Science.gov

Sample records for 3d ultrasound computer

  1. Glasses for 3D ultrasound computer tomography: phase compensation

    NASA Astrophysics Data System (ADS)

    Zapf, M.; Hopp, T.; Ruiter, N. V.

    2016-03-01

    Ultrasound Computer Tomography (USCT), developed at KIT, is a promising new imaging system for breast cancer diagnosis, and was successfully tested in a pilot study. The 3D USCT II prototype consists of several hundreds of ultrasound (US) transducers on a semi-ellipsoidal aperture. Spherical waves are sequentially emitted by individual transducers and received in parallel by many transducers. Reflectivity volumes are reconstructed by synthetic aperture focusing (SAFT). However, straight forward SAFT imaging leads to blurred images due to system imperfections. We present an extension of a previously proposed approach to enhance the images. This approach includes additional a priori information and system characteristics. Now spatial phase compensation was included. The approach was evaluated with a simulation and clinical data sets. An increase in the image quality was observed and quantitatively measured by SNR and other metrics.

  2. 3D ultrasound computer tomography: update from a clinical study

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Zapf, M.; Kretzek, E.; Henrich, J.; Tukalo, A.; Gemmeke, H.; Kaiser, C.; Knaudt, J.; Ruiter, N. V.

    2016-04-01

    Ultrasound Computer Tomography (USCT) is a promising new imaging method for breast cancer diagnosis. We developed a 3D USCT system and tested it in a pilot study with encouraging results: 3D USCT was able to depict two carcinomas, which were present in contrast enhanced MRI volumes serving as ground truth. To overcome severe differences in the breast shape, an image registration was applied. We analyzed the correlation between average sound speed in the breast and the breast density estimated from segmented MRIs and found a positive correlation with R=0.70. Based on the results of the pilot study we now carry out a successive clinical study with 200 patients. For this we integrated our reconstruction methods and image post-processing into a comprehensive workflow. It includes a dedicated DICOM viewer for interactive assessment of fused USCT images. A new preview mode now allows intuitive and faster patient positioning. We updated the USCT system to decrease the data acquisition time by approximately factor two and to increase the penetration depth of the breast into the USCT aperture by 1 cm. Furthermore the compute-intensive reflectivity reconstruction was considerably accelerated, now allowing a sub-millimeter volume reconstruction in approximately 16 minutes. The updates made it possible to successfully image first patients in our ongoing clinical study.

  3. Computer-Assisted Hepatocellular Carcinoma Ablation Planning Based on 3-D Ultrasound Imaging.

    PubMed

    Li, Kai; Su, Zhongzhen; Xu, Erjiao; Guan, Peishan; Li, Liu-Jun; Zheng, Rongqin

    2016-08-01

    To evaluate computer-assisted hepatocellular carcinoma (HCC) ablation planning based on 3-D ultrasound, 3-D ultrasound images of 60 HCC lesions from 58 patients were obtained and transferred to a research toolkit. Compared with virtual manual ablation planning (MAP), virtual computer-assisted ablation planning (CAP) consumed less time and needle insertion numbers and exhibited a higher rate of complete tumor coverage and lower rate of critical structure injury. In MAP, junior operators used less time, but had more critical structure injury than senior operators. For large lesions, CAP performed better than MAP. For lesions near critical structures, CAP resulted in better outcomes than MAP. Compared with MAP, CAP based on 3-D ultrasound imaging was more effective and achieved a higher rate of complete tumor coverage and a lower rate of critical structure injury; it is especially useful for junior operators and with large lesions, and lesions near critical structures. PMID:27126243

  4. Distributed Network, Wireless and Cloud Computing Enabled 3-D Ultrasound; a New Medical Technology Paradigm

    PubMed Central

    Meir, Arie; Rubinsky, Boris

    2009-01-01

    Medical technologies are indispensable to modern medicine. However, they have become exceedingly expensive and complex and are not available to the economically disadvantaged majority of the world population in underdeveloped as well as developed parts of the world. For example, according to the World Health Organization about two thirds of the world population does not have access to medical imaging. In this paper we introduce a new medical technology paradigm centered on wireless technology and cloud computing that was designed to overcome the problems of increasing health technology costs. We demonstrate the value of the concept with an example; the design of a wireless, distributed network and central (cloud) computing enabled three-dimensional (3-D) ultrasound system. Specifically, we demonstrate the feasibility of producing a 3-D high end ultrasound scan at a central computing facility using the raw data acquired at the remote patient site with an inexpensive low end ultrasound transducer designed for 2-D, through a mobile device and wireless connection link between them. Producing high-end 3D ultrasound images with simple low-end transducers reduces the cost of imaging by orders of magnitude. It also removes the requirement of having a highly trained imaging expert at the patient site, since the need for hand-eye coordination and the ability to reconstruct a 3-D mental image from 2-D scans, which is a necessity for high quality ultrasound imaging, is eliminated. This could enable relatively untrained medical workers in developing nations to administer imaging and a more accurate diagnosis, effectively saving the lives of people. PMID:19936236

  5. Distributed network, wireless and cloud computing enabled 3-D ultrasound; a new medical technology paradigm.

    PubMed

    Meir, Arie; Rubinsky, Boris

    2009-01-01

    Medical technologies are indispensable to modern medicine. However, they have become exceedingly expensive and complex and are not available to the economically disadvantaged majority of the world population in underdeveloped as well as developed parts of the world. For example, according to the World Health Organization about two thirds of the world population does not have access to medical imaging. In this paper we introduce a new medical technology paradigm centered on wireless technology and cloud computing that was designed to overcome the problems of increasing health technology costs. We demonstrate the value of the concept with an example; the design of a wireless, distributed network and central (cloud) computing enabled three-dimensional (3-D) ultrasound system. Specifically, we demonstrate the feasibility of producing a 3-D high end ultrasound scan at a central computing facility using the raw data acquired at the remote patient site with an inexpensive low end ultrasound transducer designed for 2-D, through a mobile device and wireless connection link between them. Producing high-end 3D ultrasound images with simple low-end transducers reduces the cost of imaging by orders of magnitude. It also removes the requirement of having a highly trained imaging expert at the patient site, since the need for hand-eye coordination and the ability to reconstruct a 3-D mental image from 2-D scans, which is a necessity for high quality ultrasound imaging, is eliminated. This could enable relatively untrained medical workers in developing nations to administer imaging and a more accurate diagnosis, effectively saving the lives of people. PMID:19936236

  6. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible. PMID:7919882

  7. A visual probe localization and calibration system for cost-effective computer-aided 3D ultrasound.

    PubMed

    Ali, Aziah; Logeswaran, Rajasvaran

    2007-08-01

    The 3D ultrasound systems produce much better reproductions than 2D ultrasound, but their prohibitively high cost deprives many less affluent organization this benefit. This paper proposes using the conventional 2D ultrasound equipment readily available in most hospitals, along with a single conventional digital camera, to construct 3D ultrasound images. The proposed system applies computer vision to extract position information of the ultrasound probe while the scanning takes place. The probe, calibrated in order to calculate the offset of the ultrasound scan from the position of the marker attached to it, is used to scan a number of geometrical objects. Using the proposed system, the 3D volumes of the objects were successfully reconstructed. The system was tested in clinical situations where human body parts were scanned. The results presented, and confirmed by medical staff, are very encouraging for cost-effective implementation of computer-aided 3D ultrasound using a simple setup with 2D ultrasound equipment and a conventional digital camera. PMID:17126314

  8. Registration of 3D ultrasound computer tomography and MRI for evaluation of tissue correspondences

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Dapp, R.; Zapf, M.; Kretzek, E.; Gemmeke, H.; Ruiter, N. V.

    2015-03-01

    3D Ultrasound Computer Tomography (USCT) is a new imaging method for breast cancer diagnosis. In the current state of development it is essential to correlate USCT with a known imaging modality like MRI to evaluate how different tissue types are depicted. Due to different imaging conditions, e.g. with the breast subject to buoyancy in USCT, a direct correlation is demanding. We present a 3D image registration method to reduce positioning differences and allow direct side-by-side comparison of USCT and MRI volumes. It is based on a two-step approach including a buoyancy simulation with a biomechanical model and free form deformations using cubic B-Splines for a surface refinement. Simulation parameters are optimized patient-specifically in a simulated annealing scheme. The method was evaluated with in-vivo datasets resulting in an average registration error below 5mm. Correlating tissue structures can thereby be located in the same or nearby slices in both modalities and three-dimensional non-linear deformations due to the buoyancy are reduced. Image fusion of MRI volumes and USCT sound speed volumes was performed for intuitive display. By applying the registration to data of our first in-vivo study with the KIT 3D USCT, we could correlate several tissue structures in MRI and USCT images and learn how connective tissue, carcinomas and breast implants observed in the MRI are depicted in the USCT imaging modes.

  9. A computational model for estimating tumor margins in complementary tactile and 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Shamsil, Arefin; Escoto, Abelardo; Naish, Michael D.; Patel, Rajni V.

    2016-03-01

    Conventional surgical methods are effective for treating lung tumors; however, they impose high trauma and pain to patients. Minimally invasive surgery is a safer alternative as smaller incisions are required to reach the lung; however, it is challenging due to inadequate intraoperative tumor localization. To address this issue, a mechatronic palpation device was developed that incorporates tactile and ultrasound sensors capable of acquiring surface and cross-sectional images of palpated tissue. Initial work focused on tactile image segmentation and fusion of position-tracked tactile images, resulting in a reconstruction of the palpated surface to compute the spatial locations of underlying tumors. This paper presents a computational model capable of analyzing orthogonally-paired tactile and ultrasound images to compute the surface circumference and depth margins of a tumor. The framework also integrates an error compensation technique and an algebraic model to align all of the image pairs and to estimate the tumor depths within the tracked thickness of a palpated tissue. For validation, an ex vivo experimental study was conducted involving the complete palpation of 11 porcine liver tissues injected with iodine-agar tumors of varying sizes and shapes. The resulting tactile and ultrasound images were then processed using the proposed model to compute the tumor margins and compare them to fluoroscopy based physical measurements. The results show a good negative correlation (r = -0.783, p = 0.004) between the tumor surface margins and a good positive correlation (r = 0.743, p = 0.009) between the tumor depth margins.

  10. Computer-generated 3D ultrasound images of the carotid artery

    NASA Technical Reports Server (NTRS)

    Selzer, Robert H.; Lee, Paul L.; Lai, June Y.; Frieden, Howard J.; Blankenhorn, David H.

    1989-01-01

    A method is under development to measure carotid artery lesions from a computer-generated three-dimensional ultrasound image. For each image, the position of the transducer in six coordinates (x, y, z, azimuth, elevation, and roll) is recorded and used to position each B-mode picture element in its proper spatial position in a three-dimensional memory array. After all B-mode images have been assembled in the memory, the three-dimensional image is filtered and resampled to produce a new series of parallel-plane two-dimensional images from which arterial boundaries are determined using edge tracking methods.

  11. Three different strategies for real-time prostate capsule volume computation from 3-D end-fire transrectal ultrasound.

    PubMed

    Barqawi, Albaha B; Lu, Li; Crawford, E David; Fenster, Aaron; Werahera, Priya N; Kumar, Dinesh; Miller, Steve; Suri, Jasjit S

    2007-01-01

    estimation of prostate capsule volume via segmentation of the prostate from 3-D ultrasound volumetric ultrasound images is a valuable clinical tool, especially during biopsy. Normally, a physician traces the boundaries of the prostate manually, but this process is tedious, laborious, and subject to errors. The prostate capsule edge is computed using three different strategies: (a) least square approach, (b) level set approach, and (c) Discrete Dynamic Contour approach. (a) In the least square method, edge points are defined by searching for the optimal edge based on the average signal characteristics. These edge points constitute an initial curve which is later refined; (b) Level set approach. The images are modeled as piece-wise constant, and the energy functional is defined and minimized. This method is also automated; and (c) The Discrete Dynamic Contour (DDC). A trained user selects several points in the first image and an initial contour is obtained by a model based initialization. Based on this initialization condition, the contour is deformed automatically to better fit the image. This method is semi-automatic. The three methods were tested on database consisting of 15 prostate phantom volumes acquired using a Philips ultrasound machine using an end-fire TRUS. The ground truth (GT) is developed by tracing the boundary of prostate on a slice-by-slice basis. The mean volumes using the least square, level set and DDC techniques were 15.84 cc, 15.55 cc and 16.33 cc, respectively. We validated the methods by calculating the volume with GT and we got an average volume of 15. PMID:18002081

  12. High definition 3D ultrasound imaging.

    PubMed

    Morimoto, A K; Krumm, J C; Kozlowski, D M; Kuhlmann, J L; Wilson, C; Little, C; Dickey, F M; Kwok, K S; Rogers, B; Walsh, N

    1997-01-01

    We have demonstrated high definition and improved resolution using a novel scanning system integrated with a commercial ultrasound machine. The result is a volumetric 3D ultrasound data set that can be visualized using standard techniques. Unlike other 3D ultrasound images, image quality is improved from standard 2D data. Image definition and bandwidth is improved using patent pending techniques. The system can be used to image patients or wounded soldiers for general imaging of anatomy such as abdominal organs, extremities, and the neck. Although the risks associated with x-ray carcinogenesis are relatively low at diagnostic dose levels, concerns remain for individuals in high risk categories. In addition, cost and portability of CT and MRI machines can be prohibitive. In comparison, ultrasound can provide portable, low-cost, non-ionizing imaging. Previous clinical trials comparing ultrasound to CT were used to demonstrate qualitative and quantitative improvements of ultrasound using the Sandia technologies. Transverse leg images demonstrated much higher clarity and lower noise than is seen in traditional ultrasound images. An x-ray CT scan was provided of the same cross-section for comparison. The results of our most recent trials demonstrate the advantages of 3D ultrasound and motion compensation compared with 2D ultrasound. Metal objects can also be observed within the anatomy. PMID:10168958

  13. 3D ultrafast ultrasound imaging in vivo

    NASA Astrophysics Data System (ADS)

    Provost, Jean; Papadacci, Clement; Esteban Arango, Juan; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-10-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra—and inter-observer variability.

  14. 3D Ultrafast Ultrasound Imaging In Vivo

    PubMed Central

    Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-01-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32×32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 3-D Ultrafast Doppler Imaging and finally 3D Ultrafast combined Tissue and Flow Doppler. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3-D Ultrafast Doppler was used to obtain 3-D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, for the first time, the complex 3-D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, and the 3-D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3-D Ultrafast Ultrasound Imaging for the 3-D real-time mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra- and inter-observer variability. PMID:25207828

  15. Computer-aided classification of liver tumors in 3D ultrasound images with combined deformable model segmentation and support vector machine

    NASA Astrophysics Data System (ADS)

    Lee, Myungeun; Kim, Jong Hyo; Park, Moon Ho; Kim, Ye-Hoon; Seong, Yeong Kyeong; Cho, Baek Hwan; Woo, Kyoung-Gu

    2014-03-01

    In this study, we propose a computer-aided classification scheme of liver tumor in 3D ultrasound by using a combination of deformable model segmentation and support vector machine. For segmentation of tumors in 3D ultrasound images, a novel segmentation model was used which combined edge, region, and contour smoothness energies. Then four features were extracted from the segmented tumor including tumor edge, roundness, contrast, and internal texture. We used a support vector machine for the classification of features. The performance of the developed method was evaluated with a dataset of 79 cases including 20 cysts, 20 hemangiomas, and 39 hepatocellular carcinomas, as determined by the radiologist's visual scoring. Evaluation of the results showed that our proposed method produced tumor boundaries that were equal to or better than acceptable in 89.8% of cases, and achieved 93.7% accuracy in classification of cyst and hemangioma.

  16. A Longitudinal Study of Remodeling in a Revised Peripheral Artery Bypass Graft Using 3D Ultrasound Imaging and Computational Hemodynamics

    PubMed Central

    Leotta, Daniel F.; Beach, Kirk W.; Riley, James J.; Aliseda, Alberto

    2011-01-01

    We report a study of the role of hemodynamic shear stress in the remodeling and failure of a peripheral artery bypass graft. Three separate scans of a femoral to popliteal above-knee bypass graft were taken over the course of a 16 month period following a revision of the graft. The morphology of the lumen is reconstructed from data obtained by a custom 3D ultrasound system. Numerical simulations are performed with the patient-specific geometries and physiologically realistic flow rates. The ultrasound reconstructions reveal two significant areas of remodeling: a stenosis with over 85% reduction in area, which ultimately caused graft failure, and a poststenotic dilatation or widening of the lumen. Likewise, the simulations reveal a complicated hemodynamic environment within the graft. Preliminary comparisons with in vivo velocimetry also showed qualitative agreement with the flow dynamics observed in the simulations. Two distinct flow features are discerned and are hypothesized to directly initiate the observed in vivo remodeling. First, a flow separation occurs at the stenosis. A low shear recirculation region subsequently develops distal to the stenosis. The low shear region is thought to be conducive to smooth muscle cell proliferation and intimal growth. A poststenotic jet issues from the stenosis and subsequently impinges onto the lumen wall. The lumen dilation is thought to be a direct result of the high shear stress and high frequency pressure fluctuations associated with the jet impingement. PMID:21428682

  17. [An integrated segmentation method for 3D ultrasound carotid artery].

    PubMed

    Yang, Xin; Wu, Huihui; Liu, Yang; Xu, Hongwei; Liang, Huageng; Cai, Wenjuan; Fang, Mengjie; Wang, Yujie

    2013-07-01

    An integrated segmentation method for 3D ultrasound carotid artery was proposed. 3D ultrasound image was sliced into transverse, coronal and sagittal 2D images on the carotid bifurcation point. Then, the three images were processed respectively, and the carotid artery contours and thickness were obtained finally. This paper tries to overcome the disadvantages of current computer aided diagnosis method, such as high computational complexity, easily introduced subjective errors et al. The proposed method could get the carotid artery overall information rapidly, accurately and completely. It could be transplanted into clinical usage for atherosclerosis diagnosis and prevention. PMID:24195385

  18. Chest wall segmentation in automated 3D breast ultrasound scans.

    PubMed

    Tan, Tao; Platel, Bram; Mann, Ritse M; Huisman, Henkjan; Karssemeijer, Nico

    2013-12-01

    In this paper, we present an automatic method to segment the chest wall in automated 3D breast ultrasound images. Determining the location of the chest wall in automated 3D breast ultrasound images is necessary in computer-aided detection systems to remove automatically detected cancer candidates beyond the chest wall and it can be of great help for inter- and intra-modal image registration. We show that the visible part of the chest wall in an automated 3D breast ultrasound image can be accurately modeled by a cylinder. We fit the surface of our cylinder model to a set of automatically detected rib-surface points. The detection of the rib-surface points is done by a classifier using features representing local image intensity patterns and presence of rib shadows. Due to attenuation of the ultrasound signal, a clear shadow is visible behind the ribs. Evaluation of our segmentation method is done by computing the distance of manually annotated rib points to the surface of the automatically detected chest wall. We examined the performance on images obtained with the two most common 3D breast ultrasound devices in the market. In a dataset of 142 images, the average mean distance of the annotated points to the segmented chest wall was 5.59 ± 3.08 mm. PMID:23273891

  19. Investigation and optimization of a finite element simulation of transducer array systems for 3D ultrasound computer tomography with respect to electrical impedance characteristics

    NASA Astrophysics Data System (ADS)

    Kohout, B.; Pirinen, J.; Ruiter, N. V.

    2012-03-01

    The established standard screening method to detect breast cancer is X-ray mammography. However X-ray mammography often has low contrast for tumors located within glandular tissue. A new approach is 3D Ultrasound Computer Tomography (USCT), which is expected to detect small tumors at an early stage. This paper describes the development, improvement and the results of Finite Element Method (FEM) simulations of the Transducer Array System (TAS) used in our 3D USCT. The focus of this work is on researching the influence of meshing and material parameters on the electrical impedance curves. Thereafter, these findings are used to optimize the simulation model. The quality of the simulation was evaluated by comparing simulated impedance characteristics with measured data of the real TAS. The resulting FEM simulation model is a powerful tool to analyze and optimize transducer array systems applied for USCT. With this simulation model, the behavior of TAS for different geometry modifications was researched. It provides a means to understand the acoustical performances inside of any ultrasound transducer represented by its electrical impedance characteristic.

  20. Automatic needle segmentation in 3D ultrasound images using 3D improved Hough transform

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Qiu, Wu; Ding, Mingyue; Zhang, Songgen

    2008-03-01

    3D ultrasound (US) is a new technology that can be used for a variety of diagnostic applications, such as obstetrical, vascular, and urological imaging, and has been explored greatly potential in the applications of image-guided surgery and therapy. Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese woman, and a minimally invasive ablation system using a needle-like RF button electrode is widely used to destroy tumor cells or stop bleeding. To avoid accidents or death of the patient by inaccurate localizations of the electrode and the tumor position during treatment, 3D US guidance system was developed. In this paper, a new automated technique, the 3D Improved Hough Transform (3DIHT) algorithm, which is potentially fast, accurate, and robust to provide needle segmentation in 3D US image for use of 3D US imaging guidance, was presented. Based on the coarse-fine search strategy and a four parameter representation of lines in 3D space, 3DIHT algorithm can segment needles quickly, accurately and robustly. The technique was evaluated using the 3D US images acquired by scanning a water phantom. The segmentation position deviation of the line was less than 2mm and angular deviation was much less than 2°. The average computational time measured on a Pentium IV 2.80GHz PC computer with a 381×381×250 image was less than 2s.

  1. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2003-05-12

    This project is in its first full year after the combining of two previously funded projects: ''3D Code Development'' and ''Dynamic Material Properties''. The motivation behind this move was to emphasize and strengthen the ties between the experimental work and the computational model development in the materials area. The next year's activities will indicate the merging of the two efforts. The current activity is structured in two tasks. Task A, ''Simulations and Measurements'', combines all the material model development and associated numerical work with the materials-oriented experimental activities. Task B, ''ALE3D Development'', is a continuation of the non-materials related activities from the previous project.

  2. 3D ultrasound imaging for prosthesis fabrication and diagnostic imaging

    SciTech Connect

    Morimoto, A.K.; Bow, W.J.; Strong, D.S.

    1995-06-01

    The fabrication of a prosthetic socket for a below-the-knee amputee requires knowledge of the underlying bone structure in order to provide pressure relief for sensitive areas and support for load bearing areas. The goal is to enable the residual limb to bear pressure with greater ease and utility. Conventional methods of prosthesis fabrication are based on limited knowledge about the patient`s underlying bone structure. A 3D ultrasound imaging system was developed at Sandia National Laboratories. The imaging system provides information about the location of the bones in the residual limb along with the shape of the skin surface. Computer assisted design (CAD) software can use this data to design prosthetic sockets for amputees. Ultrasound was selected as the imaging modality. A computer model was developed to analyze the effect of the various scanning parameters and to assist in the design of the overall system. The 3D ultrasound imaging system combines off-the-shelf technology for image capturing, custom hardware, and control and image processing software to generate two types of image data -- volumetric and planar. Both volumetric and planar images reveal definition of skin and bone geometry with planar images providing details on muscle fascial planes, muscle/fat interfaces, and blood vessel definition. The 3D ultrasound imaging system was tested on 9 unilateral below-the- knee amputees. Image data was acquired from both the sound limb and the residual limb. The imaging system was operated in both volumetric and planar formats. An x-ray CT (Computed Tomography) scan was performed on each amputee for comparison. Results of the test indicate beneficial use of ultrasound to generate databases for fabrication of prostheses at a lower cost and with better initial fit as compared to manually fabricated prostheses.

  3. Breast tumour visualization using 3D quantitative ultrasound methods

    NASA Astrophysics Data System (ADS)

    Gangeh, Mehrdad J.; Raheem, Abdul; Tadayyon, Hadi; Liu, Simon; Hadizad, Farnoosh; Czarnota, Gregory J.

    2016-04-01

    Breast cancer is one of the most common cancer types accounting for 29% of all cancer cases. Early detection and treatment has a crucial impact on improving the survival of affected patients. Ultrasound (US) is non-ionizing, portable, inexpensive, and real-time imaging modality for screening and quantifying breast cancer. Due to these attractive attributes, the last decade has witnessed many studies on using quantitative ultrasound (QUS) methods in tissue characterization. However, these studies have mainly been limited to 2-D QUS methods using hand-held US (HHUS) scanners. With the availability of automated breast ultrasound (ABUS) technology, this study is the first to develop 3-D QUS methods for the ABUS visualization of breast tumours. Using an ABUS system, unlike the manual 2-D HHUS device, the whole patient's breast was scanned in an automated manner. The acquired frames were subsequently examined and a region of interest (ROI) was selected in each frame where tumour was identified. Standard 2-D QUS methods were used to compute spectral and backscatter coefficient (BSC) parametric maps on the selected ROIs. Next, the computed 2-D parameters were mapped to a Cartesian 3-D space, interpolated, and rendered to provide a transparent color-coded visualization of the entire breast tumour. Such 3-D visualization can potentially be used for further analysis of the breast tumours in terms of their size and extension. Moreover, the 3-D volumetric scans can be used for tissue characterization and the categorization of breast tumours as benign or malignant by quantifying the computed parametric maps over the whole tumour volume.

  4. Editorial review: pediatric 3D ultrasound

    PubMed Central

    2014-01-01

    Three-dimensional ultrasound is an established diagnostic imaging technique in many specialties. However, in neonates, infants and children three-dimensional ultrasound still is underutilized, partially due to time constraints for post-processing and restricted availability, of devices as well as dedicated pediatric transducers. Also reimbursement issues still need to be addressed. This editorial review presents more or less established pediatric three-dimensional ultrasound applications with proven diagnostic benefit as well as potential future applications of three-dimensional/four-dimensional ultrasound in infants and children, aiming at enhancing research and promoting practical use of three-dimensional ultrasound in relevant pediatric conditions. Particularly, applications in neonatal neurosonography, ultrasound of the urogenital tract as well as some other small part and miscellaneous queries are highlighted. Additional other potential and future indications are discussed briefly, also mentioning restrictions and potential future developments. In summary, three-dimensional ultrasound holds some potential to widen sonographic diagnostic capabilities throughout childhood and hopefully will be increasingly investigated and introduced into clinical practice provided respective equipment and pediatric three-dimensional/four-dimensional ultrasound transducers become available. PMID:26676068

  5. Image fusion of Ultrasound Computer Tomography volumes with X-ray mammograms using a biomechanical model based 2D/3D registration.

    PubMed

    Hopp, T; Duric, N; Ruiter, N V

    2015-03-01

    Ultrasound Computer Tomography (USCT) is a promising breast imaging modality under development. Comparison to a standard method like mammography is essential for further development. Due to significant differences in image dimensionality and compression state of the breast, correlating USCT images and X-ray mammograms is challenging. In this paper we present a 2D/3D registration method to improve the spatial correspondence and allow direct comparison of the images. It is based on biomechanical modeling of the breast and simulation of the mammographic compression. We investigate the effect of including patient-specific material parameters estimated automatically from USCT images. The method was systematically evaluated using numerical phantoms and in-vivo data. The average registration accuracy using the automated registration was 11.9mm. Based on the registered images a method for analysis of the diagnostic value of the USCT images was developed and initially applied to analyze sound speed and attenuation images based on X-ray mammograms as ground truth. Combining sound speed and attenuation allows differentiating lesions from surrounding tissue. Overlaying this information on mammograms, combines quantitative and morphological information for multimodal diagnosis. PMID:25456144

  6. 3D segmentation and reconstruction of endobronchial ultrasound

    NASA Astrophysics Data System (ADS)

    Zang, Xiaonan; Breslav, Mikhail; Higgins, William E.

    2013-03-01

    State-of-the-art practice for lung-cancer staging bronchoscopy often draws upon a combination of endobronchial ultrasound (EBUS) and multidetector computed-tomography (MDCT) imaging. While EBUS offers real-time in vivo imaging of suspicious lesions and lymph nodes, its low signal-to-noise ratio and tendency to exhibit missing region-of-interest (ROI) boundaries complicate diagnostic tasks. Furthermore, past efforts did not incorporate automated analysis of EBUS images and a subsequent fusion of the EBUS and MDCT data. To address these issues, we propose near real-time automated methods for three-dimensional (3D) EBUS segmentation and reconstruction that generate a 3D ROI model along with ROI measurements. Results derived from phantom data and lung-cancer patients show the promise of the methods. In addition, we present a preliminary image-guided intervention (IGI) system example, whereby EBUS imagery is registered to a patient's MDCT chest scan.

  7. 3D Flow reconstruction using ultrasound PIV

    NASA Astrophysics Data System (ADS)

    Poelma, C.; Mari, J. M.; Foin, N.; Tang, M.-X.; Krams, R.; Caro, C. G.; Weinberg, P. D.; Westerweel, J.

    2011-04-01

    Ultrasound particle image velocimetry (PIV) can be used to obtain velocity fields in non-transparent geometries and/or fluids. In the current study, we use this technique to document the flow in a curved tube, using ultrasound contrast bubbles as flow tracer particles. The performance of the technique is first tested in a straight tube, with both steady laminar and pulsatile flows. Both experiments confirm that the technique is capable of reliable measurements. A number of adaptations are introduced that improve the accuracy and applicability of ultrasound PIV. Firstly, due to the method of ultrasound image acquisition, a correction is required for the estimation of velocities from tracer displacements. This correction accounts for the fact that columns in the image are recorded at slightly different instances. The second improvement uses a slice-by-slice scanning approach to obtain three-dimensional velocity data. This approach is here demonstrated in a strongly curved tube. The resulting flow profiles and wall shear stress distribution shows a distinct asymmetry. To meaningfully interpret these three-dimensional results, knowledge of the measurement thickness is required. Our third contribution is a method to determine this quantity, using the correlation peak heights. The latter method can also provide the third (out-of-plane) component if the measurement thickness is known, so that all three velocity components are available using a single probe.

  8. Automatic needle segmentation in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Ding, Mingyue; Cardinal, H. Neale; Guan, Weiguang; Fenster, Aaron

    2002-05-01

    In this paper, we propose to use 2D image projections to automatically segment a needle in a 3D ultrasound image. This approach is motivated by the twin observations that the needle is more conspicuous in a projected image, and its projected area is a minimum when the rays are cast parallel to the needle direction. To avoid the computational burden of an exhaustive 2D search for the needle direction, a faster 1D search procedure is proposed. First, a plane which contains the needle direction is determined by the initial projection direction and the (estimated) direction of the needle in the corresponding projection image. Subsequently, an adaptive 1D search technique is used to adjust the projection direction iteratively until the projected needle area is minimized. In order to remove noise and complex background structure from the projection images, a priori information about the needle position and orientation is used to crop the 3D volume, and the cropped volume is rendered with Gaussian transfer functions. We have evaluated this approach experimentally using agar and turkey breast phantoms. The results show that it can find the 3D needle orientation within 1 degree, in about 1 to 3 seconds on a 500 MHz computer.

  9. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  10. A 3D airborne ultrasound scanner

    NASA Astrophysics Data System (ADS)

    Capineri, L.; Masotti, L.; Rocchi, S.

    1998-06-01

    This work investigates the feasibility of an ultrasound scanner designed to reconstruct three-dimensional profiles of objects in air. There are many industrial applications in which it is important to obtain quickly and accurately the digital reconstruction of solid objects with contactless methods. The final aim of this project was the profile reconstruction of shoe lasts in order to eliminate the mechanical tracers from the reproduction process of shoe prototypes. The feasibility of an ultrasonic scanner was investigated in laboratory conditions on wooden test objects with axial symmetry. A bistatic system based on five airborne polyvinylidenedifluoride (PVDF) transducers was mechanically moved to emulate a cylindrical array transducer that can host objects of maximum width and height 20 cm and 40 cm respectively. The object reconstruction was based on a simplified version of the synthetic aperture focusing technique (SAFT): the time of flight (TOF) of the first in time echo for each receiving transducer was taken into account, a coarse spatial sampling of the ultrasonic field reflected on the array transducer was delivered and the reconstruction algorithm was based on the ellipsoidal backprojection. Measurements on a wooden cone section provided submillimetre accuracy in a controlled environment.

  11. Automatic needle segmentation in 3D ultrasound images using 3D Hough transform

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Qiu, Wu; Ding, Mingyue; Zhang, Songgeng

    2007-12-01

    3D ultrasound (US) is a new technology that can be used for a variety of diagnostic applications, such as obstetrical, vascular, and urological imaging, and has been explored greatly potential in the applications of image-guided surgery and therapy. Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese woman, and a minimally invasive ablation system using an RF button electrode which is needle-like is being used to destroy tumor cells or stop bleeding currently. Now a 3D US guidance system has been developed to avoid accidents or death of the patient by inaccurate localizations of the electrode and the tumor position during treatment. In this paper, we described two automated techniques, the 3D Hough Transform (3DHT) and the 3D Randomized Hough Transform (3DRHT), which is potentially fast, accurate, and robust to provide needle segmentation in 3D US image for use of 3D US imaging guidance. Based on the representation (Φ , θ , ρ , α ) of straight lines in 3D space, we used the 3DHT algorithm to segment needles successfully assumed that the approximate needle position and orientation are known in priori. The 3DRHT algorithm was developed to detect needles quickly without any information of the 3D US images. The needle segmentation techniques were evaluated using the 3D US images acquired by scanning water phantoms. The experiments demonstrated the feasibility of two 3D needle segmentation algorithms described in this paper.

  12. Towards 3D ultrasound image based soft tissue tracking: a transrectal ultrasound prostate image alignment system.

    PubMed

    Baumann, Michael; Mozer, Pierre; Daanen, Vincent; Troccaz, Jocelyne

    2007-01-01

    The emergence of real-time 3D ultrasound (US) makes it possible to consider image-based tracking of subcutaneous soft tissue targets for computer guided diagnosis and therapy. We propose a 3D transrectal US based tracking system for precise prostate biopsy sample localisation. The aim is to improve sample distribution, to enable targeting of unsampled regions for repeated biopsies, and to make post-interventional quality controls possible. Since the patient is not immobilized, since the prostate is mobile and due to the fact that probe movements are only constrained by the rectum during biopsy acquisition, the tracking system must be able to estimate rigid transformations that are beyond the capture range of common image similarity measures. We propose a fast and robust multi-resolution attribute-vector registration approach that combines global and local optimization methods to solve this problem. Global optimization is performed on a probe movement model that reduces the dimensionality of the search space and thus renders optimization efficient. The method was tested on 237 prostate volumes acquired from 14 different patients for 3D to 3D and 3D to orthogonal 2D slices registration. The 3D-3D version of the algorithm converged correctly in 96.7% of all cases in 6.5s with an accuracy of 1.41mm (r.m.s.) and 3.84mm (max). The 3D to slices method yielded a success rate of 88.9% in 2.3s with an accuracy of 1.37mm (r.m.s.) and 4.3mm (max). PMID:18044549

  13. Intelligent speckle reducing anisotropic diffusion algorithm for automated 3-D ultrasound images.

    PubMed

    Wu, Jun; Wang, Yuanyuan; Yu, Jinhua; Shi, Xinling; Zhang, Junhua; Chen, Yue; Pang, Yun

    2015-02-01

    A novel 3-D filtering method is presented for speckle reduction and detail preservation in automated 3-D ultrasound images. First, texture features of an image are analyzed by using the improved quadtree (QT) decomposition. Then, the optimal homogeneous and the obvious heterogeneous regions are selected from QT decomposition results. Finally, diffusion parameters and diffusion process are automatically decided based on the properties of these two selected regions. The computing time needed for 2-D speckle reduction is very short. However, the computing time required for 3-D speckle reduction is often hundreds of times longer than 2-D speckle reduction. This may limit its potential application in practice. Because this new filter can adaptively adjust the time step of iteration, the computation time is reduced effectively. Both synthetic and real 3-D ultrasound images are used to evaluate the proposed filter. It is shown that this filter is superior to other methods in both practicality and efficiency. PMID:26366596

  14. The Application of Ultrasound in 3D Bio-Printing.

    PubMed

    Zhou, Yufeng

    2016-01-01

    Three-dimensional (3D) bioprinting is an emerging and promising technology in tissue engineering to construct tissues and organs for implantation. Alignment of self-assembly cell spheroids that are used as bioink could be very accurate after droplet ejection from bioprinter. Complex and heterogeneous tissue structures could be built using rapid additive manufacture technology and multiple cell lines. Effective vascularization in the engineered tissue samples is critical in any clinical application. In this review paper, the current technologies and processing steps (such as printing, preparation of bioink, cross-linking, tissue fusion and maturation) in 3D bio-printing are introduced, and their specifications are compared with each other. In addition, the application of ultrasound in this novel field is also introduced. Cells experience acoustic radiation force in ultrasound standing wave field (USWF) and then accumulate at the pressure node at low acoustic pressure. Formation of cell spheroids by this method is within minutes with uniform size and homogeneous cell distribution. Neovessel formation from USWF-induced endothelial cell spheroids is significant. Low-intensity ultrasound could enhance the proliferation and differentiation of stem cells. Its use is at low cost and compatible with current bioreactor. In summary, ultrasound application in 3D bio-printing may solve some challenges and enhance the outcomes. PMID:27164066

  15. 3D ultrasound image segmentation using wavelet support vector machines

    PubMed Central

    Akbari, Hamed; Fei, Baowei

    2012-01-01

    Purpose: Transrectal ultrasound (TRUS) imaging is clinically used in prostate biopsy and therapy. Segmentation of the prostate on TRUS images has many applications. In this study, a three-dimensional (3D) segmentation method for TRUS images of the prostate is presented for 3D ultrasound-guided biopsy. Methods: This segmentation method utilizes a statistical shape, texture information, and intensity profiles. A set of wavelet support vector machines (W-SVMs) is applied to the images at various subregions of the prostate. The W-SVMs are trained to adaptively capture the features of the ultrasound images in order to differentiate the prostate and nonprostate tissue. This method consists of a set of wavelet transforms for extraction of prostate texture features and a kernel-based support vector machine to classify the textures. The voxels around the surface of the prostate are labeled in sagittal, coronal, and transverse planes. The weight functions are defined for each labeled voxel on each plane and on the model at each region. In the 3D segmentation procedure, the intensity profiles around the boundary between the tentatively labeled prostate and nonprostate tissue are compared to the prostate model. Consequently, the surfaces are modified based on the model intensity profiles. The segmented prostate is updated and compared to the shape model. These two steps are repeated until they converge. Manual segmentation of the prostate serves as the gold standard and a variety of methods are used to evaluate the performance of the segmentation method. Results: The results from 40 TRUS image volumes of 20 patients show that the Dice overlap ratio is 90.3% ± 2.3% and that the sensitivity is 87.7% ± 4.9%. Conclusions: The proposed method provides a useful tool in our 3D ultrasound image-guided prostate biopsy and can also be applied to other applications in the prostate. PMID:22755682

  16. Localization of liver tumors in freehand 3D laparoscopic ultrasound

    NASA Astrophysics Data System (ADS)

    Shahin, O.; Martens, V.; Besirevic, A.; Kleemann, M.; Schlaefer, A.

    2012-02-01

    The aim of minimally invasive laparoscopic liver interventions is to completely resect or ablate tumors while minimizing the trauma caused by the operation. However, restrictions such as limited field of view and reduced depth perception can hinder the surgeon's capabilities to precisely localize the tumor. Typically, preoperative data is acquired to find the tumor(s) and plan the surgery. Nevertheless, determining the precise position of the tumor is required, not only before but also during the operation. The standard use of ultrasound in hepatic surgery is to explore the liver and identify tumors. Meanwhile, the surgeon mentally builds a 3D context to localize tumors. This work aims to upgrade the use of ultrasound in laparoscopic liver surgery. We propose an approach to segment and localize tumors intra-operatively in 3D ultrasound. We reconstruct a 3D laparoscopic ultrasound volume containing a tumor. The 3D image is then preprocessed and semi-automatically segmented using a level set algorithm. During the surgery, for each subsequent reconstructed volume, a fast update of the tumor position is accomplished via registration using the previously segmented and localized tumor as a prior knowledge. The approach was tested on a liver phantom with artificial tumors. The tumors were localized in approximately two seconds with a mean error of less than 0.5 mm. The strengths of this technique are that it can be performed intra-operatively, it helps the surgeon to accurately determine the location, shape and volume of the tumor, and it is repeatable throughout the operation.

  17. Incremental volume reconstruction and rendering for 3-D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Ohbuchi, Ryutarou; Chen, David; Fuchs, Henry

    1992-09-01

    In this paper, we present approaches toward an interactive visualization of a real time input, applied to 3-D visualizations of 2-D ultrasound echography data. The first, 3 degrees-of- freedom (DOF) incremental system visualizes a 3-D volume acquired as a stream of 2-D slices with location and orientation with 3 DOF. As each slice arrives, the system reconstructs a regular 3-D volume and renders it. Rendering is done by an incremental image-order ray- casting algorithm which stores and reuses the results of expensive resampling along the rays for speed. The second is our first experiment toward real-time 6 DOF acquisition and visualization. Two-dimensional slices with 6 DOF are reconstructed off-line, and visualized at an interactive rate using a parallel volume rendering code running on the graphics multicomputer Pixel-Planes 5.

  18. Fast and Accurate Data Extraction for Near Real-Time Registration of 3-D Ultrasound and Computed Tomography in Orthopedic Surgery.

    PubMed

    Brounstein, Anna; Hacihaliloglu, Ilker; Guy, Pierre; Hodgson, Antony; Abugharbieh, Rafeef

    2015-12-01

    Automatic, accurate and real-time registration is an important step in providing effective guidance and successful anatomic restoration in ultrasound (US)-based computer assisted orthopedic surgery. We propose a method in which local phase-based bone surfaces, extracted from intra-operative US data, are registered to pre-operatively segmented computed tomography data. Extracted bone surfaces are downsampled and reinforced with high curvature features. A novel hierarchical simplification algorithm is used to further optimize the point clouds. The final point clouds are represented as Gaussian mixture models and iteratively matched by minimizing the dissimilarity between them using an L2 metric. For 44 clinical data sets from 25 pelvic fracture patients and 49 phantom data sets, we report mean surface registration accuracies of 0.31 and 0.77 mm, respectively, with an average registration time of 1.41 s. Our results suggest the viability and potential of the chosen method for real-time intra-operative registration in orthopedic surgery. PMID:26365924

  19. Automatic multimodal 2D/3D image fusion of ultrasound computer tomography and x-ray mammography for breast cancer diagnosis

    NASA Astrophysics Data System (ADS)

    Hopp, Torsten; Duric, Neb; Ruiter, Nicole V.

    2012-03-01

    Breast cancer is the most common cancer among women. The established screening method to detect breast cancer in an early state is X-ray mammography. However, X-ray frequently provides limited contrast of tumors located within glandular tissue. A new imaging approach is Ultrasound Computer Tomography generating threedimensional volumes of the breast. Three different images are available: reflectivity, attenuation and speed of sound. The correlation of USCT volumes with X-ray mammograms is of interest for evaluation of the new imaging modality as well as for a multimodal diagnosis. Yet, both modalities differ in image dimensionality, patient positioning and deformation state of the breast. In earlier work we proposed a methodology based on Finite Element Method to register speed of sound images with the according mammogram. In this work, we enhanced the methodology to register all three image types provided by USCT. Furthermore, the methodology is now completely automated using image similarity measures to estimate rotations in datasets. A fusion methodology is proposed which combines the information of the three USCT image types with the X-ray mammogram via semitransparent overlay images. The evaluation was done using 13 datasets from a clinical study. The registration accuracy was measured by the displacement of the center of a lesion marked in both modalities. Using the automated rotation estimation, a mean displacement of 10.4 mm was achieved. Due to the clinically relevant registration accuracy, the methodology provides a basis for evaluation of the new imaging device USCT as well as for multimodal diagnosis.

