Arbitrary real-time three-dimensional corporal object sensing and reconstruction scheme

A real-time three-dimensional (3D) object sensing and reconstruction scheme is presented that can be applied on any arbitrary corporeal shape. Operation is demonstrated on several calibrated objects. The system uses curvature sensors based upon in-line fiber Bragg gratings encapsulated in a low-temperature curing synthetic silicone. New methods to quantitatively evaluate the performance of a 3D object-sensing scheme are developed and appraised. It is shown that the sensing scheme yields a volumetric error of 1% to 9%, depending on the object.

Respiratory function monitoring using a real-time three-dimensional fiber-optic shaping sensing scheme based upon fiber Bragg gratings

An array of in-line curvature sensors on a garment is used to monitor the thoracic and abdominal movements of a human during respiration. The results are used to obtain volumetric changes of the human torso in agreement with a spirometer used simultaneously at the mouth. The array of 40 in-line fiber Bragg gratings is used to produce 20 curvature sensors at different locations, each sensor consisting of two fiber Bragg gratings. The 20 curvature sensors and adjoining fiber are encapsulated into a low-temperature-cured synthetic silicone. The sensors are wavelength interrogated by a commercially available system from Moog Insensys, and the wavelength changes are calibrated to recover curvature. A three-dimensional algorithm is used to generate shape changes during respiration that allow the measurement of absolute volume changes at various sections of the torso. It is shown that the sensing scheme yields a volumetric error of 6%. Comparing the volume data obtained from the spirometer with the volume estimated with the synchronous data from the shape-sensing array yielded a correlation value 0.86 with a Pearson's correlation coefficient p <0.01.

Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Three-dimensional fluid pressure mapping in porous media using magnetic resonance imaging with gas-filled liposomes

This paper presents and demonstrates a method for using magnetic resonance imaging to measure local pressure of a fluid saturating a porous medium. The method is tested both in a static system of packed silica gel and in saturated sintered glass cylinders experiencing fluid flow. The fluid used contains 3% gas in the form of 3-μm average diameter gas filled 1,2-distearoyl-sn-glycero-3-phosphocholine (C18:0, MW: 790.16) liposomes suspended in 5% glycerol and 0.5% Methyl cellulose with water. Preliminary studies at 2.35 T demonstrate relative magnetic resonance signal changes of 20% per bar in bulk fluid for an echo time TE=40 ms, and 6-10% in consolidated porous media for TE=10 ms, over the range 0.8-1.8 bar for a spatial resolution of 0.1 mm3 and a temporal resolution of 30 s. The stability of this solution with relation to applied pressure and methods for improving sensitivity are discussed. © 2007 Elsevier Inc. All rights reserved.

Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Respiratory function monitoring using a real-time three-dimensional fiber-optic shaping sensing scheme based upon fiber Bragg gratings

An array of in-line curvature sensors on a garment is used to monitor the thoracic and abdominal movements of a human during respiration. The results are used to obtain volumetric changes of the human torso in agreement with a spirometer used simultaneously at the mouth. The array of 40 in-line fiber Bragg gratings is used to produce 20 curvature sensors at different locations, each sensor consisting of two fiber Bragg gratings. The 20 curvature sensors and adjoining fiber are encapsulated into a low-temperature-cured synthetic silicone. The sensors are wavelength interrogated by a commercially available system from Moog Insensys, and the wavelength changes are calibrated to recover curvature. A three-dimensional algorithm is used to generate shape changes during respiration that allow the measurement of absolute volume changes at various sections of the torso. It is shown that the sensing scheme yields a volumetric error of 6%. Comparing the volume data obtained from the spirometer with the volume estimated with the synchronous data from the shape-sensing array yielded a correlation value 0.86 with a Pearson's correlation coefficient p <0.01.

Estimation of uncertainty in three-dimensional coordinate measurement by comparison with calibrated points

This paper details a method of estimating the uncertainty of dimensional measurement for a three-dimensional coordinate measurement machine. An experimental procedure was developed to compare three-dimensional coordinate measurements with calibrated reference points. The reference standard used to calibrate these reference points was a fringe counting interferometer with a multilateration-like technique employed to establish three-dimensional coordinates. This is an extension of the established technique of comparing measured lengths with calibrated lengths. Specifically a distributed coordinate measurement device was tested which consisted of a network of Rotary-Laser Automatic Theodolites (R-LATs), this system is known commercially as indoor GPS (iGPS). The method was found to be practical and was used to estimate that the uncertainty of measurement for the basic iGPS system is approximately 1 mm at a 95% confidence level throughout a measurement volume of approximately 10 m × 10 m × 1.5 m. © 2010 IOP Publishing Ltd.

