ether, EtOAc and nBuOH, successively. The compounds were isolated and purified by column chromatography from the EtOAc fraction, and identified based on spectral analyses (MS, 1H-NMR, 13C-NMR). Fourteen compounds were isolated and characterized as 1, 8-dihydroxy-3, 7-dimethoxyxanthone (1), 1, 8-dihydroxy-3, 5, 7-trimethoxyxanthone (2), 7-hydroxy-3, 8-dimethoxyxanthone-1-O-β-D-glucopyranoside (3), 8-0-[β-D-xylopyranosyl-(1-6) -β-D-glucopyranosyl] -1, 7-dihydroxy-3-methoxyxanthone (4), (+) -syringaresinol (5), ferulic acid (6), trans-coniferyl aldehyde (7), sinapaldehyde (8), trans-coniferyl alcohol (9), 3, 4-dihydroxybenzoic acid (10), 2-hydroxybenzoic acid (11), isophthalic acid (12), 2-furoic acid (13), and 2-methyl-4(3H)-quinazolinone(14). Compounds 2-14 were obtained from this plant for the first time.

Registration of in vivo MR to histology of rodent brains using blockface imaging

NASA Astrophysics Data System (ADS)

Uberti, Mariano; Liu, Yutong; Dou, Huanyu; Mosley, R. Lee; Gendelman, Howard E.; Boska, Michael

2009-02-01

Registration of MRI to histopathological sections can enhance bioimaging validation for use in pathobiologic, diagnostic, and therapeutic evaluations. However, commonly used registration methods fall short of this goal due to tissue shrinkage and tearing after brain extraction and preparation. In attempts to overcome these limitations we developed a software toolbox using 3D blockface imaging as the common space of reference. This toolbox includes a semi-automatic brain extraction technique using constraint level sets (CLS), 3D reconstruction methods for the blockface and MR volume, and a 2D warping technique using thin-plate splines with landmark optimization. Using this toolbox, the rodent brain volume is first extracted from the whole head MRI using CLS. The blockface volume is reconstructed followed by 3D brain MRI registration to the blockface volume to correct the global deformations due to brain extraction and fixation. Finally, registered MRI and histological slices are warped to corresponding blockface images to correct slice specific deformations. The CLS brain extraction technique was validated by comparing manual results showing 94% overlap. The image warping technique was validated by calculating target registration error (TRE). Results showed a registration accuracy of a TRE < 1 pixel. Lastly, the registration method and the software tools developed were used to validate cell migration in murine human immunodeficiency virus type one encephalitis.

Depigmented-polymerised allergoids favour regulatory over effector T cells: enhancement by 1α, 25-dihydroxyvitamin D3.

PubMed

Urry, Zoe L; Richards, David F; Black, Cheryl; Morales, Maria; Carnés, Jerónimo; Hawrylowicz, Catherine M; Robinson, Douglas S

2014-05-29

Allergen immunotherapy (SIT) is the only treatment for allergic disease capable of modifying disease long term. To reduce the risk of anaphylaxis from SIT, allergen-extracts have been modified by polymerisation with glutaraldehyde to reduce IgE binding. It is suggested that these allergoid extracts also have reduced T cell activity, which could compromise clinical efficacy. Effective SIT is thought to act through regulatory T cells (Tregs) rather than activation of effector T cells. There is no published data on the activity of modified extracts on Tregs. We compared the capacity of modified (depigmented-polymerised) versus unmodified (native) allergen extracts of grass pollen and house dust mite to stimulate proliferation/cytokine production and to modulate Treg/effector T cell frequency in cultures of peripheral blood mononuclear cells (PBMC), from volunteers sensitised to both allergens in vitro. Depigmented-polymerised allergen extracts stimulated less proliferation of PBMC, and reduced effector cell numbers after 7 days in culture than did native extracts. However, the frequency of Foxp3+ Tregs in cultures were similar to those seen with native extract so that ratios of regulatory to effector T cells were significantly increased in cultures stimulated with depigmented-polymerised extracts. Addition of 1α, 25-dihydroxyvitamin D3 further favoured Treg, and reduced effector cytokine production, but not interleukin-10. Depigmented-polymerised allergen extracts appear to favour Treg expansion over activation of effector T cells and this may relate to their demonstrated efficacy and safety in SIT. 1α, 25-dihydroxyvitamin D3 further reduces effector T cell activation by allergen extracts and may be a useful adjuvant for SIT.

Depigmented-polymerised allergoids favour regulatory over effector T cells: enhancement by 1α, 25-dihydroxyvitamin D3

PubMed Central

2014-01-01

Background Allergen immunotherapy (SIT) is the only treatment for allergic disease capable of modifying disease long term. To reduce the risk of anaphylaxis from SIT, allergen-extracts have been modified by polymerisation with glutaraldehyde to reduce IgE binding. It is suggested that these allergoid extracts also have reduced T cell activity, which could compromise clinical efficacy. Effective SIT is thought to act through regulatory T cells (Tregs) rather than activation of effector T cells. There is no published data on the activity of modified extracts on Tregs. Results We compared the capacity of modified (depigmented-polymerised) versus unmodified (native) allergen extracts of grass pollen and house dust mite to stimulate proliferation/cytokine production and to modulate Treg/effector T cell frequency in cultures of peripheral blood mononuclear cells (PBMC), from volunteers sensitised to both allergens in vitro. Depigmented-polymerised allergen extracts stimulated less proliferation of PBMC, and reduced effector cell numbers after 7 days in culture than did native extracts. However, the frequency of Foxp3+ Tregs in cultures were similar to those seen with native extract so that ratios of regulatory to effector T cells were significantly increased in cultures stimulated with depigmented-polymerised extracts. Addition of 1α, 25-dihydroxyvitamin D3 further favoured Treg, and reduced effector cytokine production, but not interleukin-10. Conclusions Depigmented-polymerised allergen extracts appear to favour Treg expansion over activation of effector T cells and this may relate to their demonstrated efficacy and safety in SIT. 1α, 25-dihydroxyvitamin D3 further reduces effector T cell activation by allergen extracts and may be a useful adjuvant for SIT. PMID:24884430

Dispersive solid-phase extraction based on magnetic dummy molecularly imprinted microspheres for selective screening of phthalates in plastic bottled beverages.

PubMed

Qiao, Jindong; Wang, Mingyu; Yan, Hongyuan; Yang, Gengliang

2014-04-02

A new magnetic dummy molecularly imprinted dispersive solid-phase extraction (MAG-MIM-dSPE) coupled with gas chromatography-FID was developed for selective determination of phthalates in plastic bottled beverages. The new magnetic dummy molecularly imprinted microspheres (MAG-MIM) using diisononyl phthalate as a template mimic were synthesized by coprecipitation coupled with aqueous suspension polymerization and were successfully applied as the adsorbents for MAG-MIM-dSPE to extract and isolate five phthalates from plastic bottled beverages. Validation experiments showed that the MAG-MIM-dSPE method had good linearity at 0.0040-0.40 μg/mL (0.9991-0.9998), good precision (3.1-6.9%), and high recovery (89.5-101.3%), and limits of detection were obtained in a range of 0.53-1.2 μg/L. The presented MAG-MIM-dSPE method combines the quick separation of magnetic particles, special selectivity of MIM, and high extraction efficiency of dSPE, which could potentially be applied to selective screening of phthalates in beverage products.

Geopositioning with a quadcopter: Extracted feature locations and predicted accuracy without a priori sensor attitude information

NASA Astrophysics Data System (ADS)

Dolloff, John; Hottel, Bryant; Edwards, David; Theiss, Henry; Braun, Aaron

2017-05-01

This paper presents an overview of the Full Motion Video-Geopositioning Test Bed (FMV-GTB) developed to investigate algorithm performance and issues related to the registration of motion imagery and subsequent extraction of feature locations along with predicted accuracy. A case study is included corresponding to a video taken from a quadcopter. Registration of the corresponding video frames is performed without the benefit of a priori sensor attitude (pointing) information. In particular, tie points are automatically measured between adjacent frames using standard optical flow matching techniques from computer vision, an a priori estimate of sensor attitude is then computed based on supplied GPS sensor positions contained in the video metadata and a photogrammetric/search-based structure from motion algorithm, and then a Weighted Least Squares adjustment of all a priori metadata across the frames is performed. Extraction of absolute 3D feature locations, including their predicted accuracy based on the principles of rigorous error propagation, is then performed using a subset of the registered frames. Results are compared to known locations (check points) over a test site. Throughout this entire process, no external control information (e.g. surveyed points) is used other than for evaluation of solution errors and corresponding accuracy.

Aviation obstacle auto-extraction using remote sensing information

NASA Astrophysics Data System (ADS)

Zimmer, N.; Lugsch, W.; Ravenscroft, D.; Schiefele, J.

2008-10-01

An Obstacle, in the aviation context, may be any natural, man-made, fixed or movable object, permanent or temporary. Currently, the most common way to detect relevant aviation obstacles from an aircraft or helicopter for navigation purposes and collision avoidance is the use of merged infrared and synthetic information of obstacle data. Several algorithms have been established to utilize synthetic and infrared images to generate obstacle information. There might be a situation however where the system is error-prone and may not be able to consistently determine the current environment. This situation can be avoided when the system knows the true position of the obstacle. The quality characteristics of the obstacle data strongly depends on the quality of the source data such as maps and official publications. In some countries such as newly industrializing and developing countries, quality and quantity of obstacle information is not available. The aviation world has two specifications - RTCA DO-276A and ICAO ANNEX 15 Ch. 10 - which describe the requirements for aviation obstacles. It is essential to meet these requirements to be compliant with the specifications and to support systems based on these specifications, e.g. 3D obstacle warning systems where accurate coordinates based on WGS-84 is a necessity. Existing aerial and satellite or soon to exist high quality remote sensing data makes it feasible to think about automated aviation obstacle data origination. This paper will describe the feasibility to auto-extract aviation obstacles from remote sensing data considering limitations of image and extraction technologies. Quality parameters and possible resolution of auto-extracted obstacle data will be discussed and presented.

Toward Enhancing Solar Cell Performance: An Effective and "Green" Additive.

PubMed

Tan, Long; Li, Pandeng; Zhang, Qingzhe; Izquierdo, Ricardo; Chaker, Mohamed; Ma, Dongling

2018-02-21

Performance of bulk heterojunction polymer solar cells (PSCs) highly relies on the morphology of the photoactive layer involving conjugated polymers and fullerene derivatives as donors and acceptors, respectively. Herein, butylamine was found to be able to optimize the morphology of the donor/acceptor (D/A) film composed of a blend of poly(3-hexylthiophene-2,5-diyl) (P3HT) and phenyl-C 61 -butyric acid methyl ester (PCBM). Compared to the commonly used alkane dithiols and halogenated additives with high boiling points, butylamine has a much lower boiling point between 77 and 79 °C, and it is also much "greener". A specific interaction between butylamine and PCBM was demonstrated to account for the morphology improvement. Essentially, butylamine can selectively dissolve PCBM in the P3HT:PCBM blend and facilitate the diffusion of PCBM in the film fabrication processes. Atomic force microscopy and X-ray photoelectron spectroscopy investigations confirmed the formation of the P3HT-enriched top surface and the abundance of PCBM at the bottom side, i.e., the formation of vertical phase segregation, as a consequence of the specific PCBM-butylamine interaction. The D/A film with inhomogeneously distributed D and A components in the vertical film direction, with more P3HT at the hole extraction side and more PCBM at the electron extraction side, enables more efficient charge extraction in the D/A film, reflected by the largely enhanced fill factor. The power conversion efficiency of devices reached 4.03 and 4.61%, respectively, depending on the thickness of the D/A film, and these are among the best values reported for P3HT:PCBM-based devices. As compared to the devices fabricated without the introduction of butylamine under otherwise the same processing conditions, they represented 19.6 and 21.6% improvement in the efficiency, respectively. The discovery of butylamine as a new, effective additive in enhancing the performance of PSCs strongly suggests that the differential affinity of additives toward donors and acceptors likely plays a more important role in morphology optimization than their boiling point, different from what was reported previously. The finding provides useful information for realizing large-area PSC fabrication, where a "greener" additive is always preferred.

Correction of a liquid lens for 3D imaging systems

NASA Astrophysics Data System (ADS)

Bower, Andrew J.; Bunch, Robert M.; Leisher, Paul O.; Li, Weixu; Christopher, Lauren A.

2012-06-01

3D imaging systems are currently being developed using liquid lens technology for use in medical devices as well as in consumer electronics. Liquid lenses operate on the principle of electrowetting to control the curvature of a buried surface, allowing for a voltage-controlled change in focal length. Imaging systems which utilize a liquid lens allow extraction of depth information from the object field through a controlled introduction of defocus into the system. The design of such a system must be carefully considered in order to simultaneously deliver good image quality and meet the depth of field requirements for image processing. In this work a corrective model has been designed for use with the Varioptic Arctic 316 liquid lens. The design is able to be optimized for depth of field while minimizing aberrations for a 3D imaging application. The modeled performance is compared to the measured performance of the corrected system over a large range of focal lengths.

High-resolution extraction of particle size via Fourier Ptychography

NASA Astrophysics Data System (ADS)

Li, Shengfu; Zhao, Yu; Chen, Guanghua; Luo, Zhenxiong; Ye, Yan

2017-11-01

This paper proposes a method which can extract the particle size information with a resolution beyond λ/NA. This is achieved by applying Fourier Ptychographic (FP) ideas to the present problem. In a typical FP imaging platform, a 2D LED array is used as light sources for angle-varied illuminations, a series of low-resolution images was taken by a full sequential scan of the array of LEDs. Here, we demonstrate the particle size information is extracted by turning on each single LED on a circle. The simulated results show that the proposed method can reduce the total number of images, without loss of reliability in the results.

Fabrication of Al2O3 coated 2D TiO2 nanoparticle photonic crystal layers by reverse nano-imprint lithography and plasma enhanced atomic layer deposition.

PubMed

Kim, Ki-Kang; Ko, Ki-Young; Ahn, Jinho

2013-10-01

This paper reports simple process to enhance the extraction efficiency of photoluminescence (PL) from Eu-doped yttrium oxide (Y2O3:Eu3+) thin-film phosphor (TFP). Two-dimensional (2D) photonic crystal layer (PCL) was fabricated on Y2O3:Eu3+ phosphor films by reverse nano-imprint method using TiO2 nanoparticle solution as a nano-imprint resin and a 2D hole-patterned PDMS stamp. Atomic scale controlled Al2O3 deposition was performed onto this 2D nanoparticle PCL for the optimization of the photonic crystal pattern size and stabilization of TiO2 nanoparticle column structure. As a result, the light extraction efficiency of the Y2O3:Eu3+ phosphor film was improved by 2.0 times compared to the conventional Y2O3:Eu3+ phosphor film.

A 3D particle visualization system for temperature management

NASA Astrophysics Data System (ADS)

Lange, B.; Rodriguez, N.; Puech, W.; Rey, H.; Vasques, X.

2011-01-01

This paper deals with a 3D visualization technique proposed to analyze and manage energy efficiency from a data center. Data are extracted from sensors located in the IBM Green Data Center in Montpellier France. These sensors measure different information such as hygrometry, pressure and temperature. We want to visualize in real-time the large among of data produced by these sensors. A visualization engine has been designed, based on particles system and a client server paradigm. In order to solve performance problems, a Level Of Detail solution has been developed. These methods are based on the earlier work introduced by J. Clark in 1976. In this paper we introduce a particle method used for this work and subsequently we explain different simplification methods applied to improve our solution.

Quantum Chemical Simulation of the Interaction of Functional Groups in Polyurethanes with 3 d-Metal Ions During Their Extraction from Aqueous Solutions

NASA Astrophysics Data System (ADS)

Ksenofontov, M. A.; Bobkova, E. Yu.; Shundalau, M. B.; Ostrovskaya, L. E.; Vasil'eva, V. S.

2017-11-01

The interaction of the functional groups in the polyurethane foam adsorbent Penopurm® with the cations of some 3d-metals upon their extraction from aqueous solutions has been studied by atomic emission spectroscopy, UV/Vis and vibrational IR spectroscopy, and quantum chemical simulation using density functional theory. Penopurm® absorbs 3d-metal cations from aqueous solutions in the pH range 5-7. Some spectral criteria have been found indicating a predominant interaction of Ni2+ ions with various fragments of the polyurethane foam structure.

Observation of the immune response of cells and tissue through multimodal label-free microscopy

NASA Astrophysics Data System (ADS)

Pavillon, Nicolas; Smith, Nicholas I.

