A novel phantom and method for comprehensive 3-dimensional measurement and correction of geometric distortion in magnetic resonance imaging

A phantom that can be used for mapping geometric distortion in magnetic resonance imaging (MRI) is described. This phantom provides an array of densely distributed control points in three-dimensional (3D) space. These points form the basis of a comprehensive measurement method to correct for geometric distortion in MR images arising principally from gradient field non-linearity and magnet field inhomogeneity. The phantom was designed based on the concept that a point in space can be defined using three orthogonal planes. This novel design approach allows for as many control points as desired. Employing this novel design, a highly accurate method has been developed that enables the positions of the control points to be measured to sub-voxel accuracy. The phantom described in this paper was constructed to fit into a body coil of a MRI scanner, (external dimensions of the phantom were: 310 mm x 310 mm x 310 mm), and it contained 10,830 control points. With this phantom, the mean errors in the measured coordinates of the control points were on the order of 0.1 mm or less, which were less than one tenth of the voxel's dimensions of the phantom image. The calculated three-dimensional distortion map, i.e., the differences between the image positions and true positions of the control points, can then be used to compensate for geometric distortion for a full image restoration. It is anticipated that this novel method will have an impact on the applicability of MRI in both clinical and research settings. especially in areas where geometric accuracy is highly required, such as in MR neuro-imaging. (C) 2004 Elsevier Inc. All rights reserved.

Geometric distortion in clinical MRI systems - Part I: evaluation using a 3D phantom

Recently, a 3D phantom that can provide a comprehensive and accurate measurement of the geometric distortion in MRI has been developed. Using this phantom, a full assessment of the geometric distortion in a number of clinical MRI systems (GE and Siemens) has been carried out and detailed results are presented in this paper. As expected, the main source of geometric distortion in modern superconducting MRI systems arises from the gradient field nonlinearity. Significantly large distortions with maximum absolute geometric errors ranged between 10 and 25 mm within a volume of 240 x 240 x 240 mm(3) were observed when imaging with the new generation of gradient systems that employs shorter coils. By comparison, the geometric distortion was much less in the older-generation gradient systems. With the vendor's correction method, the geometric distortion measured was significantly reduced but only within the plane in which these 2D correction methods were applied. Distortion along the axis normal to the plane was, as expected, virtually unchanged. Two-dimensional correction methods are a convenient approach and in principle they are the only methods that can be applied to correct geometric distortion in a single slice or in multiple noncontiguous slices. However, these methods only provide an incomplete solution to the problem and their value can be significantly reduced if the distortion along the normal of the correction plane is not small. (C) 2004 Elsevier Inc. All rights reserved.

Developments in contact lens measurement:a comparative study of industry standard geometric inspection and optical coherence tomography

Purpose: The aim of this study was to compare a developmental optical coherence tomography (OCT) based contact lens inspection instrument to a widely used geometric inspection instrument (Optimec JCF), to establish the capability of a market focused OCT system. Methods: Measurements of 27 soft spherical contact lenses were made using the Optimec JCF and a new OCT based instrument, the Optimec is830. Twelve of the lenses analysed were specially commissioned from a traditional hydrogel (Contamac GM Advance 49%) and 12 from a silicone hydrogel (Contamac Definitive 65), each set with a range of back optic zone radius (BOZR) and centre thickness (CT) values. Three commercial lenses were also measured; CooperVision MyDay (Stenfilcon A) in −10D, −3D and +6D powers. Two measurements of BOZR, CT and total diameter were made for each lens in temperature controlled saline on both instruments. Results: The results showed that the is830 and JCF measurements were comparable, but that the is830 had a better repeatability coefficient for BOZR (0.065 mm compared to 0.151 mm) and CT (0.008 mm compared to 0.027 mm). Both instruments had similar results for total diameter (0.041 mm compared to 0.044 mm). Conclusions: The OCT based instrument assessed in this study is able to match and improve on the JCF instrument for the measurement of total diameter, back optic zone radius and centre thickness for soft contact lenses in temperature controlled saline.

Characterization of time-resolved laser differential phase using 3D complementary cumulative distribution functions

An experimental method for characterizing the time-resolved phase noise of a fast switching tunable laser is discussed. The method experimentally determines a complementary cumulative distribution function of the laser's differential phase as a function of time after a switching event. A time resolved bit error rate of differential quadrature phase shift keying formatted data, calculated using the phase noise measurements, was fitted to an experimental time-resolved bit error rate measurement using a field programmable gate array, finding a good agreement between the time-resolved bit error rates.

Integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre for DNA probe immobilization

In this paper, we demonstrate the integration of a 3D hydrogel matrix within a hollow core photonic crystal fibre (HC-PCF). In addition, we also show the fluorescence of Cy5-labelled DNA molecules immobilized within the hydrogel formed in two different types of HC-PCF. The 3D hydrogel matrix is designed to bind with the amino groups of biomolecules using an appropriate cross-linker, providing higher sensitivity and selectivity than the standard 2D coverage, enabling a greater number of probe molecules to be available per unit area. The HC-PCFs, on the other hand, can be designed to maximize the capture of fluorescence to improve sensitivity and provide longer interaction lengths. This could enable the development of fibre-based point-of-care and remote systems, where the enhanced sensitivity would relax the constraints placed on sources and detectors. In this paper, we will discuss the formation of such polyethylene glycol diacrylate (PEGDA) hydrogels within a HC-PCF, including their optical properties such as light propagation and auto-fluorescence.

2D-3D registration of CT vertebra volume to fluoroscopy projection:a calibration model assessment

This study extends a previous research concerning intervertebral motion registration by means of 2D dynamic fluoroscopy to obtain a more comprehensive 3D description of vertebral kinematics. The problem of estimating the 3D rigid pose of a CT volume of a vertebra from its 2D X-ray fluoroscopy projection is addressed. 2D-3D registration is obtained maximising a measure of similarity between Digitally Reconstructed Radiographs (obtained from the CT volume) and real fluoroscopic projection. X-ray energy correction was performed. To assess the method a calibration model was realised a sheep dry vertebra was rigidly fixed to a frame of reference including metallic markers. Accurate measurement of 3D orientation was obtained via single-camera calibration of the markers and held as true 3D vertebra position; then, vertebra 3D pose was estimated and results compared. Error analysis revealed accuracy of the order of 0.1 degree for the rotation angles of about 1mm for displacements parallel to the fluoroscopic plane, and of order of 10mm for the orthogonal displacement. © 2010 P. Bifulco et al.

Advanced Applications of 3D Dosimetry and 3D Printing in Radiation Therapy

As complex radiotherapy techniques become more readily-practiced, comprehensive 3D dosimetry is a growing necessity for advanced quality assurance. However, clinical implementation has been impeded by a wide variety of factors, including the expense of dedicated optical dosimeter readout tools, high operational costs, and the overall difficulty of use. To address these issues, a novel dry-tank optical CT scanner was designed for PRESAGE 3D dosimeter readout, relying on 3D printed components and omitting costly parts from preceding optical scanners. This work details the design, prototyping, and basic commissioning of the Duke Integrated-lens Optical Scanner (DIOS).

The convex scanning geometry was designed in ScanSim, an in-house Monte Carlo optical ray-tracing simulation. ScanSim parameters were used to build a 3D rendering of a convex ‘solid tank’ for optical-CT, which is capable of collimating a point light source into telecentric geometry without significant quantities of refractive-index matched fluid. The model was 3D printed, processed, and converted into a negative mold via rubber casting to produce a transparent polyurethane scanning tank. The DIOS was assembled with the solid tank, a 3W red LED light source, a computer-controlled rotation stage, and a 12-bit CCD camera. Initial optical phantom studies show negligible spatial inaccuracies in 2D projection images and 3D tomographic reconstructions. A PRESAGE 3D dose measurement for a 4-field box treatment plan from Eclipse shows 95% of voxels passing gamma analysis at 3%/3mm criteria. Gamma analysis between tomographic images of the same dosimeter in the DIOS and DLOS systems show 93.1% agreement at 5%/1mm criteria. From this initial study, the DIOS has demonstrated promise as an economically-viable optical-CT scanner. However, further improvements will be necessary to fully develop this system into an accurate and reliable tool for advanced QA.

Pre-clinical animal studies are used as a conventional means of translational research, as a midpoint between in-vitro cell studies and clinical implementation. However, modern small animal radiotherapy platforms are primitive in comparison with conventional linear accelerators. This work also investigates a series of 3D printed tools to expand the treatment capabilities of the X-RAD 225Cx orthovoltage irradiator, and applies them to a feasibility study of hippocampal avoidance in rodent whole-brain radiotherapy.

As an alternative material to lead, a novel 3D-printable tungsten-composite ABS plastic, GMASS, was tested to create precisely-shaped blocks. Film studies show virtually all primary radiation at 225 kVp can be attenuated by GMASS blocks of 0.5cm thickness. A state-of-the-art software, BlockGen, was used to create custom hippocampus-shaped blocks from medical image data, for any possible axial treatment field arrangement. A custom 3D printed bite block was developed to immobilize and position a supine rat for optimal hippocampal conformity. An immobilized rat CT with digitally-inserted blocks was imported into the SmART-Plan Monte-Carlo simulation software to determine the optimal beam arrangement. Protocols with 4 and 7 equally-spaced fields were considered as viable treatment options, featuring improved hippocampal conformity and whole-brain coverage when compared to prior lateral-opposed protocols. Custom rodent-morphic PRESAGE dosimeters were developed to accurately reflect these treatment scenarios, and a 3D dosimetry study was performed to confirm the SmART-Plan simulations. Measured doses indicate significant hippocampal sparing and moderate whole-brain coverage.

