Digital surface model, hillshade and orthophoto of the world's largest fossil oyster reef, links to GeoTIFFs

The world's largest fossil oyster reef, formed by the giant oyster Crassostrea gryphoides and located in Stetten (north of Vienna, Austria) is studied by Harzhauser et al., 2015, 2016; Djuricic et al., 2016. Digital documentation of the unique geological site is provided by terrestrial laser scanning (TLS) at the millimeter scale. Obtaining meaningful results is not merely a matter of data acquisition with a suitable device; it requires proper planning, data management, and postprocessing. Terrestrial laser scanning technology has a high potential for providing precise 3D mapping that serves as the basis for automatic object detection in different scenarios; however, it faces challenges in the presence of large amounts of data and the irregular geometry of an oyster reef. We provide a detailed description of the techniques and strategy used for data collection and processing in Djuricic et al., 2016. The use of laser scanning provided the ability to measure surface points of 46,840 (estimated) shells. They are up to 60-cm-long oyster specimens, and their surfaces are modeled with a high accuracy of 1 mm. In addition to laser scanning measurements, more than 300 photographs were captured, and an orthophoto mosaic was generated with a ground sampling distance (GSD) of 0.5 mm. This high-resolution 3D information and the photographic texture serve as the basis for ongoing and future geological and paleontological analyses. Moreover, they provide unprecedented documentation for conservation issues at a unique natural heritage site.

On precise three-dimensional environment modeling via UAV-based photogrammetric systems

Abstract : Images acquired from unmanned aerial vehicles (UAVs) can provide data with unprecedented spatial and temporal resolution for three-dimensional (3D) modeling. Solutions developed for this purpose are mainly operating based on photogrammetry concepts, namely UAV-Photogrammetry Systems (UAV-PS). Such systems are used in applications where both geospatial and visual information of the environment is required. These applications include, but are not limited to, natural resource management such as precision agriculture, military and police-related services such as traffic-law enforcement, precision engineering such as infrastructure inspection, and health services such as epidemic emergency management. UAV-photogrammetry systems can be differentiated based on their spatial characteristics in terms of accuracy and resolution. That is some applications, such as precision engineering, require high-resolution and high-accuracy information of the environment (e.g. 3D modeling with less than one centimeter accuracy and resolution). In other applications, lower levels of accuracy might be sufficient, (e.g. wildlife management needing few decimeters of resolution). However, even in those applications, the specific characteristics of UAV-PSs should be well considered in the steps of both system development and application in order to yield satisfying results. In this regard, this thesis presents a comprehensive review of the applications of unmanned aerial imagery, where the objective was to determine the challenges that remote-sensing applications of UAV systems currently face. This review also allowed recognizing the specific characteristics and requirements of UAV-PSs, which are mostly ignored or not thoroughly assessed in recent studies. Accordingly, the focus of the first part of this thesis is on exploring the methodological and experimental aspects of implementing a UAV-PS. The developed system was extensively evaluated for precise modeling of an open-pit gravel mine and performing volumetric-change measurements. This application was selected for two main reasons. Firstly, this case study provided a challenging environment for 3D modeling, in terms of scale changes, terrain relief variations as well as structure and texture diversities. Secondly, open-pit-mine monitoring demands high levels of accuracy, which justifies our efforts to improve the developed UAV-PS to its maximum capacities. The hardware of the system consisted of an electric-powered helicopter, a high-resolution digital camera, and an inertial navigation system. The software of the system included the in-house programs specifically designed for camera calibration, platform calibration, system integration, onboard data acquisition, flight planning and ground control point (GCP) detection. The detailed features of the system are discussed in the thesis, and solutions are proposed in order to enhance the system and its photogrammetric outputs. The accuracy of the results was evaluated under various mapping conditions, including direct georeferencing and indirect georeferencing with different numbers, distributions and types of ground control points. Additionally, the effects of imaging configuration and network stability on modeling accuracy were assessed. The second part of this thesis concentrates on improving the techniques of sparse and dense reconstruction. The proposed solutions are alternatives to traditional aerial photogrammetry techniques, properly adapted to specific characteristics of unmanned, low-altitude imagery. Firstly, a method was developed for robust sparse matching and epipolar-geometry estimation. The main achievement of this method was its capacity to handle a very high percentage of outliers (errors among corresponding points) with remarkable computational efficiency (compared to the state-of-the-art techniques). Secondly, a block bundle adjustment (BBA) strategy was proposed based on the integration of intrinsic camera calibration parameters as pseudo-observations to Gauss-Helmert model. The principal advantage of this strategy was controlling the adverse effect of unstable imaging networks and noisy image observations on the accuracy of self-calibration. The sparse implementation of this strategy was also performed, which allowed its application to data sets containing a lot of tie points. Finally, the concepts of intrinsic curves were revisited for dense stereo matching. The proposed technique could achieve a high level of accuracy and efficiency by searching only through a small fraction of the whole disparity search space as well as internally handling occlusions and matching ambiguities. These photogrammetric solutions were extensively tested using synthetic data, close-range images and the images acquired from the gravel-pit mine. Achieving absolute 3D mapping accuracy of 11±7 mm illustrated the success of this system for high-precision modeling of the environment.