2017-02-01

We present applications of a label-free approach to assess the immune response based on the combination of interferometric microscopy and Raman spectroscopy, which makes it possible to simultaneously acquire morphological and molecular information of live cells. We employ this approach to derive statistical models for predicting the activation state of macrophage cells based both on morphological parameters extracted from the high-throughput full-field quantitative phase imaging, and on the molecular content information acquired through Raman spectroscopy. We also employ a system for 3D imaging based on coherence gating, enabling specific targeting of the Raman channel to structures of interest within tissue.

New 3D-printed sorbent for extraction of steroids from human plasma preceding LC-MS analysis.

PubMed

Konieczna, Lucyna; Belka, Mariusz; Okońska, Magdalena; Pyszka, Magdalena; Bączek, Tomasz

2018-04-13

In recent years, there has been an increasing worldwide interest in the use of alternative sample preparation methods that are proceeded by separation techniques. Fused deposition modeling (FDM) is a 3D printing technique that is based the consecutive layering of softened/melted thermoplastic materials. In this study, a group of natural steroids and sexual hormones - namely, aldosterone, cortisol, β-estradiol, testosterone, dihydrotestosterone, and synthetic methyltestosterone and betamethasone - were separated and determined using an optimized high-performance liquid chromatography coupled to mass spectrometry (LC-MS) method in positive ionization mode. 3D-printed sorbents were selected as the pre-concentration technique because they are generally low cost, fast, and simple to make and automate. Furthermore, the use of 3D-printed sorbents helps to minimize potential errors due to their repeatability and reproducibility, and their ability to eliminate carry over by using one printed sorbent for a single extraction of steroids from biological matrices. The extraction procedure was optimized and the parameters influencing 3D-printed Layfomm 60 ® based sorbent and LC-MS were studied, including the type of extraction solvent used, sorption and desorption times, temperature, and the salting-out effect. To demonstrate this method's applicability for biological sample analysis, the SPME-LC-MS method was validated for its ability to simultaneously quantify endogenous steroids. This evaluation confirmed good linearity and an R 2 that was between 0.9970 and 0.9990. The recovery rates for human plasma samples were 86.34-93.6% for the studied steroids with intra- and inter-day RSDs of 1.44-7.42% and 1.44-9.46%, respectively. To our knowledge, this study is the first time that 3D-printed sorbents have been used to extract trace amounts of endogenous low-molecular-weight compounds, such as steroids, from biological samples, such as plasma. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrated metabolomic analysis of the nano-sized copper particle-induced hepatotoxicity and nephrotoxicity in rats: A rapid invivo screening method for nanotoxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lei Ronghui; Department of Public Health, Xi'an Jiaotong University, Xi'an 710061; Wu Chunqi

2008-10-15

Despite an increasing application of copper nanoparticles, there is a serious lack of information concerning their impact on human health and the environment. In this study, the biochemical compositions of urine, serum, and extracts of liver and kidney tissues of rats treated with nano-copper at the different doses (50, 100, and 200 mg/kg/d for 5 d) were investigated using {sup 1}H NMR techniques with the pattern recognition methods. Serum biochemical analysis and histopathological examinations of the liver and kidney of all the rats were simultaneously performed. All the results indicated that the effects produced by nano-copper at a dose ofmore » 100 or 50 mg/kg/d were less than those induced at a higher dose of 200 mg/kg/d. Nano-copper induced overt hepatotoxicity and nephrotoxicity at 200 mg/kg/d for 5 d, which mainly involved scattered dot hepatocytic necrosis and widespread renal proximal tubule necrosis. Increased citrate, succinate, trimethylamine-N-oxide, glucose, and amino acids, accompanied by decreased creatinine levels were observed in the urine; furthermore, elevated levels of lactate, 3-hydroxybutyrate, acetate, creatine, triglycerides, and phosphatide and reduced glucose levels were observed in the serum. The predominant changes identified in the liver tissue aqueous extracts included increased lactate and creatine levels together with reduced glutamine and taurine levels, and the metabolic profile of the kidney tissue aqueous extracts showed an increase in lactate and a drop in glucose. In the chloroform/methanol extracts of the liver and kidney tissues, elevated triglyceride species were identified. These changes suggested that mitochondrial failure, enhanced ketogenesis, fatty acid {beta}-oxidation, and glycolysis contributed to the hepatotoxicity and nephrotoxicity induced by nano-copper at 200 mg/kg/d for 5 d. An increase in triglycerides in the serum, liver and kidney tissues could serve as a potential sensitive biomarker reflecting the lipidosis induced by nano-copper. The data generated from the current study completely supports the fact that an integrated metabolomic approach is promising for the development of a rapid invivo screening method for nanotoxicity.« less

Development of a Novel Motor Imagery Control Technique and Application in a Gaming Environment

PubMed Central

Xue, Tao

2017-01-01

We present a methodology for a hybrid brain-computer interface (BCI) system, with the recognition of motor imagery (MI) based on EEG and blink EOG signals. We tested the BCI system in a 3D Tetris and an analogous 2D game playing environment. To enhance player's BCI control ability, the study focused on feature extraction from EEG and control strategy supporting Game-BCI system operation. We compared the numerical differences between spatial features extracted with common spatial pattern (CSP) and the proposed multifeature extraction. To demonstrate the effectiveness of 3D game environment at enhancing player's event-related desynchronization (ERD) and event-related synchronization (ERS) production ability, we set the 2D Screen Game as the comparison experiment. According to a series of statistical results, the group performing MI in the 3D Tetris environment showed more significant improvements in generating MI-associated ERD/ERS. Analysis results of game-score indicated that the players' scores presented an obvious uptrend in 3D Tetris environment but did not show an obvious downward trend in 2D Screen Game. It suggested that the immersive and rich-control environment for MI would improve the associated mental imagery and enhance MI-based BCI skills. PMID:28572817

Automatic cell identification and visualization using digital holographic microscopy with head mounted augmented reality devices.

PubMed

O'Connor, Timothy; Rawat, Siddharth; Markman, Adam; Javidi, Bahram

2018-03-01

We propose a compact imaging system that integrates an augmented reality head mounted device with digital holographic microscopy for automated cell identification and visualization. A shearing interferometer is used to produce holograms of biological cells, which are recorded using customized smart glasses containing an external camera. After image acquisition, segmentation is performed to isolate regions of interest containing biological cells in the field-of-view, followed by digital reconstruction of the cells, which is used to generate a three-dimensional (3D) pseudocolor optical path length profile. Morphological features are extracted from the cell's optical path length map, including mean optical path length, coefficient of variation, optical volume, projected area, projected area to optical volume ratio, cell skewness, and cell kurtosis. Classification is performed using the random forest classifier, support vector machines, and K-nearest neighbor, and the results are compared. Finally, the augmented reality device displays the cell's pseudocolor 3D rendering of its optical path length profile, extracted features, and the identified cell's type or class. The proposed system could allow a healthcare worker to quickly visualize cells using augmented reality smart glasses and extract the relevant information for rapid diagnosis. To the best of our knowledge, this is the first report on the integration of digital holographic microscopy with augmented reality devices for automated cell identification and visualization.

Synthesis of Two-Dimensional Materials by Selective Extraction

DOE PAGES

Naguib, Michael; Gogotsi, Yury

2014-12-09

Two-dimensional (2D) materials have attracted much attention in the past decade. They offer high specific surface area, as well as electronic structure and properties that differ from their bulk counterparts due to the low dimensionality. Graphene is the best known and the most studied 2D material, but metal oxides and hydroxides (including clays), dichalcogenides, boron nitride (BN), and other materials that are one or several atoms thick are receiving increasing attention. They may deliver a combination of properties that cannot be provided by other materials. The most common synthesis approach in general is by reacting different elements or compounds tomore » form a new compound. However, this approach does not necessarily work well for low-dimensional structures, since it favors formation of energetically preferred 3D (bulk) solids. Many 2D materials are produced by exfoliation of van der Waals solids, such as graphite or MoS2, breaking large particles into 2D layers. However, these approaches are not universal; for example, 2D transition metal carbides cannot be produced by any of them. An alternative but less studied way of material synthesis is the selective extraction process, which is based on the difference in reactivity and stability between the different components (elements or structural units) of the original material. It can be achieved using thermal, chemical, or electrochemical processes. Many 2D materials have been synthesized using selective extraction, such as graphene from SiC, transition metal oxides (TMO) from layered 3D salts, and transition metal carbides or carbonitrides (MXenes) from MAX phases. Selective extraction synthesis is critically important when the bonds between the building blocks of the material are too strong (e.g., in carbides) to be broken mechanically in order to form nanostructures. Unlike extractive metallurgy, where the extracted metal is the goal of the process, selective extraction of one or more elements from the precursor materials releases 2D structures. In this Account, in addition to graphene and TMO, we focused on MXenes as an example for the use of selective extraction synthesis to produce novel 2D materials. About 10 new carbides and carbonitrides of transition metals have been produced by this method in the past 3 years. They offer an unusual combination of metallic conductivity and hydrophilicity and show very attractive electrochemical properties. We hope that this Account will encourage researchers to extend the use of selective extraction to other layered material systems that in turn will result in expanding the world of nanomaterials in general and 2D materials in particular, generating new materials that cannot be produced by other means.« less

Synthesis of two-dimensional materials by selective extraction.

PubMed

Naguib, Michael; Gogotsi, Yury

2015-01-20

CONSPECTUS: Two-dimensional (2D) materials have attracted much attention in the past decade. They offer high specific surface area, as well as electronic structure and properties that differ from their bulk counterparts due to the low dimensionality. Graphene is the best known and the most studied 2D material, but metal oxides and hydroxides (including clays), dichalcogenides, boron nitride (BN), and other materials that are one or several atoms thick are receiving increasing attention. They may deliver a combination of properties that cannot be provided by other materials. The most common synthesis approach in general is by reacting different elements or compounds to form a new compound. However, this approach does not necessarily work well for low-dimensional structures, since it favors formation of energetically preferred 3D (bulk) solids. Many 2D materials are produced by exfoliation of van der Waals solids, such as graphite or MoS2, breaking large particles into 2D layers. However, these approaches are not universal; for example, 2D transition metal carbides cannot be produced by any of them. An alternative but less studied way of material synthesis is the selective extraction process, which is based on the difference in reactivity and stability between the different components (elements or structural units) of the original material. It can be achieved using thermal, chemical, or electrochemical processes. Many 2D materials have been synthesized using selective extraction, such as graphene from SiC, transition metal oxides (TMO) from layered 3D salts, and transition metal carbides or carbonitrides (MXenes) from MAX phases. Selective extraction synthesis is critically important when the bonds between the building blocks of the material are too strong (e.g., in carbides) to be broken mechanically in order to form nanostructures. Unlike extractive metallurgy, where the extracted metal is the goal of the process, selective extraction of one or more elements from the precursor materials releases 2D structures. In this Account, in addition to graphene and TMO, we focused on MXenes as an example for the use of selective extraction synthesis to produce novel 2D materials. About 10 new carbides and carbonitrides of transition metals have been produced by this method in the past 3 years. They offer an unusual combination of metallic conductivity and hydrophilicity and show very attractive electrochemical properties. We hope that this Account will encourage researchers to extend the use of selective extraction to other layered material systems that in turn will result in expanding the world of nanomaterials in general and 2D materials in particular, generating new materials that cannot be produced by other means.

Synthesis of Two-Dimensional Materials by Selective Extraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naguib, Michael; Gogotsi, Yury

Two-dimensional (2D) materials have attracted much attention in the past decade. They offer high specific surface area, as well as electronic structure and properties that differ from their bulk counterparts due to the low dimensionality. Graphene is the best known and the most studied 2D material, but metal oxides and hydroxides (including clays), dichalcogenides, boron nitride (BN), and other materials that are one or several atoms thick are receiving increasing attention. They may deliver a combination of properties that cannot be provided by other materials. The most common synthesis approach in general is by reacting different elements or compounds tomore » form a new compound. However, this approach does not necessarily work well for low-dimensional structures, since it favors formation of energetically preferred 3D (bulk) solids. Many 2D materials are produced by exfoliation of van der Waals solids, such as graphite or MoS2, breaking large particles into 2D layers. However, these approaches are not universal; for example, 2D transition metal carbides cannot be produced by any of them. An alternative but less studied way of material synthesis is the selective extraction process, which is based on the difference in reactivity and stability between the different components (elements or structural units) of the original material. It can be achieved using thermal, chemical, or electrochemical processes. Many 2D materials have been synthesized using selective extraction, such as graphene from SiC, transition metal oxides (TMO) from layered 3D salts, and transition metal carbides or carbonitrides (MXenes) from MAX phases. Selective extraction synthesis is critically important when the bonds between the building blocks of the material are too strong (e.g., in carbides) to be broken mechanically in order to form nanostructures. Unlike extractive metallurgy, where the extracted metal is the goal of the process, selective extraction of one or more elements from the precursor materials releases 2D structures. In this Account, in addition to graphene and TMO, we focused on MXenes as an example for the use of selective extraction synthesis to produce novel 2D materials. About 10 new carbides and carbonitrides of transition metals have been produced by this method in the past 3 years. They offer an unusual combination of metallic conductivity and hydrophilicity and show very attractive electrochemical properties. We hope that this Account will encourage researchers to extend the use of selective extraction to other layered material systems that in turn will result in expanding the world of nanomaterials in general and 2D materials in particular, generating new materials that cannot be produced by other means.« less

Discovering H-bonding rules in crystals with inductive logic programming.

PubMed

Ando, Howard Y; Dehaspe, Luc; Luyten, Walter; Van Craenenbroeck, Elke; Vandecasteele, Henk; Van Meervelt, Luc

2006-01-01

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Chromatographic Evaluation and Characterization of Components of Gentian Root Extract Used as Food Additives.

PubMed

Amakura, Yoshiaki; Yoshimura, Morio; Morimoto, Sara; Yoshida, Takashi; Tada, Atsuko; Ito, Yusai; Yamazaki, Takeshi; Sugimoto, Naoki; Akiyama, Hiroshi

2016-01-01

Gentian root extract is used as a bitter food additive in Japan. We investigated the constituents of this extract to acquire the chemical data needed for standardized specifications. Fourteen known compounds were isolated in addition to a mixture of gentisin and isogentisin: anofinic acid, 2-methoxyanofinic acid, furan-2-carboxylic acid, 5-hydroxymethyl-2-furfural, 2,3-dihydroxybenzoic acid, isovitexin, gentiopicroside, loganic acid, sweroside, vanillic acid, gentisin 7-O-primeveroside, isogentisin 3-O-primeveroside, 6'-O-glucosylgentiopicroside, and swertiajaposide D. Moreover, a new compound, loganic acid 7-(2'-hydroxy-3'-O-β-D-glucopyranosyl)benzoate (1), was also isolated. HPLC was used to analyze gentiopicroside and amarogentin, defined as the main constituents of gentian root extract in the List of Existing Food Additives in Japan.

Semi-automatic registration of 3D orthodontics models from photographs

NASA Astrophysics Data System (ADS)

Destrez, Raphaël.; Treuillet, Sylvie; Lucas, Yves; Albouy-Kissi, Benjamin

2013-03-01

In orthodontics, a common practice used to diagnose and plan the treatment is the dental cast. After digitization by a CT-scan or a laser scanner, the obtained 3D surface models can feed orthodontics numerical tools for computer-aided diagnosis and treatment planning. One of the pre-processing critical steps is the 3D registration of dental arches to obtain the occlusion of these numerical models. For this task, we propose a vision based method to automatically compute the registration based on photos of patient mouth. From a set of matched singular points between two photos and the dental 3D models, the rigid transformation to apply to the mandible to be in contact with the maxillary may be computed by minimizing the reprojection errors. During a precedent study, we established the feasibility of this visual registration approach with a manual selection of singular points. This paper addresses the issue of automatic point detection. Based on a priori knowledge, histogram thresholding and edge detection are used to extract specific points in 2D images. Concurrently, curvatures information detects 3D corresponding points. To improve the quality of the final registration, we also introduce a combined optimization of the projection matrix with the 2D/3D point positions. These new developments are evaluated on real data by considering the reprojection errors and the deviation angles after registration in respect to the manual reference occlusion realized by a specialist.