Effect of blood flow patterns on localized platelet adhesion under physiologic flow conditions using two-dimensional and three-dimensional stent models: An experimental and computational approach

This dissertation presents dynamic flow experiments with fluorescently labeled platelets to allow for spatial observation of wall attachment in inter-strut spacings, to investigate their relationship to flow patterns. Human blood with fluorescently labeled platelets was circulated through an in vitro system that produced physiologic pulsatile flow in (1) a parallel plate blow chamber that contained two-dimensional (2D) stents that feature completely recirculating flow, partially recirculating flow, and completely reattached flow, and (2) a three-dimensional (3D) cylindrical tube that contained stents of various geometric designs. ^ Flow detachment and reattachment points exhibited very low platelet deposition. Platelet deposition was very low in the recirculation regions in the 3D stents unlike the 2D stents. Deposition distal to a strut was always high in 2D and 3D stents. Spirally recirculating regions were found in 3D unlike in 2D stents, where the deposition was higher than at well-separated regions of recirculation. ^

Three-dimensional brain fiber tracking modeling in diffusion tensor imaging

This dissertation establishes the foundation for a new 3-D visual interface integrating Magnetic Resonance Imaging (MRI) to Diffusion Tensor Imaging (DTI). The need for such an interface is critical for understanding brain dynamics, and for providing more accurate diagnosis of key brain dysfunctions in terms of neuronal connectivity. ^ This work involved two research fronts: (1) the development of new image processing and visualization techniques in order to accurately establish relational positioning of neuronal fiber tracts and key landmarks in 3-D brain atlases, and (2) the obligation to address the computational requirements such that the processing time is within the practical bounds of clinical settings. The system was evaluated using data from thirty patients and volunteers with the Brain Institute at Miami Children's Hospital. ^ Innovative visualization mechanisms allow for the first time white matter fiber tracts to be displayed alongside key anatomical structures within accurately registered 3-D semi-transparent images of the brain. ^ The segmentation algorithm is based on the calculation of mathematically-tuned thresholds and region-detection modules. The uniqueness of the algorithm is in its ability to perform fast and accurate segmentation of the ventricles. In contrast to the manual selection of the ventricles, which averaged over 12 minutes, the segmentation algorithm averaged less than 10 seconds in its execution. ^ The registration algorithm established searches and compares MR with DT images of the same subject, where derived correlation measures quantify the resulting accuracy. Overall, the images were 27% more correlated after registration, while an average of 1.5 seconds is all it took to execute the processes of registration, interpolation, and re-slicing of the images all at the same time and in all the given dimensions. ^ This interface was fully embedded into a fiber-tracking software system in order to establish an optimal research environment. This highly integrated 3-D visualization system reached a practical level that makes it ready for clinical deployment. ^

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.

Cell-cell communication in three dimensional microenvironments

Cellular behavior is dependent on a variety of extracellular cues required for normal tissue function, wound healing, and activation of the immune system. Removed from their in vivo microenvironment and cultured in vitro, cells lose many environmental cues and that may result in abberant behavior, making it difficult to study cellular processes. In order to mimic native tissue environments, optical tweezer and microfluidic technologies were used to place cells within defined areas of the culture environment. To provide three dimensional supports found in natural tissues, hydrogel scaffolds of poly (ethylene glycol) diacrylate and the basement membrane matrix Matrigel were used. Optical tweezer technology allowed precision placement and formation of homotypic and heterotypic arrays of human U937, HEK 293, and porcine mesenchymal stem cells. Alternatively, two microfluidic devices were designed to pattern Matrigel scaffolds. The first microfluidic device utilized laminar flow to spatially pattern multiple cell types within the device. Gradients of soluble molecules were then be formed and manipulated across the Matrigel scaffolds. Patterning Matrigel using laminar flow techniques require microfluidic expertise and do not produce consistent patterning conditions, limiting their use difficult in most cell culture laboratories. Thus, a buried Matrigel polydimethylsiloxane (PDMS) device was developed for spatial patterning of biological scaffolds. Matrigel is injected into micron sized channels of PDMS fabricated by soft lithography and allowed to thermally cure. Following curing, a second PDMS device was placed on top of the buried Matrigel channels to support media flow. In order to validate these systems, a cell-cell communication model system was developed utilizing LPS and TNFα signaling with fluorescent reporter systems to monitor communication in real time. We demonstrated the utility of microfluidic devices to support the cell-cell communication model system by co culturing three cell types within Matrigel scaffolds and monitoring signaling activity via fluorescent reporters.