  20. 3D segmentation of prostate ultrasound images using wavelet transform

    NASA Astrophysics Data System (ADS)

    Akbari, Hamed; Yang, Xiaofeng; Halig, Luma V.; Fei, Baowei

    2011-03-01

    The current definitive diagnosis of prostate cancer is transrectal ultrasound (TRUS) guided biopsy. However, the current procedure is limited by using 2D biopsy tools to target 3D biopsy locations. This paper presents a new method for automatic segmentation of the prostate in three-dimensional transrectal ultrasound images, by extracting texture features and by statistically matching geometrical shape of the prostate. A set of Wavelet-based support vector machines (WSVMs) are located and trained at different regions of the prostate surface. The WSVMs capture texture priors of ultrasound images for classification of the prostate and non-prostate tissues in different zones around the prostate boundary. In the segmentation procedure, these W-SVMs are trained in three sagittal, coronal, and transverse planes. The pre-trained W-SVMs are employed to tentatively label each voxel around the surface of the model as a prostate or non-prostate voxel by the texture matching. The labeled voxels in three planes after post-processing is overlaid on a prostate probability model. The probability prostate model is created using 10 segmented prostate data. Consequently, each voxel has four labels: sagittal, coronal, and transverse planes and one probability label. By defining a weight function for each labeling in each region, each voxel is labeled as a prostate or non-prostate voxel. Experimental results by using real patient data show the good performance of the proposed model in segmenting the prostate from ultrasound images.

  1. GPU-Based Block-Wise Nonlocal Means Denoising for 3D Ultrasound Images

    PubMed Central

    Hou, Wenguang; Zhang, Xuming; Ding, Mingyue

    2013-01-01

    Speckle suppression plays an important role in improving ultrasound (US) image quality. While lots of algorithms have been proposed for 2D US image denoising with remarkable filtering quality, there is relatively less work done on 3D ultrasound speckle suppression, where the whole volume data rather than just one frame needs to be considered. Then, the most crucial problem with 3D US denoising is that the computational complexity increases tremendously. The nonlocal means (NLM) provides an effective method for speckle suppression in US images. In this paper, a programmable graphic-processor-unit- (GPU-) based fast NLM filter is proposed for 3D ultrasound speckle reduction. A Gamma distribution noise model, which is able to reliably capture image statistics for Log-compressed ultrasound images, was used for the 3D block-wise NLM filter on basis of Bayesian framework. The most significant aspect of our method was the adopting of powerful data-parallel computing capability of GPU to improve the overall efficiency. Experimental results demonstrate that the proposed method can enormously accelerate the algorithm. PMID:24348747

  2. Real-time, 3-D ultrasound with multiple transducer arrays.

    PubMed

    Fronheiser, Matthew P; Light, Edward D; Idriss, Salim F; Wolf, Patrick D; Smith, Stephen W

    2006-01-01

    Modifications were made to a commercial real-time, three-dimensional (3-D) ultrasound system for near simultaneous 3-D scanning with two matrix array transducers. As a first illustration, a transducer cable assembly was modified to incorporate two independent, 3-D intra-cardiac echo catheters, a 7 Fr (2.3 mm O.D.) side scanning catheter and a 14 Fr (4.7 mm O.D) forward viewing catheter with accessory port, each catheter using 85 channels operating at 5 MHz. For applications in treatment of atrial fibrillation, the goal is to place the sideviewing catheter within the coronary sinus to view the whole left atrium, including a pulmonary vein. Meanwhile, the forward-viewing catheter inserted within the left atrium is directed toward the ostium of a pulmonary vein for therapy using the integrated accessory port. Using preloaded, phasing data, the scanner switches between catheters automatically, at the push of a button, with a delay of about 1 second, so that the clinician can view the therapy catheter with the coronary sinus catheter and vice versa. Preliminary imaging studies in a tissue phantom and in vivo show that our system successfully guided the forward-viewing catheter toward a target while being imaged with the sideviewing catheter. The forward-viewing catheter then was activated to monitor the target while we mimicked therapy delivery. In the future, the system will switch between 3-D probes on a line-by-line basis and display both volumes simultaneously. PMID:16471436

  3. Density-tapered spiral arrays for ultrasound 3-D imaging.

    PubMed

    Ramalli, Alessandro; Boni, Enrico; Savoia, Alessandro Stuart; Tortoli, Piero

    2015-08-01

    The current high interest in 3-D ultrasound imaging is pushing the development of 2-D probes with a challenging number of active elements. The most popular approach to limit this number is the sparse array technique, which designs the array layout by means of complex optimization algorithms. These algorithms are typically constrained by a few steering conditions, and, as such, cannot guarantee uniform side-lobe performance at all angles. The performance may be improved by the ungridded extensions of the sparse array technique, but this result is achieved at the expense of a further complication of the optimization process. In this paper, a method to design the layout of large circular arrays with a limited number of elements according to Fermat's spiral seeds and spatial density modulation is proposed and shown to be suitable for application to 3-D ultrasound imaging. This deterministic, aperiodic, and balanced positioning procedure attempts to guarantee uniform performance over a wide range of steering angles. The capabilities of the method are demonstrated by simulating and comparing the performance of spiral and dense arrays. A good trade-off for small vessel imaging is found, e.g., in the 60λ spiral array with 1.0λ elements and Blackman density tapering window. Here, the grating lobe level is -16 dB, the lateral resolution is lower than 6λ the depth of field is 120λ and, the average contrast is 10.3 dB, while the sensitivity remains in a 5 dB range for a wide selection of steering angles. The simulation results may represent a reference guide to the design of spiral sparse array probes for different application fields. PMID:26285181

  4. Integration of 3D intraoperative ultrasound for enhanced neuronavigation

    NASA Astrophysics Data System (ADS)

    Paulsen, Keith D.; Ji, Songbai; Hartov, Alex; Fan, Xiaoyao; Roberts, David W.

    2012-03-01

    True three-dimensional (3D) volumetric ultrasound (US) acquisitions stand to benefit intraoperative neuronavigation on multiple fronts. While traditional two-dimensional (2D) US and its tracked, hand-swept version have been recognized for many years to advantage significantly image-guided neurosurgery, especially when coregistered with preoperative MR scans, its unregulated and incomplete sampling of the surgical volume of interest have limited certain intraoperative uses of the information that are overcome through direct volume acquisition (i.e., through 2D scan-head transducer arrays). In this paper, we illustrate several of these advantages, including image-based intraoperative registration (and reregistration) and automated, volumetric displacement mapping for intraoperative image updating. These applications of 3D US are enabled by algorithmic advances in US image calibration, and volume rasterization and interpolation for multi-acquisition synthesis that will also be highlighted. We expect to demonstrate that coregistered 3D US is well worth incorporating into the standard neurosurgical navigational environment relative to traditional tracked, hand-swept 2D US.

  5. 3D Simulation of Ultrasound in the Ultra-Distal Human Radius

    NASA Astrophysics Data System (ADS)

    Kaufman, Jonathan J.; Luo, Gangming; Siffert, Robert S.

    The overall objective of this research is to develop an ultrasonic method for non-invasive assessment of the ultradistal radius (UDR). The specific objective of this study was to examine the propagation of ultrasound through the UDR and determine the relationships between bone mass and ultrasound, as well as the ability of ultrasound to discriminate between fracture and non-fracture cases. High-resolution peripheral-QCT (HR-pQCT) images were obtained from a set of 110 subjects that were part of a larger study on osteoporosis. Twenty-three of the subjects had experienced a UDR fracture within the past 2 years; the other 87 subjects served as controls. Each 3D image was used to simulate ultrasound measurements that would result from propagation through the UDR, from its anterior to its posterior surfaces. The simulation was carried out using Wave3000 (CyberLogic, Inc., New York, USA), which solves the full 3D viscoelastic wave equation using a finite difference time domain method. Bone mineral density associated with each radius was computed for each subject, and an ultrasound parameter known as net time delay (NTD) was evaluated. NTD has been shown to be highly correlated with total bone mass in both in vitro and clinical studies. Significant correlations were found between NTD and total bone mass (R2 = 0.91, p < 0.001). The data also showed a statistically significant difference in the NTD for the fracture and non-fracture cases (i.e., a decrease in mean NTD of 14% (P < 0.001), with a t-test statistic of 3.8). The study shows that ultrasound is correlated with bone mass at the UDR, as well as with fracture incidence. Therefore ultrasound may prove useful as a simple and convenient method for non-invasive assessment of osteoporosis and fracture risk. Work is ongoing to compare the simulated ultrasound data with clinical ultrasound measurements made on the same individuals.

  6. A navigation system for flexible endoscopes using abdominal 3D ultrasound.

    PubMed

    Hoffmann, R; Kaar, M; Bathia, Amon; Bathia, Amar; Lampret, A; Birkfellner, W; Hummel, J; Figl, M

    2014-09-21

    A navigation system for flexible endoscopes equipped with ultrasound (US) scan heads is presented. In contrast to similar systems, abdominal 3D-US is used for image fusion of the pre-interventional computed tomography (CT) to the endoscopic US. A 3D-US scan, tracked with an optical tracking system (OTS), is taken pre-operatively together with the CT scan. The CT is calibrated using the OTS, providing the transformation from CT to 3D-US. Immediately before intervention a 3D-US tracked with an electromagnetic tracking system (EMTS) is acquired and registered intra-modal to the preoperative 3D-US. The endoscopic US is calibrated using the EMTS and registered to the pre-operative CT by an intra-modal 3D-US/3D-US registration. Phantom studies showed a registration error for the US to CT registration of 5.1 mm±2.8 mm. 3D-US/3D-US registration of patient data gave an error of 4.1 mm compared to 2.8 mm with the phantom. From this we estimate an error on patient experiments of 5.6 mm. PMID:25170913

  7. Integrated endoscope for real-time 3D ultrasound imaging and hyperthermia: feasibility study.

    PubMed

    Pua, Eric C; Qiu, Yupeng; Smith, S W

    2007-01-01

    The goal of this research is to determine the feasibility of using a single endoscopic probe for the combined purpose of real-time 3D (RT3D) ultrasound imaging of a target organ and the delivery of ultrasound therapy to facilitate the absorption of compounds for cancer treatment. Recent research in ultrasound therapy has shown that ultrasound-mediated drug delivery improves absorption of treatments for prostate, cervical and esophageal cancer. The ability to combine ultrasound hyperthermia and 3D imaging could improve visualization and targeting of cancerous tissues. In this study, numerical modeling and experimental measurements were developed to determine the feasibility of combined therapy and imaging with a 1 cm diameter endoscopic RT3D probe with 504 transmitters and 252 receive channels. This device operates at 5 MHz and has a 6.3 mm x 6.3 mm aperture to produce real time 3D pyramidal scans of 60-120 degrees incorporating 64 x 64 = 4096 image lines at 30 volumes/sec interleaved with a 3D steerable therapy beam. A finite-element mesh was constructed with over 128,000 elements in LS-DYNA to simulate the induced temperature rise from our transducer with a 3 cm deep focus in tissue. Quarter-symmetry of the transducer was used to reduce mesh size and computation time. Based on intensity values calculated in Field II using the transducer's array geometry, a minimum I(SPTA) of 3.6 W/cm2 is required from our endoscope probe in order to induce a temperature rise of 4 degrees C within five minutes. Experimental measurements of the array's power output capabilities were conducted using a PVDF hydrophone placed 3 cm away from the face of the transducer in a watertank. Using a PDA14 Signatec data acquisition board to capture full volumes of transmitted ultrasound data, it was determined that the probe can presently maintain intensity values up to 2.4 W/cm2 over indefinite times for therapeutic applications combined with intermittent 3D scanning to maintain targeting

  8. A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect: a simulation study

    NASA Astrophysics Data System (ADS)

    Yang, R.; Song, A.; Li, X. D.; Lu, Y.; Yan, R.; Xu, B.; Li, X.

    2014-10-01

    A 3D reconstruction solution to ultrasound Joule heat density tomography based on acousto-electric effect by deconvolution is proposed for noninvasive imaging of biological tissue. Compared with ultrasound current source density imaging, ultrasound Joule heat density tomography doesn't require any priori knowledge of conductivity distribution and lead fields, so it can gain better imaging result, more adaptive to environment and with wider application scope. For a general 3D volume conductor with broadly distributed current density field, in the AE equation the ultrasound pressure can't simply be separated from the 3D integration, so it is not a common modulation and basebanding (heterodyning) method is no longer suitable to separate Joule heat density from the AE signals. In the proposed method the measurement signal is viewed as the output of Joule heat density convolving with ultrasound wave. As a result, the internal 3D Joule heat density can be reconstructed by means of Wiener deconvolution. A series of computer simulations set for breast cancer imaging applications, with consideration of ultrasound beam diameter, noise level, conductivity contrast, position dependency and size of simulated tumors, have been conducted to evaluate the feasibility and performance of the proposed reconstruction method. The computer simulation results demonstrate that high spatial resolution 3D ultrasound Joule heat density imaging is feasible using the proposed method, and it has potential applications to breast cancer detection and imaging of other organs.

  9. METHODS FOR USING 3-D ULTRASOUND SPECKLE TRACKING IN BIAXIAL MECHANICAL TESTING OF BIOLOGICAL TISSUE SAMPLES

    PubMed Central

    Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang

    2014-01-01

    Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation. PMID:25616585

  10. Registration of Real-Time 3-D Ultrasound to Tomographic Images of the Abdominal Aorta.

    PubMed

    Brekken, Reidar; Iversen, Daniel Høyer; Tangen, Geir Arne; Dahl, Torbjørn

    2016-08-01

    The purpose of this study was to develop an image-based method for registration of real-time 3-D ultrasound to computed tomography (CT) of the abdominal aorta, targeting future use in ultrasound-guided endovascular intervention. We proposed a method in which a surface model of the aortic wall was segmented from CT, and the approximate initial location of this model relative to the ultrasound volume was manually indicated. The model was iteratively transformed to automatically optimize correspondence to the ultrasound data. Feasibility was studied using data from a silicon phantom and in vivo data from a volunteer with previously acquired CT. Through visual evaluation, the ultrasound and CT data were seen to correspond well after registration. Both aortic lumen and branching arteries were well aligned. The processing was done offline, and the registration took approximately 0.2 s per ultrasound volume. The results encourage further patient studies to investigate accuracy, robustness and clinical value of the approach. PMID:27156015

  11. Development of a Wireless and Near Real-Time 3D Ultrasound Strain Imaging System.

    PubMed

    Chen, Zhaohong; Chen, Yongdong; Huang, Qinghua

    2016-04-01

    Ultrasound elastography is an important medical imaging tool for characterization of lesions. In this paper, we present a wireless and near real-time 3D ultrasound strain imaging system. It uses a 3D translating device to control a commercial linear ultrasound transducer to collect pre-compression and post-compression radio-frequency (RF) echo signal frames. The RF frames are wirelessly transferred to a high-performance server via a local area network (LAN). A dynamic programming strain estimation algorithm is implemented with the compute unified device architecture (CUDA) on the graphic processing unit (GPU) in the server to calculate the strain image after receiving a pre-compression RF frame and a post-compression RF frame at the same position. Each strain image is inserted into a strain volume which can be rendered in near real-time. We take full advantage of the translating device to precisely control the probe movement and compression. The GPU-based parallel computing techniques are designed to reduce the computation time. Phantom and in vivo experimental results demonstrate that our system can generate strain volumes with good quality and display an incrementally reconstructed volume image in near real-time. PMID:26954841

  12. Preliminary results in large bone segmentation from 3D freehand ultrasound

    NASA Astrophysics Data System (ADS)

    Fanti, Zian; Torres, Fabian; Arámbula Cosío, Fernando

    2013-11-01

    Computer Assisted Orthopedic Surgery (CAOS) requires a correct registration between the patient in the operating room and the virtual models representing the patient in the computer. In order to increase the precision and accuracy of the registration a set of new techniques that eliminated the need to use fiducial markers have been developed. The majority of these newly developed registration systems are based on costly intraoperative imaging systems like Computed Tomography (CT scan) or Magnetic resonance imaging (MRI). An alternative to these methods is the use of an Ultrasound (US) imaging system for the implementation of a more cost efficient intraoperative registration solution. In order to develop the registration solution with the US imaging system, the bone surface is segmented in both preoperative and intraoperative images, and the registration is done using the acquire surface. In this paper, we present the a preliminary results of a new approach to segment bone surface from ultrasound volumes acquired by means 3D freehand ultrasound. The method is based on the enhancement of the voxels that belongs to surface and its posterior segmentation. The enhancement process is based on the information provided by eigenanalisis of the multiscale 3D Hessian matrix. The preliminary results shows that from the enhance volume the final bone surfaces can be extracted using a singular value thresholding.

  13. Computing Radiative Transfer in a 3D Medium

    NASA Technical Reports Server (NTRS)

    Von Allmen, Paul; Lee, Seungwon

    2012-01-01

    A package of software computes the time-dependent propagation of a narrow laser beam in an arbitrary three- dimensional (3D) medium with absorption and scattering, using the transient-discrete-ordinates method and a direct integration method. Unlike prior software that utilizes a Monte Carlo method, this software enables simulation at very small signal-to-noise ratios. The ability to simulate propagation of a narrow laser beam in a 3D medium is an improvement over other discrete-ordinate software. Unlike other direct-integration software, this software is not limited to simulation of propagation of thermal radiation with broad angular spread in three dimensions or of a laser pulse with narrow angular spread in two dimensions. Uses for this software include (1) computing scattering of a pulsed laser beam on a material having given elastic scattering and absorption profiles, and (2) evaluating concepts for laser-based instruments for sensing oceanic turbulence and related measurements of oceanic mixed-layer depths. With suitable augmentation, this software could be used to compute radiative transfer in ultrasound imaging in biological tissues, radiative transfer in the upper Earth crust for oil exploration, and propagation of laser pulses in telecommunication applications.

  14. Accuracy assessment of high frequency 3D ultrasound for digital impression-taking of prepared teeth

    NASA Astrophysics Data System (ADS)

    Heger, Stefan; Vollborn, Thorsten; Tinschert, Joachim; Wolfart, Stefan; Radermacher, Klaus

    2013-03-01

    Silicone based impression-taking of prepared teeth followed by plaster casting is well-established but potentially less reliable, error-prone and inefficient, particularly in combination with emerging techniques like computer aided design and manufacturing (CAD/CAM) of dental prosthesis. Intra-oral optical scanners for digital impression-taking have been introduced but until now some drawbacks still exist. Because optical waves can hardly penetrate liquids or soft-tissues, sub-gingival preparations still need to be uncovered invasively prior to scanning. High frequency ultrasound (HFUS) based micro-scanning has been recently investigated as an alternative to optical intra-oral scanning. Ultrasound is less sensitive against oral fluids and in principal able to penetrate gingiva without invasively exposing of sub-gingival preparations. Nevertheless, spatial resolution as well as digitization accuracy of an ultrasound based micro-scanning system remains a critical parameter because the ultrasound wavelength in water-like media such as gingiva is typically smaller than that of optical waves. In this contribution, the in-vitro accuracy of ultrasound based micro-scanning for tooth geometry reconstruction is being investigated and compared to its extra-oral optical counterpart. In order to increase the spatial resolution of the system, 2nd harmonic frequencies from a mechanically driven focused single element transducer were separated and corresponding 3D surface models were calculated for both fundamentals and 2nd harmonics. Measurements on phantoms, model teeth and human teeth were carried out for evaluation of spatial resolution and surface detection accuracy. Comparison of optical and ultrasound digital impression taking indicate that, in terms of accuracy, ultrasound based tooth digitization can be an alternative for optical impression-taking.

  15. Benchmarking of state-of-the-art needle detection algorithms in 3D ultrasound data volumes

    NASA Astrophysics Data System (ADS)

    Pourtaherian, Arash; Zinger, Svitlana; de With, Peter H. N.; Korsten, Hendrikus H. M.; Mihajlovic, Nenad

    2015-03-01

    Ultrasound-guided needle interventions are widely practiced in medical diagnostics and therapy, i.e. for biopsy guidance, regional anesthesia or for brachytherapy. Needle guidance using 2D ultrasound can be very challenging due to the poor needle visibility and the limited field of view. Since 3D ultrasound transducers are becoming more widely used, needle guidance can be improved and simplified with appropriate computer-aided analyses. In this paper, we compare two state-of-the-art 3D needle detection techniques: a technique based on line filtering from literature and a system employing Gabor transformation. Both algorithms utilize supervised classification to pre-select candidate needle voxels in the volume and then fit a model of the needle on the selected voxels. The major differences between the two approaches are in extracting the feature vectors for classification and selecting the criterion for fitting. We evaluate the performance of the two techniques using manually-annotated ground truth in several ex-vivo situations of different complexities, containing three different needle types with various insertion angles. This extensive evaluation provides better understanding on the limitations and advantages of each technique under different acquisition conditions, which is leading to the development of improved techniques for more reliable and accurate localization. Benchmarking results that the Gabor features are better capable of distinguishing the needle voxels in all datasets. Moreover, it is shown that the complete processing chain of the Gabor-based method outperforms the line filtering in accuracy and stability of the detection results.

  16. Bone segmentation and fracture detection in ultrasound using 3D local phase features.

    PubMed

    Hacihaliloglu, Ilker; Abugharbieh, Rafeef; Hodgson, Antony; Rohling, Robert

    2008-01-01

    3D ultrasound (US) is increasingly considered as a viable alternative imaging modality in computer-assisted orthopaedic surgery (CAOS) applications. Automatic bone segmentation from US images, however, remains a challenge due to speckle noise and various other artifacts inherent to US. In this paper, we present intensity invariant three dimensional (3D) local image phase features, obtained using 3D Log-Gabor filter banks, for extracting ridge-like features similar to those that occur at soft tissue/bone interfaces. Our contributions include the novel extension of 2D phase symmetry features to 3D and their use in automatic extraction of bone surfaces and fractured fragments in 3D US. We validate our technique using phantom, in vitro, and in vivo experiments. Qualitative and quantitative results demonstrate remarkably clear segmentations results of bone surfaces with a localization accuracy of better than 0.62 mm and mean errors in estimating fracture displacements below 0.65 mm, which will likely be of strong clinical utility. PMID:18979759

  17. Mapping 3D Strains with Ultrasound Speckle Tracking: Method Validation and Initial Results in Porcine Scleral Inflation.

    PubMed

    Cruz Perez, Benjamin; Pavlatos, Elias; Morris, Hugh J; Chen, Hong; Pan, Xueliang; Hart, Richard T; Liu, Jun

    2016-07-01

    This study aimed to develop and validate a high frequency ultrasound method for measuring distributive, 3D strains in the sclera during elevations of intraocular pressure. A 3D cross-correlation based speckle-tracking algorithm was implemented to compute the 3D displacement vector and strain tensor at each tracking point. Simulated ultrasound radiofrequency data from a sclera-like structure at undeformed and deformed states with known strains were used to evaluate the accuracy and signal-to-noise ratio (SNR) of strain estimation. An experimental high frequency ultrasound (55 MHz) system was built to acquire 3D scans of porcine eyes inflated from 15 to 17 and then 19 mmHg. Simulations confirmed good strain estimation accuracy and SNR (e.g., the axial strains had less than 4.5% error with SNRs greater than 16.5 for strains from 0.005 to 0.05). Experimental data in porcine eyes showed increasing tensile, compressive, and shear strains in the posterior sclera during inflation, with a volume ratio close to one suggesting near-incompressibility. This study established the feasibility of using high frequency ultrasound speckle tracking for measuring 3D tissue strains and its potential to characterize physiological deformations in the posterior eye. PMID:26563101

  18. Automatic segmentation of the fetal cerebellum on ultrasound volumes, using a 3D statistical shape model.

    PubMed

    Gutiérrez-Becker, Benjamín; Arámbula Cosío, Fernando; Guzmán Huerta, Mario E; Benavides-Serralde, Jesús Andrés; Camargo-Marín, Lisbeth; Medina Bañuelos, Verónica

    2013-09-01

    Previous work has shown that the segmentation of anatomical structures on 3D ultrasound data sets provides an important tool for the assessment of the fetal health. In this work, we present an algorithm based on a 3D statistical shape model to segment the fetal cerebellum on 3D ultrasound volumes. This model is adjusted using an ad hoc objective function which is in turn optimized using the Nelder-Mead simplex algorithm. Our algorithm was tested on ultrasound volumes of the fetal brain taken from 20 pregnant women, between 18 and 24 gestational weeks. An intraclass correlation coefficient of 0.8528 and a mean Dice coefficient of 0.8 between cerebellar volumes measured using manual techniques and the volumes calculated using our algorithm were obtained. As far as we know, this is the first effort to automatically segment fetal intracranial structures on 3D ultrasound data. PMID:23686392

  19. Fast myocardial strain estimation from 3D ultrasound through elastic image registration with analytic regularization

    NASA Astrophysics Data System (ADS)

    Chakraborty, Bidisha; Heyde, Brecht; Alessandrini, Martino; D'hooge, Jan

    2016-04-01

    Image registration techniques using free-form deformation models have shown promising results for 3D myocardial strain estimation from ultrasound. However, the use of this technique has mostly been limited to research institutes due to the high computational demand, which is primarily due to the computational load of the regularization term ensuring spatially smooth cardiac strain estimates. Indeed, this term typically requires evaluating derivatives of the transformation field numerically in each voxel of the image during every iteration of the optimization process. In this paper, we replace this time-consuming step with a closed-form solution directly associated with the transformation field resulting in a speed up factor of ~10-60,000, for a typical 3D B-mode image of 2503 and 5003 voxels, depending upon the size and the parametrization of the transformation field. The performance of the numeric and the analytic solutions was contrasted by computing tracking and strain accuracy on two realistic synthetic 3D cardiac ultrasound sequences, mimicking two ischemic motion patterns. Mean and standard deviation of the displacement errors over the cardiac cycle for the numeric and analytic solutions were 0.68+/-0.40 mm and 0.75+/-0.43 mm respectively. Correlations for the radial, longitudinal and circumferential strain components at end-systole were 0.89, 0.83 and 0.95 versus 0.90, 0.88 and 0.92 for the numeric and analytic regularization respectively. The analytic solution matched the performance of the numeric solution as no statistically significant differences (p>0.05) were found when expressed in terms of bias or limits-of-agreement.

  20. Visualization of a newborn's hip joint using 3D ultrasound and automatic image processing

    NASA Astrophysics Data System (ADS)

    Overhoff, Heinrich M.; Lazovic, Djordje; von Jan, Ute

    1999-05-01

    Graf's method is a successful procedure for the diagnostic screening of developmental dysplasia of the hip. In a defined 2-D ultrasound (US) scan, which virtually cuts the hip joint, landmarks are interactively identified to derive congruence indicators. As the indicators do not reflect the spatial joint structure, and the femoral head is not clearly visible in the US scan, here 3-D US is used to gain insight to the hip joint in its spatial form. Hip joints of newborns were free-hand scanned using a conventional ultrasound transducer and a localizer system fixed on the scanhead. To overcome examiner- dependent findings the landmarks were detected by automatic segmentation of the image volume. The landmark image volumes and an automatically determined virtual sphere approximating the femoral head were visualized color-coded on a computer screen. The visualization was found to be intuitive and to simplify the diagnostic substantially. By the visualization of the 3-D relations between acetabulum and femoral head the reliability of diagnostics is improved by finding the entire joint geometry.

  1. Validation of 3D surface reconstruction of vertebrae and spinal column using 3D ultrasound data--a pilot study.

    PubMed

    Nguyen, Duc V; Vo, Quang N; Le, Lawrence H; Lou, Edmond H M

    2015-02-01

    Adolescent idiopathic scoliosis (AIS) is a three-dimensional deformity of spine associated with vertebra rotation. The Cobb angle and axial vertebral rotation are important parameters to assess the severity of scoliosis. However, the vertebral rotation is seldom measured from radiographs due to time consuming. Different techniques have been developed to extract 3D spinal information. Among many techniques, ultrasound imaging is a promising method. This pilot study reported an image processing method to reconstruct the posterior surface of vertebrae from 3D ultrasound data. Three cadaver vertebrae, a Sawbones spine phantom, and a spine from a child with AIS were used to validate the development. The in-vitro result showed the surface of the reconstructed image was visually similar to the original objects. The dimension measurement error was <5 mm and the Pearson correlation was >0.99. The results also showed a high accuracy in vertebral rotation with errors of 0.8 ± 0.3°, 2.8 ± 0.3° and 3.6 ± 0.5° for the rotation values of 0°, 15° and 30°, respectively. Meanwhile, the difference in the Cobb angle between the phantom and the image was 4° and the vertebral rotation at the apex was 2°. The Cobb angle measured from the in-vivo ultrasound image was 4° different from the radiograph. PMID:25550193

  2. 3-D statistical cancer atlas-based targeting of prostate biopsy using ultrasound image guidance

    NASA Astrophysics Data System (ADS)

    Narayanan, Ramkrishnan; Shen, Dinggang; Davatzikos, Christos A.; Crawford, E. David; Barqawi, Albaha; Werahera, Priya; Kumar, Dinesh; Suri, Jasjit S.

    2008-03-01

    Prostate cancer is a multifocal disease and lesions are not distributed uniformly within the gland. Several biopsy protocols concerning spatially specific targeting have been reported urology literature. Recently a statistical cancer atlas of the prostate was constructed providing voxelwise probabilities of cancers in the prostate. Additionally an optimized set of biopsy sites was computed with 94 - 96% detection accuracy was reported using only 6-7 needles. Here we discuss the warping of this atlas to prostate segmented side-fire ultrasound images of the patient. A shape model was used to speed up registration. The model was trained from over 38 expert segmented subjects off-line. This training yielded as few as 15-20 degrees of freedom that were optimized to warp the atlas surface to the patient's ultrasound image followed by elastic interpolation of the 3-D atlas. As a result the atlas is completely mapped to the patient's prostate anatomy along with optimal predetermined needle locations for biopsy. These do not preclude the use of additional biopsies if desired. A color overlay of the atlas is also displayed on the ultrasound image showing high cancer zones within the prostate. Finally current biopsy locations are saved in the atlas space and may be used to update the atlas based on the pathology report. In addition to the optimal atlas plan, previous biopsy locations and alternate plans can also be stored in the atlas space and warped to the patient with no additional time overhead.

  3. CASTLE3D - A Computer Aided System for Labelling Archaeological Excavations in 3D

    NASA Astrophysics Data System (ADS)

    Houshiar, H.; Borrmann, D.; Elseberg, J.; Nüchter, A.; Näth, F.; Winkler, S.

    2015-08-01

    Documentation of archaeological excavation sites with conventional methods and tools such as hand drawings, measuring tape and archaeological notes is time consuming. This process is prone to human errors and the quality of the documentation depends on the qualification of the archaeologist on site. Use of modern technology and methods in 3D surveying and 3D robotics facilitate and improve this process. Computer-aided systems and databases improve the documentation quality and increase the speed of data acquisition. 3D laser scanning is the state of the art in modelling archaeological excavation sites, historical sites and even entire cities or landscapes. Modern laser scanners are capable of data acquisition of up to 1 million points per second. This provides a very detailed 3D point cloud of the environment. 3D point clouds and 3D models of an excavation site provide a better representation of the environment for the archaeologist and for documentation. The point cloud can be used both for further studies on the excavation and for the presentation of results. This paper introduces a Computer aided system for labelling archaeological excavations in 3D (CASTLE3D). Consisting of a set of tools for recording and georeferencing the 3D data from an excavation site, CASTLE3D is a novel documentation approach in industrial archaeology. It provides a 2D and 3D visualisation of the data and an easy-to-use interface that enables the archaeologist to select regions of interest and to interact with the data in both representations. The 2D visualisation and a 3D orthogonal view of the data provide cuts of the environment that resemble the traditional hand drawings. The 3D perspective view gives a realistic view of the environment. CASTLE3D is designed as an easy-to-use on-site semantic mapping tool for archaeologists. Each project contains a predefined set of semantic information that can be used to label findings in the data. Multiple regions of interest can be joined under

  4. A molecular image-directed, 3D ultrasound-guided biopsy system for the prostate

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Schuster, David M.; Master, Viraj; Akbari, Hamed; Fenster, Aaron; Nieh, Peter

    2012-02-01

    Systematic transrectal ultrasound (TRUS)-guided biopsy is the standard method for a definitive diagnosis of prostate cancer. However, this biopsy approach uses two-dimensional (2D) ultrasound images to guide biopsy and can miss up to 30% of prostate cancers. We are developing a molecular image-directed, three-dimensional (3D) ultrasound imageguided biopsy system for improved detection of prostate cancer. The system consists of a 3D mechanical localization system and software workstation for image segmentation, registration, and biopsy planning. In order to plan biopsy in a 3D prostate, we developed an automatic segmentation method based wavelet transform. In order to incorporate PET/CT images into ultrasound-guided biopsy, we developed image registration methods to fuse TRUS and PET/CT images. The segmentation method was tested in ten patients with a DICE overlap ratio of 92.4% +/- 1.1 %. The registration method has been tested in phantoms. The biopsy system was tested in prostate phantoms and 3D ultrasound images were acquired from two human patients. We are integrating the system for PET/CT directed, 3D ultrasound-guided, targeted biopsy in human patients.

  5. A novel two-axis micromechanical scanning transducer for handheld 3D ultrasound and photoacoustic imaging

    NASA Astrophysics Data System (ADS)

    Huang, Chih-Hsien; Zou, Jun

    2016-03-01

    This paper reports the development of a new two-axis micromechanical scanning transducer for handheld 3D ultrasound imaging. It consists of a miniaturized single-element ultrasound transducer driven by a unique 2-axis liquid-immersible electromagnetic microactuator. With a mechanical scanning frequency of 19.532 Hz and an ultrasound pulse repetition rate of 5 kHz, the scanning transducer was scanned along 60 concentric paths with 256 detection points on each to simulate a physical 2D ultrasound transducer array of 60 × 256 elements. Using the scanning transducer, 3D pulse-echo ultrasound imaging of two silicon discs immersed in water as the imaging target was successfully conducted. The lateral resolution of the 3D ultrasound image was further improved with the synthetic aperture focusing technique (SAFT). The new two-axis micromechanical scanning transducer doesn't require complex and expensive multi-channel data acquisition (DAQ) electronics. Therefore, it could provide a new approach to achieve compact and low-cost 3D ultrasound and photoacoustic imaging systems, especially for handheld operations.

  6. Computational 3-D inversion for seismic exploration

    SciTech Connect

    Gavrilov, E.M.; Forslund, D.W.; Fehler, M.C.

    1997-10-01

    This is the final report of a four-month, Laboratory Directed Research and Development (LDRD) project carried out at the Los Alamos National Laboratory (LANL). There is a great need for a new and effective technology with a wide scope of industrial applications to investigate media internal properties of which can be explored only from the backscattered data. The project was dedicated to the development of a three-dimensional computational inversion tool for seismic exploration. The new computational concept of the inversion algorithm was suggested. The goal of the project was to prove the concept and the practical validity of the algorithm for petroleum exploration.

  7. Real-Time 3D Contrast-Enhanced Transcranial Ultrasound and Aberration Correction

    PubMed Central

    Ivancevich, Nikolas M.; Pinton, Gianmarco F.; Nicoletto, Heather A.; Bennett, Ellen; Laskowitz, Daniel T.; Smith, Stephen W.

    2008-01-01

    Contrast-enhanced (CE) transcranial ultrasound (US) and reconstructed 3D transcranial ultrasound have shown advantages over traditional methods in a variety of cerebrovascular diseases. We present the results from a novel ultrasound technique, namely real-time 3D contrast-enhanced transcranial ultrasound. Using real-time 3D (RT3D) ultrasound and micro-bubble contrast agent, we scanned 17 healthy volunteers via a single temporal window and 9 via the sub-occipital window and report our detection rates for the major cerebral vessels. In 71% of subjects, both of our observers identified the ipsilateral circle of Willis from the temporal window, and in 59% we imaged the entire circle of Willis. From the sub-occipital window, both observers detected the entire vertebrobasilar circulation in 22% of subjects, and in 44% the basilar artery. After performing phase aberration correction on one subject, we were able to increase the diagnostic value of the scan, detecting a vessel not present in the uncorrected scan. These preliminary results suggest that RT3D CE transcranial US and RT3D CE transcranial US with phase aberration correction have the potential to greatly impact the field of neurosonology. PMID:18395321

  8. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  9. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data.

    PubMed

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUS s t a r t ) and after (3D-iCEUS e n d ) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUS s t a r t and 3D-iCEUS e n d data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  10. 3D temperature field reconstruction using ultrasound sensing system

    NASA Astrophysics Data System (ADS)

    Liu, Yuqian; Ma, Tong; Cao, Chengyu; Wang, Xingwei

    2016-04-01

    3D temperature field reconstruction is of practical interest to the power, transportation and aviation industries and it also opens up opportunities for real time control or optimization of high temperature fluid or combustion process. In our paper, a new distributed optical fiber sensing system consisting of a series of elements will be used to generate and receive acoustic signals. This system is the first active temperature field sensing system that features the advantages of the optical fiber sensors (distributed sensing capability) and the acoustic sensors (non-contact measurement). Signals along multiple paths will be measured simultaneously enabled by a code division multiple access (CDMA) technique. Then a proposed Gaussian Radial Basis Functions (GRBF)-based approach can approximate the temperature field as a finite summation of space-dependent basis functions and time-dependent coefficients. The travel time of the acoustic signals depends on the temperature of the media. On this basis, the Gaussian functions are integrated along a number of paths which are determined by the number and distribution of sensors. The inversion problem to estimate the unknown parameters of the Gaussian functions can be solved with the measured times-of-flight (ToF) of acoustic waves and the length of propagation paths using the recursive least square method (RLS). The simulation results show an approximation error less than 2% in 2D and 5% in 3D respectively. It demonstrates the availability and efficiency of our proposed 3D temperature field reconstruction mechanism.

  11. 3D endobronchial ultrasound reconstruction and analysis for multimodal image-guided bronchoscopy

    NASA Astrophysics Data System (ADS)

    Zang, Xiaonan; Bascom, Rebecca; Gilbert, Christopher R.; Toth, Jennifer W.; Higgins, William E.

    2014-03-01

    State-of-the-art image-guided intervention (IGI) systems for lung-cancer management draw upon high-resolution three-dimensional multi-detector computed-tomography (MDCT) images and bronchoscopic video. An MDCT scan provides a high-resolution three-dimensional (3D) image of the chest that is used for preoperative procedure planning, while bronchoscopy gives live intraoperative video of the endobronchial airway tree structure. However, because neither source provides live extraluminal information on suspect nodules or lymph nodes, endobronchial ultrasound (EBUS) is often introduced during a procedure. Unfortunately, existing IGI systems provide no direct synergistic linkage between the MDCT/video data and EBUS data. Hence, EBUS proves difficult to use and can lead to inaccurate interpretations. To address this drawback, we present a prototype of a multimodal IGI system that brings together the various image sources. The system enables 3D reconstruction and visualization of structures depicted in the 2D EBUS video stream. It also provides a set of graphical tools that link the EBUS data directly to the 3D MDCT and bronchoscopic video. Results using phantom and human data indicate that the new system could potentially enable smooth natural incorporation of EBUS into the system-level work flow of bronchoscopy.

  12. Optimizing nonrigid registration performance between volumetric true 3D ultrasound images in image-guided neurosurgery

    NASA Astrophysics Data System (ADS)

    Ji, Songbai; Fan, Xiaoyao; Roberts, David W.; Hartov, Alex; Paulsen, Keith D.

    2011-03-01

    Compensating for brain shift as surgery progresses is important to ensure sufficient accuracy in patient-to-image registration in the operating room (OR) for reliable neuronavigation. Ultrasound has emerged as an important and practical imaging technique for brain shift compensation either by itself or through computational modeling that estimates whole-brain deformation. Using volumetric true 3D ultrasound (3DUS), it is possible to nonrigidly (e.g., based on B-splines) register two temporally different 3DUS images directly to generate feature displacement maps for data assimilation in the biomechanical model. Because of a large amount of data and number of degrees-of-freedom (DOFs) involved, however, a significant computational cost may be required that can adversely influence the clinical feasibility of the technique for efficiently generating model-updated MR (uMR) in the OR. This paper parametrically investigates three B-splines registration parameters and their influence on the computational cost and registration accuracy: number of grid nodes along each direction, floating image volume down-sampling rate, and number of iterations. A simulated rigid body displacement field was employed as a ground-truth against which the accuracy of displacements generated from the B-splines nonrigid registration was compared. A set of optimal parameters was then determined empirically that result in a registration computational cost of less than 1 min and a sub-millimetric accuracy in displacement measurement. These resulting parameters were further applied to a clinical surgery case to demonstrate their practical use. Our results indicate that the optimal set of parameters result in sufficient accuracy and computational efficiency in model computation, which is important for future application of the overall biomechanical modeling to generate uMR for image-guidance in the OR.

  13. The Ultrasound Brain Helmet: Simultaneous Multi-transducer 3D Transcranial Ultrasound Imaging

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.

    In this work, I examine the problem of rapid imaging of stroke and present ultrasound-based approaches for addressing it. Specifically, this dissertation discusses aberration and attenuation due to the skull as sources of image degradation and presents a prototype system for simultaneous 3D bilateral imaging via both temporal acoustic windows. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging via both temporal acoustic windows, allowing for registration and fusion of multiple real-time 3D scans of cerebral vasculature. I examine hardware considerations for new matrix arrays—transducer design and interconnects—in this application. Specifically, it is proposed that signal-to-noise ratio (SNR) may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented depicting cerebral arteries with and without the use of microbubble contrast agent that have been registered and fused using a search algorithm which maximizes normalized cross-correlation. The scanning geometry of a brain helmet-type system is also utilized to allow each matrix array to serve as a correction source for the opposing array. Aberration is estimated using cross-correlation of RF channel signals followed by least mean squares solution of the resulting overdetermined system. Delay maps are updated and real-time 3D scanning resumes. A first attempt is made at using multiple arrival time maps to correct multiple unique aberrators within a single transcranial imaging volume, i.e. several isoplanatic patches. This adaptive imaging technique, which uses steered unfocused waves transmitted by the opposing or

  14. Automated 3D ultrasound image segmentation for assistant diagnosis of breast cancer

    NASA Astrophysics Data System (ADS)

    Wang, Yuxin; Gu, Peng; Lee, Won-Mean; Roubidoux, Marilyn A.; Du, Sidan; Yuan, Jie; Wang, Xueding; Carson, Paul L.