Availability of heavy metals in minesoils measured by different methods

NASA Astrophysics Data System (ADS)

Lago, Manoel; Arenas, Daniel; Vega, Flora; Andrade, Luisa

2013-04-01

Most of environmental regulations concerning soil pollution commonly include the total heavy metal content as the reference for determining contamination levels. Nevertheless the total content includes all different chemical forms and it rarely gives information on mobility, availability and toxicity (Pueyo et al., 2004). To be able to determine the concentrations of contaminants that cause toxicity it is important to study the available content, the one that can interact with an organism and be incorporated in its structure (Vangronsveld and Cunningham, 1998). There are many techniques that determine the operationally defined as available content in soils. Most of them use a reagent that causes the displacement of the ions by electrostatic attraction (Pueyo et al., 2004). The aim of this work is to compare the agreement among different extractants (Cl2Ca, EDTA, DTPA, bidistilled water (BDW) and low molecular weight organic acids (LMWOA) when Ni and Zn concentrations are measured in the extractions from five mine soils (Touro, Spain). The sequence of soils according to total contents of Ni and Zn is S4>S5>S1>S3>S2 and S4>S1>S5>S2>S3, respectively. In all cases Zn total contents are higher than Ni varying from two times higher (S5) to four times higher (S2). Zn concentration is also higher than Ni in the Cl2Ca extractions but the opposite happens in DTPA extractions. Both metal concentrations in the EDTA, BDW and LMWOA extractions are quite similar in each soil. This first approximation already shows there is no agreement among the different techniques used for determining heavy metal availability in soils. Nevertheless it was found that soils sequence according to Zn and Ni concentrations in all available extractions techniques (with the exception of BDW) is the same. According to the Ni and Zn contents in Cl2Ca, DTPA, EDTA and LMWOA extractions the sequence is S3> S4> S5> S1> S2. The S3 is the soil with the highest content of available Ni and Zn whilst it is the soil with the lowest total Zn content and one of those with the lowest Ni one. Even the sequence obtained from BDW extractions is different (S4> S3> S2> S1> S5) the S3 soil also possess one of the highest amounts of available Ni and Zn. Therefore the information given by the BDW technique is different than the other ones used for determining available contents of Ni and Zn since DTPA, Cl2Ca, EDTA and LMWOA cause the displacement of both ions from soil matrix towards the soil solution. Acknowledgments This research was supported by Project CGL2010-16765 (MICINN-FEDER). F.A. Vega and D. Arenas-Lago acknowledge the Ministry of Science and Innovation and the University of Vigo for the Ramón y Cajal and FPI-MICINN, respectively. References Pueyo, M., López-Sánchez, J.F., Rauret, G. 2004. Analytica Chimica Acta. 504. 217-226. Vangronsveld, J.; Cunningham, S.D. 1998. Metal-Contaminated Soils: In-Situ Inactivation and Phytoremediation. Springer-Verlag, Berlin, Germany.

Modeling of negative ion transport in a plasma source (invited)

NASA Astrophysics Data System (ADS)

Riz, David; Paméla, Jérôme

1998-02-01

A code called NIETZSCHE has been developed to simulate the negative ion transport in a plasma source, from their birth place to the extraction holes. The H-/D- trajectory is calculated by numerically solving the 3D motion equation, while the atomic processes of destruction, of elastic collision with H+/D+ and of charge exchange with H0/D0 are handled at each time step by a Monte Carlo procedure. This code can be used to calculate the extraction probability of a negative ion produced at any location inside the source. Calculations performed with NIETZSCHE have been allowed to explain, either quantitatively or qualitatively, several phenomena observed in negative ion sources, such as the isotopic H-/D- effect, and the influence of the plasma grid bias or of the magnetic filter on the negative ion extraction. The code has also shown that, in the type of sources contemplated for ITER, which operate at large arc power densities (>1 W cm-3), negative ions can reach the extraction region provided they are produced at a distance lower than 2 cm from the plasma grid in the case of volume production (dissociative attachment processes), or if they are produced at the plasma grid surface, in the vicinity of the extraction holes.

New procedure for extraction of algal lipids from wet biomass: a green clean and scalable process.

PubMed

Dejoye Tanzi, Celine; Abert Vian, Maryline; Chemat, Farid

2013-04-01

A new procedure, called Simultaneous Distillation and Extraction Process (SDEP), for lipid extraction from wet microalgae (Nannochloropsis oculata and Dunaliella salina) was reported. This method does not require a pre-drying of the biomass and employs alternative solvents such as d-limonene, α-pinene and p-cymene. This procedure has been compared with Soxhlet extraction (Sox) and Bligh & Dyer method (B&D). For N. oculata, results showed that SDEP-cymene provided similar lipid yields to B&D (21.45% and 23.78%), while SDEP-limonene and pinene provided lower yields (18.73% and 18.75% respectively). For D. salina, SDEP-pinene provided the maximum lipid yield (3.29%) compared to the other solvents, which is quite close to B&D result (4.03%). No significant differences in terms of distribution of lipid classes and fatty acid composition have been obtained for different techniques. Evaluation of energy consumption indicates a substantial saving in the extraction cost by SDEP compared to the conventional extraction technique, Soxhlet. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fructus ligustri lucidi ethanol extract improves bone mineral density and properties through modulating calcium absorption-related gene expression in kidney and duodenum of growing rats.

PubMed

Feng, Xin; Lyu, Ying; Wu, Zhenghao; Fang, Yuehui; Xu, Hao; Zhao, Pengling; Xu, Yajun; Feng, Haotian

2014-04-01

Optimizing peak bone mass in early life is one of key preventive strategies against osteoporosis. Fructus ligustri lucidi (FLL), the fruit of Ligustrum lucidum Ait., is a commonly prescribed herb in many kidney-tonifying traditional Chinese medicinal formulas to alleviate osteoporosis. Previously, FLL extracts have been shown to have osteoprotective effect in aged or ovariectomized rats. In the present study, we investigated the effects of FLL ethanol extract on bone mineral density (BMD) and mechanical properties in growing male rats and explored the underlying mechanisms. Male weaning Sprague-Dawley rats were randomized into four groups and orally administrated for 4 months an AIN-93G formula-based diet supplementing with different doses of FLL ethanol extract (0.40, 0.65, and 0.90 %) or vehicle control, respectively. Then calcium balance, serum level of Ca, P, 25(OH)2D3, 1,25(OH)2D3, osteocalcin (OCN), C-terminal telopeptide of type I collagen (CTX-I), and parathyroid hormone, bone microarchitecture, and calcium absorption-related genes expression in duodenum and kidney were analyzed. The results demonstrated that FLL ethanol extract increased BMD of growing rats and improved their bone microarchitecture and mechanical properties. FLL ethanol extract altered bone turnover, as evidenced by increasing a bone formation maker, OCN, and decreasing a bone resorption maker, CTX-I. Intriguingly, both Ca absorption and Ca retention rate were elevated by FLL ethanol extract treatment, possibly through the mechanisms of up-regulating the transcriptions of calcitropic genes in kidney (1α-hydroxylase) and duodenum (vitamin D receptor, calcium transporter calbindin-D9k, and transient receptor potential vanilloid 6). In conclusion, FLL ethanol extract increased bone mass gain and improved bone properties via modulating bone turnover and up-regulating calcium absorption-related gene expression in kidney and duodenum, which could then activate 1,25(OH)2D3-dependent calcium transport in male growing rats.

Semiautomatic and Automatic Cooperative Inversion of Seismic and Magnetotelluric Data

NASA Astrophysics Data System (ADS)

Le, Cuong V. A.; Harris, Brett D.; Pethick, Andrew M.; Takam Takougang, Eric M.; Howe, Brendan

2016-09-01

Natural source electromagnetic methods have the potential to recover rock property distributions from the surface to great depths. Unfortunately, results in complex 3D geo-electrical settings can be disappointing, especially where significant near-surface conductivity variations exist. In such settings, unconstrained inversion of magnetotelluric data is inexorably non-unique. We believe that: (1) correctly introduced information from seismic reflection can substantially improve MT inversion, (2) a cooperative inversion approach can be automated, and (3) massively parallel computing can make such a process viable. Nine inversion strategies including baseline unconstrained inversion and new automated/semiautomated cooperative inversion approaches are applied to industry-scale co-located 3D seismic and magnetotelluric data sets. These data sets were acquired in one of the Carlin gold deposit districts in north-central Nevada, USA. In our approach, seismic information feeds directly into the creation of sets of prior conductivity model and covariance coefficient distributions. We demonstrate how statistical analysis of the distribution of selected seismic attributes can be used to automatically extract subvolumes that form the framework for prior model 3D conductivity distribution. Our cooperative inversion strategies result in detailed subsurface conductivity distributions that are consistent with seismic, electrical logs and geochemical analysis of cores. Such 3D conductivity distributions would be expected to provide clues to 3D velocity structures that could feed back into full seismic inversion for an iterative practical and truly cooperative inversion process. We anticipate that, with the aid of parallel computing, cooperative inversion of seismic and magnetotelluric data can be fully automated, and we hold confidence that significant and practical advances in this direction have been accomplished.

[Population data analysis of miniSTR loci: D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland].

PubMed

Kodroń, Agata; Rychlicka, Edyta; Milewska, Iwona; Woźniak, Marcin; Grzybowski, Tomasz

2010-01-01

This paper presents the allele frequencies and forensic parameters of the three miniSTR loci D10S1248, D14S1434 and D22S1045 in the Pomerania-Kujawy region of Poland. Genomic DNA was extracted by a standard phenol-chloroform extraction procedure. The three miniSTR loci D10S1248, D14S1434 and D22S1045 were amplified in a triplex polymerase chain reaction with the primer sets designed by Coble and Butler in a GeneAmp PCR System 9700 (Applied Biosystems). The amplified products were separated and detected by capillary electrophoresis on an ABI PRISM 3100 Genetic Analyzer (Applied Biosystems).The genotype frequency distributions showed no deviations from Hardy-Weinberg equilibrium expectations. The values of forensic parameters confirm that D10S1248 and D22S1045 are highly informative genetic markers, whereas D14S1434 is a moderately useful for forensic genetic identification purposes.

Study on the Polar Extracts of Dendrobium nobile, D. officinale, D. loddigesii, and Flickingeria fimbriata: Metabolite Identification, Content Evaluation, and Bioactivity Assay.

PubMed

Chen, Huiping; Li, Xuewen; Xu, Yongli; Lo, Kakei; Zheng, Huizhen; Hu, Haiyan; Wang, Jun; Lin, Yongcheng

2018-05-15

The polar extract of the Dendrobium species or F. fimbriata (a substitute of Dendrobium ), between the fat-soluble extract and polysaccharide has barely been researched. This report worked on the qualitative and quantitative studies of polar extracts from D. nobile , D. officinale , D. loddigesii , and F. fimbriata . Eight water-soluble metabolites containing a new diglucoside, flifimdioside A ( 1 ), and a rare imidazolium-type alkaloid, anosmine ( 4 ), were identified using chromatography as well as spectroscopic techniques. Their contents in the four herbs were high, approximately 0.9⁻3.7 mg/g based on the analysis of quantitative nuclear magnetic resonance (qNMR) spectroscopy. Biological activity evaluation showed that the polar extract of F. fimbriata or its pure component had good antioxidant and neuroprotective activity; compounds 1 ‒ 4 and shihunine ( 8 ) showed weak α-glucosidase inhibitory activity; 4 and 8 had weak anti-inflammatory activity. Under trial conditions, all samples had no cytotoxic activity.

Information Extraction of Tourist Geological Resources Based on 3d Visualization Remote Sensing Image

NASA Astrophysics Data System (ADS)

Wang, X.

2018-04-01

Tourism geological resources are of high value in admiration, scientific research and universal education, which need to be protected and rationally utilized. In the past, most of the remote sensing investigations of tourism geological resources used two-dimensional remote sensing interpretation method, which made it difficult for some geological heritages to be interpreted and led to the omission of some information. This aim of this paper is to assess the value of a method using the three-dimensional visual remote sensing image to extract information of geological heritages. skyline software system is applied to fuse the 0.36 m aerial images and 5m interval DEM to establish the digital earth model. Based on the three-dimensional shape, color tone, shadow, texture and other image features, the distribution of tourism geological resources in Shandong Province and the location of geological heritage sites were obtained, such as geological structure, DaiGu landform, granite landform, Volcanic landform, sandy landform, Waterscapes, etc. The results show that using this method for remote sensing interpretation is highly recognizable, making the interpretation more accurate and comprehensive.

Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

PubMed Central

Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

2016-01-01

Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaofan; Varga, Tamas; Liu, Chongxuan

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to farming, forest management and climate change. X-ray computed tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and our own code was used to noninvasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure at 31µm resolution, and extract quantitative information (root volume and surface area) from the 3D data, respectively. Based on themore » mesh generated from the root structure, computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soil hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. The flow variability and soil water distributions under different scenarios were investigated. Parameterizations were evaluated to show their impacts on the average conductivity. The pore-scale modeling approach provides realistic simulations of rhizosphere flow processes and provides useful information that can be linked to upscaled models.« less

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras.

PubMed

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-06-24

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system.

Geometrical modeling of complete dental shapes by using panoramic X-ray, digital mouth data and anatomical templates.

PubMed

Barone, Sandro; Paoli, Alessandro; Razionale, Armando Viviano

2015-07-01

In the field of orthodontic planning, the creation of a complete digital dental model to simulate and predict treatments is of utmost importance. Nowadays, orthodontists use panoramic radiographs (PAN) and dental crown representations obtained by optical scanning. However, these data do not contain any 3D information regarding tooth root geometries. A reliable orthodontic treatment should instead take into account entire geometrical models of dental shapes in order to better predict tooth movements. This paper presents a methodology to create complete 3D patient dental anatomies by combining digital mouth models and panoramic radiographs. The modeling process is based on using crown surfaces, reconstructed by optical scanning, and root geometries, obtained by adapting anatomical CAD templates over patient specific information extracted from radiographic data. The radiographic process is virtually replicated on crown digital geometries through the Discrete Radon Transform (DRT). The resulting virtual PAN image is used to integrate the actual radiographic data and the digital mouth model. This procedure provides the root references on the 3D digital crown models, which guide a shape adjustment of the dental CAD templates. The entire geometrical models are finally created by merging dental crowns, captured by optical scanning, and root geometries, obtained from the CAD templates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Normalized Metadata Generation for Human Retrieval Using Multiple Video Surveillance Cameras

PubMed Central

Jung, Jaehoon; Yoon, Inhye; Lee, Seungwon; Paik, Joonki

2016-01-01

Since it is impossible for surveillance personnel to keep monitoring videos from a multiple camera-based surveillance system, an efficient technique is needed to help recognize important situations by retrieving the metadata of an object-of-interest. In a multiple camera-based surveillance system, an object detected in a camera has a different shape in another camera, which is a critical issue of wide-range, real-time surveillance systems. In order to address the problem, this paper presents an object retrieval method by extracting the normalized metadata of an object-of-interest from multiple, heterogeneous cameras. The proposed metadata generation algorithm consists of three steps: (i) generation of a three-dimensional (3D) human model; (ii) human object-based automatic scene calibration; and (iii) metadata generation. More specifically, an appropriately-generated 3D human model provides the foot-to-head direction information that is used as the input of the automatic calibration of each camera. The normalized object information is used to retrieve an object-of-interest in a wide-range, multiple-camera surveillance system in the form of metadata. Experimental results show that the 3D human model matches the ground truth, and automatic calibration-based normalization of metadata enables a successful retrieval and tracking of a human object in the multiple-camera video surveillance system. PMID:27347961

Use of mesophilic and thermophilic bacteria for the improvement of copper extraction from a low-grade ore

NASA Astrophysics Data System (ADS)

Darezereshki, E.; Schaffie, M.; Lotfalian, M.; Seiedbaghery, S. A.; Ranjbar, M.

2011-04-01

Bioleaching was examined for copper extraction from a low grade ore using mesophilic and moderate thermophilic bacteria. Five equal size columns were used for the leaching of the ore. Sulfuric acid solution with a flow rate of 3.12 L·m-2·h-1 and pH 1.5 passed through each column continuously for 90 d. In the first and the second column, bioleaching was performed without agglomeration of the ore and on the agglomerated ore, respectively. 28wt% of the copper was extracted in the first column after 40 d, while this figure was 38wt% in the second column. After 90 d, however, the overall extractions were almost the same for both of them. Bioleaching with mesophilic bacteria was performed in the third column without agglomeration of the ore and in the fourth column on the agglomerated ore. After 40 d, copper extractions in the third and the fourth columns were 62wt% and 70wt%, respectively. Copper extractions were 75wt% for both the columns after 90 d. For the last column, bioleaching was performed with moderate thermophilic bacteria and agglomerated ore. Copper extractions were 80wt% and 85wt% after 40 and 90 d, respectively. It was concluded that crushing and agglomeration of the ore using bacteria could enhance the copper extraction considerably.