Three dimensional numerical simulation of thermohaline currents of the Persian Gulf

Observational data and a three dimensional numerical model (POM) are used to investigate the Persian Gulf outflow structure and its spreading pathway into the Oman Sea. The model is based on orthogonal curvilinear coordinate system in horizontal and train following coordinate (sigma coordinate) system in vertical. In the simulation, the horizontal diffusivity coefficients are calculated form Smogorinsky diffusivity formula and the eddy vertical diffusivities are obtained from a second turbulence closure model (namely Mellor-Yamada level 2.5 model of turbulence). The modeling area includes the east of the Persian Gulf, the Oman Sea and a part of the north-east of the Indian Ocean. In the model, the horizontal grid spacing was assumed to be about 3.5 km and the number of vertical levels was set to 32. The simulations show that the mean salinity of the PG outflow does not change substantially during the year and is about 39 psu, while its temperature exhibits seasonal variations. These lead to variations in outflow density in a way that is has its maximum density in late winter (March) and its minimum in mid-summer (August). At the entrance to the Oman Sea, the PG outflow turns to the right due to Coriolis Effect and falls down on the continental slope until it gains its equilibrium depth. The highest density of the outflow during March causes it to sink more into the deeper depths in contrast to that of August which the density is the lowest one. Hence, the neutral buoyancy depths of the outflow are about 500 m and 250 m for March and August respectively. Then, the outflow spreads in its equilibrium depths in the Oman Sea in vicinity of western and southern boundaries until it approach the Ras al Hamra Cape where the water depth suddenly begins to increase. Therefore, during March, the outflow that is deeper and wider relative to August, is more affected by the steep slope topography and as a result of vortex stretching mechanism and conservation of potential vorticity it separates from the lateral boundaries and finally forms an anti-cyclonic eddy in the Oman Sea. But during August the outflow moves as before in vicinity of lateral boundaries. In addition, the interaction of the PG outflow with tide in the Strait of Hormuz leads to intermittency in outflow movement into the Oman Sea and it could be the major reason for generations of Peddy (Peddies) in the Oman Sea.

Three-dimensional kinetic adaptations of gait throughout pregnancy and postpartum

Biomechanical adaptations that occur during pregnancy can lead to changes on gait pattern. Nevertheless, these adaptations of gait are still not fully understood. The purpose was to determine the effect of pregnancy on the biomechanical pattern of walking, regarding the kinetic parameters. A three-dimensional analysis was performed in eleven participants. The kinetic parameters in the joints of the lower limb during gait were compared at the end of the first, second, and third trimesters of pregnancy and in the postpartum period, in healthy pregnant women. The main results showed a reduction in the normalized vertical reaction forces, throughout pregnancy, particularly the third peak. Pregnant women showed, during most of the stance phase, medial reaction forces as a motor response to promote the body stability. Bilateral changes were observed in hip joint, with a decrease in the participation of the hip extensors and in the eccentric contraction of hip flexors. In ankle joint a decrease in the participation of ankle plantar flexors was found. In conclusion, the overall results point to biomechanical adjustments that showed a decrease of the mechanical load of women throughout pregnancy, with exception for few unilateral changes of hip joint moments.

Three-dimensional kinetic adaptations of gait throughout pregnancy and postpartum

Biomechanical adaptations that occur during pregnancy can lead to changes on gait pattern. Nevertheless, these adaptations of gait are still not fully understood. The purpose was to determine the effect of pregnancy on the biomechanical pattern of walking, regarding the kinetic parameters. A three-dimensional analysis was performed in eleven participants. The kinetic parameters in the joints of the lower limb during gait were compared at the end of the first, second, and third trimesters of pregnancy and in the postpartum period, in healthy pregnant women. The main results showed a reduction in the normalized vertical reaction forces, throughout pregnancy, particularly the third peak. Pregnant women showed, during most of the stance phase, medial reaction forces as a motor response to promote the body stability. Bilateral changes were observed in hip joint, with a decrease in the participation of the hip extensors and in the eccentric contraction of hip flexors. In ankle joint a decrease in the participation of ankle plantar flexors was found. In conclusion, the overall results point to biomechanical adjustments that showed a decrease of the mechanical load of women throughout pregnancy, with exception for few unilateral changes of hip joint moments.

Effects Of High Pressure Homogenization On The Activity, Stability, Kinetics And Three-dimensional Conformation Of A Glucose Oxidase Produced By Aspergillus Niger.

High pressure homogenization (HPH) is a non-thermal method, which has been employed to change the activity and stability of biotechnologically relevant enzymes. This work investigated how HPH affects the structural and functional characteristics of a glucose oxidase (GO) from Aspergillus niger. The enzyme was homogenized at 75 and 150 MPa and the effects were evaluated with respect to the enzyme activity, stability, kinetic parameters and molecular structure. The enzyme showed a pH-dependent response to the HPH treatment, with reduction or maintenance of activity at pH 4.5-6.0 and a remarkable activity increase (30-300%) at pH 6.5 in all tested temperatures (15, 50 and 75°C). The enzyme thermal tolerance was reduced due to HPH treatment and the storage for 24 h at high temperatures (50 and 75°C) also caused a reduction of activity. Interestingly, at lower temperatures (15°C) the activity levels were slightly higher than that observed for native enzyme or at least maintained. These effects of HPH treatment on function and stability of GO were further investigated by spectroscopic methods. Both fluorescence and circular dichroism revealed conformational changes in the molecular structure of the enzyme that might be associated with the distinct functional and stability behavior of GO.