3D modelling of mango fruit skin blush in the tree canopy

The fruit of certain mango cultivars (e.g., 'Honey Gold') can develop blush on their skin. Skin blush due to red pigmentation is from the accumulation of anthocyanins. Anthocyanin biosynthesis is related to environmental determinants, including light received by the fruit. It has been observed that mango skin blush varies with position in the tree canopy. However, little investigation into this spatial relationship has been conducted. The objective of this preliminary study was to describe a 'Honey Gold' mango tree by capturing its three-dimensional (3D) architecture. A light path tracing model QuasiMC was then used to predict light received by fruit. The use of this 3D model was to better understand the relationship between mango fruit skin blush and fruit position in the canopy. The digitised mango tree mimicked the real tree at a high level of detail. Observations on mango skin blush distribution supported the proposition that sunlight exposure is an absolute requirement for anthocyanin development. No blush development occurred on shaded skin. It was affirmed that 3D mapping could allow for virtual experiments. For example, for virtual canopy thinning (e.g., 'window pruning') to admit more sunlight with a view to improve fruit blush. Improvements to 3D modelling of mango skin blush could focus on increasing accuracy, e.g., measurement of leaf light reflectance and transmission and the inclusion of the effect shading by branches.

Estudio comparativo de la fiabilidad y reproducibilidad en la medición de los tamaños dentarios y las medidas de las arcadas dentarias entre registros manuales y digitales 3d obtenidos por escaneado intraoral y extraoral

Tradicionalmente, los ortodoncistas han realizado las mediciones dentales en los modelos de yeso, pero los avances tecnológicos permiten ahora a los ortodoncistas realizar esas mediciones en los modelos digitales. El propósito de este estudio fue comparar la fiabilidad y reproducibilidad de las medidas de los tamaños dentarios y las arcadas dentarias entre el método manual y los métodos digitales 3D obtenidos por un escáner intraoral CEREC Omnicam (Sirona Dental Systems) y dos escáneres extraorales: inEos X5 (Sirona Dental Systems) y Dental Scanner SMART (Open Technologies). Un modelo de yeso, un escaneado intraoral y dos modelos digitales con un escáner extraoral fueron realizadas para cada uno de los 20 sujetos. Las medidas de los tamaños dentarios, la distancia intercanina y la distancia intermolar de los modelos digitales se compararon con los correspondientes modelos de yeso (estándar de oro) Se utilizó el test de ANOVA para establecer la fiabilidad entre los cuatro métodos y el coeficiente de correlación intraclase fue calculado para determinar la reproducibilidad intra- e inter-examinador. Los resultados encontrados fueron que no existieron diferencias estadísticamente significativas entre las medidas hechas directamente en los modelos de yeso y los modelos digitales. Los coeficientes de correlación intraclase tanto intra- e inter-examinador fue alto y considerado bueno para los cuatro métodos de medición. CCI> 0.90. Se concluyó que las mediciones en los modelos digitales obtenidos con un escáner extraoral e intraoral son fiables y reproducibles

POSE ESTIMATION AND 3D RECONSTRUCTION USING SENSOR FUSION

A camera maps 3-dimensional (3D) world space to a 2-dimensional (2D) image space. In the process it loses the depth information, i.e., the distance from the camera focal point to the imaged objects. It is impossible to recover this information from a single image. However, by using two or more images from different viewing angles this information can be recovered, which in turn can be used to obtain the pose (position and orientation) of the camera. Using this pose, a 3D reconstruction of imaged objects in the world can be computed. Numerous algorithms have been proposed and implemented to solve the above problem; these algorithms are commonly called Structure from Motion (SfM). State-of-the-art SfM techniques have been shown to give promising results. However, unlike a Global Positioning System (GPS) or an Inertial Measurement Unit (IMU) which directly give the position and orientation respectively, the camera system estimates it after implementing SfM as mentioned above. This makes the pose obtained from a camera highly sensitive to the images captured and other effects, such as low lighting conditions, poor focus or improper viewing angles. In some applications, for example, an Unmanned Aerial Vehicle (UAV) inspecting a bridge or a robot mapping an environment using Simultaneous Localization and Mapping (SLAM), it is often difficult to capture images with ideal conditions. This report examines the use of SfM methods in such applications and the role of combining multiple sensors, viz., sensor fusion, to achieve more accurate and usable position and reconstruction information. This project investigates the role of sensor fusion in accurately estimating the pose of a camera for the application of 3D reconstruction of a scene. The first set of experiments is conducted in a motion capture room. These results are assumed as ground truth in order to evaluate the strengths and weaknesses of each sensor and to map their coordinate systems. Then a number of scenarios are targeted where SfM fails. The pose estimates obtained from SfM are replaced by those obtained from other sensors and the 3D reconstruction is completed. Quantitative and qualitative comparisons are made between the 3D reconstruction obtained by using only a camera versus that obtained by using the camera along with a LIDAR and/or an IMU. Additionally, the project also works towards the performance issue faced while handling large data sets of high-resolution images by implementing the system on the Superior high performance computing cluster at Michigan Technological University.