Design of Streaming Media Panoramic Video System Based on WebGL

2016 is the outbreak year of the virtual reality industry. In the field of virtual reality, 3D surveying plays an important role. Nowadays, 3D surveying technology has received increasing attention. This project aims to establish and optimize a WebGL three-dimensional broadcast platform combined with streaming media technology. It takes streaming media server and panoramic video broadcast in browser as the application background. Simultaneously, it discusses about the architecture from streaming media server to panoramic media player and analyzing relevant theory problem. This paper focuses on the debugging of streaming media platform, the structure of WebGL player environment, different types of ball model analysis, and the 3D mapping technology. The main work contains the following points: Initially, relay on Easy Darwin open source streaming media server, built a streaming service platform. It can realize the transmission from RTSP stream to streaming media server, and forwards HLS slice video to clients; Then, wrote a WebGL panoramic video player based on Three.js lib with JQuery browser playback controls. Set up a HTML5 panoramic video player; Next, analyzed the latitude and longitude sphere model which from Three.js library according to WebGL rendering method. Pointed out the drawbacks of this model and the breakthrough point of improvement; After that, on the basis of Schneider transform principle, established the Schneider sphere projection model, and converted the output OBJ file to JS file for media player reading. Finally implemented real time panoramic video high precision playing without plugin; At last, I summarized the whole project. Put forward the direction of future optimization and extensible market.

3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents

Tuberculosis (TB) is the primary cause of mortality among infectious diseases. Mycobacterium tuberculosis monophosphate kinase (TMPKmt) is essential to DNA replication. Thus, this enzyme represents a promising target for developing new drugs against TB. In the present study, the receptor-independent, RI, 4D-QSAR method has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 81 thymidine analogues, and two corresponding subsets, reported as inhibitors of TMPKmt. The resulting optimized models are not only statistically significant with r (2) ranging from 0.83 to 0.92 and q (2) from 0.78 to 0.88, but also are robustly predictive based on test set predictions. The most and the least potent inhibitors in their respective postulated active conformations, derived from each of the models, were docked in the active site of the TMPKmt crystal structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. Moreover, the QSAR models provide insights regarding a probable mechanism of action of the analogues.

Rational Design and 3D-Pharmacophore Mapping of 5 `-Thiourea-Substituted alpha-Thymidine Analogues as Mycobacterial TMPK Inhibitors

Thymidine monophosphate kinase (TMPK) has emerged as an attractive target for developing inhibitors of Mycobacterium tuberculosis growth. In this study the receptor-independent (RI) 4D-QSAR formalism has been used to develop QSAR models and corresponding 3D-pharmacophores for a set of 5`-thiourea-substituted alpha-thymidine inhibitors. Models were developed for the entire training set and for a subset of the training set consisting of the most potent inhibitors. The optimized (RI) 4D-QSAR models are statistically significant (r(2) = 0.90, q(2) = 0.83 entire set, r(2) = 0.86, q(2) = 0.80 high potency subset) and also possess good predictivity based on test set predictions. The most and least potent inhibitors, in their respective postulated active conformations derived from the models, were docked in the active site of the TMPK crystallographic structure. There is a solid consistency between the 3D-pharmacophore sites defined by the QSAR models and interactions with binding site residues. This model identifies new regions of the inhibitors that contain pharmacophore sites, such as the sugar-pyrimidine ring structure and the region of the 5`-arylthiourea moiety. These new regions of the ligands can be further explored and possibly exploited to identify new, novel, and, perhaps, better antituberculosis inhibitors of TMPKmt. Furthermore, the 3D-pharmacophores defined by these models can be used as a starting point for future receptor-dependent antituberculosis drug design as well as to elucidate candidate sites for substituent addition to optimize ADMET properties of analog inhibitors.