    2016-04-01

    Segmentation of an ultrasound image into functional tissues is of great importance to clinical diagnosis of breast cancer. However, many studies are found to segment only the mass of interest and not all major tissues. Differences and inconsistencies in ultrasound interpretation call for an automated segmentation method to make results operator-independent. Furthermore, manual segmentation of entire three-dimensional (3D) ultrasound volumes is time-consuming, resource-intensive, and clinically impractical. Here, we propose an automated algorithm to segment 3D ultrasound volumes into three major tissue types: cyst/mass, fatty tissue, and fibro-glandular tissue. To test its efficacy and consistency, the proposed automated method was employed on a database of 21 cases of whole breast ultrasound. Experimental results show that our proposed method not only distinguishes fat and non-fat tissues correctly, but performs well in classifying cyst/mass. Comparison of density assessment between the automated method and manual segmentation demonstrates good consistency with an accuracy of 85.7%. Quantitative comparison of corresponding tissue volumes, which uses overlap ratio, gives an average similarity of 74.54%, consistent with values seen in MRI brain segmentations. Thus, our proposed method exhibits great potential as an automated approach to segment 3D whole breast ultrasound volumes into functionally distinct tissues that may help to correct ultrasound speed of sound aberrations and assist in density based prognosis of breast cancer.

  15. Automated 3D ultrasound image segmentation to aid breast cancer image interpretation.

    PubMed

    Gu, Peng; Lee, Won-Mean; Roubidoux, Marilyn A; Yuan, Jie; Wang, Xueding; Carson, Paul L

    2016-02-01

    Segmentation of an ultrasound image into functional tissues is of great importance to clinical diagnosis of breast cancer. However, many studies are found to segment only the mass of interest and not all major tissues. Differences and inconsistencies in ultrasound interpretation call for an automated segmentation method to make results operator-independent. Furthermore, manual segmentation of entire three-dimensional (3D) ultrasound volumes is time-consuming, resource-intensive, and clinically impractical. Here, we propose an automated algorithm to segment 3D ultrasound volumes into three major tissue types: cyst/mass, fatty tissue, and fibro-glandular tissue. To test its efficacy and consistency, the proposed automated method was employed on a database of 21 cases of whole breast ultrasound. Experimental results show that our proposed method not only distinguishes fat and non-fat tissues correctly, but performs well in classifying cyst/mass. Comparison of density assessment between the automated method and manual segmentation demonstrates good consistency with an accuracy of 85.7%. Quantitative comparison of corresponding tissue volumes, which uses overlap ratio, gives an average similarity of 74.54%, consistent with values seen in MRI brain segmentations. Thus, our proposed method exhibits great potential as an automated approach to segment 3D whole breast ultrasound volumes into functionally distinct tissues that may help to correct ultrasound speed of sound aberrations and assist in density based prognosis of breast cancer. PMID:26547117

  16. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. PMID:26689764

  17. 3D freehand ultrasound for medical assistance in diagnosis and treatment of breast cancer: preliminary results

    NASA Astrophysics Data System (ADS)

    Torres, Fabian; Fanti, Zian; Arambula Cosío, F.

    2013-11-01

    Image-guided interventions allow the physician to have a better planning and visualization of a procedure. 3D freehand ultrasound is a non-invasive and low-cost imaging tool that can be used to assist medical procedures. This tool can be used in the diagnosis and treatment of breast cancer. There are common medical practices that involve large needles to obtain an accurate diagnosis and treatment of breast cancer. In this study we propose the use of 3D freehand ultrasound for planning and guiding such procedures as core needle biopsy and radiofrequency ablation. The proposed system will help the physician to identify the lesion area, using image-processing techniques in the 3D freehand ultrasound images, and guide the needle to this area using the information of position and orientation of the surgical tools. We think that this system can upgrade the accuracy and efficiency of these procedures.

  18. Automatic 3D segmentation of ultrasound images using atlas registration and statistical texture prior

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Schuster, David; Master, Viraj; Nieh, Peter; Fenster, Aaron; Fei, Baowei

    2011-03-01

    We are developing a molecular image-directed, 3D ultrasound-guided, targeted biopsy system for improved detection of prostate cancer. In this paper, we propose an automatic 3D segmentation method for transrectal ultrasound (TRUS) images, which is based on multi-atlas registration and statistical texture prior. The atlas database includes registered TRUS images from previous patients and their segmented prostate surfaces. Three orthogonal Gabor filter banks are used to extract texture features from each image in the database. Patient-specific Gabor features from the atlas database are used to train kernel support vector machines (KSVMs) and then to segment the prostate image from a new patient. The segmentation method was tested in TRUS data from 5 patients. The average surface distance between our method and manual segmentation is 1.61 +/- 0.35 mm, indicating that the atlas-based automatic segmentation method works well and could be used for 3D ultrasound-guided prostate biopsy.

  19. FPGA-based real-time anisotropic diffusion filtering of 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Castro-Pareja, Carlos R.; Dandekar, Omkar S.; Shekhar, Raj

    2005-02-01

    Three-dimensional ultrasonic imaging, especially the emerging real-time version of it, is particularly valuable in medical applications such as echocardiography, obstetrics and surgical navigation. A known problem with ultrasound images is their high level of speckle noise. Anisotropic diffusion filtering has been shown to be effective in enhancing the visual quality of 3D ultrasound images and as preprocessing prior to advanced image processing. However, due to its arithmetic complexity and the sheer size of 3D ultrasound images, it is not possible to perform online, real-time anisotropic diffusion filtering using standard software implementations. We present an FPGA-based architecture that allows performing anisotropic diffusion filtering of 3D images at acquisition rates, thus enabling the use of this filtering technique in real-time applications, such as visualization, registration and volume rendering.

  20. Proximal femoral focal deficiency of the fetus - early 3D/4D prenatal ultrasound diagnosis.

    PubMed

    Kudla, Marek J; Beczkowska-Kielek, Aleksandra; Kutta, Katarzyna; Partyka-Lasota, Justyna

    2016-09-01

    Proximal Femoral Focal Deficiency (PFFD) is a rare congenital syndrome of unknown etiology. Additional disorders can be present up to 70% of PFFD cases. Management (including termination) depends on the severity of the malformation. We present a case of a 32-year-old woman referred for routine ultrasound examination in the 12th week of pregnancy. Detailed 3D/4D evaluation revealed asymmetry of lower limbs and diagnosis of isolated PFFD was established. Parents were fully informed and decided to continue the pregnancy. We stress here the importance of early 3D/4D ultrasound diagnosis. Our paper presents the earliest case where the diagnosis of PFFD was established with 3D/4D ultrasound. PMID:27622419

  1. 3D reconstruction of a carotid bifurcation from 2D transversal ultrasound images.

    PubMed

    Yeom, Eunseop; Nam, Kweon-Ho; Jin, Changzhu; Paeng, Dong-Guk; Lee, Sang-Joon

    2014-12-01

    Visualizing and analyzing the morphological structure of carotid bifurcations are important for understanding the etiology of carotid atherosclerosis, which is a major cause of stroke and transient ischemic attack. For delineation of vasculatures in the carotid artery, ultrasound examinations have been widely employed because of a noninvasive procedure without ionizing radiation. However, conventional 2D ultrasound imaging has technical limitations in observing the complicated 3D shapes and asymmetric vasodilation of bifurcations. This study aims to propose image-processing techniques for better 3D reconstruction of a carotid bifurcation in a rat by using 2D cross-sectional ultrasound images. A high-resolution ultrasound imaging system with a probe centered at 40MHz was employed to obtain 2D transversal images. The lumen boundaries in each transverse ultrasound image were detected by using three different techniques; an ellipse-fitting, a correlation mapping to visualize the decorrelation of blood flow, and the ellipse-fitting on the correlation map. When the results are compared, the third technique provides relatively good boundary extraction. The incomplete boundaries of arterial lumen caused by acoustic artifacts are somewhat resolved by adopting the correlation mapping and the distortion in the boundary detection near the bifurcation apex was largely reduced by using the ellipse-fitting technique. The 3D lumen geometry of a carotid artery was obtained by volumetric rendering of several 2D slices. For the 3D vasodilatation of the carotid bifurcation, lumen geometries at the contraction and expansion states were simultaneously depicted at various view angles. The present 3D reconstruction methods would be useful for efficient extraction and construction of the 3D lumen geometries of carotid bifurcations from 2D ultrasound images. PMID:24965564

  2. A framework for human spine imaging using a freehand 3D ultrasound system.

    PubMed

    Purnama, Ketut E; Wilkinson, Michael H F; Veldhuizen, Albert G; van Ooijen, Peter M A; Lubbers, Jaap; Burgerhof, Johannes G M; Sardjono, Tri A; Verkerke, Gijbertus J

    2010-01-01

    The use of 3D ultrasound imaging to follow the progression of scoliosis, i.e., a 3D deformation of the spine, is described. Unlike other current examination modalities, in particular based on X-ray, its non-detrimental effect enables it to be used frequently to follow the progression of scoliosis which sometimes may develop rapidly. Furthermore, 3D ultrasound imaging provides information in 3D directly in contrast to projection methods. This paper describes a feasibility study of an ultrasound system to provide a 3D image of the human spine, and presents a framework of procedures to perform this task. The framework consist of an ultrasound image acquisition procedure to image a large part of the human spine by means of a freehand 3D ultrasound system and a volume reconstruction procedure which was performed in four stages: bin-filling, hole-filling, volume segment alignment, and volume segment compounding. The overall results of the procedures in this framework show that imaging of the human spine using ultrasound is feasible. Vertebral parts such as the transverse processes, laminae, superior articular processes, and spinous process of the vertebrae appear as clouds of voxels having intensities higher than the surrounding voxels. In sagittal slices, a string of transverse processes appears representing the curvature of the spine. In the bin-filling stage the estimated mean absolute noise level of a single measurement of a single voxel was determined. Our comparative study for the hole-filling methods based on rank sum statistics proved that the pixel nearest neighbour (PNN) method with variable radius and with the proposed olympic operation is the best method. Its mean absolute grey value error was less in magnitude than the noise level of a single measurement. PMID:20231799

  3. Parallel algorithm for computing 3-D reachable workspaces

    NASA Astrophysics Data System (ADS)

    Alameldin, Tarek K.; Sobh, Tarek M.

    1992-03-01

    The problem of computing the 3-D workspace for redundant articulated chains has applications in a variety of fields such as robotics, computer aided design, and computer graphics. The computational complexity of the workspace problem is at least NP-hard. The recent advent of parallel computers has made practical solutions for the workspace problem possible. Parallel algorithms for computing the 3-D workspace for redundant articulated chains with joint limits are presented. The first phase of these algorithms computes workspace points in parallel. The second phase uses workspace points that are computed in the first phase and fits a 3-D surface around the volume that encompasses the workspace points. The second phase also maps the 3- D points into slices, uses region filling to detect the holes and voids in the workspace, extracts the workspace boundary points by testing the neighboring cells, and tiles the consecutive contours with triangles. The proposed algorithms are efficient for computing the 3-D reachable workspace for articulated linkages, not only those with redundant degrees of freedom but also those with joint limits.

  4. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  5. A compact mechatronic system for 3D ultrasound guided prostate interventions

    SciTech Connect

    Bax, Jeffrey; Smith, David; Bartha, Laura; Montreuil, Jacques; Sherebrin, Shi; Gardi, Lori; Edirisinghe, Chandima; Fenster, Aaron

    2011-02-15

    Purpose: Ultrasound imaging has improved the treatment of prostate cancer by producing increasingly higher quality images and influencing sophisticated targeting procedures for the insertion of radioactive seeds during brachytherapy. However, it is critical that the needles be placed accurately within the prostate to deliver the therapy to the planned location and avoid complications of damaging surrounding tissues. Methods: The authors have developed a compact mechatronic system, as well as an effective method for guiding and controlling the insertion of transperineal needles into the prostate. This system has been designed to allow guidance of a needle obliquely in 3D space into the prostate, thereby reducing pubic arch interference. The choice of needle trajectory and location in the prostate can be adjusted manually or with computer control. Results: To validate the system, a series of experiments were performed on phantoms. The 3D scan of the string phantom produced minimal geometric error, which was less than 0.4 mm. Needle guidance accuracy tests in agar prostate phantoms showed that the mean error of bead placement was less then 1.6 mm along parallel needle paths that were within 1.2 mm of the intended target and 1 deg. from the preplanned trajectory. At oblique angles of up to 15 deg. relative to the probe axis, beads were placed to within 3.0 mm along a trajectory that were within 2.0 mm of the target with an angular error less than 2 deg. Conclusions: By combining 3D TRUS imaging system to a needle tracking linkage, this system should improve the physician's ability to target and accurately guide a needle to selected targets without the need for the computer to directly manipulate and insert the needle. This would be beneficial as the physician has complete control of the system and can safely maneuver the needle guide around obstacles such as previously placed needles.

  6. Automated benign & malignant thyroid lesion characterization and classification in 3D contrast-enhanced ultrasound.

    PubMed

    Acharya, U Rajendra; S, Vinitha Sree; Molinari, Filippo; Garberoglio, Roberto; Witkowska, Agnieszka; Suri, Jasjit S

    2012-01-01

    In this work, we present a Computer Aided Diagnosis (CAD) based technique for automatic classification of benign and malignant thyroid lesions in 3D contrast-enhanced ultrasound images. The images were obtained from 20 patients. Fine needle aspiration biopsy and histology confirmed malignancy. Discrete Wavelet Transform (DWT) and texture based features were extracted from the thyroid images. The resulting feature vectors were used to train and test three different classifiers: K-Nearest Neighbor (K-NN), Probabilistic Neural Network (PNN), and Decision Tree (DeTr) using ten-fold cross validation technique. Our results show that combination of DWT and texture features in the K-NN classifier resulted in a classification accuracy of 98.9%, a sensitivity of 98%, and a specificity of 99.8%. Thus, the preliminary results of the proposed technique show that it could be adapted as an adjunct tool that can give valuable second opinions to the doctors regarding the nature of the thyroid nodule. The technique is cost-effective, non-invasive, fast, completely automated and gives more objective and reproducible results compared to manual analysis of the ultrasound images. We however intend to establish the clinical applicability of this technique by evaluating it with more data in the future. PMID:23365926

  7. A method for 3D reconstruction of coronary arteries using biplane angiography and intravascular ultrasound images.

    PubMed

    Bourantas, Christos V; Kourtis, Iraklis C; Plissiti, Marina E; Fotiadis, Dimitrios I; Katsouras, Christos S; Papafaklis, Michail I; Michalis, Lampros K

    2005-12-01

    The aim of this study is to describe a new method for the three-dimensional reconstruction of coronary arteries and its quantitative validation. Our approach is based on the fusion of the data provided by intravascular ultrasound images (IVUS) and biplane angiographies. A specific segmentation algorithm is used for the detection of the regions of interest in intravascular ultrasound images. A new methodology is also introduced for the accurate extraction of the catheter path. In detail, a cubic B-spline is used for approximating the catheter path in each biplane projection. Each B-spline curve is swept along the normal direction of its X-ray angiographic plane forming a surface. The intersection of the two surfaces is a 3D curve, which represents the reconstructed path. The detected regions of interest in the IVUS images are placed perpendicularly onto the path and their relative axial twist is computed using the sequential triangulation algorithm. Then, an efficient algorithm is applied to estimate the absolute orientation of the first IVUS frame. In order to obtain 3D visualization the commercial package Geomagic Studio 4.0 is used. The performance of the proposed method is assessed using a validation methodology which addresses the separate validation of each step followed for obtaining the coronary reconstruction. The performance of the segmentation algorithm was examined in 80 IVUS images. The reliability of the path extraction method was studied in vitro using a metal wire model and in vivo in a dataset of 11 patients. The performance of the sequential triangulation algorithm was tested in two gutter models and in the coronary arteries (marked with metal clips) of six cadaveric sheep hearts. Finally, the accuracy in the estimation of the first IVUS frame absolute orientation was examined in the same set of cadaveric sheep hearts. The obtained results demonstrate that the proposed reconstruction method is reliable and capable of depicting the morphology of

  8. Registration of 2D cardiac images to real-time 3D ultrasound volumes for 3D stress echocardiography

    NASA Astrophysics Data System (ADS)

    Leung, K. Y. Esther; van Stralen, Marijn; Voormolen, Marco M.; van Burken, Gerard; Nemes, Attila; ten Cate, Folkert J.; Geleijnse, Marcel L.; de Jong, Nico; van der Steen, Antonius F. W.; Reiber, Johan H. C.; Bosch, Johan G.

    2006-03-01

    Three-dimensional (3D) stress echocardiography is a novel technique for diagnosing cardiac dysfunction, by comparing wall motion of the left ventricle under different stages of stress. For quantitative comparison of this motion, it is essential to register the ultrasound data. We propose an intensity based rigid registration method to retrieve two-dimensional (2D) four-chamber (4C), two-chamber, and short-axis planes from the 3D data set acquired in the stress stage, using manually selected 2D planes in the rest stage as reference. The algorithm uses the Nelder-Mead simplex optimization to find the optimal transformation of one uniform scaling, three rotation, and three translation parameters. We compared registration using the SAD, SSD, and NCC metrics, performed on four resolution levels of a Gaussian pyramid. The registration's effectiveness was assessed by comparing the 3D positions of the registered apex and mitral valve midpoints and 4C direction with the manually selected results. The registration was tested on data from 20 patients. Best results were found using the NCC metric on data downsampled with factor two: mean registration errors were 8.1mm, 5.4mm, and 8.0° in the apex position, mitral valve position, and 4C direction respectively. The errors were close to the interobserver (7.1mm, 3.8mm, 7.4°) and intraobserver variability (5.2mm, 3.3mm, 7.0°), and better than the error before registration (9.4mm, 9.0mm, 9.9°). We demonstrated that the registration algorithm visually and quantitatively improves the alignment of rest and stress data sets, performing similar to manual alignment. This will improve automated analysis in 3D stress echocardiography.

  9. 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.

  10. Recovery of liver motion and deformation due to respiration using laparoscopic freehand 3D ultrasound system.

    PubMed

    Nakamoto, Masahiko; Hirayama, Hiroaki; Sato, Yoshinobu; Konishi, Kozo; Kakeji, Yoshihiro; Hashizume, Makoto; Tamura, Shinichi

    2006-01-01

    This paper describes a rapid method for intraoperative recovery of liver motion and deformation due to respiration by using a laparoscopic freehand 3D ultrasound (US) system. Using the proposed method, 3D US images of the liver can be extended to 4D US images by acquiring additional several sequences of 2D US images during a couple of respiration cycles. Time-varying 2D US images are acquired on several sagittal image planes and their 3D positions and orientations are measured using a laparoscopic ultrasound probe to which a miniature magnetic 3D position sensor is attached. During the acquisition, the probe is assumed to move together with the liver surface. In-plane 2D deformation fields and respiratory phase are estimated from the time-varying 2D US images, and then the time-varying 3D deformation fields on the sagittal image planes are obtained by combining 3D positions and orientations of the image planes. The time-varying 3D deformation field of the volume is obtained by interpolating the 3D deformation fields estimated on several planes. The proposed method was evaluated by in vivo experiments using a pig liver. PMID:17354794

  11. Consequences of Intermodality Registration Errors for Intramodality 3D Ultrasound IGRT.

    PubMed

    van der Meer, Skadi; Seravalli, Enrica; Fontanarosa, Davide; Bloemen-van Gurp, Esther J; Verhaegen, Frank

    2016-08-01

    Intramodality ultrasound image-guided radiotherapy systems compare daily ultrasound to reference ultrasound images. Nevertheless, because the actual treatment planning is based on a reference computed tomography image, and not on a reference ultrasound image, their accuracy depends partially on the correct intermodality registration of the reference ultrasound and computed tomography images for treatment planning. The error propagation in daily patient positioning due to potential registration errors at the planning stage was assessed in this work. Five different scenarios were simulated involving shifts or rotations of ultrasound or computed tomography images. The consequences of several workflow procedures were tested with a phantom setup. As long as the reference ultrasound and computed tomography images are made to match, the patient will be in the correct treatment position. In an example with a phantom measurement, the accuracy of the performed manual fusion was found to be ≤2 mm. In clinical practice, manual registration of patient images is expected to be more difficult. Uncorrected mismatches will lead to a systematically incorrect final patient position because there will be no indication that there was a misregistration between the computed tomography and reference ultrasound images. In the treatment room, the fusion with the computed tomography image will not be visible and based on the ultrasound images the patient position seems correct. PMID:26048909

  12. 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.

  13. Novel 3-D laparoscopic magnetic ultrasound image guidance for lesion targeting

    PubMed Central

    Sindram, David; McKillop, Iain H; Martinie, John B; Iannitti, David A

    2010-01-01

    Objectives: Accurate laparoscopic liver lesion targeting for biopsy or ablation depends on the ability to merge laparoscopic and ultrasound images with proprioceptive instrument positioning, a skill that can be acquired only through extensive experience. The aim of this study was to determine whether using magnetic positional tracking to provide three-dimensional, real-time guidance improves accuracy during laparoscopic needle placement. Methods: Magnetic sensors were embedded into a needle and laparoscopic ultrasound transducer. These sensors interrupted the magnetic fields produced by an electromagnetic field generator, allowing for real-time, 3-D guidance on a stereoscopic monitor. Targets measuring 5 mm were embedded 3–5 cm deep in agar and placed inside a laparoscopic trainer box. Two novices (a college student and an intern) and two experts (hepatopancreatobiliary surgeons) targeted the lesions out of the ultrasound plane using either traditional or 3-D guidance. Results: Each subject targeted 22 lesions, 11 with traditional and 11 with the novel guidance (n = 88). Hit rates of 32% (14/44) and 100% (44/44) were observed with the traditional approach and the 3-D magnetic guidance approach, respectively. The novices were essentially unable to hit the targets using the traditional approach, but did not miss using the novel system. The hit rate of experts improved from 59% (13/22) to 100% (22/22) (P < 0.0001). Conclusions: The novel magnetic 3-D laparoscopic ultrasound guidance results in perfect targeting of 5-mm lesions, even by surgical novices. PMID:21083797

  14. Visualization of hepatic arteries with 3D ultrasound during intra-arterial therapies

    NASA Astrophysics Data System (ADS)

    Gérard, Maxime; Tang, An; Badoual, Anaïs.; Michaud, François; Bigot, Alexandre; Soulez, Gilles; Kadoury, Samuel

    2016-03-01

    Liver cancer represents the second most common cause of cancer-related mortality worldwide. The prognosis is poor with an overall mortality of 95%. Moreover, most hepatic tumors are unresectable due to their advanced stage at discovery or poor underlying liver function. Tumor embolization by intra-arterial approaches is the current standard of care for advanced cases of hepatocellular carcinoma. These therapies rely on the fact that the blood supply of primary hepatic tumors is predominantly arterial. Feedback on blood flow velocities in the hepatic arteries is crucial to ensure maximal treatment efficacy on the targeted masses. Based on these velocities, the intra-arterial injection rate is modulated for optimal infusion of the chemotherapeutic drugs into the tumorous tissue. While Doppler ultrasound is a well-documented technique for the assessment of blood flow, 3D visualization of vascular anatomy with ultrasound remains challenging. In this paper we present an image-guidance pipeline that enables the localization of the hepatic arterial branches within a 3D ultrasound image of the liver. A diagnostic Magnetic resonance angiography (MRA) is first processed to automatically segment the hepatic arteries. A non-rigid registration method is then applied on the portal phase of the MRA volume with a 3D ultrasound to enable the visualization of the 3D mesh of the hepatic arteries in the Doppler images. To evaluate the performance of the proposed workflow, we present initial results from porcine models and patient images.

  15. Validity Study of Vertebral Rotation Measurement Using 3-D Ultrasound in Adolescent Idiopathic Scoliosis.

    PubMed

    Wang, Qian; Li, Meng; Lou, Edmond H M; Chu, Winnie C W; Lam, Tsz-Ping; Cheng, Jack C Y; Wong, Man-Sang

    2016-07-01

    This study aimed to assess the validity of 3-D ultrasound measurements on the vertebral rotation of adolescent idiopathic scoliosis (AIS) under clinical settings. Thirty curves (mean Cobb angle: 21.7° ± 15.9°) from 16 patients with AIS were recruited. 3-D ultrasound and magnetic resonance imaging scans were performed at the supine position. Each of the two raters measured the apical vertebral rotation using the center of laminae (COL) method in the 3-D ultrasound images and the Aaro-Dahlborn method in the magnetic resonance images. The intra- and inter-reliability of the COL method was demonstrated by the intra-class correlation coefficient (ICC) (both [2, K] >0.9, p < 0.05). The COL method showed no significant difference (p < 0.05) compared with the Aaro-Dahlborn method. Furthermore, the agreement between these two methods was demonstrated by the Bland-Altman method, and high correlation was found (r > 0.9, p < 0.05). These results validated the proposed 3-D ultrasound method in the measurements of vertebral rotation in the patients with AIS. PMID:27083978

  16. Modeling of multi-view 3D freehand radio frequency ultrasound.

    PubMed

    Klein, T; Hansson, M; Navab, Nassir

    2012-01-01

    Nowadays ultrasound (US) examinations are typically performed with conventional machines providing two dimensional imagery. However, there exist a multitude of applications where doctors could benefit from three dimensional ultrasound providing better judgment, due to the extended spatial view. 3D freehand US allows acquisition of images by means of a tracking device attached to the ultrasound transducer. Unfortunately, view dependency makes the 3D representation of ultrasound a non-trivial task. To address this we model speckle statistics, in envelope-detected radio frequency (RF) data, using a finite mixture model (FMM), assuming a parametric representation of data, in which the multiple views are treated as components of the FMM. The proposed model is show-cased with registration, using an ultrasound specific distribution based pseudo-distance, and reconstruction tasks, performed on the manifold of Gamma model parameters. Example field of application is neurology using transcranial US, as this domain requires high accuracy and data systematically features low SNR, making intensity based registration difficult. In particular, 3D US can be specifically used to improve differential diagnosis of Parkinson's disease (PD) compared to conventional approaches and is therefore of high relevance for future application. PMID:23285579

  17. OVERALL PROCEDURES PROTOCOL AND PATIENT ENROLLMENT PROTOCOL: TESTING FEASIBILITY OF 3D ULTRASOUND DATA ACQUISITION AND RELIABILITY OF DATA RETRIEVAL FROM STORED 3D IMAGES

    EPA Science Inventory

    The purpose of this study is to examine the feasibility of collecting, transmitting,

    and analyzing 3-D ultrasound data in the context of a multi-center study of pregnant

    women. The study will also examine the reliability of measurements obtained from 3-D

    imag...

  18. Semiautomatic registration of 3D transabdominal ultrasound images for patient repositioning during postprostatectomy radiotherapy

    SciTech Connect

    Presles, Benoît Rit, Simon; Sarrut, David; Fargier-Voiron, Marie; Liebgott, Hervé; Biston, Marie-Claude; Munoz, Alexandre; Pommier, Pascal; Lynch, Rod

    2014-12-15

    Purpose: The aim of the present work is to propose and evaluate registration algorithms of three-dimensional (3D) transabdominal (TA) ultrasound (US) images to setup postprostatectomy patients during radiation therapy. Methods: Three registration methods have been developed and evaluated to register a reference 3D-TA-US image acquired during the planning CT session and a 3D-TA-US image acquired before each treatment session. The first method (method A) uses only gray value information, whereas the second one (method B) uses only gradient information. The third one (method C) combines both sets of information. All methods restrict the comparison to a region of interest computed from the dilated reference positioning volume drawn on the reference image and use mutual information as a similarity measure. The considered geometric transformations are translations and have been optimized by using the adaptive stochastic gradient descent algorithm. Validation has been carried out using manual registration by three operators of the same set of image pairs as the algorithms. Sixty-two treatment US images of seven patients irradiated after a prostatectomy have been registered to their corresponding reference US image. The reference registration has been defined as the average of the manual registration values. Registration error has been calculated by subtracting the reference registration from the algorithm result. For each session, the method has been considered a failure if the registration error was above both the interoperator variability of the session and a global threshold of 3.0 mm. Results: All proposed registration algorithms have no systematic bias. Method B leads to the best results with mean errors of −0.6, 0.7, and −0.2 mm in left–right (LR), superior–inferior (SI), and anterior–posterior (AP) directions, respectively. With this method, the standard deviations of the mean error are of 1.7, 2.4, and 2.6 mm in LR, SI, and AP directions, respectively

  19. Model based assessment of vestibular jawbone thickness using high frequency 3D ultrasound micro-scanning

    NASA Astrophysics Data System (ADS)

    Habor, Daniel; Neuhaus, Sarah; Vollborn, Thorsten; Wolfart, Stefan; Radermacher, Klaus; Heger, Stefan

    2013-03-01

    Endosseous implants are well-established in modern dentistry. However, without appropriate therapeutic intervention, progressive peri-implant bone loss may lead to failing implants. Conventionally, the particularly relevant vestibular jawbone thickness is monitored using radiographic 3D imaging methods. Ionizing radiation, as well as imaging artifacts caused by metallic implants and superstructures are major drawbacks of these imaging modalities. In this study, a high frequency ultrasound (HFUS) based approach to assess the vestibular jawbone thickness is being introduced. It should be emphasized that the presented method does not require ultrasound penetration of the jawbone. An in-vitro study using two porcine specimens with inserted endosseous implants has been carried out to assess the accuracy of our approach. The implant of the first specimen was equipped with a gingiva former while a polymer superstructure was mounted onto the implant of the second specimen. Ultrasound data has been acquired using a 4 degree of freedom (DOF) high frequency (<50MHz) laboratory ultrasound scanner. The ultrasound raw data has been converted to polygon meshes including the surfaces of bone, gingiva, gingiva former (first specimen) and superstructure (second specimen). The meshes are matched with a-priori acquired 3D models of the implant, the superstructure and the gingiva former using a best-fit algorithm. Finally, the vestibular peri-implant bone thickness has been assessed in the resulting 3D models. The accuracy of this approach has been evaluated by comparing the ultrasound based thickness measurement with a reference measurement acquired with an optical extra-oral 3D scanner prior to covering the specimens with gingiva. As a final result, the bone thicknesses of the two specimens were measured yielding an error of -46+/-89μm (first specimen) and 70+/-93μm (second specimen).

  20. An optical system for detecting 3D high-speed oscillation of a single ultrasound microbubble

    PubMed Central

    Liu, Yuan; Yuan, Baohong

    2013-01-01

    As contrast agents, microbubbles have been playing significant roles in ultrasound imaging. Investigation of microbubble oscillation is crucial for microbubble characterization and detection. Unfortunately, 3-dimensional (3D) observation of microbubble oscillation is challenging and costly because of the bubble size—a few microns in diameter—and the high-speed dynamics under MHz ultrasound pressure waves. In this study, a cost-efficient optical confocal microscopic system combined with a gated and intensified charge-coupled device (ICCD) camera were developed to detect 3D microbubble oscillation. The capability of imaging microbubble high-speed oscillation with much lower costs than with an ultra-fast framing or streak camera system was demonstrated. In addition, microbubble oscillations along both lateral (x and y) and axial (z) directions were demonstrated. Accordingly, this system is an excellent alternative for 3D investigation of microbubble high-speed oscillation, especially when budgets are limited. PMID:24049677

  1. Quantitative Assessment of Cancer Vascular Architecture by Skeletonization of High-resolution 3-D Contrast-enhanced Ultrasound Images

    PubMed Central

    Molinari, F.; Meiburger, K. M.; Giustetto, P.; Rizzitelli, S.; Boffa, C.; Castano, M.; Terreno, E.

    2014-01-01

    The accurate characterization and description of the vascular network of a cancer lesion is of paramount importance in clinical practice and cancer research in order to improve diagnostic accuracy or to assess the effectiveness of a treatment. The aim of this study was to show the effectiveness of liposomes as an ultrasound contrast agent to describe the 3-D vascular architecture of a tumor. Eight C57BL/6 mice grafted with syngeneic B16-F10 murine melanoma cells were injected with a bolus of 1,2-Distearoyl-sn-glycero-3-phosphocoline (DSPC)-based non-targeted liposomes and with a bolus of microbubbles. 3-D contrast-enhanced images of the tumor lesions were acquired in three conditions: pre-contrast, after the injection of microbubbles, and after the injection of liposomes. By using a previously developed reconstruction and characterization image processing technique, we obtained the 3-D representation of the vascular architecture in these three conditions. Six descriptive parameters of these networks were also computed: the number of vascular trees (NT), the vascular density (VD), the number of branches, the 2-D curvature measure, the number of vascular flexes of the vessels, and the 3-D curvature. Results showed that all the vascular descriptors obtained by liposome-based images were statistically equal to those obtained by using microbubbles, except the VD which was found to be lower for liposome images. All the six descriptors computed in pre-contrast conditions had values that were statistically lower than those computed in presence of contrast, both for liposomes and microbubbles. Liposomes have already been used in cancer therapy for the selective ultrasound-mediated delivery of drugs. This work demonstrated their effectiveness also as vascular diagnostic contrast agents, therefore proving that liposomes can be used as efficient “theranostic” (i.e. therapeutic + diagnostic) ultrasound probes. PMID:24206210

  2. Chest-wall segmentation in automated 3D breast ultrasound images using thoracic volume classification

    NASA Astrophysics Data System (ADS)

    Tan, Tao; van Zelst, Jan; Zhang, Wei; Mann, Ritse M.; Platel, Bram; Karssemeijer, Nico

    2014-03-01

    Computer-aided detection (CAD) systems are expected to improve effectiveness and efficiency of radiologists in reading automated 3D breast ultrasound (ABUS) images. One challenging task on developing CAD is to reduce a large number of false positives. A large amount of false positives originate from acoustic shadowing caused by ribs. Therefore determining the location of the chestwall in ABUS is necessary in CAD systems to remove these false positives. Additionally it can be used as an anatomical landmark for inter- and intra-modal image registration. In this work, we extended our previous developed chestwall segmentation method that fits a cylinder to automated detected rib-surface points and we fit the cylinder model by minimizing a cost function which adopted a term of region cost computed from a thoracic volume classifier to improve segmentation accuracy. We examined the performance on a dataset of 52 images where our previous developed method fails. Using region-based cost, the average mean distance of the annotated points to the segmented chest wall decreased from 7.57±2.76 mm to 6.22±2.86 mm.art.

  3. Tubular Enhanced Geodesic Active Contours for Continuum Robot Detection using 3D Ultrasound

    PubMed Central

    Ren, Hongliang; Dupont, Pierre E.

    2013-01-01

    Three dimensional ultrasound is a promising imaging modality for minimally invasive robotic surgery. As the robots are typically metallic, they interact strongly with the sound waves in ways that are not modeled by the ultrasound system’s signal processing algorithms. Consequently, they produce substantial imaging artifacts that can make image guidance difficult, even for experienced surgeons. This paper introduces a new approach for detecting curved continuum robots in 3D ultrasound images. The proposed approach combines geodesic active contours with a speed function that is based on enhancing the “tubularity” of the continuum robot. In particular, it takes advantage of the known robot diameter along its length. It also takes advantage of the fact that the robot surface facing the ultrasound probe provides the most accurate image. This method, termed Tubular Enhanced Geodesic Active Contours (TEGAC), is demonstrated through ex vivo intracardiac experiments to offer superior performance compared to conventional active contours. PMID:24231880

  4. A non-disruptive technology for robust 3D tool tracking for ultrasound-guided interventions.

    PubMed

    Mung, Jay; Vignon, Francois; Jain, Ameet

    2011-01-01

    In the past decade ultrasound (US) has become the preferred modality for a number of interventional procedures, offering excellent soft tissue visualization. The main limitation however is limited visualization of surgical tools. A new method is proposed for robust 3D tracking and US image enhancement of surgical tools under US guidance. Small US sensors are mounted on existing surgical tools. As the imager emits acoustic energy, the electrical signal from the sensor is analyzed to reconstruct its 3D coordinates. These coordinates can then be used for 3D surgical navigation, similar to current day tracking systems. A system with real-time 3D tool tracking and image enhancement was implemented on a commercial ultrasound scanner and 3D probe. Extensive water tank experiments with a tracked 0.2mm sensor show robust performance in a wide range of imaging conditions and tool position/orientations. The 3D tracking accuracy was 0.36 +/- 0.16mm throughout the imaging volume of 55 degrees x 27 degrees x 150mm. Additionally, the tool was successfully tracked inside a beating heart phantom. This paper proposes an image enhancement and tool tracking technology with sub-mm accuracy for US-guided interventions. The technology is non-disruptive, both in terms of existing clinical workflow and commercial considerations, showing promise for large scale clinical impact. PMID:22003612

  5. Segmentation of multiple heart cavities in 3-D transesophageal ultrasound images.

    PubMed

    Haak, Alexander; Vegas-Sánchez-Ferrero, Gonzalo; Mulder, Harriët W; Ren, Ben; Kirişli, Hortense A; Metz, Coert; van Burken, Gerard; van Stralen, Marijn; Pluim, Josien P W; van der Steen, Antonius F W; van Walsum, Theo; Bosch, Johannes G

    2015-06-01

    Three-dimensional transesophageal echocardiography (TEE) is an excellent modality for real-time visualization of the heart and monitoring of interventions. To improve the usability of 3-D TEE for intervention monitoring and catheter guidance, automated segmentation is desired. However, 3-D TEE segmentation is still a challenging task due to the complex anatomy with multiple cavities, the limited TEE field of view, and typical ultrasound artifacts. We propose to segment all cavities within the TEE view with a multi-cavity active shape model (ASM) in conjunction with a tissue/blood classification based on a gamma mixture model (GMM). 3-D TEE image data of twenty patients were acquired with a Philips X7-2t matrix TEE probe. Tissue probability maps were estimated by a two-class (blood/tissue) GMM. A statistical shape model containing the left ventricle, right ventricle, left atrium, right atrium, and aorta was derived from computed tomography angiography (CTA) segmentations by principal component analysis. ASMs of the whole heart and individual cavities were generated and consecutively fitted to tissue probability maps. First, an average whole-heart model was aligned with the 3-D TEE based on three manually indicated anatomical landmarks. Second, pose and shape of the whole-heart ASM were fitted by a weighted update scheme excluding parts outside of the image sector. Third, pose and shape of ASM for individual heart cavities were initialized by the previous whole heart ASM and updated in a regularized manner to fit the tissue probability maps. The ASM segmentations were validated against manual outlines by two observers and CTA derived segmentations. Dice coefficients and point-to-surface distances were used to determine segmentation accuracy. ASM segmentations were successful in 19 of 20 cases. The median Dice coefficient for all successful segmentations versus the average observer ranged from 90% to 71% compared with an inter-observer range of 95% to 84%. The

  6. Multi-resolution Gabor wavelet feature extraction for needle detection in 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Pourtaherian, Arash; Zinger, Svitlana; Mihajlovic, Nenad; de With, Peter H. N.; Huang, Jinfeng; Ng, Gary C.; Korsten, Hendrikus H. M.

    2015-12-01

    Ultrasound imaging is employed for needle guidance in various minimally invasive procedures such as biopsy guidance, regional anesthesia and brachytherapy. Unfortunately, a needle guidance using 2D ultrasound is very challenging, due to a poor needle visibility and a limited field of view. Nowadays, 3D ultrasound systems are available and more widely used. Consequently, with an appropriate 3D image-based needle detection technique, needle guidance and interventions may significantly be improved and simplified. In this paper, we present a multi-resolution Gabor transformation for an automated and reliable extraction of the needle-like structures in a 3D ultrasound volume. We study and identify the best combination of the Gabor wavelet frequencies. High precision in detecting the needle voxels leads to a robust and accurate localization of the needle for the intervention support. Evaluation in several ex-vivo cases shows that the multi-resolution analysis significantly improves the precision of the needle voxel detection from 0.23 to 0.32 at a high recall rate of 0.75 (gain 40%), where a better robustness and confidence were confirmed in the practical experiments.

  7. Skeletonization approach for characterization of benign vs. malignant single thyroid nodules using 3D contrast enhanced ultrasound

    NASA Astrophysics Data System (ADS)

    Molinari, Filippo; Mantovani, Alice; Deandrea, Maurilio; Limone, Paolo; Garberoglio, Roberto; Suri, Jasjit S.

    2011-03-01

    High-resolution ultrasonography (HRUS) has potentialities in differential diagnosis between malignant and benign thyroid lesions, but interpretative pitfalls remain and accuracy is still poor. We developed an image processing technique for characterizing the intra-nodular vascularization of thyroid lesions. Twenty nodules (ten malignant) were analyzed by 3-D contrast-enhanced ultrasound imaging. The 3-D volumes were preprocessed and skeletonized. Seven vascular parameters were computed on the skeletons: number of vascular trees (NT); vascular density (VD); number of branching nodes (or branching points) (NB); mean vessel radius (MR); 2-D (DM) and 3-D (SOAM) tortuosity; and inflection count metric (ICM). Results showed that the malignant nodules had higher values of NT (83.1 vs. 18.1), VD (00.4 vs. 0.01), NB (1453 vs. 552), DM (51 vs. 18), ICM (19.9 vs. 8.7), and SOAM (26 vs. 11). Quantification of nodular vascularization based on 3-D contrast-enhanced ultrasound and skeletonization could help differential diagnosis of thyroid lesions.

  8. Towards intraoperative monitoring of ablation using tracked 3D ultrasound elastography and internal palpation

    NASA Astrophysics Data System (ADS)

    Foroughi, Pezhman; Burgner, Jessica; Choti, Michael A.; Webster, Robert J., III; Hager, Gregory D.; Boctor, Emad M.

    2012-03-01

    B-mode ultrasound is widely used in liver ablation. However, the necrosis zone is typically not visible under b-mode ultrasound, since ablation does not necessarily change the acoustic properties of the tissue. In contrast, the change in tissue stiffness makes elastography ideal for monitoring ablation. Tissue palpation for elastography is typically applied at the imaging probe, by indenting it slightly into the tissue surface. However, in this paper we propose an alternate approach, where palpation is applied by a surgical instrument located inside the tissue. In our approach, the ablation needle is placed inside a steerable device called an active cannula and inserted into the tissue. A controlled motion is applied to the center of the ablation zone via the active cannula. Since the type and direction of motion is known, displacement can then be computed from two frames with the desired motion. The elastography results show the ablated region around the needle. While internal palpation provides excellent local contrast, freehand palpation from outside of the tissue via the transducer can provide a more global view of the region of the interest. For this purpose, we used a tracked 3D transducer to generate volumetric elastography images covering the ablated region. The tracking information is employed to improve the elastography results by selecting volume pairs suitable for elastography. This is an extension of our 2D frame selection technique which can cope with uncertainties associated with intra-operative elastography. In our experiments with phantom and ex-vivo tissue, we were able to generate high-quality images depicting the boundaries of the hard lesions.

  9. Integrated Interventional Devices For Real Time 3D Ultrasound Imaging and Therapy

    NASA Astrophysics Data System (ADS)

    Smith, Stephen W.; Lee, Warren; Gentry, Kenneth L.; Pua, Eric C.; Light, Edward D.