Eulerian-Lagrangian definition of coarse bed-load transport: Theory and verification with low-cost inertial measurement units

Fluvial sediment transport is controlled by hydraulics, sediment properties and arrangement, and flow history across a range of time scales. This physical complexity has led to ambiguous definition of the reference frame (Lagrangian or Eulerian) in which sediment transport is analysed. A general Eulerian-Lagrangian approach accounts for inertial characteristics of particles in a Lagrangian (particle fixed) frame, and for the hydrodynamics in an independent Eulerian frame. The necessary Eulerian-Lagrangian transformations are simplified under the assumption of an ideal Inertial Measurement Unit (IMU), rigidly attached at the centre of the mass of a sediment particle. Real, commercially available IMU sensors can provide high frequency data on accelerations and angular velocities (hence forces and energy) experienced by grains during entrainment and motion, if adequately customized. IMUs are subjected to significant error accu- mulation but they can be used for statistical parametrisation of an Eulerian-Lagrangian model, for coarse sediment particles and over the temporal scale of individual entrainment events. In this thesis an Eulerian-Lagrangian model is introduced and evaluated experimentally. Absolute inertial accelerations were recorded at a 4 Hz frequency from a spherical instrumented particle (111 mm diameter and 2383 kg/m3 density) in a series of entrainment threshold experiments on a fixed idealised bed. The grain-top inertial acceleration entrainment threshold was approximated at 44 and 51 mg for slopes 0.026 and 0.037 respectively. The saddle inertial acceleration entrainment threshold was at 32 and 25 mg for slopes 0.044 and 0.057 respectively. For the evaluation of the complete Eulerian-Lagrangian model two prototype sensors are presented: an idealised (spherical) with a diameter of 90 mm and an ellipsoidal with axes 100, 70 and 30 mm. Both are instrumented with a complete IMU, capable of sampling 3D inertial accelerations and 3D angular velocities at 50 Hz. After signal analysis, the results can be used to parametrize sediment movement but they do not contain positional information. The two sensors (spherical and ellipsoidal) were tested in a series of entrainment experiments, similar to the evaluation of the 111 mm prototype, for a slope of 0.02. The spherical sensor entrained at discharges of 24.8 ± 1.8 l/s while the same threshold for the ellipsoidal sensor was 45.2 ± 2.2 l/s. Kinetic energy calculations were used to quantify the particle-bed energy exchange under fluvial (discharge at 30 l/s) and non-fluvial conditions. All the experiments suggest that the effect of the inertial characteristics of coarse sediments on their motion is comparable to the effect hydrodynamic forces. The coupling of IMU sensors with advanced telemetric systems can lead to the tracking of Lagrangian particle trajectories, at a frequency and accuracy that will permit the testing of diffusion/dispersion models across the range of particle diameters.

Improving magnetic coupling for battery charging through 3D magnetic flux

The spatial distribution of the magnetic field and the coupling between the coils in the Wireless Power Transfer (WPT) systems is an important aspect to consider in the system design and efficiency optimization. The presented study in this paper is based on tests performed on a physical model. The transmitting (primary) equipment, is an electrical three-phase system, capable to be connected in star or delta (both electrically and geometrically). The measured results allow to describe graphically the magnetic field distribution in three dimensions. The analytical formulas aim to help to understand and to quantify the physical phenomena but they cannot be considered a universal approach and the measurement results help to understand better the observable facts. In the WPT, the key issues that will influence the efficiency, are the alignment of the coils, the spatial orientation of the magnetic field, the detachment and the tilt between the windings, all they changing the magnetic coupling between the transmitter and the receiver of energy. This research is directed not only to the magnetic field distribution but finally, to optimize the energy transfer efficiency.