Feasibility of T2* mapping for the evaluation of hip joint cartilage at 1.5T using a three-dimensional (3D), gradient-echo (GRE) sequence: a prospective study

This study defines the feasibility of utilizing three-dimensional (3D) gradient-echo (GRE) MRI at 1.5T for T(2)* mapping to assess hip joint cartilage degenerative changes using standard morphological MR grading while comparing it to delayed gadolinium-enhanced MRI of cartilage (dGEMRIC). MRI was obtained from 10 asymptomatic young adult volunteers and 33 patients with symptomatic femoroacetabular impingement (FAI). The protocol included T(2)* mapping without gadolinium-enhancement utilizing a 3D-GRE sequence with six echoes, and after gadolinium injection, routine hip sequences, and a dual-flip-angle 3D-GRE sequence for dGEMRIC T(1) mapping. Cartilage was classified as normal, with mild changes, or with severe degenerative changes based on morphological MRI. T(1) and T(2)* findings were subsequently correlated. There were significant differences between volunteers and patients in normally-rated cartilage only for T(1) values. Both T(1) and T(2)* values decreased significantly with the various grades of cartilage damage. There was a statistically significant correlation between standard MRI and T(2)* (T(1)) (P < 0.05). High intraclass correlation was noted for both T(1) and T(2)*. Correlation factor was 0.860 to 0.954 (T(2)*-T(1) intraobserver) and 0.826 to 0.867 (T(2)*-T(1) interobserver). It is feasible to gather further information about cartilage status within the hip joint using GRE T(2)* mapping at 1.5T.

Caracterização e modelação de fissuras em edifícios utilizando 3D laser scanning, com vista à sua reabilitação

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil

Is multidimensional scaling suitable for mapping the input respiratory impedance in subjects and patients?

This paper presents the application of multidimensional scaling (MDS) analysis to data emerging from noninvasive lung function tests, namely the input respiratory impedance. The aim is to obtain a geometrical mapping of the diseases in a 3D space representation, allowing analysis of (dis)similarities between subjects within the same pathology groups, as well as between the various groups. The adult patient groups investigated were healthy, diagnosed chronic obstructive pulmonary disease (COPD) and diagnosed kyphoscoliosis, respectively. The children patient groups were healthy, asthma and cystic fibrosis. The results suggest that MDS can be successfully employed for mapping purposes of restrictive (kyphoscoliosis) and obstructive (COPD) pathologies. Hence, MDS tools can be further examined to define clear limits between pools of patients for clinical classification, and used as a training aid for medical traineeship.

Virtual Campus for the University of Jaume I, Castelló, Spain: 3D Modelling of the Campus Buildings using CityEngine

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Preliminary regional rockfall hazard mapping using LIDAR-based slope frequency distribution and CONEFALL modeling

A factor limiting preliminary rockfall hazard mapping at regional scale is often the lack of knowledge of potential source areas. Nowadays, high resolution topographic data (LiDAR) can account for realistic landscape details even at large scale. With such fine-scale morphological variability, quantitative geomorphometric analyses become a relevant approach for delineating potential rockfall instabilities. Using digital elevation model (DEM)-based ?slope families? concept over areas of similar lithology and cliffs and screes zones available from the 1:25,000 topographic map, a susceptibility rockfall hazard map was drawn up in the canton of Vaud, Switzerland, in order to provide a relevant hazard overview. Slope surfaces over morphometrically-defined thresholds angles were considered as rockfall source zones. 3D modelling (CONEFALL) was then applied on each of the estimated source zones in order to assess the maximum runout length. Comparison with known events and other rockfall hazard assessments are in good agreement, showing that it is possible to assess rockfall activities over large areas from DEM-based parameters and topographical elements.

MP2RAGE, a self bias-field corrected sequence for improved segmentation and T-1-mapping at high field

The large spatial inhomogeneity in transmit B, field (B-1(+)) observable in human MR images at hi h static magnetic fields (B-0) severely impairs image quality. To overcome this effect in brain T-1-weighted images the, MPRAGE sequence was modified to generate two different images at different inversion times MP2RAGE By combining the two images in a novel fashion, it was possible to create T-1-weigthed images where the result image was free of proton density contrast, T-2* contrast, reception bias field, and, to first order transmit field inhomogeneity. MP2RAGE sequence parameters were optimized using Bloch equations to maximize contrast-to-noise ratio per unit of time between brain tissues and minimize the effect of B-1(+) variations through space. Images of high anatomical quality and excellent brain tissue differentiation suitable for applications such as segmentation and voxel-based morphometry were obtained at 3 and 7 T. From such T-1-weighted images, acquired within 12 min, high-resolution 3D T-1 maps were routinely calculated at 7 T with sub-millimeter voxel resolution (0.65-0.85 mm isotropic). T-1 maps were validated in phantom experiments. In humans, the T, values obtained at 7 T were 1.15 +/- 0.06 s for white matter (WM) and 1.92 +/- 0.16 s for grey matter (GM), in good agreement with literature values obtained at lower spatial resolution. At 3 T, where whole-brain acquisitions with 1 mm isotropic voxels were acquired in 8 min the T-1 values obtained (0.81 +/- 0.03 S for WM and 1.35 +/- 0.05 for GM) were once again found to be in very good agreement with values in the literature. (C) 2009 Elsevier Inc. All rights reserved.