    2006-05-01

    Two recent advances have expanded the potential of medical ultrasound: the introduction of real-time 3-D ultrasound imaging with catheter, transesophageal and laparoscopic probes and the development of interventional ultrasound therapeutic systems for focused ultrasound surgery, ablation and ultrasound enhanced drug delivery. This work describes devices combining both technologies. A series of transducer probes have been designed, fabricated and tested including: 1) a 12 French side scanning catheter incorporating a 64 element matrix array for imaging at 5MHz and a piston ablation transducer operating at 10 MHz. 2) a 14 Fr forward-scanning catheter integrating a 112 element 2-D array for imaging at 5 MHz encircled by an ablation annulus operating at 10 MHz. Finite element modeling was then used to simulate catheter annular and linear phased array transducers for ablation. 3) Linear phased array transducers were built to confirm the finite element analysis at 4 and 8 MHz including a mechanically focused 86 element 9 MHz array which transmits an ISPTA of 29.3 W/cm2 and creates a lesion in 2 minutes. 4) 2-D arrays of 504 channels operating at 5 MHz have been developed for transesophageal and laparascopic 3D imaging as well as therapeutic heating. All the devices image the heart anatomy including atria, valves, septa and en face views of the pulmonary veins.

  10. Simulated 3D ultrasound LV cardiac images for active shape model training

    NASA Astrophysics Data System (ADS)

    Butakoff, Constantine; Balocco, Simone; Ordas, Sebastian; Frangi, Alejandro F.

    2007-03-01

    In this paper a study of 3D ultrasound cardiac segmentation using Active Shape Models (ASM) is presented. The proposed approach is based on a combination of a point distribution model constructed from a multitude of high resolution MRI scans and the appearance model obtained from simulated 3D ultrasound images. Usually the appearance model is learnt from a set of landmarked images. The significant level of noise, the low resolution of 3D ultrasound images (3D US) and the frequent failure to capture the complete wall of the left ventricle (LV) makes automatic or manual landmarking difficult. One possible solution is to use artificially simulated 3D US images since the generated images will match exactly the shape in question. In this way, by varying simulation parameters and generating corresponding images, it is possible to obtain a training set where the image matches the shape exactly. In this work the simulation of ultrasound images is performed by a convolutional approach. The evaluation of segmentation accuracy is performed on both simulated and in vivo images. The results obtained on 567 simulated images had an average error of 1.9 mm (1.73 +/- 0.05 mm for epicardium and 2 +/- 0.07 mm for endocardium, with 95% confidence) with voxel size being 1.1 × 1.1 × 0.7 mm. The error on 20 in vivo data was 3.5 mm (3.44 +/- 0.4 mm for epicardium and 3.73 +/- 0.4 mm for endocardium). In most images the model was able to approximate the borders of myocardium even when the latter was indistinguishable from the surrounding tissues.

  11. Real-time 3D ultrasound imaging on a next-generation media processor

    NASA Astrophysics Data System (ADS)

    Pagoulatos, Niko; Noraz, Frederic; Kim, Yongmin

    2001-05-01

    3D ultrasound (US) provides physicians with a better understanding of human anatomy. By manipulating the 3D US data set, physicians can observe the anatomy in 3D from a number of different view directions and obtain 2D US images that would not be possible to directly acquire with the US probe. In order for 3D US to be in widespread clinical use, creation and manipulation of the 3D US data should be done at interactive times. This is a challenging task due to the large amount of data to be processed. Our group previously reported interactive 3D US imaging using a programmable mediaprocessor, Texas Instruments TMS320C80, which has been in clinical use. In this work, we present the algorithms we have developed for real-time 3D US using a newer and more powerful mediaprocessor, called MAP-CA. MAP-CA is a very long instruction word (VLIW) processor developed for multimedia applications. It has multiple execution units, a 32-kbyte data cache and a programmable DMA controller called the data streamer (DS). A forward mapping 6 DOF (for a freehand 3D US system based on magnetic position sensor for tracking the US probe) reconstruction algorithm with zero- order interpolation is achieved in 11.8 msec (84.7 frame/sec) per 512x512 8-bit US image. For 3D visualization of the reconstructed 3D US data sets, we used volume rendering and in particular the shear-warp factorization with the maximum intensity projection (MIP) rendering. 3D visualization is achieved in 53.6 msec (18.6 frames/sec) for a 128x128x128 8-bit volume and in 410.3 msec (2.4 frames/sec) for a 256x256x256 8-bit volume.

  12. Education System Using Interactive 3D Computer Graphics (3D-CG) Animation and Scenario Language for Teaching Materials

    ERIC Educational Resources Information Center

    Matsuda, Hiroshi; Shindo, Yoshiaki

    2006-01-01

    The 3D computer graphics (3D-CG) animation using a virtual actor's speaking is very effective as an educational medium. But it takes a long time to produce a 3D-CG animation. To reduce the cost of producing 3D-CG educational contents and improve the capability of the education system, we have developed a new education system using Virtual Actor.…

  13. Development of a 3D ultrasound-guided prostate biopsy system

    NASA Astrophysics Data System (ADS)

    Cool, Derek; Sherebrin, Shi; Izawa, Jonathan; Fenster, Aaron

    2007-03-01

    Biopsy of the prostate using ultrasound guidance is the clinical gold standard for diagnosis of prostate adenocarinoma. However, because early stage tumors are rarely visible under US, the procedure carries high false-negative rates and often patients require multiple biopsies before cancer is detected. To improve cancer detection, it is imperative that throughout the biopsy procedure, physicians know where they are within the prostate and where they have sampled during prior biopsies. The current biopsy procedure is limited to using only 2D ultrasound images to find and record target biopsy core sample sites. This information leaves ambiguity as the physician tries to interpret the 2D information and apply it to their 3D workspace. We have developed a 3D ultrasound-guided prostate biopsy system that provides 3D intra-biopsy information to physicians for needle guidance and biopsy location recording. The system is designed to conform to the workflow of the current prostate biopsy procedure, making it easier for clinical integration. In this paper, we describe the system design and validate its accuracy by performing an in vitro biopsy procedure on US/CT multi-modal patient-specific prostate phantoms. A clinical sextant biopsy was performed by a urologist on the phantoms and the 3D models of the prostates were generated with volume errors less than 4% and mean boundary errors of less than 1 mm. Using the 3D biopsy system, needles were guided to within 1.36 +/- 0.83 mm of 3D targets and the position of the biopsy sites were accurately localized to 1.06 +/- 0.89 mm for the two prostates.

  14. Reconstruction of 3D ultrasound images based on Cyclic Regularized Savitzky-Golay filters.

    PubMed

    Toonkum, Pollakrit; Suwanwela, Nijasri C; Chinrungrueng, Chedsada

    2011-02-01

    This paper presents a new three-dimensional (3D) ultrasound reconstruction algorithm for generation of 3D images from a series of two-dimensional (2D) B-scans acquired in the mechanical linear scanning framework. Unlike most existing 3D ultrasound reconstruction algorithms, which have been developed and evaluated in the freehand scanning framework, the new algorithm has been designed to capitalize the regularity pattern of the mechanical linear scanning, where all the B-scan slices are precisely parallel and evenly spaced. The new reconstruction algorithm, referred to as the Cyclic Regularized Savitzky-Golay (CRSG) filter, is a new variant of the Savitzky-Golay (SG) smoothing filter. The CRSG filter has been improved upon the original SG filter in two respects: First, the cyclic indicator function has been incorporated into the least square cost function to enable the CRSG filter to approximate nonuniformly spaced data of the unobserved image intensities contained in unfilled voxels and reduce speckle noise of the observed image intensities contained in filled voxels. Second, the regularization function has been augmented to the least squares cost function as a mechanism to balance between the degree of speckle reduction and the degree of detail preservation. The CRSG filter has been evaluated and compared with the Voxel Nearest-Neighbor (VNN) interpolation post-processed by the Adaptive Speckle Reduction (ASR) filter, the VNN interpolation post-processed by the Adaptive Weighted Median (AWM) filter, the Distance-Weighted (DW) interpolation, and the Adaptive Distance-Weighted (ADW) interpolation, on reconstructing a synthetic 3D spherical image and a clinical 3D carotid artery bifurcation in the mechanical linear scanning framework. This preliminary evaluation indicates that the CRSG filter is more effective in both speckle reduction and geometric reconstruction of 3D ultrasound images than the other methods. PMID:20696448

  15. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  16. 2D array transducers for real-time 3D ultrasound guidance of interventional devices

    NASA Astrophysics Data System (ADS)

    Light, Edward D.; Smith, Stephen W.

    2009-02-01

    We describe catheter ring arrays for real-time 3D ultrasound guidance of devices such as vascular grafts, heart valves and vena cava filters. We have constructed several prototypes operating at 5 MHz and consisting of 54 elements using the W.L. Gore & Associates, Inc. micro-miniature ribbon cables. We have recently constructed a new transducer using a braided wiring technology from Precision Interconnect. This transducer consists of 54 elements at 4.8 MHz with pitch of 0.20 mm and typical -6 dB bandwidth of 22%. In all cases, the transducer and wiring assembly were integrated with an 11 French catheter of a Cook Medical deployment device for vena cava filters. Preliminary in vivo and in vitro testing is ongoing including simultaneous 3D ultrasound and x-ray fluoroscopy.

  17. FUN3D and CFL3D Computations for the First High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Lee-Rausch, Elizabeth M.; Rumsey, Christopher L.

    2011-01-01

    Two Reynolds-averaged Navier-Stokes codes were used to compute flow over the NASA Trapezoidal Wing at high lift conditions for the 1st AIAA CFD High Lift Prediction Workshop, held in Chicago in June 2010. The unstructured-grid code FUN3D and the structured-grid code CFL3D were applied to several different grid systems. The effects of code, grid system, turbulence model, viscous term treatment, and brackets were studied. The SST model on this configuration predicted lower lift than the Spalart-Allmaras model at high angles of attack; the Spalart-Allmaras model agreed better with experiment. Neglecting viscous cross-derivative terms caused poorer prediction in the wing tip vortex region. Output-based grid adaptation was applied to the unstructured-grid solutions. The adapted grids better resolved wake structures and reduced flap flow separation, which was also observed in uniform grid refinement studies. Limitations of the adaptation method as well as areas for future improvement were identified.

  18. Fast and robust 3D ultrasound registration--block and game theoretic matching.

    PubMed

    Banerjee, Jyotirmoy; Klink, Camiel; Peters, Edward D; Niessen, Wiro J; Moelker, Adriaan; van Walsum, Theo

    2015-02-01

    Real-time 3D US has potential for image guidance in minimally invasive liver interventions. However, motion caused by patient breathing makes it hard to visualize a localized area, and to maintain alignment with pre-operative information. In this work we develop a fast affine registration framework to compensate in real-time for liver motion/displacement due to breathing. The affine registration of two consecutive ultrasound volumes in time is performed using block-matching. For a set of evenly distributed points in one volume and their correspondences in the other volume, we propose a robust outlier rejection method to reject false matches. The inliers are then used to determine the affine transformation. The approach is evaluated on 13 4D ultrasound sequences acquired from 8 subjects. For 91 pairs of 3D ultrasound volumes selected from these sequences, a mean registration error of 1.8mm is achieved. A graphics processing unit (GPU) implementation runs the 3D US registration at 8 Hz. PMID:25484018

  19. Random walk based segmentation for the prostate on 3D transrectal ultrasound images

    NASA Astrophysics Data System (ADS)

    Ma, Ling; Guo, Rongrong; Tian, Zhiqiang; Venkataraman, Rajesh; Sarkar, Saradwata; Liu, Xiabi; Nieh, Peter T.; Master, Viraj V.; Schuster, David M.; Fei, Baowei

    2016-03-01

    This paper proposes a new semi-automatic segmentation method for the prostate on 3D transrectal ultrasound images (TRUS) by combining the region and classification information. We use a random walk algorithm to express the region information efficiently and flexibly because it can avoid segmentation leakage and shrinking bias. We further use the decision tree as the classifier to distinguish the prostate from the non-prostate tissue because of its fast speed and superior performance, especially for a binary classification problem. Our segmentation algorithm is initialized with the user roughly marking the prostate and non-prostate points on the mid-gland slice which are fitted into an ellipse for obtaining more points. Based on these fitted seed points, we run the random walk algorithm to segment the prostate on the mid-gland slice. The segmented contour and the information from the decision tree classification are combined to determine the initial seed points for the other slices. The random walk algorithm is then used to segment the prostate on the adjacent slice. We propagate the process until all slices are segmented. The segmentation method was tested in 32 3D transrectal ultrasound images. Manual segmentation by a radiologist serves as the gold standard for the validation. The experimental results show that the proposed method achieved a Dice similarity coefficient of 91.37+/-0.05%. The segmentation method can be applied to 3D ultrasound-guided prostate biopsy and other applications.

  20. 3D ultrasound Nakagami imaging for radiation-induced vaginal fibrosis

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Rossi, Peter; Shelton, Joseph; Bruner, Debrorah; Tridandapani, Srini; Liu, Tian

    2014-03-01

    Radiation-induced vaginal fibrosis is a debilitating side-effect affecting up to 80% of women receiving radiotherapy for their gynecological (GYN) malignancies. Despite the significant incidence and severity, little research has been conducted to identify the pathophysiologic changes of vaginal toxicity. In a previous study, we have demonstrated that ultrasound Nakagami shape and PDF parameters can be used to quantify radiation-induced vaginal toxicity. These Nakagami parameters are derived from the statistics of ultrasound backscattered signals to capture the physical properties (e.g., arrangement and distribution) of the biological tissues. In this paper, we propose to expand this Nakagami imaging concept from 2D to 3D to fully characterize radiation-induced changes to the vaginal wall within the radiation treatment field. A pilot study with 5 post-radiotherapy GYN patients was conducted using a clinical ultrasound scanner (6 MHz) with a mechanical stepper. A serial of 2D ultrasound images, with radio-frequency (RF) signals, were acquired at 1 mm step size. The 2D Nakagami shape and PDF parameters were calculated from the RF signal envelope with a sliding window, and then 3D Nakagami parameter images were generated from the parallel 2D images. This imaging method may be useful as we try to monitor radiation-induced vaginal injury, and address vaginal toxicities and sexual dysfunction in women after radiotherapy for GYN malignancies.

  1. Automatic nipple detection on 3D images of an automated breast ultrasound system (ABUS)

    NASA Astrophysics Data System (ADS)

    Javanshir Moghaddam, Mandana; Tan, Tao; Karssemeijer, Nico; Platel, Bram

    2014-03-01

    Recent studies have demonstrated that applying Automated Breast Ultrasound in addition to mammography in women with dense breasts can lead to additional detection of small, early stage breast cancers which are occult in corresponding mammograms. In this paper, we proposed a fully automatic method for detecting the nipple location in 3D ultrasound breast images acquired from Automated Breast Ultrasound Systems. The nipple location is a valuable landmark to report the position of possible abnormalities in a breast or to guide image registration. To detect the nipple location, all images were normalized. Subsequently, features have been extracted in a multi scale approach and classification experiments were performed using a gentle boost classifier to identify the nipple location. The method was applied on a dataset of 100 patients with 294 different 3D ultrasound views from Siemens and U-systems acquisition systems. Our database is a representative sample of cases obtained in clinical practice by four medical centers. The automatic method could accurately locate the nipple in 90% of AP (Anterior-Posterior) views and in 79% of the other views.

  2. Computations of Emissions Using a 3-D Combustor Program

    NASA Technical Reports Server (NTRS)

    Srivatsa, S. K.

    1983-01-01

    A general 3-D combustor performance program developed by Garrett was extended to predict soot and NOx emissions. The soot formation and oxidation rates were computed by quasi-global models, taking into account the influence of turbulence. Radiation heat transfer was computed by the six-flux radiation mode. The radiation properties include the influence of CO2 and H2O in addition to soot. NOx emissions were computed from a global four-step hydrocarbon oxidation scheme and a set of rate-controlled reactions involving radicals and nitrogen oxides.

  3. NASA's 3D Flight Computer for Space Applications

    NASA Technical Reports Server (NTRS)

    Alkalai, Leon

    2000-01-01

    The New Millennium Program (NMP) Integrated Product Development Team (IPDT) for Microelectronics Systems was planning to validate a newly developed 3D Flight Computer system on its first deep-space flight, DS1, launched in October 1998. This computer, developed in the 1995-97 time frame, contains many new computer technologies previously never used in deep-space systems. They include: advanced 3D packaging architecture for future low-mass and low-volume avionics systems; high-density 3D packaged chip-stacks for both volatile and non-volatile mass memory: 400 Mbytes of local DRAM memory, and 128 Mbytes of Flash memory; high-bandwidth Peripheral Component Interface (Per) local-bus with a bridge to VME; high-bandwidth (20 Mbps) fiber-optic serial bus; and other attributes, such as standard support for Design for Testability (DFT). Even though this computer system did not complete on time for delivery to the DS1 project, it was an important development along a technology roadmap towards highly integrated and highly miniaturized avionics systems for deep-space applications. This continued technology development is now being performed by NASA's Deep Space System Development Program (also known as X2000) and within JPL's Center for Integrated Space Microsystems (CISM).

  4. 3D deformable organ model based liver motion tracking in ultrasound videos

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Bae; Hwang, Youngkyoo; Oh, Young-Taek; Bang, Won-Chul; Lee, Heesae; Kim, James D. K.; Kim, Chang Yeong

    2013-03-01

    This paper presents a novel method of using 2D ultrasound (US) cine images during image-guided therapy to accurately track the 3D position of a tumor even when the organ of interest is in motion due to patient respiration. Tracking is possible thanks to a 3D deformable organ model we have developed. The method consists of three processes in succession. The first process is organ modeling where we generate a personalized 3D organ model from high quality 3D CT or MR data sets captured during three different respiratory phases. The model includes the organ surface, vessel and tumor, which can all deform and move in accord with patient respiration. The second process is registration of the organ model to 3D US images. From 133 respiratory phase candidates generated from the deformable organ model, we resolve the candidate that best matches the 3D US images according to vessel centerline and surface. As a result, we can determine the position of the US probe. The final process is real-time tracking using 2D US cine images captured by the US probe. We determine the respiratory phase by tracking the diaphragm on the image. The 3D model is then deformed according to respiration phase and is fitted to the image by considering the positions of the vessels. The tumor's 3D positions are then inferred based on respiration phase. Testing our method on real patient data, we have found the accuracy of 3D position is within 3.79mm and processing time is 5.4ms during tracking.

  5. A 5 MHz Cylindrical Dual-Layer Transducer Array for 3-D Transrectal Ultrasound Imaging

    PubMed Central

    Chen, Yuling; Nguyen, Man; Yen, Jesse T.

    2012-01-01

    2-D transrectal ultrasound (TRUS) is being used in guiding prostate biopsies and treatments. In many cases, the TRUS probes are moved manually or mechanically to acquire volumetric information, making the imaging slow, user-dependent and unreliable. A real-time 3-D TRUS system could improve reliability and volume rates of imaging during these procedures. In this paper, we present a 5 MHz cylindrical dual-layer transducer array capable of real-time 3-D transrectal ultrasound without any mechanically moving parts. Compared to fully-sampled 2-D arrays, this design substantially reduces the channel count and fabrication complexity. This dual-layer transducer uses PZT elements for transmit and P[VDF-TrFE] copolymer elements for receive, respectively. The mechanical flexibility of both diced PZT and copolymer makes it practical for transrectal applications. Full synthetic aperture 3-D data sets were acquired by interfacing the transducer with a Verasonics Data Acquisition System (VDAS). Offline 3-D beamforming was then performed to obtain volumes of two wire phantoms and a cyst phantom. Generalized coherence factor (GCF) was applied to improve the contrast of images. The measured −6 dB fractional bandwidth of the transducer was 62% with a center frequency of 5.66 MHz. The measured lateral beamwidths were 1.28 mm and 0.91 mm in transverse and longitudinal directions respectively, compared with a simulated beamwidth of 0.92 mm and 0.74 mm. PMID:22972914

  6. 3D ultrasound volume stitching using phase symmetry and harris corner detection for orthopaedic applications

    NASA Astrophysics Data System (ADS)

    Dalvi, Rupin; Hacihaliloglu, Ilker; Abugharbieh, Rafeef

    2010-03-01

    Stitching of volumes obtained from three dimensional (3D) ultrasound (US) scanners improves visualization of anatomy in many clinical applications. Fast but accurate volume registration remains the key challenge in this area.We propose a volume stitching method based on efficient registration of 3D US volumes obtained from a tracked US probe. Since the volumes, after adjusting for probe motion, are coarsely registered, we obtain salient correspondence points in the central slices of these volumes. This is done by first removing artifacts in the US slices using intensity invariant local phase image processing and then applying the Harris Corner detection algorithm. Fast sub-volume registration on a small neighborhood around the points then gives fast, accurate 3D registration parameters. The method has been tested on 3D US scans of phantom and real human radius and pelvis bones and a phantom human fetus. The method has also been compared to volumetric registration, as well as feature based registration using 3D-SIFT. Quantitative results show average post-registration error of 0.33mm which is comparable to volumetric registration accuracy (0.31mm) and much better than 3D-SIFT based registration which failed to register the volumes. The proposed method was also much faster than volumetric registration (~4.5 seconds versus 83 seconds).

  7. Advanced computational tools for 3-D seismic analysis

    SciTech Connect

    Barhen, J.; Glover, C.W.; Protopopescu, V.A.

    1996-06-01

    The global objective of this effort is to develop advanced computational tools for 3-D seismic analysis, and test the products using a model dataset developed under the joint aegis of the United States` Society of Exploration Geophysicists (SEG) and the European Association of Exploration Geophysicists (EAEG). The goal is to enhance the value to the oil industry of the SEG/EAEG modeling project, carried out with US Department of Energy (DOE) funding in FY` 93-95. The primary objective of the ORNL Center for Engineering Systems Advanced Research (CESAR) is to spearhead the computational innovations techniques that would enable a revolutionary advance in 3-D seismic analysis. The CESAR effort is carried out in collaboration with world-class domain experts from leading universities, and in close coordination with other national laboratories and oil industry partners.

  8. Majority logic gate for 3D magnetic computing.

    PubMed

    Eichwald, Irina; Breitkreutz, Stephan; Ziemys, Grazvydas; Csaba, György; Porod, Wolfgang; Becherer, Markus

    2014-08-22

    For decades now, microelectronic circuits have been exclusively built from transistors. An alternative way is to use nano-scaled magnets for the realization of digital circuits. This technology, known as nanomagnetic logic (NML), may offer significant improvements in terms of power consumption and integration densities. Further advantages of NML are: non-volatility, radiation hardness, and operation at room temperature. Recent research focuses on the three-dimensional (3D) integration of nanomagnets. Here we show, for the first time, a 3D programmable magnetic logic gate. Its computing operation is based on physically field-interacting nanometer-scaled magnets arranged in a 3D manner. The magnets possess a bistable magnetization state representing the Boolean logic states '0' and '1.' Magneto-optical and magnetic force microscopy measurements prove the correct operation of the gate over many computing cycles. Furthermore, micromagnetic simulations confirm the correct functionality of the gate even for a size in the nanometer-domain. The presented device demonstrates the potential of NML for three-dimensional digital computing, enabling the highest integration densities. PMID:25073985

  9. Majority logic gate for 3D magnetic computing

    NASA Astrophysics Data System (ADS)

    Eichwald, Irina; Breitkreutz, Stephan; Ziemys, Grazvydas; Csaba, György; Porod, Wolfgang; Becherer, Markus

    2014-08-01

    For decades now, microelectronic circuits have been exclusively built from transistors. An alternative way is to use nano-scaled magnets for the realization of digital circuits. This technology, known as nanomagnetic logic (NML), may offer significant improvements in terms of power consumption and integration densities. Further advantages of NML are: non-volatility, radiation hardness, and operation at room temperature. Recent research focuses on the three-dimensional (3D) integration of nanomagnets. Here we show, for the first time, a 3D programmable magnetic logic gate. Its computing operation is based on physically field-interacting nanometer-scaled magnets arranged in a 3D manner. The magnets possess a bistable magnetization state representing the Boolean logic states ‘0’ and ‘1.’ Magneto-optical and magnetic force microscopy measurements prove the correct operation of the gate over many computing cycles. Furthermore, micromagnetic simulations confirm the correct functionality of the gate even for a size in the nanometer-domain. The presented device demonstrates the potential of NML for three-dimensional digital computing, enabling the highest integration densities.

  10. 2-D and 3-D computations of curved accelerator magnets

    SciTech Connect

    Turner, L.R.

    1991-01-01

    In order to save computer memory, a long accelerator magnet may be computed by treating the long central region and the end regions separately. The dipole magnets for the injector synchrotron of the Advanced Photon Source (APS), now under construction at Argonne National Laboratory (ANL), employ magnet iron consisting of parallel laminations, stacked with a uniform radius of curvature of 33.379 m. Laplace's equation for the magnetic scalar potential has a different form for a straight magnet (x-y coordinates), a magnet with surfaces curved about a common center (r-{theta} coordinates), and a magnet with parallel laminations like the APS injector dipole. Yet pseudo 2-D computations for the three geometries give basically identical results, even for a much more strongly curved magnet. Hence 2-D (x-y) computations of the central region and 3-D computations of the end regions can be combined to determine the overall magnetic behavior of the magnets. 1 ref., 6 figs.

  11. Model fitting using RANSAC for surgical tool localization in 3-D ultrasound images.

    PubMed

    Uhercík, Marián; Kybic, Jan; Liebgott, Hervé; Cachard, Christian

    2010-08-01

    Ultrasound guidance is used for many surgical interventions such as biopsy and electrode insertion. We present a method to localize a thin surgical tool such as a biopsy needle or a microelectrode in a 3-D ultrasound image. The proposed method starts with thresholding and model fitting using random sample consensus for robust localization of the axis. Subsequent local optimization refines its position. Two different tool image models are presented: one is simple and fast and the second uses learned a priori information about the tool's voxel intensities and the background. Finally, the tip of the tool is localized by finding an intensity drop along the axis. The simulation study shows that our algorithm can localize the tool at nearly real-time speed, even using a MATLAB implementation, with accuracy better than 1 mm. In an experimental comparison with several alternative localization methods, our method appears to be the fastest and the most robust one. We also show the results on real 3-D ultrasound data from a PVA cryogel phantom, turkey breast, and breast biopsy. PMID:20483680

  12. Breast Density Analysis with Automated Whole-Breast Ultrasound: Comparison with 3-D Magnetic Resonance Imaging.

    PubMed

    Chen, Jeon-Hor; Lee, Yan-Wei; Chan, Si-Wa; Yeh, Dah-Cherng; Chang, Ruey-Feng

    2016-05-01

    In this study, a semi-automatic breast segmentation method was proposed on the basis of the rib shadow to extract breast regions from 3-D automated whole-breast ultrasound (ABUS) images. The density results were correlated with breast density values acquired with 3-D magnetic resonance imaging (MRI). MRI images of 46 breasts were collected from 23 women without a history of breast disease. Each subject also underwent ABUS. We used Otsu's thresholding method on ABUS images to obtain local rib shadow information, which was combined with the global rib shadow information (extracted from all slice projections) and integrated with the anatomy's breast tissue structure to determine the chest wall line. The fuzzy C-means classifier was used to extract the fibroglandular tissues from the acquired images. Whole-breast volume (WBV) and breast percentage density (BPD) were calculated in both modalities. Linear regression was used to compute the correlation of density results between the two modalities. The consistency of density measurement was also analyzed on the basis of intra- and inter-operator variation. There was a high correlation of density results between MRI and ABUS (R(2) = 0.798 for WBV, R(2) = 0.825 for PBD). The mean WBV from ABUS images was slightly smaller than the mean WBV from MR images (MRI: 342.24 ± 128.08 cm(3), ABUS: 325.47 ± 136.16 cm(3), p < 0.05). In addition, the BPD calculated from MR images was smaller than the BPD from ABUS images (MRI: 24.71 ± 15.16%, ABUS: 28.90 ± 17.73%, p < 0.05). The intra-operator and inter-operator variant analysis results indicated that there was no statistically significant difference in breast density measurement variation between the two modalities. Our results revealed a high correlation in WBV and BPD between MRI and ABUS. Our study suggests that ABUS provides breast density information useful in the assessment of breast health. PMID:26831342

  13. Pitch–Catch Phase Aberration Correction of Multiple Isoplanatic Patches for 3-D Transcranial Ultrasound Imaging

    PubMed Central

    Lindsey, Brooks D.; Smith, Stephen W.

    2013-01-01

    Having previously presented the ultrasound brain helmet, a system for simultaneous 3-D ultrasound imaging via both temporal bone acoustic windows, the scanning geometry of this system is utilized to allow each matrix array to serve as a correction source for the opposing array. Aberration is estimated using cross-correlation of RF channel signals, followed by least mean squares solution of the resulting overdetermined system. Delay maps are updated and real-time 3-D scanning resumes. A first attempt is made at using multiple arrival time maps to correct multiple unique aberrators within a single transcranial imaging volume, i.e., several isoplanatic patches. This adaptive imaging technique, which uses steered unfocused waves transmitted by the opposing, or beacon, array, updates the transmit and receive delays of 5 isoplanatic patches within a 64° × 64° volume. In phantom experiments, color flow voxels above a common threshold have also increased by an average of 92%, whereas color flow variance decreased by an average of 10%. This approach has been applied to both temporal acoustic windows of two human subjects, yielding increases in echo brightness in 5 isoplanatic patches with a mean value of 24.3 ± 9.1%, suggesting that such a technique may be beneficial in the future for performing noninvasive 3-D color flow imaging of cerebrovascular disease, including stroke. PMID:23475914

  14. Development of a 3D ultrasound-guided system for thermal ablation of liver tumors

    NASA Astrophysics Data System (ADS)

    Neshat, Hamid R. S.; Cool, Derek W.; Barker, Kevin; Gardi, Lori; Kakani, Nirmal; Fenster, Aaron

    2013-03-01

    Two-dimensional ultrasound (2D US) imaging is commonly used for diagnostic and intraoperative guidance of interventional abdominal procedures including percutaneous thermal ablation of focal liver tumors with radiofrequency (RF) or microwave (MW) induced energy. However, in many situations 2D US may not provide enough anatomical detail and guidance information. Therefore, intra-procedural CT or MR imaging are used in many centers for guidance purposes. These modalities are costly and are mainly utilized to confirm tool placement rather than guiding the insertion. Three-dimensional ultrasound (3D US) has been introduced to address these issues. In this paper, we present our integrated solution to provide 3D US images using a newly developed mechanical transducer with a large field-ofview and without the need for external tracking devices to combine diagnostic and planning information of different modalities for intraoperative guidance. The system provides tools to segment the target(s), plan the treatment, and detect the ablation applicators during the procedure for guiding purposes. We present experimental results used to ensure that our system generates accurate measurements and our early clinical evaluation results. The results suggest that 3D US used for focal liver ablation can provide a more reliable planning and guidance tool compared to 2D US only, and in many cases offers comparable measurements to other alternatives at significantly lower cost, faster time and with no harmful radiation.

  15. Accuracy of volume measurement using 3D ultrasound and development of CT-3D US image fusion algorithm for prostate cancer radiotherapy

    SciTech Connect

    Baek, Jihye; Huh, Jangyoung; Hyun An, So; Oh, Yoonjin; Kim, Myungsoo; Kim, DongYoung; Chung, Kwangzoo; Cho, Sungho; Lee, Rena

    2013-02-15

    Purpose: To evaluate the accuracy of measuring volumes using three-dimensional ultrasound (3D US), and to verify the feasibility of the replacement of CT-MR fusion images with CT-3D US in radiotherapy treatment planning. Methods: Phantoms, consisting of water, contrast agent, and agarose, were manufactured. The volume was measured using 3D US, CT, and MR devices. A CT-3D US and MR-3D US image fusion software was developed using the Insight Toolkit library in order to acquire three-dimensional fusion images. The quality of the image fusion was evaluated using metric value and fusion images. Results: Volume measurement, using 3D US, shows a 2.8 {+-} 1.5% error, 4.4 {+-} 3.0% error for CT, and 3.1 {+-} 2.0% error for MR. The results imply that volume measurement using the 3D US devices has a similar accuracy level to that of CT and MR. Three-dimensional image fusion of CT-3D US and MR-3D US was successfully performed using phantom images. Moreover, MR-3D US image fusion was performed using human bladder images. Conclusions: 3D US could be used in the volume measurement of human bladders and prostates. CT-3D US image fusion could be used in monitoring the target position in each fraction of external beam radiation therapy. Moreover, the feasibility of replacing the CT-MR image fusion to the CT-3D US in radiotherapy treatment planning was verified.

  16. 3D seismic imaging on massively parallel computers

    SciTech Connect

    Womble, D.E.; Ober, C.C.; Oldfield, R.

    1997-02-01

    The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is a key to reducing the risk and cost associated with oil and gas exploration. Imaging these structures, however, is computationally expensive. Datasets can be terabytes in size, and the processing time required for the multiple iterations needed to produce a velocity model can take months, even with the massively parallel computers available today. Some algorithms, such as 3D, finite-difference, prestack, depth migration remain beyond the capacity of production seismic processing. Massively parallel processors (MPPs) and algorithms research are the tools that will enable this project to provide new seismic processing capabilities to the oil and gas industry. The goals of this work are to (1) develop finite-difference algorithms for 3D, prestack, depth migration; (2) develop efficient computational approaches for seismic imaging and for processing terabyte datasets on massively parallel computers; and (3) develop a modular, portable, seismic imaging code.

  17. Femoroacetabular impingement with chronic acetabular rim fracture - 3D computed tomography, 3D magnetic resonance imaging and arthroscopic correlation

    PubMed Central

    Chhabra, Avneesh; Nordeck, Shaun; Wadhwa, Vibhor; Madhavapeddi, Sai; Robertson, William J

    2015-01-01

    Femoroacetabular impingement is uncommonly associated with a large rim fragment of bone along the superolateral acetabulum. We report an unusual case of femoroacetabular impingement (FAI) with chronic acetabular rim fracture. Radiographic, 3D computed tomography, 3D magnetic resonance imaging and arthroscopy correlation is presented with discussion of relative advantages and disadvantages of various modalities in the context of FAI. PMID:26191497

  18. Improved Visualization of Intracranial Vessels with Intraoperative Coregistration of Rotational Digital Subtraction Angiography and Intraoperative 3D Ultrasound

    PubMed Central

    Podlesek, Dino; Meyer, Tobias; Morgenstern, Ute; Schackert, Gabriele; Kirsch, Matthias

    2015-01-01

    Introduction Ultrasound can visualize and update the vessel status in real time during cerebral vascular surgery. We studied the depiction of parent vessels and aneurysms with a high-resolution 3D intraoperative ultrasound imaging system during aneurysm clipping using rotational digital subtraction angiography as a reference. Methods We analyzed 3D intraoperative ultrasound in 39 patients with cerebral aneurysms to visualize the aneurysm intraoperatively and the nearby vascular tree before and after clipping. Simultaneous coregistration of preoperative subtraction angiography data with 3D intraoperative ultrasound was performed to verify the anatomical assignment. Results Intraoperative ultrasound detected 35 of 43 aneurysms (81%) in 39 patients. Thirty-nine intraoperative ultrasound measurements were matched with rotational digital subtraction angiography and were successfully reconstructed during the procedure. In 7 patients, the aneurysm was partially visualized by 3D-ioUS or was not in field of view. Post-clipping intraoperative ultrasound was obtained in 26 and successfully reconstructed in 18 patients (69%) despite clip related artefacts. The overlap between 3D-ioUS aneurysm volume and preoperative rDSA aneurysm volume resulted in a mean accuracy of 0.71 (Dice coefficient). Conclusions Intraoperative coregistration of 3D intraoperative ultrasound data with preoperative rotational digital subtraction angiography is possible with high accuracy. It allows the immediate visualization of vessels beyond the microscopic field, as well as parallel assessment of blood velocity, aneurysm and vascular tree configuration. Although spatial resolution is lower than for standard angiography, the method provides an excellent vascular overview, advantageous interpretation of 3D-ioUS and immediate intraoperative feedback of the vascular status. A prerequisite for understanding vascular intraoperative ultrasound is image quality and a successful match with preoperative

  19. Can 3D ultrasound identify trochlea dysplasia in newborns? Evaluation and applicability of a technique.

    PubMed

    Kohlhof, Hendrik; Heidt, Christoph; Bähler, Alexandrine; Kohl, Sandro; Gravius, Sascha; Friedrich, Max J; Ziebarth, Kai; Stranzinger, Enno

    2015-06-01

    Femoro-patellar dysplasia is considered as a significant risk factor of patellar instability. Different studies suggest that the shape of the trochlea is already developed in early childhood. Therefore early identification of a dysplastic configuration might be relevant information for the treating physician. An easy applicable routine screening of the trochlea is yet not available. The purpose of this study was to establish and evaluate a screening method for femoro-patellar dysplasia using 3D ultrasound. From 2012 to 2013 we prospectively imaged 160 consecutive femoro-patellar joints in 80 newborns from the 36th to 61st gestational week that underwent a routine hip sonography (Graf). All ultrasounds were performed by a pediatric radiologist with only minimal additional time to the routine hip ultrasound. In 30° flexion of the knee, axial, coronal, and sagittal reformats were used to standardize a reconstructed axial plane through the femoral condyle and the mid-patella. The sulcus angle, the lateral-to-medial facet ratio of the trochlea and the shape of the patella (Wiberg Classification) were evaluated. In all examinations reconstruction of the standardized axial plane was achieved, the mean trochlea angle was 149.1° (SD 4.9°), the lateral-to-medial facet ratio of the trochlea ratio was 1.3 (SD 0.22), and a Wiberg type I patella was found in 95% of the newborn. No statistical difference was detected between boys and girls. Using standardized reconstructions of the axial plane allows measurements to be made with lower operator dependency and higher accuracy in a short time. Therefore 3D ultrasound is an easy applicable and powerful tool to identify trochlea dysplasia in newborns and might be used for screening for trochlea dysplasia. PMID:25843417

  20. Vision-based endoscope tracking for 3D ultrasound image-guided surgical navigation.

    PubMed

    Yang, L; Wang, J; Ando, T; Kubota, A; Yamashita, H; Sakuma, I; Chiba, T; Kobayashi, E

    2015-03-01

    This work introduces a self-contained framework for endoscopic camera tracking by combining 3D ultrasonography with endoscopy. The approach can be readily incorporated into surgical workflows without installing external tracking devices. By fusing the ultrasound-constructed scene geometry with endoscopic vision, this integrated approach addresses issues related to initialization, scale ambiguity, and interest point inadequacy that may be faced by conventional vision-based approaches when applied to fetoscopic procedures. Vision-based pose estimations were demonstrated by phantom and ex vivo monkey placenta imaging. The potential contribution of this method may extend beyond fetoscopic procedures to include general augmented reality applications in minimally invasive procedures. PMID:25263644

  1. Aerofoil characteristics from 3D CFD rotor computations

    NASA Astrophysics Data System (ADS)

    Johansen, Jeppe; Sørensen, Niels N.

    2004-10-01

    This article describes a method for extracting aerofoil characteristics from 3D computational fluid dynamics (CFD) rotor computations. Based on the knowledge of the detailed flow in the rotor plane, the average sectional axial induction is determined for each wind speed. Based on this, the local angle of attack is determined when knowing the rotational speed and the local blade twist angle. The local aerofoil characteristics, i.e. Cl and Cd, are then computed from the forces acting on the blade. The extracted Cl and Cd are used in a standard blade element momentum (BEM) code, where no corrections are made for the rotational augmentation of forces or for the tip effect, since these are directly included in the aerofoil characteristics. Three stall-regulated wind turbine rotors are used as test cases. The computed mechanical power is overpredicted at high wind speeds using steady Reynolds-averaged Navier-Stokes computations, but using advanced turbulence models, e.g. detached eddy simulation, or a transition prediction model improves the computations. The agreement between the mechanical power (or low-speed shaft torque) predicted by CFD and BEM is good, even though a small but consistent difference in induction prediction is present. With the proposed method and a sufficiently accurate CFD computation it is possible to obtain aerofoil characteristics from a given wind turbine design without using empirical stall corrections models. Alternatively, new correction models can be derived using the extracted aerofoil characteristics. Copyright

  2. 3D Ultrasound Can Contribute to Planning CT to Define the Target for Partial Breast Radiotherapy

    SciTech Connect

    Berrang, Tanya S.; Truong, Pauline T. Popescu, Carmen; Drever, Laura; Kader, Hosam A.; Hilts, Michelle L.; Mitchell, Tracy; Soh, S.Y.; Sands, Letricia; Silver, Stuart; Olivotto, Ivo A.

    2009-02-01

    Purpose: The role of three-dimensional breast ultrasound (3D US) in planning partial breast radiotherapy (PBRT) is unknown. This study evaluated the accuracy of coregistration of 3D US to planning computerized tomography (CT) images, the seroma contouring consistency of radiation oncologists using the two imaging modalities and the clinical situations in which US was associated with improved contouring consistency compared to CT. Materials and Methods: Twenty consecutive women with early-stage breast cancer were enrolled prospectively after breast-conserving surgery. Subjects underwent 3D US at CT simulation for adjuvant RT. Three radiation oncologists independently contoured the seroma on separate CT and 3D US image sets. Seroma clarity, seroma volumes, and interobserver contouring consistency were compared between the imaging modalities. Associations between clinical characteristics and seroma clarity were examined using Pearson correlation statistics. Results: 3D US and CT coregistration was accurate to within 2 mm or less in 19/20 (95%) cases. CT seroma clarity was reduced with dense breast parenchyma (p = 0.035), small seroma volume (p < 0.001), and small volume of excised breast tissue (p = 0.01). US seroma clarity was not affected by these factors (p = NS). US was associated with improved interobserver consistency compared with CT in 8/20 (40%) cases. Of these 8 cases, 7 had low CT seroma clarity scores and 4 had heterogeneously to extremely dense breast parenchyma. Conclusion: 3D US can be a useful adjunct to CT in planning PBRT. Radiation oncologists were able to use US images to contour the seroma target, with improved interobserver consistency compared with CT in cases with dense breast parenchyma and poor CT seroma clarity.

  3. 3D conformal MRI-guided transurethral ultrasound therapy: results of gel phantom experiments

    NASA Astrophysics Data System (ADS)

    N'Djin, W. A.; Burtnyk, M.; McCormick, S.; Bronskill, M.; Chopra, R.