Evaluation of Cholesterol-lowering Activity of Standardized Extract of Mangifera indica in Albino Wistar Rats

PubMed Central

Gururaja, G. M.; Mundkinajeddu, Deepak; Kumar, A. Senthil; Dethe, Shekhar Michael; Allan, J. Joshua; Agarwal, Amit

2017-01-01

Introduction: Cholesterol lowering activity of Mangifera indica L. has been determined by earlier researchers and kernel, leaf and bark have shown significant activity. However, the specific cholesterol lowering activity of leaf methanol extract has not been determined. Materials and Methods: The present study involved evaluation of cholesterol lowering potential of methanol extract of M. indica leaves using high cholesterol diet model in albino Wistar rats. The acute oral toxicity at a dose of 5000 mg/ kg body weight was also determined in female albino Wistar rats. Phytoconstituents Iriflophenone 3-C-β-D-glucoside and mangiferin were quantified in methanol extracts of different varieties of mango leaves using high performance liquid chromatography. Results and Discussion: Significant cholesterol lowering activity was observed with methanol extract of M. indica leaves, at dose of 90 mg/kg body weight in rats and it was also found to be safe at dose of 5000 mg/kg rat body. Iriflophenone 3-C-β-D-glucoside and mangiferin were found to be in the range of 1.2 to 2.8% w/w and 3.9 to 4.6% w/w, respectively which along with 3 β taraxerol and other sterols could be contributing to the cholesterol lowering activity of mango leaves extract. Conclusions: The phytosterols rich extract of Mangifera indica leaves is a good source of nutraceutical ingredient that have the potential to lower serum cholesterol levels. SUMMARY The Mangifera indica leaves methanolic extract showed significant cholesterol lowering activity in high cholesterol diet induced hypercholesterolaemia model in rats when evaluated at a dose of 90 mg/kg rat body weight. The extract was found to contain Iriflophenone 3-C-β-D-glucoside and mangiferin which along with 3 β taraxerol and other sterols could be contributing to the cholesterol lowering activity. PMID:28250649

Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

PubMed Central

Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen

2016-01-01

Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236

Spermatoprotective activity of the leaf extract of Psidium guajava Linn.

PubMed

Akinola, O B; Oladosu, O S; Dosumu, O O

2007-12-01

The leaves of Psidium guajava Linn. (guava) contain several natural antioxidants. We therefore designed the present study to evaluate the effect of ethanol extract of guava leaves on gossypol-associated sperm toxicity in Wistar rats. Animal groups 1, 2, and 3 (n=6 each) were treated orally with crude cottonseed oil to provide 14 mg/kg/d of free gossypol for 53 d. Besides, groups 1 and 2 rats were supplemented orally with 250 mg/kg/d and 500 mg/kg/d respectively of guava leaf extract (GLE) for the same period. Group 4 animals (control, n=6) received normal saline. No significant difference (P>0.05) occurred in the sperm count of group 1 rats compared to control. In animal group 2, significant increase (P<0.05) in sperm count occurred, as opposed to group 3 animals, where this parameter decreased significantly (P<0.05). Besides, mean values of 78 %, 82 %, 30 %, and 65 % respectively were obtained for sperm motility in animal groups 1, 2, 3, and 4. Our findings suggest that ethanol extract of guava leaves possesses beneficial effect on gossypol-associated sperm toxicity, and may therefore enhance male fertility, possibly owing to its rich constituents of natural antioxidants.

Sub-Saharan Africa Report, No. 2869.

DTIC Science & Technology

1983-11-10

QUui-r^^ 33D< FBiS FOREIGN BROADCAST INFORMATION SERVICE REPRODUCED BY NATIONAL TECHNICAL INFORMATION SERVICE U.S. DEPARTMENT OF COMMERCE...8217 SPRINGFIELD, VA. 22161 / 6? 1^ NOTE JPRS publications contain information primarily from foreign newspapers, periodicals and books, but also from...indicate how the original information was processed. Where no processing indicator is given, the infor- mation was summarized or extracted. Unfamiliar

Real-time 3D visualization of the thoraco-abdominal surface during breathing with body movement and deformation extraction.

PubMed

Povšič, K; Jezeršek, M; Možina, J

2015-07-01

Real-time 3D visualization of the breathing displacements can be a useful diagnostic tool in order to immediately observe the most active regions on the thoraco-abdominal surface. The developed method is capable of separating non-relevant torso movement and deformations from the deformations that are solely related to breathing. This makes it possible to visualize only the breathing displacements. The system is based on the structured laser triangulation principle, with simultaneous spatial and color data acquisition of the thoraco-abdominal region. Based on the tracking of the attached passive markers, the torso movement and deformation is compensated using rigid and non-rigid transformation models on the three-dimensional (3D) data. The total time of 3D data processing together with visualization equals 20 ms per cycle.In vitro verification of the rigid movement extraction was performed using the iterative closest point algorithm as a reference. Furthermore, a volumetric evaluation on a live subject was performed to establish the accuracy of the rigid and non-rigid model. The root mean square deviation between the measured and the reference volumes shows an error of  ±0.08 dm(3) for rigid movement extraction. Similarly, the error was calculated to be  ±0.02 dm(3) for torsional deformation extraction and  ±0.11 dm(3) for lateral bending deformation extraction. The results confirm that during the torso movement and deformation, the proposed method is sufficiently accurate to visualize only the displacements related to breathing. The method can be used, for example, during the breathing exercise on an indoor bicycle or a treadmill.

Enhanced and green extraction polyphenols and furanocoumarins from Fig (Ficus carica L.) leaves using deep eutectic solvents.

PubMed

Wang, Tong; Jiao, Jiao; Gai, Qing-Yan; Wang, Peng; Guo, Na; Niu, Li-Li; Fu, Yu-Jie

2017-10-25

Nowadays, green extraction of bioactive compounds from medicinal plants has gained increasing attention. As green solvent, deep eutectic solvent (DES) have been highly rated to replace toxic organic solvents in extraction process. In present study, to simultaneous extraction five main bioactive compounds from fig leaves, DES was tailor-made. The tailor-made DES composed of a 3:3:3 molar ratio of glycerol, xylitol and D-(-)-Fructose showed enhanced extraction yields for five target compounds simultaneously compared with traditional methanol and non-tailor DESs. Then, the tailor-made DES based extraction methods have compared and microwave-assisted extraction was selected and optimized due to its high extraction yields with lower time consumption. The influencing parameters including extraction temperature, liquid-solid ratio, and extraction time were optimized using response surface methodology (RSM). Under optimal conditions the extraction yield of caffeoylmalic acid, psoralic acid-glucoside, rutin, psoralen and bergapten was 6.482mg/g, 16.34mg/g, 5.207mg/g, 15.22mg/g and 2.475mg/g, respectively. Macroporous resin D101 has been used to recovery target compounds with recovery yields of 79.2%, 83.4%, 85.5%, 81.2% and 75.3% for caffeoylmalic acid, psoralic acid-glucoside, rutin, psoralen and bergapten, respectively. The present study suggests that DESs are truly designer and efficient solvents and the method we developed was efficient and sustainable for extraction main compounds from Fig leaves.mg/g. Copyright © 2017 Elsevier B.V. All rights reserved.

A new C-Glycosylflavone from Encyclia michuacana

NASA Astrophysics Data System (ADS)

Tovar-Gijón, Claudia E.; Hernández-Carlos, Beatriz; Burgueño-Tapia, Eleuterio; Cedillo-Portugal, Ernestina; Joseph-Nathan, Pedro

2006-02-01

The methanol extracts from Encyclia michuacana tubercles yielded the new 8- C-(6-deoxy-β- D-glucopyranosyl)apigenin ( 1) together with known 1-(3'-hydroxy-5'-methoxyphenyl)-2-(4″-hydroxy-5″-methoxyphenyl)ethane ( 2) and 2-(4-hydroxybenzyl)malic acid ( 3). The new structure was elucidated using spectroscopic methods, mainly 1D and 2D NMR. The β-anomer for 1 was supported by comparison of the experimental 1H- 1H coupling constant values with those generated employing a generalized Karplus-type relationship using dihedral angles extracted from DFT calculations.

Characterization of Chemical Compounds with Antioxidant and Cytotoxic Activities in Bougainvillea x buttiana Holttum and Standl, (var. Rose) Extracts

PubMed Central

Abarca-Vargas, Rodolfo; Peña Malacara, Carlos F.; Petricevich, Vera L.

2016-01-01

Bougainvillea is widely used in traditional Mexican medicine to treat several diseases. This study was designed to characterize the chemical constituents of B. x buttiana extracts with antioxidant and cytotoxic activities using different solvents. The extraction solvents used were as follows: distilled water (dH2O), methanol (MeOH), acetone (DMK), ethanol (EtOH), ethyl acetate (EtOAc), dichloromethane (DCM), and hexane (Hex) (100%) at an extraction temperature of 26 °C. Analysis of bioactive compounds present in the B. x buttiana extracts included the application of common phytochemical screening assays, GC-MS analysis, and cytotoxicity and antioxidant assays. The results show that the highest extraction yield was observed with water and methanol. The maximum total phenolic content amount and highest antioxidant potential were obtained when extraction with methanol was used. With the exceptions of water and ethanol extractions, all other extracts showed cytotoxicity ranging between 31% and 50%. The prevailing compounds in water, methanol, ethanol, and acetone solvents were as follows: 4H-pyran-4-one, 2,3-dihydro-3, 5-dihydroxy-6-methyl (2), 2-propenoic acid, 3-(2-hydrophenyl)-(E)- (3), and 3-O-methyl-d-glucose (6). By contrast, the major components in the experiments using solvents such as EtOH, DMK, EtOAc, DCM, and Hex were n-hexadecanoic acid (8), 9,12-octadecadienoic acid (Z,Z) (12); 9-octadecenoic acid (E)- (13), and stigmasta-5,22-dien-3-ol (28). PMID:27918436

Single shot laser speckle based 3D acquisition system for medical applications

NASA Astrophysics Data System (ADS)

Khan, Danish; Shirazi, Muhammad Ayaz; Kim, Min Young

2018-06-01

The state of the art techniques used by medical practitioners to extract the three-dimensional (3D) geometry of different body parts requires a series of images/frames such as laser line profiling or structured light scanning. Movement of the patients during scanning process often leads to inaccurate measurements due to sequential image acquisition. Single shot structured techniques are robust to motion but the prevalent challenges in single shot structured light methods are the low density and algorithm complexity. In this research, a single shot 3D measurement system is presented that extracts the 3D point cloud of human skin by projecting a laser speckle pattern using a single pair of images captured by two synchronized cameras. In contrast to conventional laser speckle 3D measurement systems that realize stereo correspondence by digital correlation of projected speckle patterns, the proposed system employs KLT tracking method to locate the corresponding points. The 3D point cloud contains no outliers and sufficient quality of 3D reconstruction is achieved. The 3D shape acquisition of human body parts validates the potential application of the proposed system in the medical industry.

TU-F-12A-05: Sensitivity of Textural Features to 3D Vs. 4D FDG-PET/CT Imaging in NSCLC Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, F; Nyflot, M; Bowen, S

2014-06-15

Purpose: Neighborhood Gray-level difference matrices (NGLDM) based texture parameters extracted from conventional (3D) 18F-FDG PET scans in patients with NSCLC have been previously shown to associate with response to chemoradiation and poorer patient outcome. However, the change in these parameters when utilizing respiratory-correlated (4D) FDG-PET scans has not yet been characterized for NSCLC. The Objectives: of this study was to assess the extent to which NGLDM-based texture parameters on 4D PET images vary with reference to values derived from 3D scans in NSCLC. Methods: Eight patients with newly diagnosed NSCLC treated with concomitant chemoradiotherapy were included in this study. 4Dmore » PET scans were reconstructed with OSEM-IR in 5 respiratory phase-binned images and corresponding CT data of each phase were employed for attenuation correction. NGLDM-based texture features, consisting of coarseness, contrast, busyness, complexity and strength, were evaluated for gross tumor volumes defined on 3D/4D PET scans by radiation oncologists. Variation of the obtained texture parameters over the respiratory cycle were examined with respect to values extracted from 3D scans. Results: Differences between texture parameters derived from 4D scans at different respiratory phases and those extracted from 3D scans ranged from −30% to 13% for coarseness, −12% to 40% for contrast, −5% to 50% for busyness, −7% to 38% for complexity, and −43% to 20% for strength. Furthermore, no evident correlations were observed between respiratory phase and 4D scan texture parameters. Conclusion: Results of the current study showed that NGLDM-based texture parameters varied considerably based on choice of 3D PET and 4D PET reconstruction of NSCLC patient images, indicating that standardized image acquisition and analysis protocols need to be established for clinical studies, especially multicenter clinical trials, intending to validate prognostic values of texture features for NSCLC.« less

The 2D analytic signal for envelope detection and feature extraction on ultrasound images.

PubMed

Wachinger, Christian; Klein, Tassilo; Navab, Nassir

2012-08-01

The fundamental property of the analytic signal is the split of identity, meaning the separation of qualitative and quantitative information in form of the local phase and the local amplitude, respectively. Especially the structural representation, independent of brightness and contrast, of the local phase is interesting for numerous image processing tasks. Recently, the extension of the analytic signal from 1D to 2D, covering also intrinsic 2D structures, was proposed. We show the advantages of this improved concept on ultrasound RF and B-mode images. Precisely, we use the 2D analytic signal for the envelope detection of RF data. This leads to advantages for the extraction of the information-bearing signal from the modulated carrier wave. We illustrate this, first, by visual assessment of the images, and second, by performing goodness-of-fit tests to a Nakagami distribution, indicating a clear improvement of statistical properties. The evaluation is performed for multiple window sizes and parameter estimation techniques. Finally, we show that the 2D analytic signal allows for an improved estimation of local features on B-mode images. Copyright © 2012 Elsevier B.V. All rights reserved.

Sugarcane Crop Extraction Using Object-Oriented Method from ZY-3 High Resolution Satellite Tlc Image

NASA Astrophysics Data System (ADS)

Luo, H.; Ling, Z. Y.; Shao, G. Z.; Huang, Y.; He, Y. Q.; Ning, W. Y.; Zhong, Z.

2018-04-01

Sugarcane is one of the most important crops in Guangxi, China. As the development of satellite remote sensing technology, more remotely sensed images can be used for monitoring sugarcane crop. With the help of Three Line Camera (TLC) images, wide coverage and stereoscopic mapping ability, Chinese ZY-3 high resolution stereoscopic mapping satellite is useful in attaining more information for sugarcane crop monitoring, such as spectral, shape, texture difference between forward, nadir and backward images. Digital surface model (DSM) derived from ZY-3 TLC images are also able to provide height information for sugarcane crop. In this study, we make attempt to extract sugarcane crop from ZY-3 images, which are acquired in harvest period. Ortho-rectified TLC images, fused image, DSM are processed for our extraction. Then Object-oriented method is used in image segmentation, example collection, and feature extraction. The results of our study show that with the help of ZY-3 TLC image, the information of sugarcane crop in harvest time can be automatic extracted, with an overall accuracy of about 85.3 %.

Perform Thermodynamics Measurements on Fuel Cycle Case Study Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Leigh R.

This document was prepared to meet FCR&D level 3 milestone M3FT-14IN0304022, “Perform Thermodynamics Measurements on Fuel Cycle Case Study Systems.” This work was carried out under the auspices of the Thermodynamics and Kinetics FCR&D work package. This document reports preliminary work in support of determining the thermodynamic parameters for the ALSEP process. The ALSEP process is a mixed extractant system comprised of a cation exchanger 2-ethylhexyl-phosphonic acid mono-2-ethylhexyl ester (HEH[EHP]) and a neutral solvating extractant N,N,N’,N’-tetraoctyldiglycolamide (TODGA). The extractant combination produces complex organic phase chemistry that is challenging for traditional measurement techniques. To neutralize the complexity, temperature dependent solvent extractionmore » experiments were conducted with neat TODGA and scaled down concentrations of the ALSEP formulation to determine the enthalpies of extraction for the two conditions. A full set of thermodynamic data for Eu, Am, and Cm extraction by TODGA from 3.0 M HNO3 is reported. These data are compared to previous extraction results from a 1.0 M HNO3 aqueous medium, and a short discussion of the mixed HEH[EHP]/TODGA system results is offered.« less

Joint classification and contour extraction of large 3D point clouds

NASA Astrophysics Data System (ADS)

Hackel, Timo; Wegner, Jan D.; Schindler, Konrad

2017-08-01

We present an effective and efficient method for point-wise semantic classification and extraction of object contours of large-scale 3D point clouds. What makes point cloud interpretation challenging is the sheer size of several millions of points per scan and the non-grid, sparse, and uneven distribution of points. Standard image processing tools like texture filters, for example, cannot handle such data efficiently, which calls for dedicated point cloud labeling methods. It turns out that one of the major drivers for efficient computation and handling of strong variations in point density, is a careful formulation of per-point neighborhoods at multiple scales. This allows, both, to define an expressive feature set and to extract topologically meaningful object contours. Semantic classification and contour extraction are interlaced problems. Point-wise semantic classification enables extracting a meaningful candidate set of contour points while contours help generating a rich feature representation that benefits point-wise classification. These methods are tailored to have fast run time and small memory footprint for processing large-scale, unstructured, and inhomogeneous point clouds, while still achieving high classification accuracy. We evaluate our methods on the semantic3d.net benchmark for terrestrial laser scans with >109 points.