Mapping complex tissue architecture with diffusion spectrum magnetic resonance imaging.

Methods are presented to map complex fiber architectures in tissues by imaging the 3D spectra of tissue water diffusion with MR. First, theoretical considerations show why and under what conditions diffusion contrast is positive. Using this result, spin displacement spectra that are conventionally phase-encoded can be accurately reconstructed by a Fourier transform of the measured signal's modulus. Second, studies of in vitro and in vivo samples demonstrate correspondence between the orientational maxima of the diffusion spectrum and those of the fiber orientation density at each location. In specimens with complex muscular tissue, such as the tongue, diffusion spectrum images show characteristic local heterogeneities of fiber architectures, including angular dispersion and intersection. Cerebral diffusion spectra acquired in normal human subjects resolve known white matter tracts and tract intersections. Finally, the relation between the presented model-free imaging technique and other available diffusion MRI schemes is discussed.

MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field.

The large spatial inhomogeneity in transmit B(1) field (B(1)(+)) observable in human MR images at high static magnetic fields (B(0)) severely impairs image quality. To overcome this effect in brain T(1)-weighted images, the MPRAGE sequence was modified to generate two different images at different inversion times, MP2RAGE. By combining the two images in a novel fashion, it was possible to create T(1)-weighted images where the result image was free of proton density contrast, T(2) contrast, reception bias field, and, to first order, transmit field inhomogeneity. MP2RAGE sequence parameters were optimized using Bloch equations to maximize contrast-to-noise ratio per unit of time between brain tissues and minimize the effect of B(1)(+) variations through space. Images of high anatomical quality and excellent brain tissue differentiation suitable for applications such as segmentation and voxel-based morphometry were obtained at 3 and 7 T. From such T(1)-weighted images, acquired within 12 min, high-resolution 3D T(1) maps were routinely calculated at 7 T with sub-millimeter voxel resolution (0.65-0.85 mm isotropic). T(1) maps were validated in phantom experiments. In humans, the T(1) values obtained at 7 T were 1.15+/-0.06 s for white matter (WM) and 1.92+/-0.16 s for grey matter (GM), in good agreement with literature values obtained at lower spatial resolution. At 3 T, where whole-brain acquisitions with 1 mm isotropic voxels were acquired in 8 min, the T(1) values obtained (0.81+/-0.03 s for WM and 1.35+/-0.05 for GM) were once again found to be in very good agreement with values in the literature.

Ambulatory assessment of 3D ground reaction force using plantar pressure distribution.

This study aimed to use the plantar pressure insole for estimating the three-dimensional ground reaction force (GRF) as well as the frictional torque (T(F)) during walking. Eleven subjects, six healthy and five patients with ankle disease participated in the study while wearing pressure insoles during several walking trials on a force-plate. The plantar pressure distribution was analyzed and 10 principal components of 24 regional pressure values with the stance time percentage (STP) were considered for GRF and T(F) estimation. Both linear and non-linear approximators were used for estimating the GRF and T(F) based on two learning strategies using intra-subject and inter-subjects data. The RMS error and the correlation coefficient between the approximators and the actual patterns obtained from force-plate were calculated. Our results showed better performance for non-linear approximation especially when the STP was considered as input. The least errors were observed for vertical force (4%) and anterior-posterior force (7.3%), while the medial-lateral force (11.3%) and frictional torque (14.7%) had higher errors. The result obtained for the patients showed higher error; nevertheless, when the data of the same patient were used for learning, the results were improved and in general slight differences with healthy subjects were observed. In conclusion, this study showed that ambulatory pressure insole with data normalization, an optimal choice of inputs and a well-trained nonlinear mapping function can estimate efficiently the three-dimensional ground reaction force and frictional torque in consecutive gait cycle without requiring a force-plate.