    2011-09-01

    MRI-guided transurethral ultrasound therapy shows promise for minimally invasive treatment of localized prostate cancer. Previous in-vivo studies demonstrated the feasibility of performing conservative treatments using real-time temperature feedback to control accurately the establishment of coagulative lesions within circumscribed prostate regions. This in-vitro study tested device configuration and control options for achieving full prostate treatments. A multi-channel MRI compatible ultrasound therapy system was evaluated in gel phantoms using 3 canine prostate models. Prostate profiles were 5 mm-step-segmented from T2-weighted MR images performed during previous in-vivo experiments. During ultrasound exposures, each ultrasound element was controlled independently by the 3D controller. Decisions on acoustic power, frequency, and device rotation rate were made in real time based on MR thermometry feedback and prostate radii. Low and high power treatment approaches using maximum acoustic powers of 10 or 20 W.cm-2 were tested as well as single and dual-frequency strategies (4.05/13.10 MHz). The dual-frequency strategy used either the fundamental frequency or the 3rd harmonic component, depending on the prostate radius. The 20 W.cm-2 dual frequency approach was the most efficient configuration in achieving full prostate treatments. Treatment times were about half the duration of those performed with 10 W.cm-2 configurations. Full prostate coagulations were performed in 16.3±6.1 min at a rate of 1.8±0.2 cm3.min-1, and resulted in very little undertreated tissue (<3%). Surrounding organs positioned beyond a safety distance of 1.4±1.0 mm from prostate boundaries were not damaged, particularly rectal wall tissues. In this study, a 3D, MR-thermometry-guided transurethral ultrasound therapy was validated in vitro in a tissue-mimicking phantom for performing full prostate treatment. A dual-frequency configuration with 20 W.cm-2 ultrasound intensity exposure showed good

  4. Evaluation of Gastric Volumes: Comparison of 3-D Ultrasound and Magnetic Resonance Imaging.

    PubMed

    Buisman, Wijnand J; Mauritz, Femke A; Westerhuis, Wouter E; Gilja, Odd Helge; van der Zee, David C; van Herwaarden-Lindeboom, Maud Y A

    2016-07-01

    To investigate gastric accommodation, accurate measurements of gastric volumes are necessary. An excellent technique to measure gastric volumes is dynamic magnetic resonance imaging (MRI). Unfortunately, dynamic MRI is expensive and not always available. A new 3-D ultrasound (US) method using a matrix transducer was developed to measure gastric volumes. In this prospective study, 14 healthy volunteers underwent a dynamic MRI and a 3-D US. Gastric volumes were calculated with intra-gastric liquid content and total gastric volume. Mean postprandial liquid gastric content was 397 ± 96.5 mL. Mean volume difference was 1.0 mL with limits of agreement of -8.9 to 10.9 mL. When gastric air was taken into account, mean total gastric volume was 540 ± 115.4 mL SD. Mean volume difference was 2.3 mL with limits of agreement of -21.1 to 26.4 mL. The matrix 3-D US showed excellent agreement with dynamic MRI. Therefore matrix 3-D US is a reliable alternative to measure gastric volumes. PMID:27067418

  5. 3D transrectal ultrasound prostate biopsy using a mechanical imaging and needle-guidance system

    NASA Astrophysics Data System (ADS)

    Bax, Jeffrey; Cool, Derek; Gardi, Lori; Montreuil, Jacques; Gil, Elena; Bluvol, Jeremy; Knight, Kerry; Smith, David; Romagnoli, Cesare; Fenster, Aaron

    2008-03-01

    Prostate biopsy procedures are generally limited to 2D transrectal ultrasound (TRUS) imaging for biopsy needle guidance. This limitation results in needle position ambiguity and an insufficient record of biopsy core locations in cases of prostate re-biopsy. We have developed a multi-jointed mechanical device that supports a commercially available TRUS probe with an integrated needle guide for precision prostate biopsy. The device is fixed at the base, allowing the joints to be manually manipulated while fully supporting its weight throughout its full range of motion. Means are provided to track the needle trajectory and display this trajectory on a corresponding TRUS image. This allows the physician to aim the needle-guide at predefined targets within the prostate, providing true 3D navigation. The tracker has been designed for use with several end-fired transducers that can be rotated about the longitudinal axis of the probe to generate 3D images. The tracker reduces the variability associated with conventional hand-held probes, while preserving user familiarity and procedural workflow. In a prostate phantom, biopsy needles were guided to within 2 mm of their targets, and the 3D location of the biopsy core was accurate to within 3 mm. The 3D navigation system is validated in the presence of prostate motion in a preliminary patient study.

  6. Accuracy evaluation of a 3D ultrasound-guided biopsy system

    NASA Astrophysics Data System (ADS)

    Wooten, Walter J.; Nye, Jonathan A.; Schuster, David M.; Nieh, Peter T.; Master, Viraj A.; Votaw, John R.; Fei, Baowei

    2013-03-01

    Early detection of prostate cancer is critical in maximizing the probability of successful treatment. Current systematic biopsy approach takes 12 or more randomly distributed core tissue samples within the prostate and can have a high potential, especially with early disease, for a false negative diagnosis. The purpose of this study is to determine the accuracy of a 3D ultrasound-guided biopsy system. Testing was conducted on prostate phantoms created from an agar mixture which had embedded markers. The phantoms were scanned and the 3D ultrasound system was used to direct the biopsy. Each phantom was analyzed with a CT scan to obtain needle deflection measurements. The deflection experienced throughout the biopsy process was dependent on the depth of the biopsy target. The results for markers at a depth of less than 20 mm, 20-30 mm, and greater than 30 mm were 3.3 mm, 4.7 mm, and 6.2 mm, respectively. This measurement encapsulates the entire biopsy process, from the scanning of the phantom to the firing of the biopsy needle. Increased depth of the biopsy target caused a greater deflection from the intended path in most cases which was due to an angular incidence of the biopsy needle. Although some deflection was present, this system exhibits a clear advantage in the targeted biopsy of prostate cancer and has the potential to reduce the number of false negative biopsies for large lesions.

  7. Accuracy Evaluation of a 3D Ultrasound-guided Biopsy System

    PubMed Central

    Wooten, Walter J.; Nye, Jonathan A.; Schuster, David M.; Nieh, Peter T.; Master, Viraj A.; Votaw, John R.; Fei, Baowei

    2013-01-01

    Early detection of prostate cancer is critical in maximizing the probability of successful treatment. Current systematic biopsy approach takes 12 or more randomly distributed core tissue samples within the prostate and can have a high potential, especially with early disease, for a false negative diagnosis. The purpose of this study is to determine the accuracy of a 3D ultrasound-guided biopsy system. Testing was conducted on prostate phantoms created from an agar mixture which had embedded markers. The phantoms were scanned and the 3D ultrasound system was used to direct the biopsy. Each phantom was analyzed with a CT scan to obtain needle deflection measurements. The deflection experienced throughout the biopsy process was dependent on the depth of the biopsy target. The results for markers at a depth of less than 20 mm, 20-30 mm, and greater than 30 mm were 3.3 mm, 4.7 mm, and 6.2 mm, respectively. This measurement encapsulates the entire biopsy process, from the scanning of the phantom to the firing of the biopsy needle. Increased depth of the biopsy target caused a greater deflection from the intended path in most cases which was due to an angular incidence of the biopsy needle. Although some deflection was present, this system exhibits a clear advantage in the targeted biopsy of prostate cancer and has the potential to reduce the number of false negative biopsies for large lesions. PMID:24392206

  8. Thermal analysis of the surrounding anatomy during 3-D MRI-guided transurethral ultrasound prostate therapy

    NASA Astrophysics Data System (ADS)

    Burtnyk, Mathieu; Chopra, Rajiv; Bronskill, Michael

    2010-03-01

    Previous numerical simulations have shown that MRI-guided transurethral ultrasound therapy can generate highly accurate volumes of thermal coagulation conforming to 3-D human prostate geometries. The goal of this work is to simulate, quantify and evaluate the thermal impact of these treatments on the rectum, pelvic bone, neurovascular bundles (NVB) and urinary sphincters. This study used twenty 3-D anatomical models of prostate cancer patients and detailed bio-acoustic simulations incorporating an active feedback algorithm which controlled a rotating, planar ultrasound transducer (17-4×3 mm elements, 4.7/9.7 MHz, 10 Wac/cm2). Heating of the adjacent surrounding anatomy was evaluated using thermal tolerances reported in the literature. Heating of the rectum poses the most important safety concern and is influenced largely by the water temperature flowing through an endorectal cooling device; temperatures of 7-37° C are required to limit potential damage to less than 10 mm3 on the outer 1 mm layer of rectum. Significant heating of the pelvic bone was predicted in 30% of the patient models with an ultrasound frequency of 4.7 MHz; setting the frequency to 9.7 MHz when the bone is less than 10 mm away from the prostate reduced heating in all cases below the threshold for irreversible damage. Heating of the NVB was significant in 75% of the patient models in the absence of treatment planning; this proportion was reduced to 5% by using treatment margins of up to 4 mm. To avoid damaging the urinary sphincters, margins from the transducer of 2-4 mm should be used, depending on the transurethral cooling temperature. Simulations show that MRI-guided transurethral therapy can treat the entire prostate accurately. Strategies have been developed which, along with careful treatment planning, can be used to avoid causing thermal injury to the rectum, pelvic bone, NVB and urinary sphincters.

  9. Visualizing ultrasound through computational modeling

    NASA Technical Reports Server (NTRS)

    Guo, Theresa W.

    2004-01-01

    The Doppler Ultrasound Hematocrit Project (DHP) hopes to find non-invasive methods of determining a person s blood characteristics. Because of the limits of microgravity and the space travel environment, it is important to find non-invasive methods of evaluating the health of persons in space. Presently, there is no well developed method of determining blood composition non-invasively. This projects hopes to use ultrasound and Doppler signals to evaluate the characteristic of hematocrit, the percentage by volume of red blood cells within whole blood. These non-invasive techniques may also be developed to be used on earth for trauma patients where invasive measure might be detrimental. Computational modeling is a useful tool for collecting preliminary information and predictions for the laboratory research. We hope to find and develop a computer program that will be able to simulate the ultrasound signals the project will work with. Simulated models of test conditions will more easily show what might be expected from laboratory results thus help the research group make informed decisions before and during experimentation. There are several existing Matlab based computer programs available, designed to interpret and simulate ultrasound signals. These programs will be evaluated to find which is best suited for the project needs. The criteria of evaluation that will be used are 1) the program must be able to specify transducer properties and specify transmitting and receiving signals, 2) the program must be able to simulate ultrasound signals through different attenuating mediums, 3) the program must be able to process moving targets in order to simulate the Doppler effects that are associated with blood flow, 4) the program should be user friendly and adaptable to various models. After a computer program is chosen, two simulation models will be constructed. These models will simulate and interpret an RF data signal and a Doppler signal.

  10. [Cesarean scar ectopic pregnancy: diagnosis with 2D, three-dimensional (3D) ultrasound and 3D power doppler of a case and review of the literature].

    PubMed

    Pavlova, E; Gunev, D; Diavolov, V; Slavchev, B

    2013-01-01

    Cesarean scar pregnancy is rare type of ectopic pregnancy. It is associated with severe complication if it is not diagnosed early in pregnancy. We present a case of difficult first-trimester diagnosis of Cesarean scar pregnancy. In this paper we discuss the incidence of this condition, the antenatal diagnosis, the prognosis and management and the importance of 2D and 3D ultrasound technique as a diagnostic tool. PMID:24501880

  11. Computational approaches to 3D modeling of RNA.

    PubMed

    Laing, Christian; Schlick, Tamar

    2010-07-21

    Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research. PMID:21399271

  12. Intracranial Catheter for Integrated 3D Ultrasound Imaging & Hyperthermia: Feasibility Study

    NASA Astrophysics Data System (ADS)

    Herickhoff, Carl D.; Light, Edward D.; Bing, Kristin Frinkley; Mukundan, Srinivasan; Grant, Gerald A.; Wolf, Patrick D.; Dixon-Tulloch, Ellen; Shih, Timothy; Hsu, Stephen J.; Smith, Stephen W.

    2009-04-01

    In this study, we investigated the feasibility of an intracranial catheter transducer capable of real-time 3D (RT3D) imaging and ultrasound hyperthermia, for application in the visualization and treatment of tumors in the brain. We designed and constructed a 12 Fr, integrated matrix and linear array catheter transducer prototype for combined RT3D imaging and heating capability. This dual-mode catheter incorporated 153 matrix array elements and 11 linear array elements, on a 0.2 mm pitch, with a total aperture size of 8.4 mm×2.3 mm. This array achieved a 3.5° C in vitro temperature rise at a 2 cm focal distance in tissue-mimicking material. The dual-mode catheter prototype was compared with a Siemens 10 Fr AcuNav™ catheter as a gold standard in experiments assessing image quality and therapeutic potential, and both probes were used in a canine brain model to image anatomical structures and color Doppler blood flow and to attempt in vivo heating.

  13. Semiautomated segmentation and 3D reconstruction of coronary trees: biplane angiography and intravascular ultrasound data fusion

    NASA Astrophysics Data System (ADS)

    Prause, Guido P. M.; DeJong, Steven C.; McKay, Charles R.; Sonka, Milan

    1996-04-01

    In this paper, we describe an approach to 3D reconstruction of the coronary tree based on combined use of biplane coronary angiography and intravascular ultrasound (IVUS). Shortly before the start of a constant-speed IVUS pullback, radiopaque dye is injected into the examined coronary tree and the heart is imaged with a calibrated biplane X-ray system. The 3D centerline of the coronary tree is reconstructed from the geometrically corrected biplane angiograms using an automated segmentation method and manual matching of corresponding branching points. The borders of vessel wall and plaque are automatically detected in the acquired pullback images and the IVUS cross sections are mapped perpendicular to the previously reconstructed 3D vessel centerline. In addition, the twist of the IVUS probe due to the curvature of the coronary artery is calculated for a torsion-free catheter and the whole vessel reconstruction is rotationally adjusted using available anatomic landmarks. The accuracy of the biplane reconstruction procedure is validated by means of a left coronary tree phantom. The feasibility of the entire approach is demonstrated in a cadaveric pig heart.

  14. A new combined prior based reconstruction method for compressed sensing in 3D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Uddin, Muhammad S.; Islam, Rafiqul; Tahtali, Murat; Lambert, Andrew J.; Pickering, Mark R.

    2015-03-01

    Ultrasound (US) imaging is one of the most popular medical imaging modalities, with 3D US imaging gaining popularity recently due to its considerable advantages over 2D US imaging. However, as it is limited by long acquisition times and the huge amount of data processing it requires, methods for reducing these factors have attracted considerable research interest. Compressed sensing (CS) is one of the best candidates for accelerating the acquisition rate and reducing the data processing time without degrading image quality. However, CS is prone to introduce noise-like artefacts due to random under-sampling. To address this issue, we propose a combined prior-based reconstruction method for 3D US imaging. A Laplacian mixture model (LMM) constraint in the wavelet domain is combined with a total variation (TV) constraint to create a new regularization regularization prior. An experimental evaluation conducted to validate our method using synthetic 3D US images shows that it performs better than other approaches in terms of both qualitative and quantitative measures.

  15. 3D finite-difference seismic migration with parallel computers

    SciTech Connect

    Ober, C.C.; Gjertsen, R.; Minkoff, S.; Womble, D.E.

    1998-11-01

    The ability to image complex geologies such as salt domes in the Gulf of Mexico and thrusts in mountainous regions is essential for reducing the risk associated with oil exploration. Imaging these structures, however, is computationally expensive as datasets can be terabytes in size. Traditional ray-tracing migration methods cannot handle complex velocity variations commonly found near such salt structures. Instead the authors use the full 3D acoustic wave equation, discretized via a finite difference algorithm. They reduce the cost of solving the apraxial wave equation by a number of numerical techniques including the method of fractional steps and pipelining the tridiagonal solves. The imaging code, Salvo, uses both frequency parallelism (generally 90% efficient) and spatial parallelism (65% efficient). Salvo has been tested on synthetic and real data and produces clear images of the subsurface even beneath complicated salt structures.

  16. Computing 3D head orientation from a monocular image sequence

    NASA Astrophysics Data System (ADS)

    Horprasert, Thanarat; Yacoob, Yaser; Davis, Larry S.

    1997-02-01

    An approach for estimating 3D head orientation in a monocular image sequence is proposed. The approach employs recently developed image-based parameterized tracking for face and face features to locate the area in which a sub- pixel parameterized shape estimation of the eye's boundary is performed. This involves tracking of five points (four at the eye corners and the fifth is the tip of the nose). We describe an approach that relies on the coarse structure of the face to compute orientation relative to the camera plane. Our approach employs projective invariance of the cross-ratios of the eye corners and anthropometric statistics to estimate the head yaw, roll and pitch. Analytical and experimental results are reported.

  17. Parallelization of ARC3D with Computer-Aided Tools

    NASA Technical Reports Server (NTRS)

    Jin, Haoqiang; Hribar, Michelle; Yan, Jerry; Saini, Subhash (Technical Monitor)

    1998-01-01

    A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

  18. Software-based geometry operations for 3D computer graphics

    NASA Astrophysics Data System (ADS)

    Sima, Mihai; Iancu, Daniel; Glossner, John; Schulte, Michael; Mamidi, Suman

    2006-02-01

    In order to support a broad dynamic range and a high degree of precision, many of 3D renderings fundamental algorithms have been traditionally performed in floating-point. However, fixed-point data representation is preferable over floating-point representation in graphics applications on embedded devices where performance is of paramount importance, while the dynamic range and precision requirements are limited due to the small display sizes (current PDA's are 640 × 480 (VGA), while cell-phones are even smaller). In this paper we analyze the efficiency of a CORDIC-augmented Sandbridge processor when implementing a vertex processor in software using fixed-point arithmetic. A CORDIC-based solution for vertex processing exhibits a number of advantages over classical Multiply-and-Acumulate solutions. First, since a single primitive is used to describe the computation, the code can easily be vectorized and multithreaded, and thus fits the major Sandbridge architectural features. Second, since a CORDIC iteration consists of only a shift operation followed by an addition, the computation may be deeply pipelined. Initially, we outline the Sandbridge architecture extension which encompasses a CORDIC functional unit and the associated instructions. Then, we consider rigid-body rotation, lighting, exponentiation, vector normalization, and perspective division (which are some of the most important data-intensive 3D graphics kernels) and propose a scheme to implement them on the CORDIC-augmented Sandbridge processor. Preliminary results indicate that the performance improvement within the extended instruction set ranges from 3× to 10× (with the exception of rigid body rotation).

  19. Quantification of cerebral ventricle volume change of preterm neonates using 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chen, Yimin; Kishimoto, Jessica; Qiu, Wu; de Ribaupierre, Sandrine; Fenster, Aaron; Chiu, Bernard

    2015-03-01

    Intraventricular hemorrhage (IVH) is a major cause of brain injury in preterm neonates. Quantitative measurement of ventricular dilation or shrinkage is important for monitoring patients and in evaluation of treatment options. 3D ultrasound (US) has been used to monitor the ventricle volume as a biomarker for ventricular dilation. However, volumetric quantification does not provide information as to where dilation occurs. The location where dilation occurs may be related to specific neurological problems later in life. For example, posterior horn enlargement, with thinning of the corpus callosum and parietal white matter fibres, could be linked to poor visuo-spatial abilities seen in hydrocephalic children. In this work, we report on the development and application of a method used to analyze local surface change of the ventricles of preterm neonates with IVH from 3D US images. The technique is evaluated using manual segmentations from 3D US images acquired in two imaging sessions. The surfaces from baseline and follow-up were registered and then matched on a point-by-point basis. The distance between each pair of corresponding points served as an estimate of local surface change of the brain ventricle at each vertex. The measurements of local surface change were then superimposed on the ventricle surface to produce the 3D local surface change map that provide information on the spatio-temporal dilation pattern of brain ventricles following IVH. This tool can be used to monitor responses to different treatment options, and may provide important information for elucidating the deficiencies a patient will have later in life.

  20. Segmentation of the common carotid artery with active shape models from 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Yang, Xin; Jin, Jiaoying; He, Wanji; Yuchi, Ming; Ding, Mingyue

    2012-03-01

    Carotid atherosclerosis is a major cause of stroke, a leading cause of death and disability. In this paper, we develop and evaluate a new segmentation method for outlining both lumen and adventitia (inner and outer walls) of common carotid artery (CCA) from three-dimensional ultrasound (3D US) images for carotid atherosclerosis diagnosis and evaluation. The data set consists of sixty-eight, 17× 2× 2, 3D US volume data acquired from the left and right carotid arteries of seventeen patients (eight treated with 80mg atorvastain and nine with placebo), who had carotid stenosis of 60% or more, at baseline and after three months of treatment. We investigate the use of Active Shape Models (ASMs) to segment CCA inner and outer walls after statin therapy. The proposed method was evaluated with respect to expert manually outlined boundaries as a surrogate for ground truth. For the lumen and adventitia segmentations, respectively, the algorithm yielded Dice Similarity Coefficient (DSC) of 93.6%+/- 2.6%, 91.8%+/- 3.5%, mean absolute distances (MAD) of 0.28+/- 0.17mm and 0.34 +/- 0.19mm, maximum absolute distances (MAXD) of 0.87 +/- 0.37mm and 0.74 +/- 0.49mm. The proposed algorithm took 4.4 +/- 0.6min to segment a single 3D US images, compared to 11.7+/-1.2min for manual segmentation. Therefore, the method would promote the translation of carotid 3D US to clinical care for the fast, safety and economical monitoring of the atherosclerotic disease progression and regression during therapy.

  1. Non-invasive transcranial ultrasound therapy based on a 3D CT scan: protocol validation and in vitro results

    NASA Astrophysics Data System (ADS)

    Marquet, F.; Pernot, M.; Aubry, J.-F.; Montaldo, G.; Marsac, L.; Tanter, M.; Fink, M.

    2009-05-01

    A non-invasive protocol for transcranial brain tissue ablation with ultrasound is studied and validated in vitro. The skull induces strong aberrations both in phase and in amplitude, resulting in a severe degradation of the beam shape. Adaptive corrections of the distortions induced by the skull bone are performed using a previous 3D computational tomography scan acquisition (CT) of the skull bone structure. These CT scan data are used as entry parameters in a FDTD (finite differences time domain) simulation of the full wave propagation equation. A numerical computation is used to deduce the impulse response relating the targeted location and the ultrasound therapeutic array, thus providing a virtual time-reversal mirror. This impulse response is then time-reversed and transmitted experimentally by a therapeutic array positioned exactly in the same referential frame as the one used during CT scan acquisitions. In vitro experiments are conducted on monkey and human skull specimens using an array of 300 transmit elements working at a central frequency of 1 MHz. These experiments show a precise refocusing of the ultrasonic beam at the targeted location with a positioning error lower than 0.7 mm. The complete validation of this transcranial adaptive focusing procedure paves the way to in vivo animal and human transcranial HIFU investigations.

  2. 3D in vivo imaging of rat hearts by high frequency ultrasound and its application in myofiber orientation wrapping

    NASA Astrophysics Data System (ADS)

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Lerakis, Stamatios; Wagner, Mary B.; Fei, Baowei

    2015-03-01

    Cardiac ultrasound plays an important role in the imaging of hearts in basic cardiovascular research and clinical examinations. 3D ultrasound imaging can provide the geometry or motion information of the heart. Especially, the wrapping of cardiac fiber orientations to the ultrasound volume could supply useful information on the stress distributions and electric action spreading. However, how to acquire 3D ultrasound volumes of the heart of small animals in vivo for cardiac fiber wrapping is still a challenging problem. In this study, we provide an approach to acquire 3D ultrasound volumes of the rat hearts in vivo. The comparison between both in vivo and ex vivo geometries indicated 90.1% Dice similarity. In this preliminary study, the evaluations of the cardiac fiber orientation wrapping errors were 24.7° for the acute angle error and were 22.4° for the inclination angle error. This 3D ultrasound imaging and fiber orientation estimation technique have potential applications in cardiac imaging.

  3. 3D in vivo imaging of rat hearts by high frequency ultrasound and its application in myofiber orientation wrapping

    PubMed Central

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Lerakis, Stamatios; Wagner, Mary B.; Fei, Baowei

    2015-01-01

    Cardiac ultrasound plays an important role in the imaging of hearts in basic cardiovascular research and clinical examinations. 3D ultrasound imaging can provide the geometry or motion information of the heart. Especially, the wrapping of cardiac fiber orientations to the ultrasound volume could supply useful information on the stress distributions and electric action spreading. However, how to acquire 3D ultrasound volumes of the heart of small animals in vivo for cardiac fiber wrapping is still a challenging problem. In this study, we provide an approach to acquire 3D ultrasound volumes of the rat hearts in vivo. The comparison between both in vivo and ex vivo geometries indicated 90.1% Dice similarity. In this preliminary study, the evaluations of the cardiac fiber orientation wrapping errors were 24.7° for the acute angle error and were 22.4° for the inclination angle error. This 3D ultrasound imaging and fiber orientation estimation technique have potential applications in cardiac imaging. PMID:26412926

  4. Automated 3D ultrasound elastography of the breast: a phantom validation study

    NASA Astrophysics Data System (ADS)

    Hendriks, Gijs A. G. M.; Holländer, Branislav; Menssen, Jan; Milkowski, Andy; Hansen, Hendrik H. G.; de Korte, Chris L.

    2016-04-01

    In breast cancer screening, the automated breast volume scanner (ABVS) was introduced as an alternative for mammography since the latter technique is less suitable for women with dense breasts. Although clinical studies show promising results, clinicians report two disadvantages: long acquisition times (>90 s) introducing breathing artefacts, and high recall rates due to detection of many small lesions of uncertain malignant potential. Technical improvements for faster image acquisition and better discrimination between benign and malignant lesions are thus required. Therefore, the aim of this study was to investigate if 3D ultrasound elastography using plane-wave imaging is feasible. Strain images of a breast elastography phantom were acquired by an ABVS-mimicking device that allowed axial and elevational movement of the attached transducer. Pre- and post-deformation volumes were acquired with different constant speeds (between 1.25 and 40.0 mm s-1) and by three protocols: Go-Go (pre- and post-volumes with identical start and end positions), Go-Return (similar to Go-Go with opposite scanning directions) and Control (pre- and post-volumes acquired per position, this protocol can be seen as reference). Afterwards, 2D and 3D cross-correlation and strain algorithms were applied to the acquired volumes and the results were compared. The Go-Go protocol was shown to be superior with better strain image quality (CNRe and SNRe) than Go-Return and to be similar as Control. This can be attributed to applying opposite mechanical forces to the phantom during the Go-Return protocol, leading to out-of-plane motion. This motion was partly compensated by using 3D cross-correlation. However, the quality was still inferior to Go-Go. Since these results were obtained in a phantom study with controlled deformations, the effect of possible uncontrolled in vivo tissue motion artefacts has to be addressed in future studies. In conclusion, it seems feasible to implement 3D ultrasound

  5. Automated 3D ultrasound elastography of the breast: a phantom validation study.

    PubMed

    Hendriks, Gijs A G M; Holländer, Branislav; Menssen, Jan; Milkowski, Andy; Hansen, Hendrik H G; de Korte, Chris L

    2016-04-01

    In breast cancer screening, the automated breast volume scanner (ABVS) was introduced as an alternative for mammography since the latter technique is less suitable for women with dense breasts. Although clinical studies show promising results, clinicians report two disadvantages: long acquisition times (>90 s) introducing breathing artefacts, and high recall rates due to detection of many small lesions of uncertain malignant potential. Technical improvements for faster image acquisition and better discrimination between benign and malignant lesions are thus required. Therefore, the aim of this study was to investigate if 3D ultrasound elastography using plane-wave imaging is feasible. Strain images of a breast elastography phantom were acquired by an ABVS-mimicking device that allowed axial and elevational movement of the attached transducer. Pre- and post-deformation volumes were acquired with different constant speeds (between 1.25 and 40.0 mm s(-1)) and by three protocols: Go-Go (pre- and post-volumes with identical start and end positions), Go-Return (similar to Go-Go with opposite scanning directions) and Control (pre- and post-volumes acquired per position, this protocol can be seen as reference). Afterwards, 2D and 3D cross-correlation and strain algorithms were applied to the acquired volumes and the results were compared. The Go-Go protocol was shown to be superior with better strain image quality (CNRe and SNRe) than Go-Return and to be similar as Control. This can be attributed to applying opposite mechanical forces to the phantom during the Go-Return protocol, leading to out-of-plane motion. This motion was partly compensated by using 3D cross-correlation. However, the quality was still inferior to Go-Go. Since these results were obtained in a phantom study with controlled deformations, the effect of possible uncontrolled in vivo tissue motion artefacts has to be addressed in future studies. In conclusion, it seems feasible to implement 3D

  6. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

    Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein

  7. 3D prostate boundary segmentation from ultrasound images using 2D active shape models.

    PubMed

    Hodge, Adam C; Ladak, Hanif M

    2006-01-01

    Boundary outlining, or segmentation, of the prostate is an important task in diagnosis and treatment planning for prostate cancer. This paper describes an algorithm for semi-automatic, three-dimensional (3D) segmentation of the prostate boundary from ultrasound images based on two-dimensional (2D) active shape models (ASM) and rotation-based slicing. Evaluation of the algorithm used distance- and volume-based error metrics to compare algorithm generated boundary outlines to gold standard (manually generated) boundary outlines. The mean absolute distance between the algorithm and gold standard boundaries was 1.09+/-0.49 mm, the average percent absolute volume difference was 3.28+/-3.16%, and a 5x speed increase as compared manual planimetry was achieved. PMID:17946106

  8. 3D prostate segmentation of ultrasound images combining longitudinal image registration and machine learning

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Fei, Baowei

    2012-02-01

    We developed a three-dimensional (3D) segmentation method for transrectal ultrasound (TRUS) images, which is based on longitudinal image registration and machine learning. Using longitudinal images of each individual patient, we register previously acquired images to the new images of the same subject. Three orthogonal Gabor filter banks were used to extract texture features from each registered image. Patient-specific Gabor features from the registered images are used to train kernel support vector machines (KSVMs) and then to segment the newly acquired prostate image. The segmentation method was tested in TRUS data from five patients. The average surface distance between our and manual segmentation is 1.18 +/- 0.31 mm, indicating that our automatic segmentation method based on longitudinal image registration is feasible for segmenting the prostate in TRUS images.

  9. A phantom with reduced complexity for spatial 3-D ultrasound calibration.

    PubMed

    Dandekar, Sangita; Li, Yinbo; Molloy, Janelle; Hossack, John

    2005-08-01

    The design of a new phantom for 3-D ultrasound calibration is presented. The phantom provides a viable alternative to existing phantoms that are significantly more complex and require high precision fabrication. The phantom, referred to as a "plane-of-wires" phantom, consists of two wires mounted at the same fixed height above the bottom of a water tank. Data collection for calibration involved rotating and translating the phantom so that the wires remained in a single plane parallel to the tank bottom. The mean reconstruction accuracy of the plane-of-wires calibration is 0.66 mm at a mean depth of 12.3 mm, with a precision of 1.23 mm at the same mean depth. The calibration was used to determine the volume of a cube with known volume with an error of 2.51%. The calibration performance achieved is comparable with that of existing approaches. PMID:16085099

  10. Simulation of autonomous robotic multiple-core biopsy by 3D ultrasound guidance.

    PubMed

    Liang, Kaicheng; Rogers, Albert J; Light, Edward D; Von Allmen, Daniel; Smith, Stephen W

    2010-04-01

    An autonomous multiple-core biopsy system guided by real-time 3D ultrasound and operated by a robotic arm with 6+1 degrees of freedom has been developed. Using a specimen of turkey breast as a tissue phantom, our system was able to first autonomously locate the phantom in the image volume and then perform needle sticks in each of eight sectors in the phantom in a single session, with no human intervention required. Based on the fraction of eight sectors successfully sampled in an experiment of five trials, a success rate of 93% was recorded. This system could have relevance in clinical procedures that involve multiple needle-core sampling such as prostate or breast biopsy. PMID:20687279

  11. 3D transrectal ultrasound (TRUS) prostate segmentation based on optimal feature learning framework

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Rossi, Peter J.; Jani, Ashesh B.; Mao, Hui; Curran, Walter J.; Liu, Tian

    2016-03-01

    We propose a 3D prostate segmentation method for transrectal ultrasound (TRUS) images, which is based on patch-based feature learning framework. Patient-specific anatomical features are extracted from aligned training images and adopted as signatures for each voxel. The most robust and informative features are identified by the feature selection process to train the kernel support vector machine (KSVM). The well-trained SVM was used to localize the prostate of the new patient. Our segmentation technique was validated with a clinical study of 10 patients. The accuracy of our approach was assessed using the manual segmentations (gold standard). The mean volume Dice overlap coefficient was 89.7%. In this study, we have developed a new prostate segmentation approach based on the optimal feature learning framework, demonstrated its clinical feasibility, and validated its accuracy with manual segmentations.

  12. Constitutive Modeling of Porcine Liver in Indentation Using 3D Ultrasound Imaging

    PubMed Central

    Jordan, P.; Socrate, S.; Zickler, T.E.; Howe, R.D.

    2009-01-01

    In this work we present an inverse finite-element modeling framework for constitutive modeling and parameter estimation of soft tissues using full-field volumetric deformation data obtained from 3D ultrasound. The finite-element model is coupled to full-field visual measurements by regularization springs attached at nodal locations. The free ends of the springs are displaced according to the locally estimated tissue motion and the normalized potential energy stored in all springs serves as a measure of model-experiment agreement for material parameter optimization. We demonstrate good accuracy of estimated parameters and consistent convergence properties on synthetically generated data. We present constitutive model selection and parameter estimation for perfused porcine liver in indentation and demonstrate that a quasilinear viscoelastic model with shear modulus relaxation offers good model-experiment agreement in terms of indenter displacement (0.19 mm RMS error) and tissue displacement field (0.97 mm RMS error). PMID:19627823

  13. Computational and methodological developments towards 3D full waveform inversion

    NASA Astrophysics Data System (ADS)

    Etienne, V.; Virieux, J.; Hu, G.; Jia, Y.; Operto, S.

    2010-12-01

    Full waveform inversion (FWI) is one of the most promising techniques for seismic imaging. It relies on a formalism taking into account every piece of information contained in the seismic data as opposed to more classical techniques such as travel time tomography. As a result, FWI is a high resolution imaging process able to reach a spatial accuracy equal to half a wavelength. FWI is based on a local optimization scheme and therefore the main limitation concerns the starting model which has to be closed enough to the real one in order to converge to the global minimum. Another counterpart of FWI is the required computational resources when considering models and frequencies of interest. The task becomes even more tremendous when one tends to perform the inversion using the elastic equation instead of using the acoustic approximation. This is the reason why until recently most studies were limited to 2D cases. In the last few years, due to the increase of the available computational power, FWI has focused a lot of interests and continuous efforts towards inversion of 3D models, leading to remarkable applications up to the continental scale. We investigate the computational burden induced by FWI in 3D elastic media and propose some strategic features leading to the reduction of the numerical cost while providing a great flexibility in the inversion parametrization. First, in order to release the memory requirements, we developed our FWI algorithm in the frequency domain and take benefit of the wave-number redundancy in the seismic data to process a quite reduced number of frequencies. To do so, we extract frequency solutions from time marching techniques which are efficient for 3D structures. Moreover, this frequency approach permits a multi-resolution strategy by proceeding from low to high frequencies: the final model at one frequency is used as the starting model for the next frequency. This procedure overcomes partially the non-linear behavior of the inversion

  14. Transvaginal 3D Image-Guided High Intensity Focused Ultrasound Array

    NASA Astrophysics Data System (ADS)

    Held, Robert; Nguyen, Thuc Nghi; Vaezy, Shahram

    2005-03-01

    The goal of this project is to develop a transvaginal image-guided High Intensity Focused Ultrasound (HIFU) device using piezocomposite HIFU array technology, and commercially-available ultrasound imaging. Potential applications include treatment of uterine fibroids and abnormal uterine bleeding. The HIFU transducer was an annular phased array, with a focal length range of 30-60 mm, an elliptically-shaped aperture of 35×60 mm, and an operating frequency of 3 MHz. A pillow-shaped bag with water circulation will be used for coupling the HIFU energy into the tissue. An intra-cavity imaging probe (C9-5, Philips) was integrated with the HIFU array such that the focal axis of the HIFU transducer was within the image plane. The entire device will be covered by a gel-filled condom when inserted in the vaginal cavity. To control it, software packages were developed in the LabView programming environment. An imaging algorithm processed the ultrasound image to remove noise patterns due to the HIFU signal. The device will be equipped with a three-dimensional tracking system, using a six-degrees-of-freedom articulating arm. Necrotic lesions were produced in a tissue-mimicking phantom and a turkey breast sample for all focal lengths. Various HIFU doses allow various necrotic lesion shapes, including thin ellipsoidal, spherical, wide cylindrical, and teardrop-shaped. Software control of the device allows multiple foci to be activated sequentially for desired lesion patterns. Ultrasound imaging synchronization can be achieved using hardware signals obtained from the imaging system, or software signals determined empirically for various imaging probes. The image-guided HIFU device will provide a valuable tool in visualization of uterine fibroid tumors for the purposes of planning and subsequent HIFU treatment of the tumor, all in a 3D environment. The control system allows for various lesions of different shapes to be optimally positioned in the tumor to cover the entire tumor

  15. Catheter-Based Ultrasound for 3D Control of Thermal Therapy

    NASA Astrophysics Data System (ADS)

    Diederich, Chris; Chen, Xin; Wootton, Jeffery; Juang, Titania; Nau, Will H.; Kinsey, Adam; Hsu, I.-Chow; Rieke, Viola; Pauly, Kim Butts; Sommer, Graham; Bouley, Donna

    2009-04-01

    Catheter-based ultrasound applicators have been investigated for delivering hyperthermia and thermal ablation for the treatment of cancer and benign diseases. Technology includes an intrauterine applicator integrated with an HDR ring applicator, interstitial applicators for hyperthermia delivery during brachytherapy, interstitial applicators for tumor ablation, and transurethral devices for conformal prostate ablation. Arrays of multiple sectored tubular transducers have been fabricated for interstitial and intrauterine hyperthermia applicators. High-power interstitial versions have been evaluated for percutaneous implantation with directional or dynamic angular control of thermal ablation. Transurethral applicators include curvilinear transducers with rotational sweeping of narrow heating patterns, and multi-sectored tubular devices capable of dynamic angular control without applicator movement. Performance was evaluated in phantom, excised tissue, in vivo experiments in canine prostate under MR temperature monitoring, clinical hyperthermia, and 3D-biothermal simulations with patient anatomy. Interstitial and intrauterine devices can tailor hyperthermia to large treatment volumes, with multisectored control useful to limit exposure to rectum and bladder. Curvilinear transurethral devices with sequential rotation produce target conforming coagulation zones that can cover either the whole gland or defined focal regions. Multi-sectored transurethral applicators can dynamically control the angular heating profile and target large regions of the prostate without applicator manipulation. High-power interstitial implants with directional devices can be used to effectively ablate defined target regions while avoiding sensitive tissues. MR temperature monitoring can effectively define the extent of thermal damage and provided a means for real-time control of the applicators. In summary, these catheter-based ultrasound devices allow for dynamic control of heating profiles

  16. CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API

    NASA Astrophysics Data System (ADS)

    Boctor, Emad M.; Viswanathan, Anand; Pieper, Steve; Choti, Michael A.; Taylor, Russell H.; Kikinis, Ron; Fichtinger, Gabor

    2004-05-01

    Ultrasound has become popular in clinical/surgical applications, both as the primary image guidance modality and also in conjunction with other modalities like CT or MRI. Three dimensional ultrasound (3DUS) systems have also demonstrated usefulness in image-guided therapy (IGT). At the same time, however, current lack of open-source and open-architecture multi-modal medical visualization systems prevents 3DUS from fulfilling its potential. Several stand-alone 3DUS systems, like Stradx or In-Vivo exist today. Although these systems have been found to be useful in real clinical setting, it is difficult to augment their functionality and integrate them in versatile IGT systems. To address these limitations, a robotic/freehand 3DUS open environment (CISUS) is being integrated into the 3D Slicer, an open-source research tool developed for medical image analysis and surgical planning. In addition, the system capitalizes on generic application programming interfaces (APIs) for tracking devices and robotic control. The resulting platform-independent open-source system may serve as a valuable tool to the image guided surgery community. Other researchers could straightforwardly integrate the generic CISUS system along with other functionalities (i.e. dual view visualization, registration, real-time tracking, segmentation, etc) to rapidly create their medical/surgical applications. Our current driving clinical application is robotically assisted and freehand 3DUS-guided liver ablation, which is fully being integrated under the CISUS-3D Slicer. Initial functionality and pre-clinical feasibility are demonstrated on phantom and ex-vivo animal models.