Anthocyanin contents in the seed coat of black soya bean and their anti-human tyrosinase activity and antioxidative activity.

PubMed

Jhan, J-K; Chung, Y-C; Chen, G-H; Chang, C-H; Lu, Y-C; Hsu, C-K

2016-06-01

The seed coat of black soya bean (SCBS) contains high amount of anthocyanins and shows antioxidant and anti-mushroom tyrosinase activities. The objectives of this study were to analyse the anthocyanins in SCBS with different solvents and to find the relationship between anthocyanin profile with anti-human and anti-mushroom tyrosinase activities. SCBS was extracted with hot water, 50 and 80% ethanol, 50 and 80% acetone and 50 and 80% acidified acetone. Total phenol and total flavonoid contents in the extracts were determined. Anthocyanins in the extracts were analysed using HPLC and LC/MS/MS. A genetically engineered human tyrosinase was used to evaluate the anti-tyrosinase potential of the extracts from SCBS. 80% acetone extract from SCBS obtained the highest total phenol, total flavonoid and cyanidin-3-O-glucoside (C3G) contents among all the extracts, whereas the hot water extract showed the lowest antioxidant contents. Three anthocyanin compounds were found in all the extracts from SCBS, and the analysis of HPLC and LC/MS/MS indicated that they were C3G, delphinidin-3-O-glucoside (D3G) and peonidin-3-O-glucoside (P3G). The ratios of C3G (2.84 mg g(-1) ), D3G (0.34 mg g(-1) ) and P3G (0.35 mg g(-1) ) in 80% acidified acetone extract were 76.6, 9.1 and 9.3%, respectively. All the extracts from SCBS possessed anti-human tyrosinase activity. Moreover, a good correlation was found between the anti-human tyrosinase activities and C3G contents in the extracts. Antioxidants in SCBS also possess anti-human and anti-mushroom tyrosinase activities. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Multi-AUV Target Search Based on Bioinspired Neurodynamics Model in 3-D Underwater Environments.

PubMed

Cao, Xiang; Zhu, Daqi; Yang, Simon X

2016-11-01

Target search in 3-D underwater environments is a challenge in multiple autonomous underwater vehicles (multi-AUVs) exploration. This paper focuses on an effective strategy for multi-AUV target search in the 3-D underwater environments with obstacles. First, the Dempster-Shafer theory of evidence is applied to extract information of environment from the sonar data to build a grid map of the underwater environments. Second, a topologically organized bioinspired neurodynamics model based on the grid map is constructed to represent the dynamic environment. The target globally attracts the AUVs through the dynamic neural activity landscape of the model, while the obstacles locally push the AUVs away to avoid collision. Finally, the AUVs plan their search path to the targets autonomously by a steepest gradient descent rule. The proposed algorithm deals with various situations, such as static targets search, dynamic targets search, and one or several AUVs break down in the 3-D underwater environments with obstacles. The simulation results show that the proposed algorithm is capable of guiding multi-AUV to achieve search task of multiple targets with higher efficiency and adaptability compared with other algorithms.

3D sensor algorithms for spacecraft pose determination

NASA Astrophysics Data System (ADS)

Trenkle, John M.; Tchoryk, Peter, Jr.; Ritter, Greg A.; Pavlich, Jane C.; Hickerson, Aaron S.

2006-05-01

Researchers at the Michigan Aerospace Corporation have developed accurate and robust 3-D algorithms for pose determination (position and orientation) of satellites as part of an on-going effort supporting autonomous rendezvous, docking and space situational awareness activities. 3-D range data from a LAser Detection And Ranging (LADAR) sensor is the expected input; however, the approach is unique in that the algorithms are designed to be sensor independent. Parameterized inputs allow the algorithms to be readily adapted to any sensor of opportunity. The cornerstone of our approach is the ability to simulate realistic range data that may be tailored to the specifications of any sensor. We were able to modify an open-source raytracing package to produce point cloud information from which high-fidelity simulated range images are generated. The assumptions made in our experimentation are as follows: 1) we have access to a CAD model of the target including information about the surface scattering and reflection characteristics of the components; 2) the satellite of interest may appear at any 3-D attitude; 3) the target is not necessarily rigid, but does have a limited number of configurations; and, 4) the target is not obscured in any way and is the only object in the field of view of the sensor. Our pose estimation approach then involves rendering a large number of exemplars (100k to 5M), extracting 2-D (silhouette- and projection-based) and 3-D (surface-based) features, and then training ensembles of decision trees to predict: a) the 4-D regions on a unit hypersphere into which the unit quaternion that represents the vehicle [Q X, Q Y, Q Z, Q W] is pointing, and, b) the components of that unit quaternion. Results have been quite promising and the tools and simulation environment developed for this application may also be applied to non-cooperative spacecraft operations, Autonomous Hazard Detection and Avoidance (AHDA) for landing craft, terrain mapping, vehicle guidance, path planning and obstacle avoidance.

Extraction of the 3D local orientation of myocytes in human cardiac tissue using X-ray phase-contrast micro-tomography and multi-scale analysis.

PubMed

Varray, François; Mirea, Iulia; Langer, Max; Peyrin, Françoise; Fanton, Laurent; Magnin, Isabelle E

2017-05-01

This paper presents a methodology to access the 3D local myocyte arrangements in fresh human post-mortem heart samples. We investigated the cardiac micro-structure at a high and isotropic resolution of 3.5 µm in three dimensions using X-ray phase micro-tomography at the European Synchrotron Radiation Facility. We then processed the reconstructed volumes to extract the 3D local orientation of the myocytes using a multi-scale approach with no segmentation. We created a simplified 3D model of tissue sample made of simulated myocytes with known size and orientations, to evaluate our orientation extraction method. Afterwards, we applied it to 2D histological cuts and to eight 3D left ventricular (LV) cardiac tissue samples. Then, the variation of the helix angles, from the endocardium to the epicardium, was computed at several spatial resolutions ranging from 3.6 3  mm 3 to 112 3  µm 3 . We measure an increased range of 20° to 30° from the coarsest resolution level to the finest level in the experimental samples. This result is in line with the higher values measured from histology. The displayed tractography demonstrates a rather smooth evolution of the transmural helix angle in six LV samples and a sudden discontinuity of the helix angle in two septum samples. These measurements bring a new vision of the human heart architecture from macro- to micro-scale. Copyright © 2017 Elsevier B.V. All rights reserved.

A sea-land segmentation algorithm based on multi-feature fusion for a large-field remote sensing image

NASA Astrophysics Data System (ADS)

Li, Jing; Xie, Weixin; Pei, Jihong

2018-03-01

Sea-land segmentation is one of the key technologies of sea target detection in remote sensing images. At present, the existing algorithms have the problems of low accuracy, low universality and poor automatic performance. This paper puts forward a sea-land segmentation algorithm based on multi-feature fusion for a large-field remote sensing image removing island. Firstly, the coastline data is extracted and all of land area is labeled by using the geographic information in large-field remote sensing image. Secondly, three features (local entropy, local texture and local gradient mean) is extracted in the sea-land border area, and the three features combine a 3D feature vector. And then the MultiGaussian model is adopted to describe 3D feature vectors of sea background in the edge of the coastline. Based on this multi-gaussian sea background model, the sea pixels and land pixels near coastline are classified more precise. Finally, the coarse segmentation result and the fine segmentation result are fused to obtain the accurate sea-land segmentation. Comparing and analyzing the experimental results by subjective vision, it shows that the proposed method has high segmentation accuracy, wide applicability and strong anti-disturbance ability.

Fusion Ash Separation in the Princeton Field-Reversed Configuration Reactor

NASA Astrophysics Data System (ADS)

Abbate, Joseph; Yeh, Meagan; McGreivy, Nick; Cohen, Samuel

2016-10-01

The Princeton Field-Reversed Configuration (PFRC) concept relies on low-neutron production by D-3He fusion to enable small, safe nuclear-fusion reactors to be built, an approach requiring rapid and efficient extraction of fusion ash and energy produced by D-3He fusion reactions. The ash exhaust stream would contain energetic (0.1-1 MeV) protons, T, 3He, and 4He ions and nearly 1e5 cooler (ca. 100 eV) D ions. The T extracted from the reactor would be a valuable fusion product in that it decays into 3He, which could be used as fuel. If the T were not extracted it would be troublesome because of neutron production by the D-T reaction. This paper discusses methods to separate the various species in a PFRC reactor's exhaust stream. First, we discuss the use of curved magnetic fields to separate the energetic from the cool components. Then we discuss exploiting material properties, specifically reflection, sputtering threshold, and permeability, to allow separation of the hydrogen from the helium isotopes. DOE Contract Number DE-AC02-09CH11466.

Comparing success levels of different neural network structures in extracting discriminative information from the response patterns of a temperature-modulated resistive gas sensor

NASA Astrophysics Data System (ADS)

Hosseini-Golgoo, S. M.; Bozorgi, H.; Saberkari, A.

2015-06-01

Performances of three neural networks, consisting of a multi-layer perceptron, a radial basis function, and a neuro-fuzzy network with local linear model tree training algorithm, in modeling and extracting discriminative features from the response patterns of a temperature-modulated resistive gas sensor are quantitatively compared. For response pattern recording, a voltage staircase containing five steps each with a 20 s plateau is applied to the micro-heater of the sensor, when 12 different target gases, each at 11 concentration levels, are present. In each test, the hidden layer neuron weights are taken as the discriminatory feature vector of the target gas. These vectors are then mapped to a 3D feature space using linear discriminant analysis. The discriminative information content of the feature vectors are determined by the calculation of the Fisher’s discriminant ratio, affording quantitative comparison among the success rates achieved by the different neural network structures. The results demonstrate a superior discrimination ratio for features extracted from local linear neuro-fuzzy and radial-basis-function networks with recognition rates of 96.27% and 90.74%, respectively.

The Exponentially Embedded Family of Distributions for Effective Data Representation, Information Extraction, and Decision Making

DTIC Science & Technology

2013-03-01

information ex- traction and learning from data. First of all, it admits sufficient statistics and therefore, provides the means for selecting good models...readily found since the Kullback -Liebler divergence can be used to ascertain distances between PDFs for various hypothesis testing scenarios. We...t1, t2) Information content of T2 (x) is D(pryj,IJ2(tl, t2)11Pryj,!J2=0(tl, t2)) = reduction in distance to true PDF where D(p1llp2) is Kullback

Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

NASA Astrophysics Data System (ADS)

Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

2012-12-01

Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

Componential profile and amylase inhibiting activity of phenolic compounds from Calendula officinalis L. leaves.

PubMed

Olennikov, Daniil N; Kashchenko, Nina I

2014-01-01

An ethanolic extract and its ethyl acetate-soluble fraction from leaves of Calendula officinalis L. (Asteraceae) were found to show an inhibitory effect on amylase. From the crude extract fractions, one new phenolic acid glucoside, 6'-O-vanilloyl-β-D-glucopyranose, was isolated, together with twenty-four known compounds including five phenolic acid glucosides, five phenylpropanoids, five coumarins, and nine flavonoids. Their structures were elucidated based on chemical and spectral data. The main components, isoquercitrin, isorhamnetin-3-O-β-D-glucopyranoside, 3,5-di-O-caffeoylquinic acid, and quercetin-3-O-(6''-acetyl)-β-D-glucopyranoside, exhibited potent inhibitory effects on amylase.

Phytochemical and antioxidant activity studies on Ononis angustissima L. aerial parts: isolation of two new flavonoids.

PubMed

Mezrag, Abderrahmane; Malafronte, Nicola; Bouheroum, Mohamed; Travaglino, Carmen; Russo, Daniela; Milella, Luigi; Severino, Lorella; De Tommasi, Nunziatina; Braca, Alessandra; Dal Piaz, Fabrizio

2017-03-01

Ononis angustissima aerial parts extract and exudate were subjected to phytochemical and biological studies. Two new natural flavonoids, (3S)-7-hydroxy-4'-methoxy-isoflavanone 3'-β-d-glucopyranoside (1) and kaempferol 3-O-β-d-glucopyranoside-7-O-(2'''-acetyl)-β-d-galactopyranoside (4), and sixteen known compounds were isolated through a bio-oriented approach. Their structural characterisation was achieved using spectroscopic analyses including 2D NMR. The phytochemical profile of the extracts was also performed, and the antioxidant activity of all compounds was tested by three different assays. To get a trend in the results and to compare the antioxidant capacity among the different methods used, the obtained data were transformed to a relative antioxidant capacity index.

Mapping cardiac fiber orientations from high-resolution DTI to high-frequency 3D ultrasound

NASA Astrophysics Data System (ADS)

Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Wagner, Mary B.; Fei, Baowei

2014-03-01

The orientation of cardiac fibers affects the anatomical, mechanical, and electrophysiological properties of the heart. Although echocardiography is the most common imaging modality in clinical cardiac examination, it can only provide the cardiac geometry or motion information without cardiac fiber orientations. If the patient's cardiac fiber orientations can be mapped to his/her echocardiography images in clinical examinations, it may provide quantitative measures for diagnosis, personalized modeling, and image-guided cardiac therapies. Therefore, this project addresses the feasibility of mapping personalized cardiac fiber orientations to three-dimensional (3D) ultrasound image volumes. First, the geometry of the heart extracted from the MRI is translated to 3D ultrasound by rigid and deformable registration. Deformation fields between both geometries from MRI and ultrasound are obtained after registration. Three different deformable registration methods were utilized for the MRI-ultrasound registration. Finally, the cardiac fiber orientations imaged by DTI are mapped to ultrasound volumes based on the extracted deformation fields. Moreover, this study also demonstrated the ability to simulate electricity activations during the cardiac resynchronization therapy (CRT) process. The proposed method has been validated in two rat hearts and three canine hearts. After MRI/ultrasound image registration, the Dice similarity scores were more than 90% and the corresponding target errors were less than 0.25 mm. This proposed approach can provide cardiac fiber orientations to ultrasound images and can have a variety of potential applications in cardiac imaging.

Improving sand and gravel utilization and land-use planning. - 3D-modelling gravel resources with geospatial data.

NASA Astrophysics Data System (ADS)

Rolstad Libach, Lars; Wolden, Knut; Dagestad, Atle; Eskil Larsen, Bjørn

2017-04-01

The Norwegian aggregate industry produces approximately 14 million tons of sand and gravel aggregates annually to a value of approximately 100 million Euros. Utilization of aggregates are often linked to land-use conflicts and complex environmental impacts at the extraction site. These topics are managed on a local municipal level in Norway. The Geological Survey of Norway has a database and a web map service with information about sand and gravel deposits with considerable volumes and an importance evaluation. Some of the deposits covers large areas where the land-use conflicts are high. To ease and improve land-use planning, safeguard other important resources like groundwater and sustainable utilization of sand and gravel resources - there is a need for more detailed information of already mapped important resources. Detailed 3D-models of gravel deposits is a tool for a better land-use- and resource management. By combining seismic, GPR and resistivity geophysical profile data, borehole data, quaternary maps and lidar surface data, it has been possible to make 3D-models of deposits and to further research the possibilities for distinguishing different qualities and volumes. Good datasets and a detailed resource map is a prerequisite to assess geological resources for planners, extractors and neighbours. Future challenges lies in use of, often old, geophysical data, and combining these. What kind of information is it possible to grasp from depth-data that actually argues for a more detailed delineation of resources?

Calibration of 3D ultrasound to an electromagnetic tracking system

NASA Astrophysics Data System (ADS)

Lang, Andrew; Parthasarathy, Vijay; Jain, Ameet

2011-03-01

The use of electromagnetic (EM) tracking is an important guidance tool that can be used to aid procedures requiring accurate localization such as needle injections or catheter guidance. Using EM tracking, the information from different modalities can be easily combined using pre-procedural calibration information. These calibrations are performed individually, per modality, allowing different imaging systems to be mixed and matched according to the procedure at hand. In this work, a framework for the calibration of a 3D transesophageal echocardiography probe to EM tracking is developed. The complete calibration framework includes three required steps: data acquisition, needle segmentation, and calibration. Ultrasound (US) images of an EM tracked needle must be acquired with the position of the needles in each volume subsequently extracted by segmentation. The calibration transformation is determined through a registration between the segmented points and the recorded EM needle positions. Additionally, the speed of sound is compensated for since calibration is performed in water that has a different speed then is assumed by the US machine. A statistical validation framework has also been developed to provide further information related to the accuracy and consistency of the calibration. Further validation of the calibration showed an accuracy of 1.39 mm.