  17. Comparison of 3-D synthetic aperture phased-array ultrasound imaging and parallel beamforming.

    PubMed

    Rasmussen, Morten Fischer; Jensen, Jørgen Arendt

    2014-10-01

    This paper demonstrates that synthetic aperture imaging (SAI) can be used to achieve real-time 3-D ultrasound phased-array imaging. It investigates whether SAI increases the image quality compared with the parallel beamforming (PB) technique for real-time 3-D imaging. Data are obtained using both simulations and measurements with an ultrasound research scanner and a commercially available 3.5- MHz 1024-element 2-D transducer array. To limit the probe cable thickness, 256 active elements are used in transmit and receive for both techniques. The two imaging techniques were designed for cardiac imaging, which requires sequences designed for imaging down to 15 cm of depth and a frame rate of at least 20 Hz. The imaging quality of the two techniques is investigated through simulations as a function of depth and angle. SAI improved the full-width at half-maximum (FWHM) at low steering angles by 35%, and the 20-dB cystic resolution by up to 62%. The FWHM of the measured line spread function (LSF) at 80 mm depth showed a difference of 20% in favor of SAI. SAI reduced the cyst radius at 60 mm depth by 39% in measurements. SAI improved the contrast-to-noise ratio measured on anechoic cysts embedded in a tissue-mimicking material by 29% at 70 mm depth. The estimated penetration depth on the same tissue-mimicking phantom shows that SAI increased the penetration by 24% compared with PB. Neither SAI nor PB achieved the design goal of 15 cm penetration depth. This is likely due to the limited transducer surface area and a low SNR of the experimental scanner used. PMID:25265174

  18. Accurate 3D reconstruction of complex blood vessel geometries from intravascular ultrasound images: in vitro study.

    PubMed

    Subramanian, K R; Thubrikar, M J; Fowler, B; Mostafavi, M T; Funk, M W

    2000-01-01

    We present a technique that accurately reconstructs complex three dimensional blood vessel geometry from 2D intravascular ultrasound (IVUS) images. Biplane x-ray fluoroscopy is used to image the ultrasound catheter tip at a few key points along its path as the catheter is pulled through the blood vessel. An interpolating spline describes the continuous catheter path. The IVUS images are located orthogonal to the path, resulting in a non-uniform structured scalar volume of echo densities. Isocontour surfaces are used to view the vessel geometry, while transparency and clipping enable interactive exploration of interior structures. The two geometries studied are a bovine artery vascular graft having U-shape and a constriction, and a canine carotid artery having multiple branches and a constriction. Accuracy of the reconstructions is established by comparing the reconstructions to (1) silicone moulds of the vessel interior, (2) biplane x-ray images, and (3) the original echo images. Excellent shape and geometry correspondence was observed in both geometries. Quantitative measurements made at key locations of the 3D reconstructions also were in good agreement with those made in silicone moulds. The proposed technique is easily adoptable in clinical practice, since it uses x-rays with minimal exposure and existing IVUS technology. PMID:11105284

  19. Ultrasound and 3D Skin Imaging: Methods to Evaluate Efficacy of Striae Distensae Treatment

    PubMed Central

    Bleve, Mariella; Capra, Priscilla; Pavanetto, Franca; Perugini, Paola

    2012-01-01

    Background. Over time, the striae rubra develop into striae alba that appear white, flat, and depressed. It is very important to determine the optimum striae management. In order to evaluate the effectiveness of these therapies, objective measurement tools are necessary. Objective. The aim of this study is to evaluate if ultrasonography and PRIMOS can be used to obtain an objective assessment of stretch marks type and stage; furthermore, we aim to apply these techniques to evaluate the efficacy of a topical treatment. Methods. 20 volunteers were enrolled with a two-month study. A marketed cosmetic product was used as the active over one body area. The controlateral area with stretch marks was treated with a “placebo” formulation without active, as a control. The instrumental evaluation was carried out at the beginning of the trial (baseline values or t0), after 1 month (t1), and at the end of the study (t2). Results. PRIMOS was able to measure and document striae distensae maturation; furthermore, ultrasound imaging permitted to visualize and diagnose the striae. Statistical analysis of skin roughness demonstrated a statistically significant reduction of Rp value only in a treated group. In fact, the Rp value represented a maximum peak height in the area selected. These results demonstrated that after two months of treatment only the striae rubra can be treated successfully. Conclusions. This work demonstrated that the 22MHz ultrasound can diagnose stretch marks; PRIMOS device can detect and measure striae distensae type and maturation. Furthermore, the high-frequency ultrasound and the 3D image device, described in this work, can be successfully employed in order to evaluate the efficacy of a topical treatment. PMID:22203840

  20. Ultrasound and 3D Skin Imaging: Methods to Evaluate Efficacy of Striae Distensae Treatment.

    PubMed

    Bleve, Mariella; Capra, Priscilla; Pavanetto, Franca; Perugini, Paola

    2012-01-01

    Background. Over time, the striae rubra develop into striae alba that appear white, flat, and depressed. It is very important to determine the optimum striae management. In order to evaluate the effectiveness of these therapies, objective measurement tools are necessary. Objective. The aim of this study is to evaluate if ultrasonography and PRIMOS can be used to obtain an objective assessment of stretch marks type and stage; furthermore, we aim to apply these techniques to evaluate the efficacy of a topical treatment. Methods. 20 volunteers were enrolled with a two-month study. A marketed cosmetic product was used as the active over one body area. The controlateral area with stretch marks was treated with a "placebo" formulation without active, as a control. The instrumental evaluation was carried out at the beginning of the trial (baseline values or t(0)), after 1 month (t(1)), and at the end of the study (t(2)). Results. PRIMOS was able to measure and document striae distensae maturation; furthermore, ultrasound imaging permitted to visualize and diagnose the striae. Statistical analysis of skin roughness demonstrated a statistically significant reduction of Rp value only in a treated group. In fact, the Rp value represented a maximum peak height in the area selected. These results demonstrated that after two months of treatment only the striae rubra can be treated successfully. Conclusions. This work demonstrated that the 22MHz ultrasound can diagnose stretch marks; PRIMOS device can detect and measure striae distensae type and maturation. Furthermore, the high-frequency ultrasound and the 3D image device, described in this work, can be successfully employed in order to evaluate the efficacy of a topical treatment. PMID:22203840

  1. 3D Vectorial Time Domain Computational Integrated Photonics

    SciTech Connect

    Kallman, J S; Bond, T C; Koning, J M; Stowell, M L

    2007-02-16

    The design of integrated photonic structures poses considerable challenges. 3D-Time-Domain design tools are fundamental in enabling technologies such as all-optical logic, photonic bandgap sensors, THz imaging, and fast radiation diagnostics. Such technologies are essential to LLNL and WFO sponsors for a broad range of applications: encryption for communications and surveillance sensors (NSA, NAI and IDIV/PAT); high density optical interconnects for high-performance computing (ASCI); high-bandwidth instrumentation for NIF diagnostics; micro-sensor development for weapon miniaturization within the Stockpile Stewardship and DNT programs; and applications within HSO for CBNP detection devices. While there exist a number of photonics simulation tools on the market, they primarily model devices of interest to the communications industry. We saw the need to extend our previous software to match the Laboratory's unique emerging needs. These include modeling novel material effects (such as those of radiation induced carrier concentrations on refractive index) and device configurations (RadTracker bulk optics with radiation induced details, Optical Logic edge emitting lasers with lateral optical inputs). In addition we foresaw significant advantages to expanding our own internal simulation codes: parallel supercomputing could be incorporated from the start, and the simulation source code would be accessible for modification and extension. This work addressed Engineering's Simulation Technology Focus Area, specifically photonics. Problems addressed from the Engineering roadmap of the time included modeling the Auston switch (an important THz source/receiver), modeling Vertical Cavity Surface Emitting Lasers (VCSELs, which had been envisioned as part of fast radiation sensors), and multi-scale modeling of optical systems (for a variety of applications). We proposed to develop novel techniques to numerically solve the 3D multi-scale propagation problem for both the microchip

  2. 2-D array for 3-D Ultrasound Imaging Using Synthetic Aperture Techniques

    PubMed Central

    Daher, Nadim M.; Yen, Jesse T.

    2010-01-01

    A 2-D array of 256 × 256 = 65,536 elements, with total area 4 × 4 = 16 cm2, serves as a flexible platform for developing acquisition schemes for 3-D rectilinear ultrasound imaging at 10 MHz using synthetic aperture techniques. This innovative system combines a simplified interconnect scheme and synthetic aperture techniques with a 2-D array for 3-D imaging. A row-column addressing scheme is used to access different elements for different transmit events. This addressing scheme is achieved through a simple interconnect, consisting of one top, one bottom single layer flex circuits, which, compared to multi-layer flex circuits, are simpler to design, cheaper to manufacture and thinner so their effect on the acoustic response is minimized. We present three designs that prioritize different design objectives: volume acquisiton time, resolution, and sensitivity, while maintaining acceptable figures for the other design objectives. For example, one design overlooks time acquisition requirements, assumes good noise conditions, and optimizes for resolution, achieving −6 dB and −20 dB beamwidths of less than 0.2 and 0.5 millimeters, respectively, for an F/2 aperture. Another design can acquire an entire volume in 256 transmit events, with −6dB and −20 dB beamwidths in the order of 0.4 and 0.8 millimeters, respectively. PMID:16764446

  3. Characterization of neonatal patients with intraventricular hemorrhage using 3D ultrasound cerebral ventricle volumes

    NASA Astrophysics Data System (ADS)

    Kishimoto, Jessica; Fenster, Aaron; Lee, David S. C.; de Ribaupierre, Sandrine

    2015-03-01

    One of the major non-congenital cause of neurological impairment among neonates born very preterm is intraventricular hemorrhage (IVH) - bleeding within the lateral ventricles. Most IVH patients will have a transient period of ventricle dilation that resolves spontaneously. However, those patients most at risk of long-term impairment are those who have progressive ventricle dilation as this causes macrocephaly, an abnormally enlarged head, then later causes increases intracranial pressure (ICP). 2D ultrasound (US) images through the fontanelles of the patients are serially acquired to monitor the progression of the ventricle dilation. These images are used to determine when interventional therapies such as needle aspiration of the built up CSF might be indicated for a patient. Initial therapies usually begin during the third week of life. Such interventions have been shown to decrease morbidity and mortality in IVH patients; however, this comes with risks of further hemorrhage or infection; therefore only patients requiring it should be treated. Previously we have developed and validated a 3D US system to monitor the progression of ventricle volumes (VV) in IVH patients. This system has been validated using phantoms and a small set of patient images. The aim of this work is to determine the ability of 3D US generated VV to categorize patients into those who will require interventional therapies, and those who will have spontaneous resolution. Patients with higher risks could therefore be monitored better, by re-allocating some of the resources as the low risks infants would need less monitoring.

  4. Automatic 3D ultrasound calibration for image guided therapy using intramodality image registration

    NASA Astrophysics Data System (ADS)

    Schlosser, Jeffrey; Kirmizibayrak, Can; Shamdasani, Vijay; Metz, Steve; Hristov, Dimitre

    2013-11-01

    Many real time ultrasound (US) guided therapies can benefit from management of motion-induced anatomical changes with respect to a previously acquired computerized anatomy model. Spatial calibration is a prerequisite to transforming US image information to the reference frame of the anatomy model. We present a new method for calibrating 3D US volumes using intramodality image registration, derived from the ‘hand-eye’ calibration technique. The method is fully automated by implementing data rejection based on sensor displacements, automatic registration over overlapping image regions, and a self-consistency error metric evaluated continuously during calibration. We also present a novel method for validating US calibrations based on measurement of physical phantom displacements within US images. Both calibration and validation can be performed on arbitrary phantoms. Results indicate that normalized mutual information and localized cross correlation produce the most accurate 3D US registrations for calibration. Volumetric image alignment is more accurate and reproducible than point selection for validating the calibrations, yielding <1.5 mm root mean square error, a significant improvement relative to previously reported hand-eye US calibration results. Comparison of two different phantoms for calibration and for validation revealed significant differences for validation (p = 0.003) but not for calibration (p = 0.795).

  5. A preliminary evaluation work on a 3D ultrasound imaging system for 2D array transducer

    NASA Astrophysics Data System (ADS)

    Zhong, Xiaoli; Li, Xu; Yang, Jiali; Li, Chunyu; Song, Junjie; Ding, Mingyue; Yuchi, Ming

    2016-04-01

    This paper presents a preliminary evaluation work on a pre-designed 3-D ultrasound imaging system. The system mainly consists of four parts, a 7.5MHz, 24×24 2-D array transducer, the transmit/receive circuit, power supply, data acquisition and real-time imaging module. The row-column addressing scheme is adopted for the transducer fabrication, which greatly reduces the number of active channels . The element area of the transducer is 4.6mm by 4.6mm. Four kinds of tests were carried out to evaluate the imaging performance, including the penetration depth range, axial and lateral resolution, positioning accuracy and 3-D imaging frame rate. Several strong reflection metal objects , fixed in a water tank, were selected for the purpose of imaging due to a low signal-to-noise ratio of the transducer. The distance between the transducer and the tested objects , the thickness of aluminum, and the seam width of the aluminum sheet were measured by a calibrated micrometer to evaluate the penetration depth, the axial and lateral resolution, respectively. The experiment al results showed that the imaging penetration depth range was from 1.0cm to 6.2cm, the axial and lateral resolution were 0.32mm and 1.37mm respectively, the imaging speed was up to 27 frames per second and the positioning accuracy was 9.2%.

  6. 3D ultrasound system to investigate intraventricular hemorrhage in preterm neonates

    NASA Astrophysics Data System (ADS)

    Kishimoto, J.; de Ribaupierre, S.; Lee, D. S. C.; Mehta, R.; St. Lawrence, K.; Fenster, A.

    2013-11-01

    Intraventricular hemorrhage (IVH) is a common disorder among preterm neonates that is routinely diagnosed and monitored by 2D cranial ultrasound (US). The cerebral ventricles of patients with IVH often have a period of ventricular dilation (ventriculomegaly). This initial increase in ventricle size can either spontaneously resolve, which often shows clinically as a period of stabilization in ventricle size and eventual decline back towards a more normal size, or progressive ventricular dilation that does not stabilize and which may require interventional therapy to reduce symptoms relating to increased intracranial pressure. To improve the characterization of ventricle dilation, we developed a 3D US imaging system that can be used with a conventional clinical US scanner to image the ventricular system of preterm neonates at risk of ventriculomegaly. A motorized transducer housing was designed specifically for hand-held use inside an incubator using a transducer commonly used for cranial 2D US scans. This system was validated using geometric phantoms, US/MRI compatible ventricle volume phantoms, and patient images to determine 3D reconstruction accuracy and inter- and intra-observer volume estimation variability. 3D US geometric reconstruction was found to be accurate with an error of <0.2%. Measured volumes of a US/MRI compatible ventricle-like phantom were within 5% of gold standard water displacement measurements. Intra-class correlation for the three observers was 0.97, showing very high agreement between observers. The coefficient of variation was between 1.8-6.3% for repeated segmentations of the same patient. The minimum detectable difference was calculated to be 0.63 cm3 for a single observer. Results from ANOVA for three observers segmenting three patients of IVH grade II did not show any significant differences (p > 0.05) for the measured ventricle volumes between observers. This 3D US system can reliably produce 3D US images of the neonatal ventricular

  7. The alteration in placental volume and placental mean grey value in growth-restricted pregnancies assessed by 3D ultrasound (Growth Restriction & 3D Ultrasonography).

    PubMed

    Artunc Ulkumen, B; Pala, H G; Uyar, Y; Koyuncu, F M; Bulbul Baytur, Y

    2015-01-01

    We aimed to evaluate the volumetric and echogenic alterations in placentas between the intrauterine growth restriction (IUGR) and normal pregnancies using three-dimensional ultrasound and virtual organ computer-aided analysis (VOCAL) software. This case-control prospective study consisted of 48 singleton pregnancies complicated by IUGR and 60 healthy singleton pregnancies matched for maternal age, gestational age and parity. Placental volume (PV) and placental volumetric mean grey values (MGV) were evaluated. PV (cm(3)) was analysed using the VOCAL imaging analysis program, and 3D histogram was used to calculate the volumetric MGV (%). PV was 278.50 ± 63.68 and 370.98 ± 97.82 cm(3) in IUGR and control groups, respectively (p = 0.004). MGV of the placenta was 38.24 ± 8.41 and 38.24 ± 8.41 in IUGR and control groups, respectively (p = 0.30). receiver operator curve (ROC) curve analysis revealed that area under curve was 0.731 for PV. Correlation analysis revealed that PV was significantly associated with estimated fetal weight (r = 0.319, p = 0.003), biparietal diameter (r = 0.346, p = 0.002), head circumference (r = 0.269, p = 0.019), abdominal circumference (r = 0.344, p = 0.002) and femur length (r = 0.328, p = 0.004). PV was inversely related to the umbilical artery pulsatility index (r = - 0.244, p = 0.017). To the best of our knowledge, this is the first study evaluating volumetric MGV in IUGR placentas by comparing them with healthy pregnancies. Our study showed that PV diminishes significantly in IUGR pregnancies, whereas volumetric MGV does not alter significantly. PMID:25409488

  8. Computationally efficient storage of 3D particle intensity and position data for use in 3D PIV and 3D PTV

    NASA Astrophysics Data System (ADS)

    Atkinson, C.; Buchmann, N. A.; Soria, J.

    2013-11-01

    Three-dimensional (3D) volumetric velocity measurement techniques, such as tomographic or holographic particle image velocimetry (PIV), rely upon the computationally intensive formation, storage and localized interrogation of multiple 3D particle intensity fields. Calculation of a single velocity field typically requires the extraction of particle intensities into tens of thousands of 3D sub-volumes or discrete particle clusters, the processing of which can significantly affect the performance of 3D cross-correlation based PIV and 3D particle tracking velocimetry (PTV). In this paper, a series of popular and customized volumetric data formats are presented and investigated using synthetic particle volumes and experimental data arising from tomographic PIV measurements of a turbulent boundary layer. Results show that the use of a sub-grid ordered non-zero intensity format with a sub-grid size of 16 × 16 × 16 points provides the best performance for cross-correlation based PIV analysis, while a particle clustered non-zero intensity format provides the best format for PTV applications. In practical tomographic PIV measurements the sub-grid ordered non-zero intensity format offered a 29% improvement in reconstruction times, while providing a 93% reduction in volume data requirements and a 28% overall improvement in cross-correlation based velocity analysis and validation times.

  9. Intraoperative patient registration using volumetric true 3D ultrasound without fiducials

    PubMed Central

    Ji, Songbai; Roberts, David W.; Hartov, Alex; Paulsen, Keith D.

    2012-01-01

    Purpose: Accurate patient registration is crucial for effective image-guidance in open cranial surgery. Typically, it is accomplished by matching skin-affixed fiducials manually identified in the operating room (OR) with their counterparts in the preoperative images, which not only consumes OR time and personnel resources but also relies on the presence (and subsequent fixation) of the fiducials during the preoperative scans (until the procedure begins). In this study, the authors present a completely automatic, volumetric image-based patient registration technique that does not rely on fiducials by registering tracked (true) 3D ultrasound (3DUS) directly with preoperative magnetic resonance (MR) images. Methods: Multistart registrations between binary 3DUS and MR volumes were first executed to generate an initial starting point without incorporating prior information on the US transducer contact point location or orientation for subsequent registration between grayscale 3DUS and MR via maximization of either mutual information (MI) or correlation ratio (CR). Patient registration was then computed through concatenation of spatial transformations. Results: In ten (N = 10) patient cases, an average fiducial (marker) distance error (FDE) of 5.0 mm and 4.3 mm was achieved using MI or CR registration (FDE was smaller with CR vs MI in eight of ten cases), which are comparable to values reported for typical fiducial- or surface-based patient registrations. The translational and rotational capture ranges were found to be 24.0 mm and 27.0° for binary registrations (up to 32.8 mm and 36.4°), 12.2 mm and 25.6° for MI registrations (up to 18.3 mm and 34.4°), and 22.6 mm and 40.8° for CR registrations (up to 48.5 mm and 65.6°), respectively. The execution time to complete a patient registration was 12–15 min with parallel processing, which can be significantly reduced by confining the 3DUS transducer location to the center of craniotomy in MR before registration (an

  10. In vitro in-stent restenoses evaluated by 3D ultrasound.

    PubMed

    Lécart, Myriam; Cardinal, Marie-Hélène Roy; Qin, Zhao; Soulez, Gilles; Cloutier, Guy

    2009-02-01

    The purpose of this study was to quantify in-stent restenoses with 3D B mode and power Doppler ultrasound (U.S.) imaging. In-stent restenoses were mimicked with vascular phantoms in which a nonferromagnetic prototype stent (Boston Scientific) and a ferromagnetic clinical stainless steel stent (Palmaz P295) were embedded. Each phantom had an 80% in-stent stenosis and a 75% stenosis located outside the stent. These phantoms were compared to a reference phantom reproducing both stenoses without stent. Data sets of 2D cross-sectional U.S. images were acquired in freehand scanning using a magnetic sensor attached to the U.S. probe and in mechanical linear scanning with the probe attached to a step motor device. Each 2D image was automatically segmented before 3D reconstruction of the vessel. Results indicate that the reference phantom (without stent) was accurately assessed with errors below 1.8% for the 75% stenosis and 3.2% for the 80% stenosis in both B mode and power Doppler for the two scanning methods. The 80% in-stent stenoses in Boston Scientific and Palmaz stents were, respectively, evaluated at 73.8 (+/-3.2)% and 75.8 (+/- 3)% in B mode and at 82 (+/- 2.5)% and 86.2 (+/- 6.4)% in power Doppler when freehand scans were used. For comparison, when linear scans were selected, in-stent stenoses in the Boston Scientific or Palmaz stent were, respectively, evaluated at 77.4 (+/- 2.0)% and 73.8 (+/- 2.5)% in B mode and at 87.0 (+/- 1.3)% and 85.6 (+/- 5.8)% in power Doppler. To conclude, 3D freehand U.S. is a valuable method to quantify in-stent restenoses, particularly in B mode. It is thus hoped that, in the clinical setting, noninvasive 3D U.S. may provide sufficient precision to grade in-stent restenoses. PMID:19291990

  11. Histological Evaluation of 3D MRI-Guided Transurethral Ultrasound Therapy in the Prostate

    NASA Astrophysics Data System (ADS)

    Vedula, Siddharth; Boyes, Aaron; Chopra, Rajiv; Bronskill, Michael

    2010-03-01

    Previous work from our group has shown that transurethral ultrasound therapy, with a single ultrasound transducer guided by temperature feedback from a single MRI plane (slice), can be used to treat a targeted region accurately in the prostate gland. We have extended this approach to a larger, 3D, targeted volume within the prostate, using a multi-element transducer controlled concurrently by temperature feedback from multiple imaging planes. Animals were placed supine in a 1.5 T clinical MRI, and the transurethral heating device was positioned with image guidance. A four-element transducer (each element was 5 mm long, operating at ˜8 MHz) was rotated to treat a targeted volume around the device. Temperature maps transverse to each element were acquired during heating and used to control the acoustic power of each element and the rate of rotation of the device. T2-weighted and contrast-enhanced (CE) MR images were obtained pre- and post-heating. Following the treatment, prostates were removed and fixed, axially sliced, stained with H&E, and digitally imaged at high-resolution to outline boundaries of cell death. Slice alignment and image registration techniques were developed to enable quantitative comparison of the axial MRI images and matching histological sections. Prostate sections showed clear regions of coagulative necrosis, extending ˜20 mm along the urethra, which correlated well with CE MRI data and transducer length. After registration, the outer border of coagulative necrosis on H&E conformed well to the target isotherm, similar to results from our previous (single element) acute studies. These results confirm that our previous analysis techniques for a single transducer can be extended to multiple elements, and that a large volumetric ablation of the prostate gland is feasible with a high degree of accuracy.

  12. Compressed Sensing Reconstruction of 3D Ultrasound Data Using Dictionary Learning and Line-Wise Subsampling.

    PubMed

    Lorintiu, Oana; Liebgott, Hervé; Alessandrini, Martino; Bernard, Olivier; Friboulet, Denis

    2015-12-01

    In this paper we present a compressed sensing (CS) method adapted to 3D ultrasound imaging (US). In contrast to previous work, we propose a new approach based on the use of learned overcomplete dictionaries that allow for much sparser representations of the signals since they are optimized for a particular class of images such as US images. In this study, the dictionary was learned using the K-SVD algorithm and CS reconstruction was performed on the non-log envelope data by removing 20% to 80% of the original data. Using numerically simulated images, we evaluate the influence of the training parameters and of the sampling strategy. The latter is done by comparing the two most common sampling patterns, i.e., point-wise and line-wise random patterns. The results show in particular that line-wise sampling yields an accuracy comparable to the conventional point-wise sampling. This indicates that CS acquisition of 3D data is feasible in a relatively simple setting, and thus offers the perspective of increasing the frame rate by skipping the acquisition of RF lines. Next, we evaluated this approach on US volumes of several ex vivo and in vivo organs. We first show that the learned dictionary approach yields better performances than conventional fixed transforms such as Fourier or discrete cosine. Finally, we investigate the generality of the learned dictionary approach and show that it is possible to build a general dictionary allowing to reliably reconstruct different volumes of different ex vivo or in vivo organs. PMID:26057610

  13. Adaptive volume rendering of cardiac 3D ultrasound images: utilizing blood pool statistics

    NASA Astrophysics Data System (ADS)

    Åsen, Jon Petter; Steen, Erik; Kiss, Gabriel; Thorstensen, Anders; Rabben, Stein Inge

    2012-03-01

    In this paper we introduce and investigate an adaptive direct volume rendering (DVR) method for real-time visualization of cardiac 3D ultrasound. DVR is commonly used in cardiac ultrasound to visualize interfaces between tissue and blood. However, this is particularly challenging with ultrasound images due to variability of the signal within tissue as well as variability of noise signal within the blood pool. Standard DVR involves a global mapping of sample values to opacity by an opacity transfer function (OTF). While a global OTF may represent the interface correctly in one part of the image, it may result in tissue dropouts, or even artificial interfaces within the blood pool in other parts of the image. In order to increase correctness of the rendered image, the presented method utilizes blood pool statistics to do regional adjustments of the OTF. The regional adaptive OTF was compared with a global OTF in a dataset of apical recordings from 18 subjects. For each recording, three renderings from standard views (apical 4-chamber (A4C), inverted A4C (IA4C) and mitral valve (MV)) were generated for both methods, and each rendering was tuned to the best visual appearance by a physician echocardiographer. For each rendering we measured the mean absolute error (MAE) between the rendering depth buffer and a validated left ventricular segmentation. The difference d in MAE between the global and regional method was calculated and t-test results are reported with significant improvements for the regional adaptive method (dA4C = 1.5 +/- 0.3 mm, dIA4C = 2.5 +/- 0.4 mm, dMV = 1.7 +/- 0.2 mm, d.f. = 17, all p < 0.001). This improvement by the regional adaptive method was confirmed through qualitative visual assessment by an experienced physician echocardiographer who concluded that the regional adaptive method produced rendered images with fewer tissue dropouts and less spurious structures inside the blood pool in the vast majority of the renderings. The algorithm has been

  14. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation

    PubMed Central

    Zhou, Xuan; Castro, Nathan J.; Zhu, Wei; Cui, Haitao; Aliabouzar, Mitra; Sarkar, Kausik; Zhang, Lijie Grace

    2016-01-01

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm2 intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application. PMID:27597635

  15. Improved Human Bone Marrow Mesenchymal Stem Cell Osteogenesis in 3D Bioprinted Tissue Scaffolds with Low Intensity Pulsed Ultrasound Stimulation.

    PubMed

    Zhou, Xuan; Castro, Nathan J; Zhu, Wei; Cui, Haitao; Aliabouzar, Mitra; Sarkar, Kausik; Zhang, Lijie Grace

    2016-01-01

    3D printing and ultrasound techniques are showing great promise in the evolution of human musculoskeletal tissue repair and regeneration medicine. The uniqueness of the present study was to combine low intensity pulsed ultrasound (LIPUS) and advanced 3D printing techniques to synergistically improve growth and osteogenic differentiation of human mesenchymal stem cells (MSC). Specifically, polyethylene glycol diacrylate bioinks containing cell adhesive Arginine-Glycine-Aspartic acid-Serene (RGDS) peptide and/or nanocrystalline hydroxyapatite (nHA) were used to fabricate 3D scaffolds with different geometric patterns via novel table-top stereolithography 3D printer. The resultant scaffolds provide a highly porous and interconnected 3D environment to support cell proliferation. Scaffolds with small square pores were determined to be the optimal geometric pattern for MSC attachment and growth. The optimal LIPUS working parameters were determined to be 1.5 MHz, 20% duty cycle with 150 mW/cm(2) intensity. Results demonstrated that RGDS peptide and nHA containing 3D printed scaffolds under LIPUS treatment can greatly promote MSC proliferation, alkaline phosphatase activity, calcium deposition and total protein content. These results illustrate the effectiveness of the combination of LIPUS and biomimetic 3D printing scaffolds as a valuable combinatorial tool for improved MSC function, thus make them promising for future clinical and various regenerative medicine application. PMID:27597635

  16. 2D Ultrasound and 3D MR Image Registration of the Prostate for Brachytherapy Surgical Navigation

    PubMed Central

    Zhang, Shihui; Jiang, Shan; Yang, Zhiyong; Liu, Ranlu

    2015-01-01

    Abstract Two-dimensional (2D) ultrasound (US) images are widely used in minimally invasive prostate procedure for its noninvasive nature and convenience. However, the poor quality of US image makes it difficult to be used as guiding utility. To improve the limitation, we propose a multimodality image guided navigation module that registers 2D US images with magnetic resonance imaging (MRI) based on high quality preoperative models. A 2-step spatial registration method is used to complete the procedure which combines manual alignment and rapid mutual information (MI) optimize algorithm. In addition, a 3-dimensional (3D) reconstruction model of prostate with surrounding organs is employed to combine with the registered images to conduct the navigation. Registration accuracy is measured by calculating the target registration error (TRE). The results show that the error between the US and preoperative MR images of a polyvinyl alcohol hydrogel model phantom is 1.37 ± 0.14 mm, with a similar performance being observed in patient experiments. PMID:26448009

  17. Portable high-intensity focused ultrasound system with 3D electronic steering, real-time cavitation monitoring, and 3D image reconstruction algorithms: a preclinical study in pigs

    PubMed Central

    2014-01-01

    Purpose: The aim of this study was to evaluate the safety and accuracy of a new portable ultrasonography-guided high-intensity focused ultrasound (USg-HIFU) system with a 3-dimensional (3D) electronic steering transducer, a simultaneous ablation and imaging module, real-time cavitation monitoring, and 3D image reconstruction algorithms. Methods: To address the accuracy of the transducer, hydrophones in a water chamber were used to assess the generation of sonic fields. An animal study was also performed in five pigs by ablating in vivo thighs by single-point sonication (n=10) or volume sonication (n=10) and ex vivo kidneys by single-point sonication (n=10). Histological and statistical analyses were performed. Results: In the hydrophone study, peak voltages were detected within 1.0 mm from the targets on the y- and z-axes and within 2.0-mm intervals along the x-axis (z-axis, direction of ultrasound propagation; y- and x-axes, perpendicular to the direction of ultrasound propagation). Twenty-nine of 30 HIFU sessions successfully created ablations at the target. The in vivo porcine thigh study showed only a small discrepancy (width, 0.5-1.1 mm; length, 3.0 mm) between the planning ultrasonograms and the pathological specimens. Inordinate thermal damage was not observed in the adjacent tissues or sonic pathways in the in vivo thigh and ex vivo kidney studies. Conclusion: Our study suggests that this new USg-HIFU system may be a safe and accurate technique for ablating soft tissues and encapsulated organs. PMID:25038809

  18. Computed 3D visualisation of an extinct cephalopod using computer tomographs

    NASA Astrophysics Data System (ADS)

    Lukeneder, Alexander

    2012-08-01

    The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal.

  19. Computed 3D visualisation of an extinct cephalopod using computer tomographs

    PubMed Central

    Lukeneder, Alexander

    2012-01-01

    The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal. PMID:24850976

  20. Computed 3D visualisation of an extinct cephalopod using computer tomographs.

    PubMed

    Lukeneder, Alexander

    2012-08-01

    The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal. PMID:24850976

  1. Quantitative assessment of cancer vascular architecture by skeletonization of high-resolution 3-D contrast-enhanced ultrasound images: role of liposomes and microbubbles.

    PubMed

    Molinari, F; Meiburger, K M; Giustetto, P; Rizzitelli, S; Boffa, C; Castano, M; Terreno, E

    2014-12-01

    The accurate characterization and description of the vascular network of a cancer lesion is of paramount importance in clinical practice and cancer research in order to improve diagnostic accuracy or to assess the effectiveness of a treatment. The aim of this study was to show the effectiveness of liposomes as an ultrasound contrast agent to describe the 3-D vascular architecture of a tumor. Eight C57BL/6 mice grafted with syngeneic B16-F10 murine melanoma cells were injected with a bolus of 1,2-Distearoyl-sn-glycero-3-phosphocoline (DSPC)-based non-targeted liposomes and with a bolus of microbubbles. 3-D contrast-enhanced images of the tumor lesions were acquired in three conditions: pre-contrast, after the injection of microbubbles, and after the injection of liposomes. By using a previously developed reconstruction and characterization image processing technique, we obtained the 3-D representation of the vascular architecture in these three conditions. Six descriptive parameters of these networks were also computed: the number of vascular trees (NT), the vascular density (VD), the number of branches, the 2-D curvature measure, the number of vascular flexes of the vessels, and the 3-D curvature. Results showed that all the vascular descriptors obtained by liposome-based images were statistically equal to those obtained by using microbubbles, except the VD which was found to be lower for liposome images. All the six descriptors computed in pre-contrast conditions had values that were statistically lower than those computed in presence of contrast, both for liposomes and microbubbles. Liposomes have already been used in cancer therapy for the selective ultrasound-mediated delivery of drugs. This work demonstrated their effectiveness also as vascular diagnostic contrast agents, therefore proving that liposomes can be used as efficient "theranostic" (i.e. therapeutic 1 diagnostic) ultrasound probes. PMID:24206210

  2. Cross-Modality Validation of Acetabular Surface Models Using 3-D Ultrasound Versus Magnetic Resonance Imaging in Normal and Dysplastic Infant Hips.

    PubMed

    Diederichs, Chad; Heath, Alana; Hareendranathan, Abhilash R; Zonoobi, Dornoosh; Kuntze, Gregor; Dulai, Sukhdeep; Mabee, Myles G; Ronsky, Janet L; Jaremko, Jacob L

    2016-09-01

    Current imaging diagnosis of developmental dysplasia of the hip (DDH) in infancy relies on 2-D ultrasound (US), which is highly operator-dependent. 3-D US offers more complete, and potentially more reliable, imaging of infant hip geometry. We sought to validate the fidelity of acetabular surface models obtained by 3-D US against those obtained concurrently by magnetic resonance imaging (MRI). 3-D US and MRI scans were performed on the same d in 20 infants with normal to severely dysplastic hips (mean age, 57 d; range 13-181 d). 3-D US was performed by two observers using a Philips VL13-5 probe. Coronal 3-D multi-echo data image combination (MEDIC) magnetic resonance (MR) images (1-mm slice thickness) were obtained, usually without sedation, in a 1.5 T Siemens unit. Acetabular surface models were generated for 40 hips from 3-D US and MRI using semi-automated tracing software, separately by three observers. For each hip, the 3-D US and MRI models were co-registered to overlap as closely as possible using Amira software, and the root mean square (RMS) distances between points on the models were computed. 3-D US scans took 3.2 s each. Inter-modality variability was visually minimal. Mean RMS distance between corresponding points on the acetabular surface at 3-D US and MRI was 0.4 ± 0.3 mm, with 95% confidence interval <1 mm. Mean RMS errors for inter-observer and intra-observer comparisons were significantly less for 3-D US than for MRI, while inter-scan and inter-modality comparisons showed no significant difference. Acetabular geometry was reproduced by 3-D US surface models within 1 mm of the corresponding 3-D MRI surface model, and the 3-D US models were more reliable. This validates the fidelity of 3-D US modeling and encourages future use of 3-D US in assessing infant acetabulum anatomy, which may be useful to detect and monitor treatment of hip dysplasia. PMID:27209429

  3. Quantitative Analysis of Vascular Heterogeneity in Breast Lesions Using Contrast-Enhanced 3-D Harmonic and Subharmonic Ultrasound Imaging

    PubMed Central

    Sridharan, Anush; Eisenbrey, John R.; Machado, Priscilla; Ojeda-Fournier, Haydee; Wilkes, Annina; Sevrukov, Alexander; Mattrey, Robert F.; Wallace, Kirk; Chalek, Carl L.; Thomenius, Kai E.; Forsberg, Flemming

    2015-01-01

    Ability to visualize breast lesion vascularity and quantify the vascular heterogeneity using contrast-enhanced 3-D harmonic (HI) and subharmonic (SHI) ultrasound imaging was investigated in a clinical population. Patients (n = 134) identified with breast lesions on mammography were scanned using power Doppler imaging, contrast-enhanced 3-D HI, and 3-D SHI on a modified Logiq 9 scanner (GE Healthcare). A region of interest corresponding to ultrasound contrast agent flow was identified in 4D View (GE Medical Systems) and mapped to raw slice data to generate a map of time-intensity curves for the lesion volume. Time points corresponding to baseline, peak intensity, and washout of ultrasound contrast agent were identified and used to generate and compare vascular heterogeneity plots for malignant and benign lesions. Vascularity was observed with power Doppler imaging in 84 lesions (63 benign and 21 malignant). The 3-D HI showed flow in 8 lesions (5 benign and 3 malignant), whereas 3-D SHI visualized flow in 68 lesions (49 benign and 19 malignant). Analysis of vascular heterogeneity in the 3-D SHI volumes found benign lesions having a significant difference in vascularity between central and peripheral sections (1.71 ± 0.96 vs. 1.13 ± 0.79 dB, p < 0.001, respectively), whereas malignant lesions showed no difference (1.66 ± 1.39 vs. 1.24 ± 1.14 dB, p = 0.24), indicative of more vascular coverage. These preliminary results suggest quantitative evaluation of vascular heterogeneity in breast lesions using contrast-enhanced 3-D SHI is feasible and able to detect variations in vascularity between central and peripheral sections for benign and malignant lesions. PMID:25935933

  4. 3D thoracoscopic ultrasound volume measurement validation in an ex vivo and in vivo porcine model of lung tumours

    NASA Astrophysics Data System (ADS)

    Hornblower, V. D. M.; Yu, E.; Fenster, A.; Battista, J. J.; Malthaner, R. A.

    2007-01-01

    The purpose of this study was to validate the accuracy and reliability of volume measurements obtained using three-dimensional (3D) thoracoscopic ultrasound (US) imaging. Artificial 'tumours' were created by injecting a liquid agar mixture into spherical moulds of known volume. Once solidified, the 'tumours' were implanted into the lung tissue in both a porcine lung sample ex vivo and a surgical porcine model in vivo. 3D US images were created by mechanically rotating the thoracoscopic ultrasound probe about its long axis while the transducer was maintained in close contact with the tissue. Volume measurements were made by one observer using the ultrasound images and a manual-radial segmentation technique and these were compared with the known volumes of the agar. In vitro measurements had average accuracy and precision of 4.76% and 1.77%, respectively; in vivo measurements had average accuracy and precision of 8.18% and 1.75%, respectively. The 3D thoracoscopic ultrasound can be used to accurately and reproducibly measure 'tumour' volumes both in vivo and ex vivo.

  5. The effect of object speed and direction on the performance of 3D speckle tracking using a 3D swept-volume ultrasound probe

    NASA Astrophysics Data System (ADS)

    Harris, Emma J.; Miller, Naomi R.; Bamber, Jeffrey C.; Symonds-Tayler, J. Richard N.; Evans, Philip M.

    2011-11-01

    Three-dimensional (3D) soft tissue tracking using 3D ultrasound is of interest for monitoring organ motion during therapy. Previously we demonstrated feature tracking of respiration-induced liver motion in vivo using a 3D swept-volume ultrasound probe. The aim of this study was to investigate how object speed affects the accuracy of tracking ultrasonic speckle in the absence of any structural information, which mimics the situation in homogenous tissue for motion in the azimuthal and elevational directions. For object motion prograde and retrograde to the sweep direction of the transducer, the spatial sampling frequency increases or decreases with object speed, respectively. We examined the effect object motion direction of the transducer on tracking accuracy. We imaged a homogenous ultrasound speckle phantom whilst moving the probe with linear motion at a speed of 0-35 mm s-1. Tracking accuracy and precision were investigated as a function of speed, depth and direction of motion for fixed displacements of 2 and 4 mm. For the azimuthal direction, accuracy was better than 0.1 and 0.15 mm for displacements of 2 and 4 mm, respectively. For a 2 mm displacement in the elevational direction, accuracy was better than 0.5 mm for most speeds. For 4 mm elevational displacement with retrograde motion, accuracy and precision reduced with speed and tracking failure was observed at speeds of greater than 14 mm s-1. Tracking failure was attributed to speckle de-correlation as a result of decreasing spatial sampling frequency with increasing speed of retrograde motion. For prograde motion, tracking failure was not observed. For inter-volume displacements greater than 2 mm, only prograde motion should be tracked which will decrease temporal resolution by a factor of 2. Tracking errors of the order of 0.5 mm for prograde motion in the elevational direction indicates that using the swept probe technology speckle tracking accuracy is currently too poor to track homogenous tissue over

  6. Learning Projectile Motion with the Computer Game ``Scorched 3D``

    NASA Astrophysics Data System (ADS)

    Jurcevic, John S.

    2008-01-01

    For most of our students, video games are a normal part of their lives. We should take advantage of this medium to teach physics in a manner that is engrossing for our students. In particular, modern video games incorporate accurate physics in their game engines, and they allow us to visualize the physics through flashy and captivating graphics. I recently used the game "Scorched 3D" to help my students understand projectile motion.

  7. Computation of optimized arrays for 3-D electrical imaging surveys

    NASA Astrophysics Data System (ADS)

    Loke, M. H.; Wilkinson, P. B.; Uhlemann, S. S.; Chambers, J. E.; Oxby, L. S.

    2014-12-01

    3-D electrical resistivity surveys and inversion models are required to accurately resolve structures in areas with very complex geology where 2-D models might suffer from artefacts. Many 3-D surveys use a grid where the number of electrodes along one direction (x) is much greater than in the perpendicular direction (y). Frequently, due to limitations in the number of independent electrodes in the multi-electrode system, the surveys use a roll-along system with a small number of parallel survey lines aligned along the x-direction. The `Compare R' array optimization method previously used for 2-D surveys is adapted for such 3-D surveys. Offset versions of the inline arrays used in 2-D surveys are included in the number of possible arrays (the comprehensive data set) to improve the sensitivity to structures in between the lines. The array geometric factor and its relative error are used to filter out potentially unstable arrays in the construction of the comprehensive data set. Comparisons of the conventional (consisting of dipole-dipole and Wenner-Schlumberger arrays) and optimized arrays are made using a synthetic model and experimental measurements in a tank. The tests show that structures located between the lines are better resolved with the optimized arrays. The optimized arrays also have significantly better depth resolution compared to the conventional arrays.

  8. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization

    NASA Astrophysics Data System (ADS)

    Martínez, José M.; Jarosz, Boguslaw J.

    2015-03-01

    Thermal therapy has emerged as an independent modality of treating some tumors. In many clinics the hyperthermia, one of the thermal therapy modalities, has been used adjuvant to radio- or chemotherapy to substantially improve the clinical treatment outcomes. In this work, a methodology for building a realistic brain phantom for interstitial ultrasound low dose-rate thermal therapy of the brain is proposed. A 3D brain phantom made of the tissue mimicking material (TMM) had the acoustic and thermal properties in the 20-32 °C range, which is similar to that of a brain at 37 °C. The phantom had 10-11% by mass of bovine gelatin powder dissolved in ethylene glycol. The TMM sonicated at 1 MHz, 1.6 MHz and 2.5 MHz yielded the amplitude attenuation coefficients of 62  ±  1 dB m-1, 115  ±  4 dB m-1 and 175  ±  9 dB m-1, respectively. The density and acoustic speed determination at room temperature (~24 °C) gave 1040  ±  40 kg m-3 and 1545  ±  44 m s-1, respectively. The average thermal conductivity was 0.532 W m-1 K-1. The T1 and T2 values of the TMM were 207  ±  4 and 36.2  ±  0.4 ms, respectively. We envisage the use of our phantom for treatment planning and for quality assurance in MRI based temperature determination. Our phantom preparation methodology may be readily extended to other thermal therapy technologies.

  9. Critical assessment of intramodality 3D ultrasound imaging for prostate IGRT compared to fiducial markers

    SciTech Connect

    Meer, Skadi van der; Bloemen-van Gurp, Esther; Hermans, Jolanda; Voncken, Robert; Heuvelmans, Denys; Gubbels, Carol; Fontanarosa, Davide; Visser, Peter; Lutgens, Ludy; Gils, Francis van; Verhaegen, Frank

    2013-07-15

    Purpose: A quantitative 3D intramodality ultrasound (US) imaging system was verified for daily in-room prostate localization, and compared to prostate localization based on implanted fiducial markers (FMs).Methods: Thirteen prostate patients underwent multiple US scans during treatment. A total of 376 US-scans and 817 matches were used to determine the intra- and interoperator variability. Additionally, eight other patients underwent daily prostate localization using both US and electronic portal imaging (EPI) with FMs resulting in 244 combined US-EPI scans. Scanning was performed with minimal probe pressure and a correction for the speed of sound aberration was performed. Uncertainties of both US and FM methods were assessed. User variability of the US method was assessed.Results: The overall US user variability is 2.6 mm. The mean differences between US and FM are: 2.5 {+-} 4.0 mm (LR), 0.6 {+-} 4.9 mm (SI), and -2.3 {+-} 3.6 mm (AP). The intramodality character of this US system mitigates potential errors due to transducer pressure and speed of sound aberrations.Conclusions: The overall accuracy of US (3.0 mm) is comparable to our FM workflow (2.2 mm). Since neither US nor FM can be considered a gold standard no conclusions can be drawn on the superiority of either method. Because US imaging captures the prostate itself instead of surrogates no invasive procedure is required. It requires more effort to standardize US imaging than FM detection. Since US imaging does not involve a radiation burden, US prostate imaging offers an alternative for FM EPI positioning.

  10. New fabrication techniques for ring-array transducers for real-time 3D intravascular ultrasound.

    PubMed

    Light, Edward D; Lieu, Victor; Smith, Stephen W

    2009-10-01

    We have previously described miniature 2D array transducers integrated into a Cook Medical, Inc. vena cava filter deployment device. While functional, the fabrication technique was very labor intensive and did not lend itself well to efficient fabrication of large numbers of devices. We developed two new fabrication methods that we believe can be used to efficiently manufacture these types of devices in greater than prototype numbers. One transducer consisted of 55 elements operating near 5 MHz. The interelement spacing is 0.20 mm. It was constructed on a flat piece of copper-clad polyimide and then wrapped around an 11 French catheter of a Cook Medical, Inc. inferior vena cava (IVC) filter deployment device. We used a braided wiring technology from Tyco Electronics Corp. to connect the elements to our real-time 3D ultrasound scanner. Typical measured transducer element bandwidth was 20% centered at 4.7 MHz and the 50 Omega round trip insertion loss was --82 dB. The mean of the nearest neighbor cross talk was -37.0 dB. The second method consisted of a 46-cm long single layer flex circuit from MicroConnex that terminates in an interconnect that plugs directly into our system cable. This transducer had 70 elements at 0.157 mm interelement spacing operating at 4.8 MHz. Typical measured transducer element bandwidth was 29% and the 50 Omega round trip insertion loss was -83 dB. The mean of the nearest neighbor cross talk was -33.0 dB. PMID:20458877

  11. A 2D to 3D ultrasound image registration algorithm for robotically assisted laparoscopic radical prostatectomy

    NASA Astrophysics Data System (ADS)

    Esteghamatian, Mehdi; Pautler, Stephen E.; McKenzie, Charles A.; Peters, Terry M.

    2011-03-01

    Robotically assisted laparoscopic radical prostatectomy (RARP) is an effective approach to resect the diseased organ, with stereoscopic views of the targeted tissue improving the dexterity of the surgeons. However, since the laparoscopic view acquires only the surface image of the tissue, the underlying distribution of the cancer within the organ is not observed, making it difficult to make informed decisions on surgical margins and sparing of neurovascular bundles. One option to address this problem is to exploit registration to integrate the laparoscopic view with images of pre-operatively acquired dynamic contrast enhanced (DCE) MRI that can demonstrate the regions of malignant tissue within the prostate. Such a view potentially allows the surgeon to visualize the location of the malignancy with respect to the surrounding neurovascular structures, permitting a tissue-sparing strategy to be formulated directly based on the observed tumour distribution. If the tumour is close to the capsule, it may be determined that the adjacent neurovascular bundle (NVB) needs to be sacrificed within the surgical margin to ensure that any erupted tumour was resected. On the other hand, if the cancer is sufficiently far from the capsule, one or both NVBs may be spared. However, in order to realize such image integration, the pre-operative image needs to be fused with the laparoscopic view of the prostate. During the initial stages of the operation, the prostate must be tracked in real time so that the pre-operative MR image remains aligned with patient coordinate system. In this study, we propose and investigate a novel 2D to 3D ultrasound image registration algorithm to track the prostate motion with an accuracy of 2.68+/-1.31mm.

  12. GPU accelerated registration of a statistical shape model of the lumbar spine to 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Khallaghi, Siavash; Abolmaesumi, Purang; Gong, Ren Hui; Chen, Elvis; Gill, Sean; Boisvert, Jonathan; Pichora, David; Borschneck, Dan; Fichtinger, Gabor; Mousavi, Parvin

    2011-03-01

    We present a parallel implementation of a statistical shape model registration to 3D ultrasound images of the lumbar vertebrae (L2-L4). Covariance Matrix Adaptation Evolution Strategy optimization technique, along with Linear Correlation of Linear Combination similarity metric have been used, to improve the robustness and capture range of the registration approach. Instantiation and ultrasound simulation have been implemented on a graphics processing unit for a faster registration. Phantom studies show a mean target registration error of 3.2 mm, while 80% of all the cases yield target registration error of below 3.5 mm.

  13. Non-rigid registration between 3D ultrasound and CT images of the liver based on intensity and gradient information

    NASA Astrophysics Data System (ADS)

    Lee, Duhgoon; Nam, Woo Hyun; Lee, Jae Young; Ra, Jong Beom

    2011-01-01

    In order to utilize both ultrasound (US) and computed tomography (CT) images of the liver concurrently for medical applications such as diagnosis and image-guided intervention, non-rigid registration between these two types of images is an essential step, as local deformation between US and CT images exists due to the different respiratory phases involved and due to the probe pressure that occurs in US imaging. This paper introduces a voxel-based non-rigid registration algorithm between the 3D B-mode US and CT images of the liver. In the proposed algorithm, to improve the registration accuracy, we utilize the surface information of the liver and gallbladder in addition to the information of the vessels inside the liver. For an effective correlation between US and CT images, we treat those anatomical regions separately according to their characteristics in US and CT images. Based on a novel objective function using a 3D joint histogram of the intensity and gradient information, vessel-based non-rigid registration is followed by surface-based non-rigid registration in sequence, which improves the registration accuracy. The proposed algorithm is tested for ten clinical datasets and quantitative evaluations are conducted. Experimental results show that the registration error between anatomical features of US and CT images is less than 2 mm on average, even with local deformation due to different respiratory phases and probe pressure. In addition, the lesion registration error is less than 3 mm on average with a maximum of 4.5 mm that is considered acceptable for clinical applications.

  14. Elsevier Trophoblast Research Award Lecture: Searching for an early pregnancy 3-D morphometric ultrasound marker to predict fetal growth restriction.

    PubMed

    Collins, S L; Stevenson, G N; Noble, J A; Impey, L

    2013-03-01

    Fetal growth restriction (FGR) is a major cause of perinatal morbidity and mortality, even in term babies. An effective screening test to identify pregnancies at risk of FGR, leading to increased antenatal surveillance with timely delivery, could decrease perinatal mortality and morbidity. Placental volume, measured with commercially available packages and a novel, semi-automated technique, has been shown to predict small for gestational age babies. Placental morphology measured in 2-D in the second trimester and ex-vivo post delivery, correlates with FGR. This has also been investigated using 2-D estimates of diameter and site of cord insertion obtained using the Virtual Organ Computer-aided AnaLysis (VOCAL) software. Data is presented describing a pilot study of a novel 3-D method for defining compactness of placental shape. We prospectively recruited women with a singleton pregnancy and BMI of <35. A 3-D ultrasound scan was performed between 11 and 13 + 6 weeks' gestation. The placental volume, total placental surface area and the area of the utero-placental interface were calculated using our validated technique. From these we generated dimensionless indices including sphericity (ψ), standardised placental volume (sPlaV) and standardised functional area (sFA) using Buckingham π theorem. The marker for FGR used was small for gestational age, defined as <10th customised birth weight centile (cSGA). Regression analysis examined which of the morphometric indices were independent predictors of cSGA. Data were collected for 143 women, 20 had cSGA babies. Only sPlaV and sFA were significantly correlated to birth weight (p < 0.001). Regression demonstrated all dimensionless indices were inter-dependent co-factors. ROC curves showed no advantage for using sFA over the simpler sPlaV. The generated placental indices are not independent of placental volume this early in gestation. It is hoped that another placental ultrasound marker based on vascularity can improve the

  15. Implementation Of True 3D Cursors In Computer Graphics

    NASA Astrophysics Data System (ADS)

    Butts, David R.; McAllister, David F.

    1988-06-01

    The advances in stereoscopic image display techniques have shown an increased need for real-time interaction with the three-dimensional image. We have developed a prototype real-time stereoscopic cursor to investigate this interaction. The results have pointed out areas where hardware speeds are a limiting factor, as well as areas where various methodologies cause perceptual difficulties. This paper addresses the psychological and perceptual anomalies involved in stereo image techniques, cursor generation and motion, and the use of the device as a 3D drawing and depth measuring tool.

  16. FINAL INTERIM REPORT, CANDIDATE SITES, MACHINES IN USE, DATA STORAGE AND TRANSMISSION METHODS: TESTING FEASIBILITY OF 3D ULTRASOUND DATA ACQUISITION AND RELIABILITY OF DATA RETRIEVAL FROM STORED 3D IMAGES

    EPA Science Inventory

    The purpose of this Work Assignment, 02-03, is to examine the feasibility of collecting transmitting, and analyzing 3-D ultrasound data in the context of a multi-center study of pregnant women. The study will also examine the reliability of measurements obtained from 3-D images< ...

  17. Register cardiac fiber orientations from 3D DTI volume to 2D ultrasound image of rat hearts

    NASA Astrophysics Data System (ADS)

    Qin, Xulei; Wang, Silun; Shen, Ming; Zhang, Xiaodong; Lerakis, Stamatios; Wagner, Mary B.; Fei, Baowei

    2015-03-01

    Two-dimensional (2D) ultrasound or echocardiography is one of the most widely used examinations for the diagnosis of cardiac diseases. However, it only supplies the geometric and structural information of the myocardium. In order to supply more detailed microstructure information of the myocardium, this paper proposes a registration method to map cardiac fiber orientations from three-dimensional (3D) magnetic resonance diffusion tensor imaging (MR-DTI) volume to the 2D ultrasound image. It utilizes a 2D/3D intensity based registration procedure including rigid, log-demons, and affine transformations to search the best similar slice from the template volume. After registration, the cardiac fiber orientations are mapped to the 2D ultrasound image via fiber relocations and reorientations. This method was validated by six images of rat hearts ex vivo. The evaluation results indicated that the final Dice similarity coefficient (DSC) achieved more than 90% after geometric registrations; and the inclination angle errors (IAE) between the mapped fiber orientations and the gold standards were less than 15 degree. This method may provide a practical tool for cardiologists to examine cardiac fiber orientations on ultrasound images and have the potential to supply additional information for diagnosis of cardiac diseases.

  18. Efficient sensitivity computations in 3D air quality models

    NASA Astrophysics Data System (ADS)

    Kioutsioukis, Ioannis; Melas, Dimitrios; Zerefos, Christos; Ziomas, Ioannis

    2005-04-01

    The prediction of ground level ozone for air quality monitoring and assessment is simulated through an integrated system of gridded models (meteorological, photochemical), where the atmosphere is represented with a three-dimensional grid that may include thousands of grid cells. The continuity equation solved by the Photochemical Air Quality Model (PAQM) reproduces the atmospheric processes (dynamical, physical, chemical and radiative), such as moving and mixing air parcels from one grid cell to another, calculating chemical reactions, injecting new emissions. The whole modeling procedure includes several sources of uncertainty, especially in the large data sets that describe the status of the domain (boundary conditions, emissions, chemical reaction rates and several others). The robustness of the photochemical simulation is addressed in this work through the deterministic approach of sensitivity analysis. The automatic differentiation tool ADIFOR is applied on the 3D PAQM CAMx and augments its Fortran 77 code by introducing new lines of code that additionally calculate, in only one run, the gradient of the solution vector with respect to its input parameters. The applicability of the approach is evaluated through a sensitivity study of the modeled concentrations to perturbations at the boundary conditions and the emissions, for three essentially dissimilar European Metropolises of the Auto-Oil II programme (Athens, Milan, and London).

  19. Multi-modality fusion of CT, 3D ultrasound, and tracked strain images for breast irradiation planning

    NASA Astrophysics Data System (ADS)

    Foroughi, Pezhman; Csoma, Csaba; Rivaz, Hassan; Fichtinger, Gabor; Zellars, Richard; Hager, Gregory; Boctor, Emad

    2009-02-01

    Breast irradiation significantly reduces the risk of recurrence of cancer. There is growing evidence suggesting that irradiation of only the involved area of the breast, partial breast irradiation (PBI), is as effective as whole breast irradiation. Benefits of PBI include shortened treatment time, and perhaps fewer side effects as less tissue is treated. However, these benefits cannot be realized without precise and accurate localization of the lumpectomy cavity. Several studies have shown that accurate delineation of the cavity in CT scans is very challenging and the delineated volumes differ dramatically over time and among users. In this paper, we propose utilizing 3D ultrasound (3D-US) and tracked strain images as complementary modalities to reduce uncertainties associated with current CT planning workflow. We present the early version of an integrated system that fuses 3D-US and real-time strain images. For the first time, we employ tracking information to reduce the noise in calculation of strain image by choosing the properly compressed frames and to position the strain image within the ultrasound volume. Using this system, we provide the tools to retrieve additional information from 3D-US and strain image alongside the CT scan. We have preliminarily evaluated our proposed system in a step-by-step fashion using a breast phantom and clinical experiments.

  20. 3D optical imagery for motion compensation in a limb ultrasound system

    NASA Astrophysics Data System (ADS)

    Ranger, Bryan J.; Feigin, Micha; Zhang, Xiang; Mireault, Al; Raskar, Ramesh; Herr, Hugh M.; Anthony, Brian W.

    2016-04-01

    Conventional processes for prosthetic socket fabrication are heavily subjective, often resulting in an interface to the human body that is neither comfortable nor completely functional. With nearly 100% of amputees reporting that they experience discomfort with the wearing of their prosthetic limb, designing an effective interface to the body can significantly affect quality of life and future health outcomes. Active research in medical imaging and biomechanical tissue modeling of residual limbs has led to significant advances in computer aided prosthetic socket design, demonstrating an interest in moving toward more quantifiable processes that are still patient-specific. In our work, medical ultrasonography is being pursued to acquire data that may quantify and improve the design process and fabrication of prosthetic sockets while greatly reducing cost compared to an MRI-based framework. This paper presents a prototype limb imaging system that uses a medical ultrasound probe, mounted to a mechanical positioning system and submerged in a water bath. The limb imaging is combined with three-dimensional optical imaging for motion compensation. Images are collected circumferentially around the limb and combined into cross-sectional axial image slices, resulting in a compound image that shows tissue distributions and anatomical boundaries similar to magnetic resonance imaging. In this paper we provide a progress update on our system development, along with preliminary results as we move toward full volumetric imaging of residual limbs for prosthetic socket design. This demonstrates a novel multi-modal approach to residual limb imaging.

  1. Phase grouping-based needle segmentation in 3-D trans-rectal ultrasound-guided prostate trans-perineal therapy.

    PubMed

    Qiu, Wu; Yuchi, Ming; Ding, Mingyue

    2014-04-01

    A robust and efficient needle segmentation method used to localize and track the needle in 3-D trans-rectal ultrasound (TRUS)-guided prostate therapy is proposed. The algorithmic procedure begins by cropping the 3-D US image containing a needle; then all voxels in the cropped 3-D image are grouped into different line support regions (LSRs) based on the outer product of the adjacent voxels' gradient vector. Two different needle axis extraction methods in the candidate LSR are presented: least-squares fitting and 3-D randomized Hough transform. Subsequent local optimization refines the position of the needle axis. Finally, the needle endpoint is localized by finding an intensity drop along the needle axis. The proposed methods were validated with 3-D TRUS tissue-mimicking agar phantom images, chicken breast phantom images and patient images obtained during prostate cryotherapy. The results of the in vivo test indicate that our method can localize the needle accurately and robustly with a needle endpoint localization accuracy <1.43 mm and detection accuracy >84%, which are favorable for 3-D TRUS-guided prostate trans-perineal therapy. PMID:24462163

  2. Fast 3D dark-field reflection-mode photoacoustic microscopy in vivo with a 30-MHz ultrasound linear array

    PubMed Central

    Song, Liang; Maslov, Konstantin; Bitton, Rachel; Shung, K. Kirk; Wang, Lihong V.

    2009-01-01

    We present an in vivo dark-field reflection-mode photoacoustic microscopy system that performs cross-sectional (B-scan) imaging at 50 Hz with realtime beamforming and 3D imaging consisting of 166 B-scan frames at 1 Hz with post-beamforming. To our knowledge, this speed is currently the fastest in photoacoustic imaging. A custom-designed light delivery system is integrated with a 30-MHz ultrasound linear array to realize dark-field reflection-mode imaging. Linear mechanical scanning of the array produces 3D images. The system has axial, lateral, and elevational resolutions of 25, 70, and 200 μm, respectively, and can image 3 mm deep in scattering biological tissues. Volumetric images of subcutaneous vasculature in rats are demonstrated in vivo. Fast 3D photoacoustic microscopy is anticipated to facilitate applications of photoacoustic imaging in biomedical studies that involve dynamics and clinical procedures that demand immediate diagnosis. PMID:19021408

  3. The 3d International Workshop on Computational Electronics

    NASA Astrophysics Data System (ADS)

    Goodnick, Stephen M.

    1994-09-01

    The Third International Workshop on Computational Electronics (IWCE) was held at the Benson Hotel in downtown Portland, Oregon, on May 18, 19, and 20, 1994. The workshop was devoted to a broad range of topics in computational electronics related to the simulation of electronic transport in semiconductors and semiconductor devices, particularly those which use large computational resources. The workshop was supported by the National Science Foundation (NSF), the Office of Naval Research and the Army Research Office, as well as local support from the Oregon Joint Graduate Schools of Engineering and the Oregon Center for Advanced Technology Education. There were over 100 participants in the Portland workshop, of which more than one quarter represented research groups outside of the United States from Austria, Canada, France, Germany, Italy, Japan, Switzerland, and the United Kingdom. There were a total 81 papers presented at the workshop, 9 invited talks, 26 oral presentations and 46 poster presentations. The emphasis of the contributions reflected the interdisciplinary nature of computational electronics with researchers from the Chemistry, Computer Science, Mathematics, Engineering, and Physics communities participating in the workshop.

  4. Computational ocean acoustics: Advances in 3D ocean acoustic modeling

    NASA Astrophysics Data System (ADS)

    Schmidt, Henrik; Jensen, Finn B.

    2012-11-01

    The numerical model of ocean acoustic propagation developed in the 1980's are still in widespread use today, and the field of computational ocean acoustics is often considered a mature field. However, the explosive increase in computational power available to the community has created opportunities for modeling phenomena that earlier were beyond reach. Most notably, three-dimensional propagation and scattering problems have been prohibitive computationally, but are now addressed routinely using brute force numerical approaches such as the Finite Element Method, in particular for target scattering problems, where they are being combined with the traditional wave theory propagation models in hybrid modeling frameworks. Also, recent years has seen the development of hybrid approaches coupling oceanographic circulation models with acoustic propagation models, enabling the forecasting of sonar performance uncertainty in dynamic ocean environments. These and other advances made over the last couple of decades support the notion that the field of computational ocean acoustics is far from being mature. [Work supported by the Office of Naval Research, Code 321OA].

  5. Tools for 3D scientific visualization in computational aerodynamics

    NASA Technical Reports Server (NTRS)

    Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

    1989-01-01

    The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

  6. Computational 3-D Model of the Human Respiratory System

    EPA Science Inventory

    We are developing a comprehensive, morphologically-realistic computational model of the human respiratory system that can be used to study the inhalation, deposition, and clearance of contaminants, while being adaptable for age, race, gender, and health/disease status. The model ...

  7. Tensor3D: A computer graphics program to simulate 3D real-time deformation and visualization of geometric bodies

    NASA Astrophysics Data System (ADS)

    Pallozzi Lavorante, Luca; Dirk Ebert, Hans

    2008-07-01

    Tensor3D is a geometric modeling program with the capacity to simulate and visualize in real-time the deformation, specified through a tensor matrix and applied to triangulated models representing geological bodies. 3D visualization allows the study of deformational processes that are traditionally conducted in 2D, such as simple and pure shears. Besides geometric objects that are immediately available in the program window, the program can read other models from disk, thus being able to import objects created with different open-source or proprietary programs. A strain ellipsoid and a bounding box are simultaneously shown and instantly deformed with the main object. The principal axes of strain are visualized as well to provide graphical information about the orientation of the tensor's normal components. The deformed models can also be saved, retrieved later and deformed again, in order to study different steps of progressive strain, or to make this data available to other programs. The shape of stress ellipsoids and the corresponding Mohr circles defined by any stress tensor can also be represented. The application was written using the Visualization ToolKit, a powerful scientific visualization library in the public domain. This development choice, allied to the use of the Tcl/Tk programming language, which is independent on the host computational platform, makes the program a useful tool for the study of geometric deformations directly in three dimensions in teaching as well as research activities.

  8. SIMULTANEOUS BILATERAL REAL-TIME 3-D TRANSCRANIAL ULTRASOUND IMAGING AT 1 MHZ THROUGH POOR ACOUSTIC WINDOWS

    PubMed Central

    Lindsey, Brooks D.; Nicoletto, Heather A.; Bennett, Ellen R.; Laskowitz, Daniel T.; Smith, Stephen W.

    2013-01-01

    Ultrasound imaging has been proposed as a rapid, portable alternative imaging modality to examine stroke patients in pre-hospital or emergency room settings. However, in performing transcranial ultrasound examinations, 8%–29% of patients in a general population may present with window failure, in which case it is not possible to acquire clinically useful sonographic information through the temporal bone acoustic window. In this work, we describe the technical considerations, design and fabrication of low-frequency (1.2 MHz), large aperture (25.3 mm) sparse matrix array transducers for 3-D imaging in the event of window failure. These transducers are integrated into a system for real-time 3-D bilateral transcranial imaging—the ultrasound brain helmet—and color flow imaging capabilities at 1.2 MHz are directly compared with arrays operating at 1.8 MHz in a flow phantom with attenuation comparable to the in vivo case. Contrast-enhanced imaging allowed visualization of arteries of the Circle of Willis in 5 of 5 subjects and 8 of 10 sides of the head despite probe placement outside of the acoustic window. Results suggest that this type of transducer may allow acquisition of useful images either in individuals with poor windows or outside of the temporal acoustic window in the field. PMID:23415287

  9. GEO3D - Three-Dimensional Computer Model of a Ground Source Heat Pump System

    SciTech Connect

    James Menart

    2013-06-07

    This file is the setup file for the computer program GEO3D. GEO3D is a computer program written by Jim Menart to simulate vertical wells in conjunction with a heat pump for ground source heat pump (GSHP) systems. This is a very detailed three-dimensional computer model. This program produces detailed heat transfer and temperature field information for a vertical GSHP system.

  10. Performance of ultrasound based measurement of 3D displacement using a curvilinear probe for organ motion tracking

    NASA Astrophysics Data System (ADS)

    Harris, Emma J.; Miller, Naomi R.; Bamber, Jeffrey C.; Evans, Phillip M.; Symonds-Tayler, J. Richard N.

    2007-09-01

    Three-dimensional (3D) soft tissue tracking is of interest for monitoring organ motion during therapy. Our goal is to assess the tracking performance of a curvilinear 3D ultrasound probe in terms of the accuracy and precision of measured displacements. The first aim was to examine the depth dependence of the tracking performance. This is of interest because the spatial resolution varies with distance from the elevational focus and because the curvilinear geometry of the transducer causes the spatial sampling frequency to decrease with depth. Our second aim was to assess tracking performance as a function of the spatial sampling setting (low, medium or high sampling). These settings are incorporated onto 3D ultrasound machines to allow the user to control the trade-off between spatial sampling and temporal resolution. Volume images of a speckle-producing phantom were acquired before and after the probe had been moved by a known displacement (1, 2 or 8 mm). This allowed us to assess the optimum performance of the tracking algorithm, in the absence of motion. 3D speckle tracking was performed using 3D cross-correlation and sub-voxel displacements were estimated. The tracking performance was found to be best for axial displacements and poorest for elevational displacements. In general, the performance decreased with depth, although the nature of the depth dependence was complex. Under certain conditions, the tracking performance was sufficient to be useful for monitoring organ motion. For example, at the highest sampling setting, for a 2 mm displacement, good accuracy and precision (an error and standard deviation of <0.4 mm) were observed at all depths and for all directions of displacement. The trade-off between spatial sampling, temporal resolution and size of the field of view (FOV) is discussed.

  11. Recent advances in 3D computed tomography techniques for simulation and navigation in hepatobiliary pancreatic surgery.

    PubMed

    Uchida, Masafumi

    2014-04-01

    A few years ago it could take several hours to complete a 3D image using a 3D workstation. Thanks to advances in computer science, obtaining results of interest now requires only a few minutes. Many recent 3D workstations or multimedia computers are equipped with onboard 3D virtual patient modeling software, which enables patient-specific preoperative assessment and virtual planning, navigation, and tool positioning. Although medical 3D imaging can now be conducted using various modalities, including computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasonography (US) among others, the highest quality images are obtained using CT data, and CT images are now the most commonly used source of data for 3D simulation and navigation image. If the 2D source image is bad, no amount of 3D image manipulation in software will provide a quality 3D image. In this exhibition, the recent advances in CT imaging technique and 3D visualization of the hepatobiliary and pancreatic abnormalities are featured, including scan and image reconstruction technique, contrast-enhanced techniques, new application of advanced CT scan techniques, and new virtual reality simulation and navigation imaging. PMID:24464989

  12. Instantiation and registration of statistical shape models of the femur and pelvis using 3D ultrasound imaging.

    PubMed

    Barratt, Dean C; Chan, Carolyn S K; Edwards, Philip J; Penney, Graeme P; Slomczykowski, Mike; Carter, Timothy J; Hawkes, David J

    2008-06-01

    Statistical shape modelling potentially provides a powerful tool for generating patient-specific, 3D representations of bony anatomy for computer-aided orthopaedic surgery (CAOS) without the need for a preoperative CT scan. Furthermore, freehand 3D ultrasound (US) provides a non-invasive method for digitising bone surfaces in the operating theatre that enables a much greater region to be sampled compared with conventional direct-contact (i.e., pointer-based) digitisation techniques. In this paper, we describe how these approaches can be combined to simultaneously generate and register a patient-specific model of the femur and pelvis to the patient during surgery. In our implementation, a statistical deformation model (SDM) was constructed for the femur and pelvis by performing a principal component analysis on the B-spline control points that parameterise the freeform deformations required to non-rigidly register a training set of CT scans to a carefully segmented template CT scan. The segmented template bone surface, represented by a triangulated surface mesh, is instantiated and registered to a cloud of US-derived surface points using an iterative scheme in which the weights corresponding to the first five principal modes of variation of the SDM are optimised in addition to the rigid-body parameters. The accuracy of the method was evaluated using clinically realistic data obtained on three intact human cadavers (three whole pelves and six femurs). For each bone, a high-resolution CT scan and rigid-body registration transformation, calculated using bone-implanted fiducial markers, served as the gold standard bone geometry and registration transformation, respectively. After aligning the final instantiated model and CT-derived surfaces using the iterative closest point (ICP) algorithm, the average root-mean-square distance between the surfaces was 3.5mm over the whole bone and 3.7mm in the region of surgical interest. The corresponding distances after aligning the

  13. Development of a 3D patient-specific planning platform for interstitial and transurethral ultrasound thermal therapy

    NASA Astrophysics Data System (ADS)

    Prakash, Punit; Diederich, Chris J.

    2010-03-01

    Interstitial and transurethral catheter-based ultrasound devices are under development for treatment of prostate cancer and BPH, uterine fibroids, liver tumors and other soft tissue disease. Accurate 3D thermal modeling is essential for designing site-specific applicators, exploring treatment delivery strategies, and integration of patient-specific treatment planning of thermal ablations. We are developing a comprehensive 3D modeling and treatment planning platform for ultrasound ablation of tissue using catheter-based applicators. We explored the applicability of assessing thermal effects in tissue using critical temperature, thermal dose and Arrhenius thermal damage thresholds and performed a comparative analysis of dynamic tissue properties critical to accurate modeling. We used the model to assess the feasibility of automatic feedback control with MR thermometry, and demonstrated the utility of the modeling platform for 3D patient-specific treatment planning. We have identified critical temperature, thermal dose and thermal damage thresholds for assessing treatment endpoint. Dynamic changes in tissue attenuation/absorption and perfusion must be included for accurate prediction of temperature profiles and extents of the ablation zone. Lastly, we demonstrated use of the modeling platform for patient-specific treatment planning.

  14. Automatic registration between 3D intra-operative ultrasound and pre-operative CT images of the liver based on robust edge matching

    NASA Astrophysics Data System (ADS)

    Nam, Woo Hyun; Kang, Dong-Goo; Lee, Duhgoon; Lee, Jae Young; Ra, Jong Beom

    2012-01-01

    The registration of a three-dimensional (3D) ultrasound (US) image with a computed tomography (CT) or magnetic resonance image is beneficial in various clinical applications such as diagnosis and image-guided intervention of the liver. However, conventional methods usually require a time-consuming and inconvenient manual process for pre-alignment, and the success of this process strongly depends on the proper selection of initial transformation parameters. In this paper, we present an automatic feature-based affine registration procedure of 3D intra-operative US and pre-operative CT images of the liver. In the registration procedure, we first segment vessel lumens and the liver surface from a 3D B-mode US image. We then automatically estimate an initial registration transformation by using the proposed edge matching algorithm. The algorithm finds the most likely correspondences between the vessel centerlines of both images in a non-iterative manner based on a modified Viterbi algorithm. Finally, the registration is iteratively refined on the basis of the global affine transformation by jointly using the vessel and liver surface information. The proposed registration algorithm is validated on synthesized datasets and 20 clinical datasets, through both qualitative and quantitative evaluations. Experimental results show that automatic registration can be successfully achieved between 3D B-mode US and CT images even with a large initial misalignment.

  15. Computer-generated hologram for 3D scene from multi-view images

    NASA Astrophysics Data System (ADS)

    Chang, Eun-Young; Kang, Yun-Suk; Moon, KyungAe; Ho, Yo-Sung; Kim, Jinwoong

    2013-05-01

    Recently, the computer generated hologram (CGH) calculated from real existing objects is more actively investigated to support holographic video and TV applications. In this paper, we propose a method of generating a hologram of the natural 3-D scene from multi-view images in order to provide motion parallax viewing with a suitable navigation range. After a unified 3-D point source set describing the captured 3-D scene is obtained from multi-view images, a hologram pattern supporting motion-parallax is calculated from the set using a point-based CGH method. We confirmed that 3-D scenes are faithfully reconstructed using numerical reconstruction.

  16. 2D and 3D endoanal and translabial ultrasound measurement variation in normal postpartum measurements of the anal sphincter complex

    PubMed Central

    MERIWETHER, Kate V.; HALL, Rebecca J.; LEEMAN, Lawrence M.; MIGLIACCIO, Laura; QUALLS, Clifford; ROGERS, Rebecca G.

    2015-01-01

    Introduction Women may experience anal sphincter anatomy changes after vaginal or Cesarean delivery. Therefore, accurate and acceptable imaging options to evaluate the anal sphincter complex (ASC) are needed. ASC measurements may differ between translabial (TL-US) and endoanal ultrasound (EA-US) imaging and between 2D and 3D ultrasound. The objective of this analysis was to describe measurement variation between these modalities. Methods Primiparous women underwent 2D and 3D TL-US imaging of the ASC six months after a vaginal birth (VB) or Cesarean delivery (CD). A subset of women also underwent EA-US measurements. Measurements included the internal anal sphincter (IAS) thickness at proximal, mid, and distal levels and the external anal sphincter (EAS) at 3, 6, 9, and 12 o’clock positions as well as bilateral thickness of the pubovisceralis muscle (PVM). Results 433 women presented for US: 423 had TL-US and 64 had both TL-US and EA-US of the ASC. All IAS measurements were significantly thicker on TL-US than EA-US (all p<0.01), while EAS measurements were significantly thicker on EA-US (p<0.01). PVM measurements with 3D or 2D imaging were similar (p>0.20). On both TL-US and EA-US, there were multiple sites where significant asymmetry existed in left versus right measurements. Conclusion The ultrasound modality used to image the ASC introduces small but significant changes in measurements, and the direction of the bias depends on the muscle and location being imaged. PMID:25344221

  17. The spine in 3D. Computed tomographic reformation from 2D axial sections.

    PubMed

    Virapongse, C; Gmitro, A; Sarwar, M

    1986-01-01

    A new program (3D83, General Electric) was used to reformat three-dimensional (3D) images from two-dimensional (2D) computed tomographic axial scans in 18 patients who had routine scans of the spine. The 3D spine images were extremely true to life and could be rotated around all three principle axes (constituting a movie), so that an illusion of head-motion parallax was created. The benefit of 3D reformation with this program is primarily for preoperative planning. It appears that 3D can also effectively determine the patency of foraminal stenosis by reformatting in hemisections. Currently this program is subject to several drawbacks that require user interaction and long reconstruction time. With further improvement, 3D reformation will find increasing clinical applicability. PMID:3787319

  18. 3D ultrasound image guidance system used in RF uterine adenoma and uterine bleeding ablation system

    NASA Astrophysics Data System (ADS)

    Ding, Mingyue; Luo, Xiaoan; Cai, Chao; Zhou, Chengping; Fenster, Aaron

    2006-03-01

    Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese women. Many women lose their fertility from these diseases. Currently, a minimally invasive ablation system using an RF button electrode is being used in Chinese hospitals to destroy tumor cells or stop bleeding. In this paper, we report on a 3D US guidance system developed to avoid accidents or death of the patient by inaccurate localization of the tumor position during treatment. A 3D US imaging system using a rotational scanning approach of an abdominal probe was built. In order to reduce the distortion produced when the rotational axis is not collinear with the central beam of the probe, a new 3D reconstruction algorithm is used. Then, a fast 3D needle segmentation algorithm is used to find the electrode. Finally, the tip of electrode is determined along the segmented 3D needle and the whole electrode is displayed. Experiments with a water phantom demonstrated the feasibility of our approach.

  19. Fusion of ultrasound B-mode and vibro-elastography images for automatic 3D segmentation of the prostate.

    PubMed

    Mahdavi, S Sara; Moradi, Mehdi; Morris, William J; Goldenberg, S Larry; Salcudean, Septimiu E

    2012-11-01

    Prostate segmentation in B-mode images is a challenging task even when done manually by experts. In this paper we propose a 3D automatic prostate segmentation algorithm which makes use of information from both ultrasound B-mode and vibro-elastography data.We exploit the high contrast to noise ratio of vibro-elastography images of the prostate, in addition to the commonly used B-mode images, to implement a 2D Active Shape Model (ASM)-based segmentation algorithm on the midgland image. The prostate model is deformed by a combination of two measures: the gray level similarity and the continuity of the prostate edge in both image types. The automatically obtained mid-gland contour is then used to initialize a 3D segmentation algorithm which models the prostate as a tapered and warped ellipsoid. Vibro-elastography images are used in addition to ultrasound images to improve boundary detection.We report a Dice similarity coefficient of 0.87±0.07 and 0.87±0.08 comparing the 2D automatic contours with manual contours of two observers on 61 images. For 11 cases, a whole gland volume error of 10.2±2.2% and 13.5±4.1% and whole gland volume difference of -7.2±9.1% and -13.3±12.6% between 3D automatic and manual surfaces of two observers is obtained. This is the first validated work showing the fusion of B-mode and vibro-elastography data for automatic 3D segmentation of the prostate. PMID:22829391

  20. Three dimensional level set based semiautomatic segmentation of atherosclerotic carotid artery wall volume using 3D ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Hossain, Md. Murad; AlMuhanna, Khalid; Zhao, Limin; Lal, Brajesh K.; Sikdar, Siddhartha

    2014-03-01

    3D segmentation of carotid plaque from ultrasound (US) images is challenging due to image artifacts and poor boundary definition. Semiautomatic segmentation algorithms for calculating vessel wall volume (VWV) have been proposed for the common carotid artery (CCA) but they have not been applied on plaques in the internal carotid artery (ICA). In this work, we describe a 3D segmentation algorithm that is robust to shadowing and missing boundaries. Our algorithm uses distance regularized level set method with edge and region based energy to segment the adventitial wall boundary (AWB) and lumen-intima boundary (LIB) of plaques in the CCA, ICA and external carotid artery (ECA). The algorithm is initialized by manually placing points on the boundary of a subset of transverse slices with an interslice distance of 4mm. We propose a novel user defined stopping surface based energy to prevent leaking of evolving surface across poorly defined boundaries. Validation was performed against manual segmentation using 3D US volumes acquired from five asymptomatic patients with carotid stenosis using a linear 4D probe. A pseudo gold-standard boundary was formed from manual segmentation by three observers. The Dice similarity coefficient (DSC), Hausdor distance (HD) and modified HD (MHD) were used to compare the algorithm results against the pseudo gold-standard on 1205 cross sectional slices of 5 3D US image sets. The algorithm showed good agreement with the pseudo gold standard boundary with mean DSC of 93.3% (AWB) and 89.82% (LIB); mean MHD of 0.34 mm (AWB) and 0.24 mm (LIB); mean HD of 1.27 mm (AWB) and 0.72 mm (LIB). The proposed 3D semiautomatic segmentation is the first step towards full characterization of 3D plaque progression and longitudinal monitoring.

  1. Fast computation of the acoustic field for ultrasound elements.

    PubMed

    Güven, H Emre; Miller, Eric L; Cleveland, Robin O

    2009-09-01

    A fast method for computing the acoustic field of ultrasound transducers is presented with application to rectangular elements that are cylindrically focused. No closed-form solutions exist for this case but several numerical techniques have been described in the ultrasound imaging literature. Our motivation is the rapid calculation of imaging kernels for physics-based diagnostic imaging for which current methods are too computationally intensive. Here, the surface integral defining the acoustic field from a baffled piston is converted to a 3-D spatial convolution of the element surface and the Green's function. A 3-D version of the overlap-save method from digital signal processing is employed to obtain a fast computational algorithm based on spatial Fourier transforms. Further efficiency is gained by using a separable approximation to the Green's function through singular value decomposition and increasing the effective sampling rate by polyphase filtering. The tradeoff between accuracy and spatial sampling rate is explored to determine appropriate parameters for a specific transducer. Comparisons with standard tools such as Field II are presented, where nearly 2 orders of magnitude improvement in computation speed is observed for similar accuracy. PMID:19811993

  2. Predicate-Based Focus-and-Context Visualization for 3D Ultrasound.

    PubMed

    Schulte zu Berge, Christian; Baust, Maximilian; Kapoor, Ankur; Navab, Nassir

    2014-12-01

    Direct volume visualization techniques offer powerful insight into volumetric medical images and are part of the clinical routine for many applications. Up to now, however, their use is mostly limited to tomographic imaging modalities such as CT or MRI. With very few exceptions, such as fetal ultrasound, classic volume rendering using one-dimensional intensity-based transfer functions fails to yield satisfying results in case of ultrasound volumes. This is particularly due its gradient-like nature, a high amount of noise and speckle, and the fact that individual tissue types are rather characterized by a similar texture than by similar intensity values. Therefore, clinicians still prefer to look at 2D slices extracted from the ultrasound volume. In this work, we present an entirely novel approach to the classification and compositing stage of the volume rendering pipeline, specifically designed for use with ultrasonic images. We introduce point predicates as a generic formulation for integrating the evaluation of not only low-level information like local intensity or gradient, but also of high-level information, such as non-local image features or even anatomical models. Thus, we can successfully filter clinically relevant from non-relevant information. In order to effectively reduce the potentially high dimensionality of the predicate configuration space, we propose the predicate histogram as an intuitive user interface. This is augmented by a scribble technique to provide a comfortable metaphor for selecting predicates of interest. Assigning importance factors to the predicates allows for focus-and-context visualization that ensures to always show important (focus) regions of the data while maintaining as much context information as possible. Our method naturally integrates into standard ray casting algorithms and yields superior results in comparison to traditional methods in terms of visualizing a specific target anatomy in ultrasound volumes. PMID:26356952

  3. In vivo validation of a 3D ultrasound system for imaging the lateral ventricles of neonates

    NASA Astrophysics Data System (ADS)

    Kishimoto, J.; Fenster, A.; Chen, N.; Lee, D.; de Ribaupierre, S.

    2014-03-01

    Dilated lateral ventricles in neonates can be due to many different causes, such as brain loss, or congenital malformation; however, the main cause is hydrocephalus, which is the accumulation of fluid within the ventricular system. Hydrocephalus can raise intracranial pressure resulting in secondary brain damage, and up to 25% of patients with severely enlarged ventricles have epilepsy in later life. Ventricle enlargement is clinically monitored using 2D US through the fontanels. The sensitivity of 2D US to dilation is poor because it cannot provide accurate measurements of irregular volumes such as the ventricles, so most clinical evaluations are of a qualitative nature. We developed a 3D US system to image the cerebral ventricles of neonates within the confines of incubators that can be easily translated to more open environments. Ventricle volumes can be segmented from these images giving a quantitative volumetric measurement of ventricle enlargement without moving the patient into an imaging facility. In this paper, we report on in vivo validation studies: 1) comparing 3D US ventricle volumes before and after clinically necessary interventions removing CSF, and 2) comparing 3D US ventricle volumes to those from MRI. Post-intervention ventricle volumes were less than pre-intervention measurements for all patients and all interventions. We found high correlations (R = 0.97) between the difference in ventricle volume and the reported removed CSF with the slope not significantly different than 1 (p < 0.05). Comparisons between ventricle volumes from 3D US and MR images taken 4 (±3.8) days of each other did not show significant difference (p=0.44) between 3D US and MRI through paired t-test.

  4. Prostate boundary segmentation from ultrasound images using 2D active shape models: optimisation and extension to 3D.

    PubMed

    Hodge, Adam C; Fenster, Aaron; Downey, Dónal B; Ladak, Hanif M

    2006-12-01

    Boundary outlining, or segmentation, of the prostate is an important task in diagnosis and treatment planning for prostate cancer. This paper describes an algorithm based on two-dimensional (2D) active shape models (ASM) for semi-automatic segmentation of the prostate boundary from ultrasound images. Optimisation of the 2D ASM for prostatic ultrasound was done first by examining ASM construction and image search parameters. Extension of the algorithm to three-dimensional (3D) segmentation was then done using rotational-based slicing. Evaluation of the 3D segmentation algorithm used distance- and volume-based error metrics to compare algorithm generated boundary outlines to gold standard (manually generated) boundary outlines. Minimum description length landmark placement for ASM construction, and specific values for constraints and image search were found to be optimal. Evaluation of the algorithm versus gold standard boundaries found an average mean absolute distance of 1.09+/-0.49 mm, an average percent absolute volume difference of 3.28+/-3.16%, and a 5x speed increase versus manual segmentation. PMID:16930764

  5. Electro-holography display using computer generated hologram of 3D objects based on projection spectra

    NASA Astrophysics Data System (ADS)

    Huang, Sujuan; Wang, Duocheng; He, Chao

    2012-11-01

    A new method of synthesizing computer-generated hologram of three-dimensional (3D) objects is proposed from their projection images. A series of projection images of 3D objects are recorded with one-dimensional azimuth scanning. According to the principles of paraboloid of revolution in 3D Fourier space and 3D central slice theorem, spectra information of 3D objects can be gathered from their projection images. Considering quantization error of horizontal and vertical directions, the spectrum information from each projection image is efficiently extracted in double circle and four circles shape, to enhance the utilization of projection spectra. Then spectra information of 3D objects from all projection images is encoded into computer-generated hologram based on Fourier transform using conjugate-symmetric extension. The hologram includes 3D information of objects. Experimental results for numerical reconstruction of the CGH at different distance validate the proposed methods and show its good performance. Electro-holographic reconstruction can be realized by using an electronic addressing reflective liquid-crystal display (LCD) spatial light modulator. The CGH from the computer is loaded onto the LCD. By illuminating a reference light from a laser source to the LCD, the amplitude and phase information included in the CGH will be reconstructed due to the diffraction of the light modulated by the LCD.