Discriminating between benign and malignant breast tumors using 3D convolutional neural network in dynamic contrast enhanced-MR images

NASA Astrophysics Data System (ADS)

Li, Jing; Fan, Ming; Zhang, Juan; Li, Lihua

2017-03-01

Convolutional neural networks (CNNs) are the state-of-the-art deep learning network architectures that can be used in a range of applications, including computer vision and medical image analysis. It exhibits a powerful representation learning mechanism with an automated design to learn features directly from the data. However, the common 2D CNNs only use the two dimension spatial information without evaluating the correlation between the adjoin slices. In this study, we established a method of 3D CNNs to discriminate between malignant and benign breast tumors. To this end, 143 patients were enrolled which include 66 benign and 77 malignant instances. The MRI images were pre-processed for noise reduction and breast tumor region segmentation. Data augmentation by spatial translating, rotating and vertical and horizontal flipping is applied to the cases to reduce possible over-fitting. A region-of-interest (ROI) and a volume-of-interest (VOI) were segmented in 2D and 3D DCE-MRI, respectively. The enhancement ratio for each MR series was calculated for the 2D and 3D images. The results for the enhancement ratio images in the two series are integrated for classification. The results of the area under the ROC curve(AUC) values are 0.739 and 0.801 for 2D and 3D methods, respectively. The results for 3D CNN which combined 5 slices for each enhancement ratio images achieved a high accuracy(Acc), sensitivity(Sens) and specificity(Spec) of 0.781, 0.744 and 0.823, respectively. This study indicates that 3D CNN deep learning methods can be a promising technology for breast tumor classification without manual feature extraction.

Hierarchical human action recognition around sleeping using obscured posture information

NASA Astrophysics Data System (ADS)

Kudo, Yuta; Sashida, Takehiko; Aoki, Yoshimitsu

2015-04-01

This paper presents a new approach for human action recognition around sleeping with the human body parts locations and the positional relationship between human and sleeping environment. Body parts are estimated from the depth image obtained by a time-of-flight (TOF) sensor using oriented 3D normal vector. Issues in action recognition of sleeping situation are the demand of availability in darkness, and hiding of the human body by duvets. Therefore, the extraction of image features is difficult since color and edge features are obscured by covers. Thus, first in our method, positions of four parts of the body (head, torso, thigh, and lower leg) are estimated by using the shape model of bodily surface constructed by oriented 3D normal vector. This shape model can represent the surface shape of rough body, and is effective in robust posture estimation of the body hidden with duvets. Then, action descriptor is extracted from the position of each body part. The descriptor includes temporal variation of each part of the body and spatial vector of position of the parts and the bed. Furthermore, this paper proposes hierarchical action classes and classifiers to improve the indistinct action classification. Classifiers are composed of two layers, and recognize human action by using the action descriptor. First layer focuses on spatial descriptor and classifies action roughly. Second layer focuses on temporal descriptor and classifies action finely. This approach achieves a robust recognition of obscured human by using the posture information and the hierarchical action recognition.

MULTISCALE TENSOR ANISOTROPIC FILTERING OF FLUORESCENCE MICROSCOPY FOR DENOISING MICROVASCULATURE.

PubMed

Prasath, V B S; Pelapur, R; Glinskii, O V; Glinsky, V V; Huxley, V H; Palaniappan, K

2015-04-01

Fluorescence microscopy images are contaminated by noise and improving image quality without blurring vascular structures by filtering is an important step in automatic image analysis. The application of interest here is to automatically extract the structural components of the microvascular system with accuracy from images acquired by fluorescence microscopy. A robust denoising process is necessary in order to extract accurate vascular morphology information. For this purpose, we propose a multiscale tensor with anisotropic diffusion model which progressively and adaptively updates the amount of smoothing while preserving vessel boundaries accurately. Based on a coherency enhancing flow with planar confidence measure and fused 3D structure information, our method integrates multiple scales for microvasculature preservation and noise removal membrane structures. Experimental results on simulated synthetic images and epifluorescence images show the advantage of our improvement over other related diffusion filters. We further show that the proposed multiscale integration approach improves denoising accuracy of different tensor diffusion methods to obtain better microvasculature segmentation.

Joint detection of anatomical points on surface meshes and color images for visual registration of 3D dental models

NASA Astrophysics Data System (ADS)

Destrez, Raphaël.; Albouy-Kissi, Benjamin; Treuillet, Sylvie; Lucas, Yves

2015-04-01

Computer aided planning for orthodontic treatment requires knowing occlusion of separately scanned dental casts. A visual guided registration is conducted starting by extracting corresponding features in both photographs and 3D scans. To achieve this, dental neck and occlusion surface are firstly extracted by image segmentation and 3D curvature analysis. Then, an iterative registration process is conducted during which feature positions are refined, guided by previously found anatomic edges. The occlusal edge image detection is improved by an original algorithm which follows Canny's poorly detected edges using a priori knowledge of tooth shapes. Finally, the influence of feature extraction and position optimization is evaluated in terms of the quality of the induced registration. Best combination of feature detection and optimization leads to a positioning average error of 1.10 mm and 2.03°.

Determination of siloxanes in silicone products and potential migration to milk, formula and liquid simulants.

PubMed

Zhang, Kai; Wong, Jon W; Begley, Timothy H; Hayward, Douglas G; Limm, William

2012-08-01

A pressurised solvent extraction procedure coupled with a gas chromatography-mass spectrometry-selective ion monitoring (GC-MS-SIM) method was developed to determine three cyclic siloxanes, octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), dodecamethylcyclohexasiloxane (D6) and three linear siloxanes, octamethyltrisiloxane (L3), decamethyltetrasiloxane (L4), dodecamethylpentasiloxane (L5), in silicone products. Additionally, two different extraction methods were developed to measure these siloxanes migrating into milk, infant formula and liquid simulants (50 and 95% ethanol in water). The limits of quantification (LOQs) of the six siloxanes ranged from 6 ng/g (L3) to 15 ng/g (D6). Silicone nipples and silicone bakewares were extracted using pressurised solvent extraction (PSE) and analysed using the GC-MS-SIM method. No linear siloxanes were detected in the silicone nipple samples analysed. The three cyclic siloxanes (D4, D5 and D6) were detected in all silicone nipple samples with concentrations ranging from 0.5 to 269 µg/g. In the bakeware samples, except for L3, the other five siloxanes were detected with concentrations ranging from 0.2 µg/g (L4) to 7030 µg/g (D6). To investigate the potential migration of the six siloxanes from silicone nipples to milk and infant formula, a liquid extraction and dispersive clean-up procedure was developed for the two matrices. The procedure used a mix of hexane and ethyl acetate (1 : 1, v/v) as extraction solvent and C₁₈ powder as the dispersive clean-up sorbent. For the liquid simulants, extraction of the siloxanes was achieved using hexane without any salting out or clean-up procedures. The recoveries of the six siloxanes from the milk, infant formula and simulants fortified at 50, 100, 200, 500 and 1000 µg/l ranged from 70 to 120% with a relative standard derivation (RSD) of less than 15% (n = 4). Migration tests were performed by exposing milk, infant formula and the liquid simulants to silicone baking sheets with known concentrations of the six siloxanes at 40°C. No siloxanes were detected in milk or infant formula after 6 h of direct contact with the silicone baking sheet plaques, indicating insignificant migration of the siloxanes to milk or infant formula. Migration tests in the two simulants lasted up to 72 h and the three cyclic siloxanes were detected in 50% ethanol after an 8-h exposure and after 2 h in 95% ethanol. The highest detected concentrations of D4, D5 and D6 were 42, 36 and 155 ng/ml, respectively, indicating very limited migration of D4, D5 or D6 into the two simulants.

Single Nucleotide Polymorphism Analysis of European Archaeological M. leprae DNA

PubMed Central

Watson, Claire L.; Lockwood, Diana N. J.

2009-01-01

Background Leprosy was common in Europe eight to twelve centuries ago but molecular confirmation of this has been lacking. We have extracted M. leprae ancient DNA (aDNA) from medieval bones and single nucleotide polymorphism (SNP) typed the DNA, this provides insight into the pattern of leprosy transmission in Europe and may assist in the understanding of M. leprae evolution. Methods and Findings Skeletons have been exhumed from 3 European countries (the United Kingdom, Denmark and Croatia) and are dated around the medieval period (476 to 1350 A.D.). we tested for the presence of 3 previously identified single nucleotide polymorphisms (SNPs) in 10 aDNA extractions. M. leprae aDNA was extracted from 6 of the 10 bone samples. SNP analysis of these 6 extractions were compared to previously analysed European SNP data using the same PCR assays and were found to be the same. Testing for the presence of SNPs in M. leprae DNA extracted from ancient bone samples is a novel approach to analysing European M. leprae DNA and the findings concur with the previously published data that European M. leprae strains fall in to one group (SNP group 3). Conclusions These findings support the suggestion that the M. leprae genome is extremely stable and show that archaeological M. leprae DNA can be analysed to gain detailed information about the genotypic make-up of European leprosy, which may assist in the understanding of leprosy transmission worldwide. PMID:19847306

Application of dispersive liquid-liquid microextraction coupled with vortex-assisted hydrophobic magnetic nanoparticles based solid-phase extraction for determination of aflatoxin M1 in milk samples by sensitive micelle enhanced spectrofluorimetry.

PubMed

Amoli-Diva, Mitra; Taherimaslak, Zohreh; Allahyari, Mehdi; Pourghazi, Kamyar; Manafi, Mohammad Hanif

2015-03-01

An efficient, simple and fast low-density solvent based dispersive liquid-liquid microextraction (LDS-DLLME) followed by vortex-assisted dispersive solid phase extraction (VA-D-SPE) has been developed as a new approach for extraction and preconcentration of aflatoxin M1 in milk samples prior to its micelle enhanced spectrofluorimetic determination. In this LDS-DLLME coupled VA-D-SPE method, milk samples were first treated with methanol/water (80:20, v/v) after removing the fat layer. This solvent was directly used as the dispersing solvent in DLLME along with using 1-heptanol (as a low-density solvent with respect to water) as the extracting solvent. In VA-D-SPE approach, hydrophobic oleic acid modified Fe3O4 nanoparticles were used to retrieve the analyte from the DLLME step. It is considerably that the target of VA-D-SPE was 1-heptanol rather than the aflatoxin M1 directly. The main parameters affecting the efficiency of LDS-DLLME and VA-D-SPE procedures and signal enhancement of aflatoxin M1 were investigated and optimized. Under the optimum conditions, the method was linear in the range from 0.02 to 200 µg L(-1) with the correlation coefficient (R(2)) of 0.9989 and detection limit of 13 ng L(-1). The intra-day precision was 2.9 and 4.3% and the inter-day precision was 2.1 and 3.3% for concentration of 2 and 50 µg L(-1) respectively. The developed method was applied for extraction and preconcentration of AFM1 in three commercially available milk samples and the results were compared with the official AOAC method. Copyright © 2014 Elsevier B.V. All rights reserved.

Separate Perceptual and Neural Processing of Velocity- and Disparity-Based 3D Motion Signals

PubMed Central

Czuba, Thaddeus B.; Cormack, Lawrence K.; Huk, Alexander C.

2016-01-01

Although the visual system uses both velocity- and disparity-based binocular information for computing 3D motion, it is unknown whether (and how) these two signals interact. We found that these two binocular signals are processed distinctly at the levels of both cortical activity in human MT and perception. In human MT, adaptation to both velocity-based and disparity-based 3D motions demonstrated direction-selective neuroimaging responses. However, when adaptation to one cue was probed using the other cue, there was no evidence of interaction between them (i.e., there was no “cross-cue” adaptation). Analogous psychophysical measurements yielded correspondingly weak cross-cue motion aftereffects (MAEs) in the face of very strong within-cue adaptation. In a direct test of perceptual independence, adapting to opposite 3D directions generated by different binocular cues resulted in simultaneous, superimposed, opposite-direction MAEs. These findings suggest that velocity- and disparity-based 3D motion signals may both flow through area MT but constitute distinct signals and pathways. SIGNIFICANCE STATEMENT Recent human neuroimaging and monkey electrophysiology have revealed 3D motion selectivity in area MT, which is driven by both velocity-based and disparity-based 3D motion signals. However, to elucidate the neural mechanisms by which the brain extracts 3D motion given these binocular signals, it is essential to understand how—or indeed if—these two binocular cues interact. We show that velocity-based and disparity-based signals are mostly separate at the levels of both fMRI responses in area MT and perception. Our findings suggest that the two binocular cues for 3D motion might be processed by separate specialized mechanisms. PMID:27798134

Separate Perceptual and Neural Processing of Velocity- and Disparity-Based 3D Motion Signals.

PubMed

Joo, Sung Jun; Czuba, Thaddeus B; Cormack, Lawrence K; Huk, Alexander C

2016-10-19

Although the visual system uses both velocity- and disparity-based binocular information for computing 3D motion, it is unknown whether (and how) these two signals interact. We found that these two binocular signals are processed distinctly at the levels of both cortical activity in human MT and perception. In human MT, adaptation to both velocity-based and disparity-based 3D motions demonstrated direction-selective neuroimaging responses. However, when adaptation to one cue was probed using the other cue, there was no evidence of interaction between them (i.e., there was no "cross-cue" adaptation). Analogous psychophysical measurements yielded correspondingly weak cross-cue motion aftereffects (MAEs) in the face of very strong within-cue adaptation. In a direct test of perceptual independence, adapting to opposite 3D directions generated by different binocular cues resulted in simultaneous, superimposed, opposite-direction MAEs. These findings suggest that velocity- and disparity-based 3D motion signals may both flow through area MT but constitute distinct signals and pathways. Recent human neuroimaging and monkey electrophysiology have revealed 3D motion selectivity in area MT, which is driven by both velocity-based and disparity-based 3D motion signals. However, to elucidate the neural mechanisms by which the brain extracts 3D motion given these binocular signals, it is essential to understand how-or indeed if-these two binocular cues interact. We show that velocity-based and disparity-based signals are mostly separate at the levels of both fMRI responses in area MT and perception. Our findings suggest that the two binocular cues for 3D motion might be processed by separate specialized mechanisms. Copyright © 2016 the authors 0270-6474/16/3610791-12$15.00/0.

a Weighted Closed-Form Solution for Rgb-D Data Registration

NASA Astrophysics Data System (ADS)

Vestena, K. M.; Dos Santos, D. R.; Oilveira, E. M., Jr.; Pavan, N. L.; Khoshelham, K.

2016-06-01

Existing 3D indoor mapping of RGB-D data are prominently point-based and feature-based methods. In most cases iterative closest point (ICP) and its variants are generally used for pairwise registration process. Considering that the ICP algorithm requires an relatively accurate initial transformation and high overlap a weighted closed-form solution for RGB-D data registration is proposed. In this solution, we weighted and normalized the 3D points based on the theoretical random errors and the dual-number quaternions are used to represent the 3D rigid body motion. Basically, dual-number quaternions provide a closed-form solution by minimizing a cost function. The most important advantage of the closed-form solution is that it provides the optimal transformation in one-step, it does not need to calculate good initial estimates and expressively decreases the demand for computer resources in contrast to the iterative method. Basically, first our method exploits RGB information. We employed a scale invariant feature transformation (SIFT) for extracting, detecting, and matching features. It is able to detect and describe local features that are invariant to scaling and rotation. To detect and filter outliers, we used random sample consensus (RANSAC) algorithm, jointly with an statistical dispersion called interquartile range (IQR). After, a new RGB-D loop-closure solution is implemented based on the volumetric information between pair of point clouds and the dispersion of the random errors. The loop-closure consists to recognize when the sensor revisits some region. Finally, a globally consistent map is created to minimize the registration errors via a graph-based optimization. The effectiveness of the proposed method is demonstrated with a Kinect dataset. The experimental results show that the proposed method can properly map the indoor environment with an absolute accuracy around 1.5% of the travel of a trajectory.

Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography.

PubMed

Le Pogam, Adrien; Hatt, Mathieu; Descourt, Patrice; Boussion, Nicolas; Tsoumpas, Charalampos; Turkheimer, Federico E; Prunier-Aesch, Caroline; Baulieu, Jean-Louis; Guilloteau, Denis; Visvikis, Dimitris

2011-09-01

Partial volume effects (PVEs) are consequences of the limited spatial resolution in emission tomography leading to underestimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multiresolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low-resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model, which may introduce artifacts in regions where no significant correlation exists between anatomical and functional details. A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present, the new model outperformed the 2D global approach, avoiding artifacts and significantly improving quality of the corrected images and their quantitative accuracy. A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multiresolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information.

Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography

PubMed Central

Le Pogam, Adrien; Hatt, Mathieu; Descourt, Patrice; Boussion, Nicolas; Tsoumpas, Charalampos; Turkheimer, Federico E.; Prunier-Aesch, Caroline; Baulieu, Jean-Louis; Guilloteau, Denis; Visvikis, Dimitris

2011-01-01

Purpose Partial volume effects (PVE) are consequences of the limited spatial resolution in emission tomography leading to under-estimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multi-resolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model which may introduce artefacts in regions where no significant correlation exists between anatomical and functional details. Methods A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. Results Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present the new model outperformed the 2D global approach, avoiding artefacts and significantly improving quality of the corrected images and their quantitative accuracy. Conclusions A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multi-resolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information. PMID:21978037

Flavonoids from the grains of C1/R-S transgenic rice, the transgenic Oryza sativa spp. japonica, and their radical scavenging activities.

PubMed

Cho, Jin-Gyeong; Song, Na-Young; Nam, Tae-Gyu; Shrestha, Sabina; Park, Hee-Jung; Lyu, Ha-Na; Kim, Dae-Ok; Lee, Gihwan; Woo, Young-Min; Jeong, Tae-Sook; Baek, Nam-In

2013-10-30

The transgenic rice cultivar of Oryza sativa spp. japonica cv. Hwa-Young, C1/R-S transgenic rice (C1/R-S rice), is a flavonoid-rich cultivar of rice. The grains of C1/R-S rice were extracted with aqueous MeOH, and the concentrated extract was partitioned with EtOAc, n-BuOH, and H2O, successively. Repeated silica gel, octadecyl silica gel (ODS), and Sephadex LH-20 column chromatographies for the EtOAc and n-BuOH fractions afforded four new flavonoids (compounds 2, 3, 7, and 8) along with four known flavonoids: (+)-3'-O-methyltaxifolin (1), brassicin (4), isorhamnetin-4'-O-β-D-glucosyranoside (5), and 3'-O-methyltaxifolin-5-O-β-D-glucopyranoside (6). The new flavonoids were identified as 3'-O-methyltaxifolin-7-O-β-D-glucopyranoside (2), 3'-O-methyltaxifolin-4'-O-β-D-glucopyranoside (3), isorhamnetin-7-O-β-D-cellobioside (brassicin-4″-O-β-D-glucopyranoside) (7), and brassicin-4'-O-β-D-glucosyranoside (8) from the result of spectroscopic data including nuclear magnetic resonance spectrometry (NMR), mass spectrometry (MS), and infrared spectroscopy (IR). Also, quantitative analysis of major flavonoids (compounds 2, 3, and 8) in C1/R-S rice, O. sativa spp. japonica cv. Hwa-Young (HY), and a hybrid of two cultivar (C1/R-S rice/HY) extracts was performed using HPLC experiment. The isolated flavonoids were evaluated for their radical-scavenging effect on DPPH and ABTS radicals.

USING CARBOHYDRATES AS MOLECULAR MARKERS TO DETERMINE THE CONTRIBUTION OF AGRICULTURAL SOIL TO AMBIENT FINE AND COURSE PM

EPA Science Inventory

Project research optimized the quantification technique for carbohydrates that also allows quantification of other non-polar molecular markers based on using an isotopically labeled internal standard (D-glucose-1,2,3,4,5,6,6-d7) to monitor extraction efficiency, extraction usi...

Antiinflammatory triterpenoid saponins from the seeds of Aesculus chinensis.

PubMed

Wei, Feng; Ma, Lin-Yun; Jin, Wen-Tao; Ma, Shuang-Cheng; Han, Guo-Zhu; Khan, Ikhlas Ahmad; Lin, Rui-Chao

2004-10-01

Phytochemical study of the ethanol extract of the seeds of Aesculus chinensis led to the isolation of a new triterpenoid saponin (6), together with five known triterpenoid saponins (1-5). The structure of the new compound was elucidated on the basis of spectral data to be 21,28-di-O-acetylprotoaescigenin-3-O-[beta-D-glucopyranosyl(1-2)][beta-D-glucopyranosyl(1-4)]-beta-D-glucopyranosiduronic acid (aesculiside A, 6). The antiinflammatory activities of the four main saponins (1-4) were compared with those of total saponin extracts, and single saponins showed more potent activity than total saponin extracts in mice.

fMRI Analysis-by-Synthesis Reveals a Dorsal Hierarchy That Extracts Surface Slant.

PubMed

Ban, Hiroshi; Welchman, Andrew E

2015-07-08

The brain's skill in estimating the 3-D orientation of viewed surfaces supports a range of behaviors, from placing an object on a nearby table, to planning the best route when hill walking. This ability relies on integrating depth signals across extensive regions of space that exceed the receptive fields of early sensory neurons. Although hierarchical selection and pooling is central to understanding of the ventral visual pathway, the successive operations in the dorsal stream are poorly understood. Here we use computational modeling of human fMRI signals to probe the computations that extract 3-D surface orientation from binocular disparity. To understand how representations evolve across the hierarchy, we developed an inference approach using a series of generative models to explain the empirical fMRI data in different cortical areas. Specifically, we simulated the responses of candidate visual processing algorithms and tested how well they explained fMRI responses. Thereby we demonstrate a hierarchical refinement of visual representations moving from the representation of edges and figure-ground segmentation (V1, V2) to spatially extensive disparity gradients in V3A. We show that responses in V3A are little affected by low-level image covariates, and have a partial tolerance to the overall depth position. Finally, we show that responses in V3A parallel perceptual judgments of slant. This reveals a relatively short computational hierarchy that captures key information about the 3-D structure of nearby surfaces, and more generally demonstrates an analysis approach that may be of merit in a diverse range of brain imaging domains. Copyright © 2015 Ban and Welchman.

Anaerobic Aryl Reductive Dehalogenation of Halobenzoates by Cell Extracts of “Desulfomonile tiedjei”

PubMed Central

DeWeerd, Kim A.; Suflita, Joseph M.

1990-01-01

We studied the transformation of halogenated benzoates by cell extracts of a dehalogenating anaerobe, “Desulfomonile tiedjei.” We found that cell extracts possessed aryl reductive dehalogenation activity. The activity was heat labile and dependent on the addition of reduced methyl viologen, but not on that of reduced NAD, NADP, flavin mononucleotide, flavin adenine dinucleotide, desulfoviridin, cytochrome c3, or benzyl viologen. Dehalogenation activity in extracts was stimulated by formate, CO, or H2, but not by pyruvate plus coenzyme A or by dithionite. The pH and temperature optima for aryl dehalogenation were 8.2 and 35°C, respectively. The rate of dehalogenation was proportional to the amount of protein in the assay mixture. The substrate specificity of aryl dehalogenation activity for various aromatic compounds in “D. tiedjei” cell extracts was identical to that of whole cells, except differences were observed in the relative rates of halobenzoate transformation. Dehalogenation was 10-fold greater in “D. tiedjei” extracts prepared from cells cultured in the presence of 3-chlorobenzoate, suggesting that the activity was inducible. Aryl reductive dehalogenation in extracts was inhibited by sulfite, sulfide, and thiosulfate, but not sulfate. Experiments with combinations of substrates suggested that cell extracts dehalogenated 3-iodobenzoate more readily than either 3,5-dichlorobenzoate or 3-chlorobenzoate. Dehalogenation activity was found to be membrane associated. This is the first report characterizing aryl dehalogenation activity in cell extracts of an obligate anaerobe. PMID:16348308

The Growth of SGC-7901 Tumor Xenografts Was Suppressed by Chinese Bayberry Anthocyanin Extract through Upregulating KLF6 Gene Expression.

PubMed

Wang, Yue; Zhang, Xia-Nan; Xie, Wen-Hua; Zheng, Yi-Xiong; Cao, Jin-Ping; Cao, Pei-Rang; Chen, Qing-Jun; Li, Xian; Sun, Chong-de

2016-09-27

To investigate the antitumor effect of anthocyanins extracted from Chinese bayberry fruit ( Myrica rubra Sieb. et Zucc.), a nude mouse tumor xenograft model was established. Treatments with C3G (cyanidin-3-glucoside, an anthocyanin) significantly suppressed the growth of SGC-7901 tumor xenografts in a dose-dependent manner. Immunohistochemical staining showed a significant increase in p21 expression, indicating that the cell cycle of tumor xenografts was inhibited. qPCR screening showed that C3G treatment up-regulated the expression of the KLF6 gene, which is an important tumor suppressor gene inactivated in many human cancers. Western blot showed that C3G treatments markedly increased KLF6 and p21 protein levels, inhibited CDK4 and Cyclin D1 expression, but did not notably change the expression of p53. These results indicated that KLF6 up-regulates p21 in a p53-independent manner and significantly reduces tumor proliferation. This study provides important information for the possible mechanism of C3G-induced antitumor activity against gastric adenocarcinoma in vivo.

The Growth of SGC-7901 Tumor Xenografts Was Suppressed by Chinese Bayberry Anthocyanin Extract through Upregulating KLF6 Gene Expression

PubMed Central

Wang, Yue; Zhang, Xia-nan; Xie, Wen-hua; Zheng, Yi-xiong; Cao, Jin-ping; Cao, Pei-rang; Chen, Qing-jun; Li, Xian; Sun, Chong-de

2016-01-01

To investigate the antitumor effect of anthocyanins extracted from Chinese bayberry fruit (Myrica rubra Sieb. et Zucc.), a nude mouse tumor xenograft model was established. Treatments with C3G (cyanidin-3-glucoside, an anthocyanin) significantly suppressed the growth of SGC-7901 tumor xenografts in a dose-dependent manner. Immunohistochemical staining showed a significant increase in p21 expression, indicating that the cell cycle of tumor xenografts was inhibited. qPCR screening showed that C3G treatment up-regulated the expression of the KLF6 gene, which is an important tumor suppressor gene inactivated in many human cancers. Western blot showed that C3G treatments markedly increased KLF6 and p21 protein levels, inhibited CDK4 and Cyclin D1 expression, but did not notably change the expression of p53. These results indicated that KLF6 up-regulates p21 in a p53-independent manner and significantly reduces tumor proliferation. This study provides important information for the possible mechanism of C3G-induced antitumor activity against gastric adenocarcinoma in vivo. PMID:27690088

Two-dimensional correlation infrared spectroscopy applied to analyzing and identifying the extracts of Baeckea frutescens medicinal materials.

PubMed

Adib, Adiana Mohamed; Jamaludin, Fadzureena; Kiong, Ling Sui; Hashim, Nuziah; Abdullah, Zunoliza

2014-08-05

Baeckea frutescens or locally known as Cucur atap is used as antibacterial, antidysentery, antipyretic and diuretic agent. In Malaysia and Indonesia, they are used as an ingredient of the traditional medicine given to mothers during confinement. A three-steps infra-red (IR) macro-fingerprinting method combining conventional IR spectra, and the secondary derivative spectra with two dimensional infrared correlation spectroscopy (2D-IR) have been proved to be effective methods to examine a complicated mixture such as herbal medicines. This study investigated the feasibility of employing multi-steps IR spectroscopy in order to study the main constituents of B. frutescens and its different extracts (extracted by chloroform, ethyl acetate, methanol and aqueous in turn). The findings indicated that FT-IR and 2D-IR can provide many holistic variation rules of chemical constituents. The structural information of the samples indicated that B. frutescens and its extracts contain a large amount of flavonoids, since some characteristic absorption peaks of flavonoids, such as ∼1600cm(-1), ∼1500cm(-1), ∼1450cm(-1), and ∼1270cm(-1) can be observed. The macroscopical fingerprint characters of FT-IR and 2D-IR spectra can not only provide the information of main chemical constituents in medicinal materials and their different extracts, but also compare the components differences among the similar samples. In conclusion, the multi-steps IR macro-fingerprint method is rapid, effective, visual and accurate for pharmaceutical research. Copyright © 2014 Elsevier B.V. All rights reserved.

The Application of Chinese High-Spatial Remote Sensing Satellite Image in Land Law Enforcement Information Extraction

NASA Astrophysics Data System (ADS)

Wang, N.; Yang, R.

2018-04-01

Chinese high -resolution (HR) remote sensing satellites have made huge leap in the past decade. Commercial satellite datasets, such as GF-1, GF-2 and ZY-3 images, the panchromatic images (PAN) resolution of them are 2 m, 1 m and 2.1 m and the multispectral images (MS) resolution are 8 m, 4 m, 5.8 m respectively have been emerged in recent years. Chinese HR satellite imagery has been free downloaded for public welfare purposes using. Local government began to employ more professional technician to improve traditional land management technology. This paper focused on analysing the actual requirements of the applications in government land law enforcement in Guangxi Autonomous Region. 66 counties in Guangxi Autonomous Region were selected for illegal land utilization spot extraction with fusion Chinese HR images. The procedure contains: A. Defines illegal land utilization spot type. B. Data collection, GF-1, GF-2, and ZY-3 datasets were acquired in the first half year of 2016 and other auxiliary data were collected in 2015. C. Batch process, HR images were collected for batch preprocessing through ENVI/IDL tool. D. Illegal land utilization spot extraction by visual interpretation. E. Obtaining attribute data with ArcGIS Geoprocessor (GP) model. F. Thematic mapping and surveying. Through analysing 42 counties results, law enforcement officials found 1092 illegal land using spots and 16 suspicious illegal mining spots. The results show that Chinese HR satellite images have great potential for feature information extraction and the processing procedure appears robust.

Extracting leaf area index using viewing geometry effects-A new perspective on high-resolution unmanned aerial system photography

NASA Astrophysics Data System (ADS)

Roth, Lukas; Aasen, Helge; Walter, Achim; Liebisch, Frank

2018-07-01

Extraction of leaf area index (LAI) is an important prerequisite in numerous studies related to plant ecology, physiology and breeding. LAI is indicative for the performance of a plant canopy and of its potential for growth and yield. In this study, a novel method to estimate LAI based on RGB images taken by an unmanned aerial system (UAS) is introduced. Soybean was taken as the model crop of investigation. The method integrates viewing geometry information in an approach related to gap fraction theory. A 3-D simulation of virtual canopies helped developing and verifying the underlying model. In addition, the method includes techniques to extract plot based data from individual oblique images using image projection, as well as image segmentation applying an active learning approach. Data from a soybean field experiment were used to validate the method. The thereby measured LAI prediction accuracy was comparable with the one of a gap fraction-based handheld device (R2 of 0.92 , RMSE of 0.42 m 2m-2) and correlated well with destructive LAI measurements (R2 of 0.89 , RMSE of 0.41 m2 m-2). These results indicate that, if respecting the range (LAI ≤ 3) the method was tested for, extracting LAI from UAS derived RGB images using viewing geometry information represents a valid alternative to destructive and optical handheld device LAI measurements in soybean. Thereby, we open the door for automated, high-throughput assessment of LAI in plant and crop science.

Investigating Recombination and Charge Carrier Dynamics in a One-Dimensional Nanopillared Perovskite Absorber.

PubMed

Kwon, Hyeok-Chan; Yang, Wooseok; Lee, Daehee; Ahn, Jihoon; Lee, Eunsong; Ma, Sunihl; Kim, Kyungmi; Yun, Seong-Cheol; Moon, Jooho

2018-05-22

Organometal halide perovskite materials have become an exciting research topic as manifested by intense development of thin film solar cells. Although high-performance solar-cell-based planar and mesoscopic configurations have been reported, one-dimensional (1-D) nanostructured perovskite solar cells are rarely investigated despite their expected promising optoelectrical properties, such as enhanced charge transport/extraction. Herein, we have analyzed the 1-D nanostructure effects of organometal halide perovskite (CH 3 NH 3 PbI 3- x Cl x ) on recombination and charge carrier dynamics by utilizing a nanoporous anodized alumina oxide scaffold to fabricate a vertically aligned 1-D nanopillared array with controllable diameters. It was observed that the 1-D perovskite exhibits faster charge transport/extraction characteristics, lower defect density, and lower bulk resistance than the planar counterpart. As the aspect ratio increases in the 1-D structures, in addition, the charge transport/extraction rate is enhanced and the resistance further decreases. However, when the aspect ratio reaches 6.67 (diameter ∼30 nm), the recombination rate is aggravated due to high interface-to-volume ratio-induced defect generation. To obtain the full benefits of 1-D perovskite nanostructuring, our study provides a design rule to choose the appropriate aspect ratio of 1-D perovskite structures for improved photovoltaic and other optoelectrical applications.

3D-shape of objects with straight line-motion by simultaneous projection of color coded patterns

NASA Astrophysics Data System (ADS)

Flores, Jorge L.; Ayubi, Gaston A.; Di Martino, J. Matías; Castillo, Oscar E.; Ferrari, Jose A.

2018-05-01

In this work, we propose a novel technique to retrieve the 3D shape of dynamic objects by the simultaneous projection of a fringe pattern and a homogeneous light pattern which are both coded in two of the color channels of a RGB image. The fringe pattern, red channel, is used to retrieve the phase by phase-shift algorithms with arbitrary phase-step, while the homogeneous pattern, blue channel, is used to match pixels from the test object in consecutive images, which are acquired at different positions, and thus, to determine the speed of the object. The proposed method successfully overcomes the standard requirement of projecting fringes of two different frequencies; one frequency to extract object information and the other one to retrieve the phase. Validation experiments are presented.

New steroidal saponin and antiulcer activity from Solanum paniculatum L.

PubMed

Vieira Júnior, Gerardo Magela; da Rocha, Cláudia Quintino; de Souza Rodrigues, Tamires; Hiruma-Lima, Clélia Akiko; Vilegas, Wagner

2015-11-01

Solanum paniculatum L. (Solanaceae) is a plant species widespread throughout tropical America, especially in the Brazilian Savanna region. It is used in Brazil for culinary purposes and in folk medicine to treat liver and gastric dysfunctions, as well as hangovers. Fractionation of the ethanolic extracts (70%) from aerial parts (leaves and twigs) of S. paniculatum led to the isolation of the two new saponins (22R, 23S, 25R)-3β, 6α, 23-trihydroxy-5α-spirostane 6-O-β-D-xylopyranosyl-(1" → 3"')-O-[β-D-quinovopyranosyl(1″' → 2')]-O-[α-L-rhamnopyranosyl(1" → 3')]-O-β-D-quinovopyranoside (1) and diosgenin 3-O-β-D-glucopyranosyl(1" → 6')-O-β-D-glucopyranoside (2) together with four know compounds: caffeic acid (3), diosgenin β-D-glucopyranoside (4), rutin (5), and quercetin 3-O-α-L-rhamnopyranosyl (1"' → 6 ″)-O-β-D-galactopyranoside (6). The structures of these compounds were elucidated by extensive use of 1D and 2D NMR experiments along with HRESIMS analyses. Different doses (31.25-500 mg/kg) of ethanolic extract of leaves from S. paniculatum were evaluated against gastric ulcer induced by ethanol in rats. The lower dose of extract able to promote antiulcer effect was 125 mg/kg. The treatment with S. paniculatum by oral route was able to decrease gastric lesion area and also reduced levels of myeloperoxidase (MPO) in the gastric mucosa. Our results reveal for the first time, steroidal saponins from S. paniculatum and the antiulcer effect of this species at this lower dose. Copyright © 2014 Elsevier Ltd. All rights reserved.

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

Denoised and texture enhanced MVCT to improve soft tissue conspicuity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Ke, E-mail: ksheng@mednet.ucla.edu; Qi, Sharon X.; Gou, Shuiping

Purpose: MVCT images have been used in TomoTherapy treatment to align patients based on bony anatomies but its usefulness for soft tissue registration, delineation, and adaptive radiation therapy is limited due to insignificant photoelectric interaction components and the presence of noise resulting from low detector quantum efficiency of megavoltage x-rays. Algebraic reconstruction with sparsity regularizers as well as local denoising methods has not significantly improved the soft tissue conspicuity. The authors aim to utilize a nonlocal means denoising method and texture enhancement to recover the soft tissue information in MVCT (DeTECT). Methods: A block matching 3D (BM3D) algorithm was adaptedmore » to reduce the noise while keeping the texture information of the MVCT images. Following imaging denoising, a saliency map was created to further enhance visual conspicuity of low contrast structures. In this study, BM3D and saliency maps were applied to MVCT images of a CT imaging quality phantom, a head and neck, and four prostate patients. Following these steps, the contrast-to-noise ratios (CNRs) were quantified. Results: By applying BM3D denoising and saliency map, postprocessed MVCT images show remarkable improvements in imaging contrast without compromising resolution. For the head and neck patient, the difficult-to-see lymph nodes and vein in the carotid space in the original MVCT image became conspicuous in DeTECT. For the prostate patients, the ambiguous boundary between the bladder and the prostate in the original MVCT was clarified. The CNRs of phantom low contrast inserts were improved from 1.48 and 3.8 to 13.67 and 16.17, respectively. The CNRs of two regions-of-interest were improved from 1.5 and 3.17 to 3.14 and 15.76, respectively, for the head and neck patient. DeTECT also increased the CNR of prostate from 0.13 to 1.46 for the four prostate patients. The results are substantially better than a local denoising method using anisotropic diffusion. Conclusions: The authors showed that it is feasible to extract more soft tissue contrast information from the noisy MVCT images using a nonlocal means 3D block matching method in combination with saliency maps, revealing information that was originally unperceivable to human observers.« less

3D refraction correction and extraction of clinical parameters from spectral domain optical coherence tomography of the cornea.

PubMed

Zhao, Mingtao; Kuo, Anthony N; Izatt, Joseph A

2010-04-26

Capable of three-dimensional imaging of the cornea with micrometer-scale resolution, spectral domain-optical coherence tomography (SDOCT) offers potential advantages over Placido ring and Scheimpflug photography based systems for accurate extraction of quantitative keratometric parameters. In this work, an SDOCT scanning protocol and motion correction algorithm were implemented to minimize the effects of patient motion during data acquisition. Procedures are described for correction of image data artifacts resulting from 3D refraction of SDOCT light in the cornea and from non-idealities of the scanning system geometry performed as a pre-requisite for accurate parameter extraction. Zernike polynomial 3D reconstruction and a recursive half searching algorithm (RHSA) were implemented to extract clinical keratometric parameters including anterior and posterior radii of curvature, central cornea optical power, central corneal thickness, and thickness maps of the cornea. Accuracy and repeatability of the extracted parameters obtained using a commercial 859nm SDOCT retinal imaging system with a corneal adapter were assessed using a rigid gas permeable (RGP) contact lens as a phantom target. Extraction of these parameters was performed in vivo in 3 patients and compared to commercial Placido topography and Scheimpflug photography systems. The repeatability of SDOCT central corneal power measured in vivo was 0.18 Diopters, and the difference observed between the systems averaged 0.1 Diopters between SDOCT and Scheimpflug photography, and 0.6 Diopters between SDOCT and Placido topography.

3D GGO candidate extraction in lung CT images using multilevel thresholding on supervoxels

NASA Astrophysics Data System (ADS)

Huang, Shan; Liu, Xiabi; Han, Guanghui; Zhao, Xinming; Zhao, Yanfeng; Zhou, Chunwu

2018-02-01

The earlier detection of ground glass opacity (GGO) is of great importance since GGOs are more likely to be malignant than solid nodules. However, the detection of GGO is a difficult task in lung cancer screening. This paper proposes a novel GGO candidate extraction method, which performs multilevel thresholding on supervoxels in 3D lung CT images. Firstly, we segment the lung parenchyma based on Otsu algorithm. Secondly, the voxels which are adjacent in 3D discrete space and sharing similar grayscale are clustered into supervoxels. This procedure is used to enhance GGOs and reduce computational complexity. Thirdly, Hessian matrix is used to emphasize focal GGO candidates. Lastly, an improved adaptive multilevel thresholding method is applied on segmented clusters to extract GGO candidates. The proposed method was evaluated on a set of 19 lung CT scans containing 166 GGO lesions from the Lung CT Imaging Signs (LISS) database. The experimental results show that our proposed GGO candidate extraction method is effective, with a sensitivity of 100% and 26.3 of false positives per scan (665 GGO candidates, 499 non-GGO regions and 166 GGO regions). It can handle both focal GGOs and diffuse GGOs.

Efficient generation of holographic news ticker in holographic 3DTV

NASA Astrophysics Data System (ADS)

Kim, Seung-Cheol; Kim, Eun-Soo

2009-08-01

News ticker is used to show breaking news or news headlines in conventional 2-D broadcasting system. For the case of the breaking news, the fast creation is need, because the information should be sent quickly. In addition, if holographic 3- D broadcasting system is started in the future, news ticker will remain. On the other hands, some approaches for generation of CGH patterns have been suggested like the ray-tracing method and look-up table (LUT) method. However, these methods have some drawbacks that needs much time or needs huge memory size for look-up table. Recently, a novel LUT (N-LUT) method for fast generation of CGH patterns of 3-D objects with a dramatically reduced LUT without the loss of computational speed was proposed. Therefore, we proposed the method to efficiently generate the holographic news ticker in holographic 3DTV or 3-D movies using N-LUT method. The proposed method is largely consisted of five steps: construction of the LUT for each character, extraction of characters in news ticker, generation and shift of the CGH pattern for news ticker using the LUT for each character, composition of hologram pattern for 3-D video and hologram pattern for news ticker and reconstruct the holographic 3D video with news ticker. To confirm the proposed method, moving car in front of the castle is used as a 3D video and the words 'HOLOGRAM CAPTION GENERATOR' is used as a news ticker. From this simulation results confirmed the feasibility of the proposed method in fast generation of CGH patterns for holographic captions.

3D confocal Raman imaging of oil-rich emulsion from enzyme-assisted aqueous extraction of extruded soybean powder.

PubMed

Wu, Longkun; Wang, Limin; Qi, Baokun; Zhang, Xiaonan; Chen, Fusheng; Li, Yang; Sui, Xiaonan; Jiang, Lianzhou

2018-05-30

The understanding of the structure morphology of oil-rich emulsion from enzyme-assisted extraction processing (EAEP) was a critical step to break the oil-rich emulsion structure in order to recover oil. Albeit EAEP method has been applied as an alternative way to conventional solvent extraction method, the structure morphology of oil-rich emulsion was still unclear. The current study aimed to investigate the structure morphology of oil-rich emulsion from EAEP using 3D confocal Raman imaging technique. With increasing the enzymatic hydrolysis duration from 1 to 3 h, the stability of oil-rich emulsion was decreased as visualized in the 3D confocal Raman images that the protein and oil were mixed together. The subsequent Raman spectrum analysis further revealed that the decreased stability of oil-rich emulsion was due to the protein aggregations via SS bonds or protein-lipid interactions. The conformational transfer in protein indicated the formation of a compact structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Polysaccharide structure of tetrasporic red seaweed Tichocarpus crinitus.

PubMed

Byankina Barabanova, A O; Sokolova, E V; Anastyuk, S D; Isakov, V V; Glazunov, V P; Volod'ko, A V; Yakovleva, I M; Solov'eva, T F; Yermak, I M

2013-10-15

Sulfated polysaccharide isolated from tetrasporic plants of Tichocarpus crinitus was investigated. The polysaccharide was isolated by two methods: with water extraction at 80 °C (HT) and with a mild alkaline extraction (AE). The extracted polysaccharides were presented by non-gelling ones only, while galactose and 3,6-AG were the main monosaccharides, at the same time amount of 3,6-AG in AE polysaccharides was the similar to that of HT. According to methods of spectroscopy and mass spectrometry, the polysaccharide from tetrasporic T. crinitus contains main blocks of 1,3-linked β-D-galactopyranosyl-2,4-disulfates and 1,4-linked 3,6-anhydro-α-D-galactopyranosyl while 6-sulfated 4-linked galactopyranosyl resudies are randomly distributed along the polysaccharide chain. The alkaline treatment of HT polysaccharide results in obtaining polysaccharide with regular structure that composed of alternating 1,3-linked β-D-galactopyranosyl-2,4-disulfates and 1,4-linked 3,6-anhydro-α-D-galactopyranosyl residues. Native polysaccharide (HT) possessed both high anticoagulant and antiplatelet activity measured by fibrin clotting and platelet aggregation induced by collagen. This activity could be connected with peculiar chemical structure of HT polysaccharide which has high sulfation degree and contains also 3,6-anhydrogalactose in the polymer chain. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of NaClO-treated multiwalled carbon nanotubes as solid phase extraction sorbents for preconcentration of trace 2,4-dichlorophenoxyacetic acid in aqueous samples.

PubMed

Lu, Ping; Deng, Dayi; Ni, Xiaodan

2012-09-01

Multiwalled carbon nanotubes functionalized by oxidation of original multiwalled carbon nanotubes with NaClO were prepared and their application as solid phase extraction sorbent for 2,4-dichlorophenoxyacetic acid (2,4-D) was investigated systemically, and a new method was developed for the determination of trace 2,4-D in water samples based on extraction and preconcentration of 2,4-D with solid phase extraction columns packed with NaClO-treated multiwalled carbon nanotubes prior to its determination by HPLC. The optimum experimental parameters for preconcentration of 2,4-D, including the column activating conditions, the amount of the sorbent, pH of the sample, elution composition, and elution volume, were investigated. The results indicated 2,4-D could be quantitatively retained by 100 mg NaClO-treated multiwalled carbon nanotubes at pH 5, and then eluted completely with 10 mL 3:1 (v/v) methanol-ammonium acetate solution (0.3 mol/L). The detection limit of this method for 2,4-D was 0.15 μg/L, and the relative standard deviation was 2.3% for fortified tap water samples and 2.5% for fortified riverine water sample at the 10 μg/L level. The method was validated using fortified tap water and riverine water samples with known amount of 2,4-D at the 0.4, 10, and 30 μg/L levels, respectively. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Neuroprotective Properties of Compounds Extracted from Dianthus superbus L. against Glutamate-induced Cell Death in HT22 Cells

PubMed Central

Yun, Bo-Ra; Yang, Hye Jin; Weon, Jin Bae; Lee, Jiwoo; Eom, Min Rye; Ma, Choong Je

2016-01-01

Background: Dianthus superbus L. has been used in Chinese herbal medicine as a diuretic and anti-inflammatory agent. Objective: In this study, we isolated ten bioactive compounds from D. superbus and evaluated their neuroprotective activity against glutamate-induced cell death in the hippocampal neuronal HT22 cells. Materials and Methods: New compound, (E)-methyl-4-hydroxy-4-(8a-methyl-3-oxodecahydronaphthalen-4a-yl) (1) and, nine known compounds, diosmetin-7-O (2’’,6’’-di-O-α-L-rhamnopyranosyl)-β-D-glucopyranoside (2), 4-hydroxy-3-methoxy-pentyl ester benzenepropanoic acid (3), vanillic acid (4), 4-hydroxy-benzeneacetic acid (5), 4-methoxybenzeneacetic acid (6), (E)-4-methoxycinnamic acid (7), 3-methoxy-4-hydroxyphenylethanol (8), hydroferulic acid (9), and methyl hydroferulate (10), were isolated by bioactivity-guided separation. Structures of the isolated compounds were identified on the basis of 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional NMR spectra, while their neuroprotective properties were evaluated by performing the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Results: D. superbus extract had a neuroprotective effect and isolated 10 compounds. Among the compounds, compounds 5 and 6 effectively protected HT22 cells against glutamate toxicity. Conclusion: In conclusion, the extract of D. superbus and compounds isolated from it exhibited neuroprotective properties, suggesting therapeutic potential for applications in neurotoxic diseases. SUMMARY D. superbus extract significantly protected on glutamate-induced cell death in HT22 cellsNew compound, (E)-methyl-4-hydroxy-4-(8a-methyl-3-oxodecahydronaphthalen-4a-yl) (1) and, nine known compounds, diosmetin-7-O(2’’,6’’-di-O-α-L-rhamnopyranosyl)-β-D-glucopyranoside (2), 4-hydroxy-3-methoxy-pentyl ester benzenepropanoic acid (3), vanillic acid (4), 4-hydroxy-benzeneacetic acid (5), 4-methoxybenzeneacetic acid (6), (E)-4-methoxycinnamic acid (7), 3-methoxy-4-hydroxyphenylethanol (8), hydroferulic acid (9), and methyl hydroferulate (10) were isolated from D. superbus extract4-hydroxy-benzeneacetic acid and 4-methoxybenzeneacetic acid showed significant protective activity against glutamate-induced toxicity in HT22 cells. Abbreviations used: CNS: Central nervous system, ROS: Reactive oxygen species, CHCl3: Chloroform, EtOAc: Ethyl acetate, BuOH: Butanol, HPLC: High performance liquid chromatography, TLC: Thin layer chromatography, MPLC: Middle performance liquid chromatography, MeOH: Methanol, OD: Optical density, COSY: Correlation spectroscopy, HMQC: Heteronuclear multiple-quantum correlation, HMBC: Heteronuclear multiple-bond correlation, HR-MS: High-resolution molecular spectroscopy, MTT: 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. PMID:27076746