  6. SU-E-J-135: An Investigation of Ultrasound Imaging for 3D Intra-Fraction Prostate Motion Estimation

    SciTech Connect

    O'Shea, T; Harris, E; Bamber, J; Evans, P

    2014-06-01

    Purpose: This study investigates the use of a mechanically swept 3D ultrasound (US) probe to estimate intra-fraction motion of the prostate during radiation therapy using an US phantom and simulated transperineal imaging. Methods: A 3D motion platform was used to translate an US speckle phantom while simulating transperineal US imaging. Motion patterns for five representative types of prostate motion, generated from patient data previously acquired with a Calypso system, were using to move the phantom in 3D. The phantom was also implanted with fiducial markers and subsequently tracked using the CyberKnife kV x-ray system for comparison. A normalised cross correlation block matching algorithm was used to track speckle patterns in 3D and 2D US data. Motion estimation results were compared with known phantom translations. Results: Transperineal 3D US could track superior-inferior (axial) and anterior-posterior (lateral) motion to better than 0.8 mm root-mean-square error (RMSE) at a volume rate of 1.7 Hz (comparable with kV x-ray tracking RMSE). Motion estimation accuracy was poorest along the US probe's swept axis (right-left; RL; RMSE < 4.2 mm) but simple regularisation methods could be used to improve RMSE (< 2 mm). 2D US was found to be feasible for slowly varying motion (RMSE < 0.5 mm). 3D US could also allow accurate radiation beam gating with displacement thresholds of 2 mm and 5 mm exhibiting a RMSE of less than 0.5 mm. Conclusion: 2D and 3D US speckle tracking is feasible for prostate motion estimation during radiation delivery. Since RL prostate motion is small in magnitude and frequency, 2D or a hybrid (2D/3D) US imaging approach which also accounts for potential prostate rotations could be used. Regularisation methods could be used to ensure the accuracy of tracking data, making US a feasible approach for gating or tracking in standard or hypo-fractionated prostate treatments.

  7. Real-time 3D curved needle segmentation using combined B-mode and power Doppler ultrasound.

    PubMed

    Greer, Joseph D; Adebar, Troy K; Hwang, Gloria L; Okamura, Allison M

    2014-01-01

    This paper presents a real-time segmentation method for curved needles in biological tissue based on analysis of B-mode and power Doppler images from a tracked 2D ultrasound transducer. Mechanical vibration induced by an external voice coil results in a Doppler response along the needle shaft, which is centered around the needle section in the ultrasound image. First, B-mode image analysis is performed within regions of interest indicated by the Doppler response to create a segmentation of the needle section in the ultrasound image. Next, each needle section is decomposed into a sequence of points and transformed into a global coordinate system using the tracked transducer pose. Finally, the 3D shape is reconstructed from these points. The results of this method differ from manual segmentation by 0.71 ± 0.55 mm in needle tip location and 0.38 ± 0.27 mm along the needle shaft. This method is also fast, taking 5-10 ms to run on a standard PC, and is particularly advantageous in robotic needle steering, which involves thin, curved needles with poor echogenicity. PMID:25485402

  8. Volumetry and biomechanical parameters detected by 3D and 2D ultrasound in patients with and without an abdominal aortic aneurysm.

    PubMed

    Batagini, Nayara Cioffi; Ventura, Carlos Augusto Pinto; Raghavan, Madhavan L; Chammas, Maria Cristina; Tachibana, Adriano; da Silva, Erasmo Simão

    2016-06-01

    The objective was to demonstrate the ability of ultrasound (US) with 3D properties to evaluate volumetry and biomechanical parameters of the aorta in patients with and without abdominal aortic aneurysm (AAA). Thirty-one patients with normal aortas (group 1), 46 patients with AAA measuring 3.0-5.5 cm (group 2) and 31 patients with AAA ⩾ 5.5 cm (group 3) underwent a 2D/3D-US examination of the infra-renal aorta, and the images were post-processed prior to being analyzed. In the maximum diameter, the global circumferential strain and the global maximum rotation assessed by 2D speckle-tracking algorithms were compared among the three groups. The volumetry data obtained using 3D-US from 40 AAA patients were compared with the volumetry data obtained by a contemporary computed tomography (CT) scan. The median global circumferential strain was 2.0% (interquartile range (IR): 1.0-3.0), 1.0% (IR: 1.0-2.0) and 1.0% (IR: 1.0-1.75) in groups 1, 2 and 3, respectively (p < 0.001). The median global maximum rotation decreased progressively from group 1 to group 3 (1.38º (IR: 0.77-2.13), 0.80º (IR: 0.57-1.0) and 0.50º (IR: 0.31-0.75), p < 0.001). AAA volume estimations by 3D-US correlated well with CT (R(2) = 0.76). In conclusion, US with 3D properties is non-invasive and has the potential to evaluate volumetry and biomechanical characteristics of AAA. PMID:26896335

  9. Time- and Computation-Efficient Calibration of MEMS 3D Accelerometers and Gyroscopes

    PubMed Central

    Stančin, Sara; Tomažič, Sašo

    2014-01-01

    We propose calibration methods for microelectromechanical system (MEMS) 3D accelerometers and gyroscopes that are efficient in terms of time and computational complexity. The calibration process for both sensors is simple, does not require additional expensive equipment, and can be performed in the field before or between motion measurements. The methods rely on a small number of defined calibration measurements that are used to obtain the values of 12 calibration parameters. This process enables the static compensation of sensor inaccuracies. The values detected by the 3D sensor are interpreted using a generalized 3D sensor model. The model assumes that the values detected by the sensor are equal to the projections of the measured value on the sensor sensitivity axes. Although this finding is trivial for 3D accelerometers, its validity for 3D gyroscopes is not immediately apparent; thus, this paper elaborates on this latter topic. For an example sensor device, calibration parameters were established using calibration measurements of approximately 1.5 min in duration for the 3D accelerometer and 2.5 min in duration for the 3D gyroscope. Correction of each detected 3D value using the established calibration parameters in further measurements requires only nine addition and nine multiplication operations. PMID:25123469

  10. Optimal transcostal high-intensity focused ultrasound with combined real-time 3D movement tracking and correction

    NASA Astrophysics Data System (ADS)

    Marquet, F.; Aubry, J. F.; Pernot, M.; Fink, M.; Tanter, M.

    2011-11-01

    Recent studies have demonstrated the feasibility of transcostal high intensity focused ultrasound (HIFU) treatment in liver. However, two factors limit thermal necrosis of the liver through the ribs: the energy deposition at focus is decreased by the respiratory movement of the liver and the energy deposition on the skin is increased by the presence of highly absorbing bone structures. Ex vivo ablations were conducted to validate the feasibility of a transcostal real-time 3D movement tracking and correction mode. Experiments were conducted through a chest phantom made of three human ribs immersed in water and were placed in front of a 300 element array working at 1 MHz. A binarized apodization law introduced recently in order to spare the rib cage during treatment has been extended here with real-time electronic steering of the beam. Thermal simulations have been conducted to determine the steering limits. In vivo 3D-movement detection was performed on pigs using an ultrasonic sequence. The maximum error on the transcostal motion detection was measured to be 0.09 ± 0.097 mm on the anterior-posterior axis. Finally, a complete sequence was developed combining real-time 3D transcostal movement correction and spiral trajectory of the HIFU beam, allowing the system to treat larger areas with optimized efficiency. Lesions as large as 1 cm in diameter have been produced at focus in excised liver, whereas no necroses could be obtained with the same emitted power without correcting the movement of the tissue sample.

  11. 3D non-rigid registration using surface and local salient features for transrectal ultrasound image-guided prostate biopsy

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofeng; Akbari, Hamed; Halig, Luma; Fei, Baowei

    2011-03-01

    We present a 3D non-rigid registration algorithm for the potential use in combining PET/CT and transrectal ultrasound (TRUS) images for targeted prostate biopsy. Our registration is a hybrid approach that simultaneously optimizes the similarities from point-based registration and volume matching methods. The 3D registration is obtained by minimizing the distances of corresponding points at the surface and within the prostate and by maximizing the overlap ratio of the bladder neck on both images. The hybrid approach not only capture deformation at the prostate surface and internal landmarks but also the deformation at the bladder neck regions. The registration uses a soft assignment and deterministic annealing process. The correspondences are iteratively established in a fuzzy-to-deterministic approach. B-splines are used to generate a smooth non-rigid spatial transformation. In this study, we tested our registration with pre- and postbiopsy TRUS images of the same patients. Registration accuracy is evaluated using manual defined anatomic landmarks, i.e. calcification. The root-mean-squared (RMS) of the difference image between the reference and floating images was decreased by 62.6+/-9.1% after registration. The mean target registration error (TRE) was 0.88+/-0.16 mm, i.e. less than 3 voxels with a voxel size of 0.38×0.38×0.38 mm3 for all five patients. The experimental results demonstrate the robustness and accuracy of the 3D non-rigid registration algorithm.

  12. Computing 3-D structure of rigid objects using stereo and motion

    NASA Technical Reports Server (NTRS)

    Nguyen, Thinh V.

    1987-01-01

    Work performed as a step toward an intelligent automatic machine vision system for 3-D imaging is discussed. The problem considered is the quantitative 3-D reconstruction of rigid objects. Motion and stereo are the two clues considered in this system. The system basically consists of three processes: the low level process to extract image features, the middle level process to establish the correspondence in the stereo (spatial) and motion (temporal) modalities, and the high level process to compute the 3-D coordinates of the corner points by integrating the spatial and temporal correspondences.

  13. Numerical Modeling of 3-D Dynamics of Ultrasound Contrast Agent Microbubbles Using the Boundary Integral Method

    NASA Astrophysics Data System (ADS)

    Calvisi, Michael; Manmi, Kawa; Wang, Qianxi

    2014-11-01

    Ultrasound contrast agents (UCAs) are microbubbles stabilized with a shell typically of lipid, polymer, or protein and are emerging as a unique tool for noninvasive therapies ranging from gene delivery to tumor ablation. The nonspherical dynamics of contrast agents are thought to play an important role in both diagnostic and therapeutic applications, for example, causing the emission of subharmonic frequency components and enhancing the uptake of therapeutic agents across cell membranes and tissue interfaces. A three-dimensional model for nonspherical contrast agent dynamics based on the boundary integral method is presented. The effects of the encapsulating shell are approximated by adapting Hoff's model for thin-shell, spherical contrast agents to the nonspherical case. A high-quality mesh of the bubble surface is maintained by implementing a hybrid approach of the Lagrangian method and elastic mesh technique. Numerical analyses for the dynamics of UCAs in an infinite liquid and near a rigid wall are performed in parameter regimes of clinical relevance. The results show that the presence of a coating significantly reduces the oscillation amplitude and period, increases the ultrasound pressure amplitude required to incite jetting, and reduces the jet width and velocity.

  14. Using High Frequency Focused Water-Coupled Ultrasound for 3-D Surface Depression Profiling

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Whalen, Mike F.; Hendricks, J. Lynne; Bodis, James R.

    1999-01-01

    Surface topography is an important variable in the performance of many industrial components and is normally measured with diamond-tip profilometry over a small area or using optical scattering methods for larger area measurement. A prior study was performed demonstrating that focused air-coupled ultrasound at 1 MHz was capable of profiling surfaces with 25 micron depth resolution and 400 micron lateral resolution over a 1.4 mm depth range. In this article, the question of whether higher-frequency focused water-coupled ultrasound can improve on these specifications is addressed. 10 and 25 MHz focused ultrasonic transducers were employed in the water-coupled mode. Time-of-flight images of the sample surface were acquired and converted to depth / surface profile images using the simple relation (d = V*t/2) between distance (d), time-of-flight (t), and the velocity of sound in water (V). Results are compared for the two frequencies used and with those from the 1 MHz air-coupled configuration.

  15. Computational efficient segmentation of cell nuclei in 2D and 3D fluorescent micrographs

    NASA Astrophysics Data System (ADS)

    De Vylder, Jonas; Philips, Wilfried

    2011-02-01

    This paper proposes a new segmentation technique developed for the segmentation of cell nuclei in both 2D and 3D fluorescent micrographs. The proposed method can deal with both blurred edges as with touching nuclei. Using a dual scan line algorithm its both memory as computational efficient, making it interesting for the analysis of images coming from high throughput systems or the analysis of 3D microscopic images. Experiments show good results, i.e. recall of over 0.98.

  16. 3-D field computation: The near-triumph of commerical codes

    SciTech Connect

    Turner, L.R.

    1995-07-01

    In recent years, more and more of those who design and analyze magnets and other devices are using commercial codes rather than developing their own. This paper considers the commercial codes and the features available with them. Other recent trends with 3-D field computation include parallel computation and visualization methods such as virtual reality systems.

  17. 3D-SoftChip: A Novel Architecture for Next-Generation Adaptive Computing Systems

    NASA Astrophysics Data System (ADS)

    Kim, Chul; Rassau, Alex; Lachowicz, Stefan; Lee, Mike Myung-Ok; Eshraghian, Kamran

    2006-12-01

    This paper introduces a novel architecture for next-generation adaptive computing systems, which we term 3D-SoftChip. The 3D-SoftChip is a 3-dimensional (3D) vertically integrated adaptive computing system combining state-of-the-art processing and 3D interconnection technology. It comprises the vertical integration of two chips (a configurable array processor and an intelligent configurable switch) through an indium bump interconnection array (IBIA). The configurable array processor (CAP) is an array of heterogeneous processing elements (PEs), while the intelligent configurable switch (ICS) comprises a switch block, 32-bit dedicated RISC processor for control, on-chip program/data memory, data frame buffer, along with a direct memory access (DMA) controller. This paper introduces the novel 3D-SoftChip architecture for real-time communication and multimedia signal processing as a next-generation computing system. The paper further describes the advanced HW/SW codesign and verification methodology, including high-level system modeling of the 3D-SoftChip using SystemC, being used to determine the optimum hardware specification in the early design stage.

  18. A new 3D computational model for shaped charge jet breakup

    SciTech Connect

    Zernow, L.; Chapyak, E.J.; Mosso, S.J.

    1996-09-01

    This paper reviews prior 1D and 2D axisymmetric, analytical and computational studies, as well as empirical studies of the shaped charge jet particulation problem and discusses their associated insights and problems. It proposes a new 3D computational model of the particulation process, based upon a simplified version of the observed counter-rotating, double helical surface perturbations, found on softly recovered shaped charge jet particles, from both copper and tantalum jets. This 3D approach contrasts with the random, axisymmetric surface perturbations which have previously been used, to try to infer the observed length distribution of jet particles, on the basis of the most unstable wavelength concept, which leads to the expectation of a continuous distribution of particle lengths. The 3D model, by its very nature, leads to a non-random, periodic distribution of potential initial necking loci, on alternate sides of the stretching jet. This in turn infers a potentially periodic, overlapping, multi-modal distribution of associated jet particle lengths. Since it is unlikely that all potential initial necking sites will be activated simultaneously, the 3D model also suggests that longer jet particles containing partial, but unseparated necks, should be observed fairly often. The computational analysis is in its very early stages and the problems involved in inserting the two helical grooves and in defining the initial conditions and boundary conditions for the computation will be discussed. Available initial results from the 3D computation will be discussed and interpreted.

  19. Mitigation of Variability among 3D Echocardiography-Derived Regional Strain Values Acquired by Multiple Ultrasound Systems by Vendor Independent Analysis

    PubMed Central

    Streiff, Cole; Zhu, Meihua; Shimada, Eriko; Sahn, David J.; Ashraf, Muhammad

    2016-01-01

    Introduction This study compared the variability of 3D echo derived circumferential and longitudinal strain values computed from vendor-specific and vendor-independent analyses of images acquired using ultrasound systems from different vendors. Methods Ten freshly harvested porcine hearts were studied. Each heart was mounted on a custom designed phantom and driven to simulate normal cardiac motion. Cardiac rotation was digitally controlled and held constant at 5°, while pumped stroke volume (SV) ranged from 30-70ml. Full-volume image data was acquired using three different ultrasound systems from different vendors. The image data was analyzed for longitudinal and circumferential strains (LS, CS) using both vendor-specific and vendor-independent analysis packages. Results Good linear relationships were observed for each vendor-specific analysis package for both CS and LS at the mid-anterior segment, with correlation coefficients ranging from 0.82–0.91 (CS) and 0.86–0.89 (LS). Comparable linear regressions were observed for results determined by a vendor independent program (CS: R = 0.82–0.89; LS: R = 0.86–0.89). Variability between analysis packages was examined via a series of ANOVA tests. A statistical difference was found between vendor-specific analysis packages (p<0.001), while no such difference was observed between ultrasound systems when using the vendor-independent program (p>0.05). Conclusions Circumferential and longitudinal regional strain values differ when quantified by vendor-specific analysis packages; however, this variability is mitigated by use of a vendor-independent quantification method. These results suggest that echocardiograms acquired using different ultrasound systems could be meaningfully compared using vendor-independent software. PMID:27149685

  20. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

    PubMed Central

    Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

    2012-01-01

    Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future

  1. 3D Slicer as an image computing platform for the Quantitative Imaging Network.

    PubMed

    Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V; Pieper, Steve; Kikinis, Ron

    2012-11-01

    Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open-source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future

  2. Development of 3D ultrasound needle guidance for high-dose-rate interstitial brachytherapy of gynaecological cancers

    NASA Astrophysics Data System (ADS)

    Rodgers, J.; Tessier, D.; D'Souza, D.; Leung, E.; Hajdok, G.; Fenster, A.

    2016-04-01

    High-dose-rate (HDR) interstitial brachytherapy is often included in standard-of-care for gynaecological cancers. Needles are currently inserted through a perineal template without any standard real-time imaging modality to assist needle guidance, causing physicians to rely on pre-operative imaging, clinical examination, and experience. While two-dimensional (2D) ultrasound (US) is sometimes used for real-time guidance, visualization of needle placement and depth is difficult and subject to variability and inaccuracy in 2D images. The close proximity to critical organs, in particular the rectum and bladder, can lead to serious complications. We have developed a three-dimensional (3D) transrectal US system and are investigating its use for intra-operative visualization of needle positions used in HDR gynaecological brachytherapy. As a proof-of-concept, four patients were imaged with post-insertion 3D US and x-ray CT. Using software developed in our laboratory, manual rigid registration of the two modalities was performed based on the perineal template's vaginal cylinder. The needle tip and a second point along the needle path were identified for each needle visible in US. The difference between modalities in the needle trajectory and needle tip position was calculated for each identified needle. For the 60 needles placed, the mean trajectory difference was 3.23 +/- 1.65° across the 53 visible needle paths and the mean difference in needle tip position was 3.89 +/- 1.92 mm across the 48 visible needles tips. Based on the preliminary results, 3D transrectal US shows potential for the development of a 3D US-based needle guidance system for interstitial gynaecological brachytherapy.

  3. Computing elastic moduli on 3-D X-ray computed tomography image stacks

    NASA Astrophysics Data System (ADS)

    Garboczi, E. J.; Kushch, V. I.

    2015-03-01

    A numerical task of current interest is to compute the effective elastic properties of a random composite material by operating on a 3D digital image of its microstructure obtained via X-ray computed tomography (CT). The 3-D image is usually sub-sampled since an X-ray CT image is typically of order 10003 voxels or larger, which is considered to be a very large finite element problem. Two main questions for the validity of any such study are then: can the sub-sample size be made sufficiently large to capture enough of the important details of the random microstructure so that the computed moduli can be thought of as accurate, and what boundary conditions should be chosen for these sub-samples? This paper contributes to the answer of both questions by studying a simulated X-ray CT cylindrical microstructure with three phases, cut from a random model system with known elastic properties. A new hybrid numerical method is introduced, which makes use of finite element solutions coupled with exact solutions for elastic moduli of square arrays of parallel cylindrical fibers. The new method allows, in principle, all of the microstructural data to be used when the X-ray CT image is in the form of a cylinder, which is often the case. Appendix A describes a similar algorithm for spherical sub-samples, which may be of use when examining the mechanical properties of particles. Cubic sub-samples are also taken from this simulated X-ray CT structure to investigate the effect of two different kinds of boundary conditions: forced periodic and fixed displacements. It is found that using forced periodic displacements on the non-geometrically periodic cubic sub-samples always gave more accurate results than using fixed displacements, although with about the same precision. The larger the cubic sub-sample, the more accurate and precise was the elastic computation, and using the complete cylindrical sample with the new method gave still more accurate and precise results. Fortran 90

  4. Meta!Blast computer game: a pipeline from science to 3D art to education

    NASA Astrophysics Data System (ADS)

    Schneller, William; Campbell, P. J.; Bassham, Diane; Wurtele, Eve Syrkin

    2012-03-01

    Meta!Blast (http://www.metablast.org) is designed to address the challenges students often encounter in understanding cell and metabolic biology. Developed by faculty and students in biology, biochemistry, computer science, game design, pedagogy, art and story, Meta!Blast is being created using Maya (http://usa.autodesk.com/maya/) and the Unity 3D (http://unity3d.com/) game engine, for Macs and PCs in classrooms; it has also been exhibited in an immersive environment. Here, we describe the pipeline from protein structural data and holographic information to art to the threedimensional (3D) environment to the game engine, by which we provide a publicly-available interactive 3D cellular world that mimics a photosynthetic plant cell.

  5. Automatic left-atrial segmentation from cardiac 3D ultrasound: a dual-chamber model-based approach

    NASA Astrophysics Data System (ADS)

    Almeida, Nuno; Sarvari, Sebastian I.; Orderud, Fredrik; Gérard, Olivier; D'hooge, Jan; Samset, Eigil

    2016-04-01

    In this paper, we present an automatic solution for segmentation and quantification of the left atrium (LA) from 3D cardiac ultrasound. A model-based framework is applied, making use of (deformable) active surfaces to model the endocardial surfaces of cardiac chambers, allowing incorporation of a priori anatomical information in a simple fashion. A dual-chamber model (LA and left ventricle) is used to detect and track the atrio-ventricular (AV) plane, without any user input. Both chambers are represented by parametric surfaces and a Kalman filter is used to fit the model to the position of the endocardial walls detected in the image, providing accurate detection and tracking during the whole cardiac cycle. This framework was tested in 20 transthoracic cardiac ultrasound volumetric recordings of healthy volunteers, and evaluated using manual traces of a clinical expert as a reference. The 3D meshes obtained with the automatic method were close to the reference contours at all cardiac phases (mean distance of 0.03+/-0.6 mm). The AV plane was detected with an accuracy of -0.6+/-1.0 mm. The LA volumes assessed automatically were also in agreement with the reference (mean +/-1.96 SD): 0.4+/-5.3 ml, 2.1+/-12.6 ml, and 1.5+/-7.8 ml at end-diastolic, end-systolic and pre-atrial-contraction frames, respectively. This study shows that the proposed method can be used for automatic volumetric assessment of the LA, considerably reducing the analysis time and effort when compared to manual analysis.

  6. Noninvasive Quantification of In Vitro Osteoblastic Differentiation in 3D Engineered Tissue Constructs Using Spectral Ultrasound Imaging

    PubMed Central

    Peterson, Alexis W.; Caldwell, David J.; Stegemann, Jan P.; Deng, Cheri X.

    2014-01-01

    Non-destructive monitoring of engineered tissues is needed for translation of these products from the lab to the clinic. In this study, non-invasive, high resolution spectral ultrasound imaging (SUSI) was used to monitor the differentiation of MC3T3 pre-osteoblasts seeded within collagen hydrogels. SUSI was used to measure the diameter, concentration and acoustic attenuation of scatterers within such constructs cultured in either control or osteogenic medium over 21 days. Conventional biochemical assays were used on parallel samples to determine DNA content and calcium deposition. Construct volume and morphology were accurately imaged using ultrasound. Cell diameter was estimated to be approximately 12.5–15.5 µm using SUSI, which corresponded well to measurements of fluorescently stained cells. The total number of cells per construct assessed by quantitation of DNA content decreased from 5.6±2.4×104 at day 1 to 0.9±0.2×104 at day 21. SUSI estimation of the equivalent number of acoustic scatters showed a similar decreasing trend, except at day 21 in the osteogenic samples, which showed a marked increase in both scatterer number and acoustic impedance, suggestive of mineral deposition by the differentiating MC3T3 cells. Estimation of calcium content by SUSI was 41.7±11.4 µg/ml, which agreed well with the biochemical measurement of 38.7±16.7 µg/ml. Color coded maps of parameter values were overlaid on B-mode images to show spatiotemporal changes in cell diameter and calcium deposition. This study demonstrates the use of non-destructive ultrasound imaging to provide quantitative information on the number and differentiated state of cells embedded within 3D engineered constructs, and therefore presents a valuable tool for longitudinal monitoring of engineered tissue development. PMID:24465680

  7. Noninvasive quantification of in vitro osteoblastic differentiation in 3D engineered tissue constructs using spectral ultrasound imaging.

    PubMed

    Gudur, Madhu Sudhan Reddy; Rao, Rameshwar R; Peterson, Alexis W; Caldwell, David J; Stegemann, Jan P; Deng, Cheri X

    2014-01-01

    Non-destructive monitoring of engineered tissues is needed for translation of these products from the lab to the clinic. In this study, non-invasive, high resolution spectral ultrasound imaging (SUSI) was used to monitor the differentiation of MC3T3 pre-osteoblasts seeded within collagen hydrogels. SUSI was used to measure the diameter, concentration and acoustic attenuation of scatterers within such constructs cultured in either control or osteogenic medium over 21 days. Conventional biochemical assays were used on parallel samples to determine DNA content and calcium deposition. Construct volume and morphology were accurately imaged using ultrasound. Cell diameter was estimated to be approximately 12.5-15.5 µm using SUSI, which corresponded well to measurements of fluorescently stained cells. The total number of cells per construct assessed by quantitation of DNA content decreased from 5.6±2.4×10(4) at day 1 to 0.9±0.2×10(4) at day 21. SUSI estimation of the equivalent number of acoustic scatters showed a similar decreasing trend, except at day 21 in the osteogenic samples, which showed a marked increase in both scatterer number and acoustic impedance, suggestive of mineral deposition by the differentiating MC3T3 cells. Estimation of calcium content by SUSI was 41.7±11.4 µg/ml, which agreed well with the biochemical measurement of 38.7±16.7 µg/ml. Color coded maps of parameter values were overlaid on B-mode images to show spatiotemporal changes in cell diameter and calcium deposition. This study demonstrates the use of non-destructive ultrasound imaging to provide quantitative information on the number and differentiated state of cells embedded within 3D engineered constructs, and therefore presents a valuable tool for longitudinal monitoring of engineered tissue development. PMID:24465680

  8. Computer generated holograms of 3D objects with reduced number of projections

    NASA Astrophysics Data System (ADS)

    Huang, Su-juan; Liu, Dao-jin; Zhao, Jing-jing

    2010-11-01

    A new method for synthesizing computer-generated holograms of 3D objects has been proposed with reduced number of projections. According to the principles of paraboloid of revolution in 3D Fourier space, spectra information of 3D objects is gathered from projection images. We record a series of real projection images of 3D objects under incoherent white-light illumination by circular scanning method, and synthesize interpolated projection images by motion estimation and compensation between adjacent real projection images, then extract the spectra information of the 3D objects from all projection images in circle form. Because of quantization error, information extraction in two circles form is better than in single circle. Finally hologram is encoded based on computer-generated holography using a conjugate-symmetric extension. Our method significantly reduces the number of required real projections without increasing much of the computing time of the hologram and degrading the reconstructed image. Numerical reconstruction of the hologram shows good results.

  9. Introduction of the ASP3D Computer Program for Unsteady Aerodynamic and Aeroelastic Analyses

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    2005-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The new ASP3D code is the result of a decade of developmental work on improvements to the small perturbation formulation, performed while the author was employed as a Senior Research Scientist in the Configuration Aerodynamics Branch at the NASA Langley Research Center. The ASP3D code is a significant improvement to the state-of-the-art for transonic aeroelastic analyses over the CAP-TSD code (Computational Aeroelasticity Program Transonic Small Disturbance), which was developed principally by the author in the mid-1980s. The author is in a unique position as the developer of both computer programs to compare, contrast, and ultimately make conclusions regarding the underlying formulations and utility of each code. The paper describes the salient features of the ASP3D code including the rationale for improvements in comparison with CAP-TSD. Numerous results are presented to demonstrate the ASP3D capability. The general conclusion is that the new ASP3D capability is superior to the older CAP-TSD code because of the myriad improvements developed and incorporated.

  10. Computational methods for constructing protein structure models from 3D electron microscopy maps

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. PMID:23796504

  11. Efficient curve-skeleton computation for the analysis of biomedical 3d images - biomed 2010.

    PubMed

    Brun, Francesco; Dreossi, Diego

    2010-01-01

    Advances in three dimensional (3D) biomedical imaging techniques, such as magnetic resonance (MR) and computed tomography (CT), make it easy to reconstruct high quality 3D models of portions of human body and other biological specimens. A major challenge lies in the quantitative analysis of the resulting models thus allowing a more comprehensive characterization of the object under investigation. An interesting approach is based on curve-skeleton (or medial axis) extraction, which gives basic information concerning the topology and the geometry. Curve-skeletons have been applied in the analysis of vascular networks and the diagnosis of tracheal stenoses as well as a 3D flight path in virtual endoscopy. However curve-skeleton computation is a crucial task. An effective skeletonization algorithm was introduced by N. Cornea in [1] but it lacks in computational performances. Thanks to the advances in imaging techniques the resolution of 3D images is increasing more and more, therefore there is the need for efficient algorithms in order to analyze significant Volumes of Interest (VOIs). In the present paper an improved skeletonization algorithm based on the idea proposed in [1] is presented. A computational comparison between the original and the proposed method is also reported. The obtained results show that the proposed method allows a significant computational improvement making more appealing the adoption of the skeleton representation in biomedical image analysis applications. PMID:20467122

  12. Dynamic shape modeling of the mitral valve from real-time 3D ultrasound images using continuous medial representation

    NASA Astrophysics Data System (ADS)

    Pouch, Alison M.; Yushkevich, Paul A.; Jackson, Benjamin M.; Gorman, Joseph H., III; Gorman, Robert C.; Sehgal, Chandra M.

    2012-03-01

    Purpose: Patient-specific shape analysis of the mitral valve from real-time 3D ultrasound (rt-3DUS) has broad application to the assessment and surgical treatment of mitral valve disease. Our goal is to demonstrate that continuous medial representation (cm-rep) is an accurate valve shape representation that can be used for statistical shape modeling over the cardiac cycle from rt-3DUS images. Methods: Transesophageal rt-3DUS data acquired from 15 subjects with a range of mitral valve pathology were analyzed. User-initialized segmentation with level sets and symmetric diffeomorphic normalization delineated the mitral leaflets at each time point in the rt-3DUS data series. A deformable cm-rep was fitted to each segmented image of the mitral leaflets in the time series, producing a 4D parametric representation of valve shape in a single cardiac cycle. Model fitting accuracy was evaluated by the Dice overlap, and shape interpolation and principal component analysis (PCA) of 4D valve shape were performed. Results: Of the 289 3D images analyzed, the average Dice overlap between each fitted cm-rep and its target segmentation was 0.880+/-0.018 (max=0.912, min=0.819). The results of PCA represented variability in valve morphology and localized leaflet thickness across subjects. Conclusion: Deformable medial modeling accurately captures valve geometry in rt-3DUS images over the entire cardiac cycle and enables statistical shape analysis of the mitral valve.

  13. The Ultrasound Brain Helmet: New Transducers and Volume Registration for In Vivo Simultaneous Multi-Transducer 3-D Transcranial Imaging

    PubMed Central

    Lindsey, Brooks D.; Light, Edward D.; Nicoletto, Heather A.; Bennett, Ellen R.; Laskowitz, Daniel T.; Smith, Stephen W.

    2012-01-01

    Because stroke remains an important and time-sensitive health concern in developed nations, we present a system capable of fusing 3-D transcranial ultrasound volumes acquired from two sides of the head. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging through both temporal acoustic windows, allowing for potential registration of multiple real-time 3-D scans of cerebral vasculature. We examine hardware considerations for new matrix arrays—transducer design and interconnects—in this application. Specifically, it is proposed that SNR may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented, showing cerebral arteries with and without the use of microbubble contrast agent; they have been registered and fused using a simple algorithm which maximizes normalized cross-correlation. PMID:21693401

  14. Accurate quantification of local changes for carotid arteries in 3D ultrasound images using convex optimization-based deformable registration

    NASA Astrophysics Data System (ADS)

    Cheng, Jieyu; Qiu, Wu; Yuan, Jing; Fenster, Aaron; Chiu, Bernard

    2016-03-01

    Registration of longitudinally acquired 3D ultrasound (US) images plays an important role in monitoring and quantifying progression/regression of carotid atherosclerosis. We introduce an image-based non-rigid registration algorithm to align the baseline 3D carotid US with longitudinal images acquired over several follow-up time points. This algorithm minimizes the sum of absolute intensity differences (SAD) under a variational optical-flow perspective within a multi-scale optimization framework to capture local and global deformations. Outer wall and lumen were segmented manually on each image, and the performance of the registration algorithm was quantified by Dice similarity coefficient (DSC) and mean absolute distance (MAD) of the outer wall and lumen surfaces after registration. In this study, images for 5 subjects were registered initially by rigid registration, followed by the proposed algorithm. Mean DSC generated by the proposed algorithm was 79:3+/-3:8% for lumen and 85:9+/-4:0% for outer wall, compared to 73:9+/-3:4% and 84:7+/-3:2% generated by rigid registration. Mean MAD of 0:46+/-0:08mm and 0:52+/-0:13mm were generated for lumen and outer wall respectively by the proposed algorithm, compared to 0:55+/-0:08mm and 0:54+/-0:11mm generated by rigid registration. The mean registration time of our method per image pair was 143+/-23s.

  15. Mapping and characterizing endometrial implants by registering 2D transvaginal ultrasound to 3D pelvic magnetic resonance images.

    PubMed

    Yavariabdi, Amir; Bartoli, Adrien; Samir, Chafik; Artigues, Maxime; Canis, Michel

    2015-10-01

    We propose a new deformable slice-to-volume registration method to register a 2D Transvaginal Ultrasound (TVUS) to a 3D Magnetic Resonance (MR) volume. Our main goal is to find a cross-section of the MR volume such that the endometrial implants and their depth of infiltration can be mapped from TVUS to MR. The proposed TVUS-MR registration method uses contour to surface correspondences through a novel variational one-step deformable Iterative Closest Point (ICP) method. Specifically, we find a smooth deformation field while establishing point correspondences automatically. We demonstrate the accuracy of the proposed method by quantitative and qualitative tests on both semi-synthetic and clinical data. To generate semi-synthetic data sets, 3D surfaces are deformed with 4-40% degrees of deformation and then various intersection curves are obtained at 0-20° cutting angles. Results show an average mean square error of 5.7934±0.4615mm, average Hausdorff distance of 2.493±0.14mm, and average Dice similarity coefficient of 0.9750±0.0030. PMID:26241161

  16. Models the Electromagnetic Response of a 3D Distribution using MP COMPUTERS

    1999-05-01

    EM3D models the electromagnetic response of a 3D distribution of conductivity, dielectric permittivity and magnetic permeability within the earth for geophysical applications using massively parallel computers. The simulations are carried out in the frequency domain for either electric or magnetic sources for either scattered or total filed formulations of Maxwell''s equations. The solution is based on the method of finite differences and includes absorbing boundary conditions so that responses can be modeled up into themore » radar range where wave propagation is dominant. Recent upgrades in the software include the incorporation of finite size sources, that in addition to dipolar source fields, and a low induction number preconditioner that can significantly reduce computational run times. A graphical user interface (GUI) is bundled with the software so that complicated 3D models can be easily constructed and simulated with the software. The GUI also allows for plotting of the output.« less

  17. 3-D Multiphase Segmentation of X-Ray Micro Computed Tomography Data of Geologic Materials

    NASA Astrophysics Data System (ADS)

    Tuller, M.; Kulkarni, R.; Fink, W.

    2011-12-01

    Advancements of noninvasive imaging methods such as X-Ray Computed Tomography (CT) led to a recent surge of applications in Geoscience. While substantial efforts and resources have been devoted to advance CT technology and micro-scale analysis, the development of a stable 3-D multiphase image segmentation method applicable to large datasets is lacking. To eliminate the need for wet/dry or dual energy scans, image alignment, and subtraction analysis, commonly applied in synchrotron X-Ray micro CT, a segmentation method based on a Bayesian Markov Random Field (MRF) framework amenable to true 3-D multiphase processing was developed and evaluated. Furthermore, several heuristic and deterministic combinatorial optimization schemes required to solve the labeling problem of the MRF image model were implemented and tested for computational efficiency and their impact on segmentation results. Test results for natural and artificial porous media datasets demonstrate great potential of the MRF image model for 3-D multiphase segmentation.

  18. Mechanically assisted 3D ultrasound for pre-operative assessment and guiding percutaneous treatment of focal liver tumors

    NASA Astrophysics Data System (ADS)

    Sadeghi Neshat, Hamid; Bax, Jeffery; Barker, Kevin; Gardi, Lori; Chedalavada, Jason; Kakani, Nirmal; Fenster, Aaron

    2014-03-01

    Image-guided percutaneous ablation is the standard treatment for focal liver tumors deemed inoperable and is commonly used to maintain eligibility for patients on transplant waitlists. Radiofrequency (RFA), microwave (MWA) and cryoablation technologies are all delivered via one or a number of needle-shaped probes inserted directly into the tumor. Planning is mostly based on contrast CT/MRI. While intra-procedural CT is commonly used to confirm the intended probe placement, 2D ultrasound (US) remains the main, and in some centers the only imaging modality used for needle guidance. Corresponding intraoperative 2D US with planning and other intra-procedural imaging modalities is essential for accurate needle placement. However, identification of matching features of interest among these images is often challenging given the limited field-of-view (FOV) and low quality of 2D US images. We have developed a passive tracking arm with a motorized scan-head and software tools to improve guiding capabilities of conventional US by large FOV 3D US scans that provides more anatomical landmarks that can facilitate registration of US with both planning and intra-procedural images. The tracker arm is used to scan the whole liver with a high geometrical accuracy that facilitates multi-modality landmark based image registration. Software tools are provided to assist with the segmentation of the ablation probes and tumors, find the 2D view that best shows the probe(s) from a 3D US image, and to identify the corresponding image from planning CT scans. In this paper, evaluation results from laboratory testing and a phase 1 clinical trial for planning and guiding RFA and MWA procedures using the developed system will be presented. Early clinical results show a comparable performance to intra-procedural CT that suggests 3D US as a cost-effective alternative with no side-effects in centers where CT is not available.

  19. Automatic segmentation and 3D reconstruction of intravascular ultrasound images for a fast preliminar evaluation of vessel pathologies.

    PubMed

    Sanz-Requena, Roberto; Moratal, David; García-Sánchez, Diego Ramón; Bodí, Vicente; Rieta, José Joaquín; Sanchis, Juan Manuel

    2007-03-01

    Intravascular ultrasound (IVUS) imaging is used along with X-ray coronary angiography to detect vessel pathologies. Manual analysis of IVUS images is slow and time-consuming and it is not feasible for clinical purposes. A semi-automated method is proposed to generate 3D reconstructions from IVUS video sequences, so that a fast diagnose can be easily done, quantifying plaque length and severity as well as plaque volume of the vessels under study. The methodology described in this work has four steps: a pre-processing of IVUS images, a segmentation of media-adventitia contour, a detection of intima and plaque and a 3D reconstruction of the vessel. Preprocessing is intended to remove noise from the images without blurring the edges. Segmentation of media-adventitia contour is achieved using active contours (snakes). In particular, we use the gradient vector flow (GVF) as external force for the snakes. The detection of lumen border is obtained taking into account gray-level information of the inner part of the previously detected contours. A knowledge-based approach is used to determine which level of gray corresponds statistically to the different regions of interest: intima, plaque and lumen. The catheter region is automatically discarded. An estimate of plaque type is also given. Finally, 3D reconstruction of all detected regions is made. The suitability of this methodology has been verified for the analysis and visualization of plaque length, stenosis severity, automatic detection of the most problematic regions, calculus of plaque volumes and a preliminary estimation of plaque type obtaining for automatic measures of lumen and vessel area an average error smaller than 1mm(2) (equivalent aproximately to 10% of the average measure), for calculus of plaque and lumen volume errors smaller than 0.5mm(3) (equivalent approximately to 20% of the average measure) and for plaque type estimates a mismatch of less than 8% in the analysed frames. PMID:17215103

  20. Non-rigid registration of a 3D ultrasound and a MR image data set of the female pelvic floor using a biomechanical model

    PubMed Central

    Verhey, Janko F; Wisser, Josef; Warfield, Simon K; Rexilius, Jan; Kikinis, Ron

    2005-01-01

    Background The visual combination of different modalities is essential for many medical imaging applications in the field of Computer-Assisted medical Diagnosis (CAD) to enhance the clinical information content. Clinically, incontinence is a diagnosis with high clinical prevalence and morbidity rate. The search for a method to identify risk patients and to control the success of operations is still a challenging task. The conjunction of magnetic resonance (MR) and 3D ultrasound (US) image data sets could lead to a new clinical visual representation of the morphology as we show with corresponding data sets of the female anal canal with this paper. Methods We present a feasibility study for a non-rigid registration technique based on a biomechanical model for MR and US image data sets of the female anal canal as a base for a new innovative clinical visual representation. Results It is shown in this case study that the internal and external sphincter region could be registered elastically and the registration partially corrects the compression induced by the ultrasound transducer, so the MR data set showing the native anatomy is used as a frame for the US data set showing the same region with higher resolution but distorted by the transducer Conclusion The morphology is of special interest in the assessment of anal incontinence and the non-rigid registration of normal clinical MR and US image data sets is a new field of the adaptation of this method incorporating the advantages of both technologies. PMID:15777475

  1. Using 3D Computer Graphics Multimedia to Motivate Preservice Teachers' Learning of Geometry and Pedagogy

    ERIC Educational Resources Information Center

    Goodson-Espy, Tracy; Lynch-Davis, Kathleen; Schram, Pamela; Quickenton, Art

    2010-01-01

    This paper describes the genesis and purpose of our geometry methods course, focusing on a geometry-teaching technology we created using NVIDIA[R] Chameleon demonstration. This article presents examples from a sequence of lessons centered about a 3D computer graphics demonstration of the chameleon and its geometry. In addition, we present data…

  2. Analyzing 3D xylem networks in Vitis vinifera using High Resolution Computed Tomography (HRCT)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent developments in High Resolution Computed Tomography (HRCT) have made it possible to visualize three dimensional (3D) xylem networks without time consuming, labor intensive physical sectioning. Here we describe a new method to visualize complex vessel networks in plants and produce a quantitat...

  3. The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

    ERIC Educational Resources Information Center

    Elangovan, Tavasuria; Ismail, Zurida

    2014-01-01

    A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

  4. 3D image fusion and guidance for computer-assisted bronchoscopy

    NASA Astrophysics Data System (ADS)

    Higgins, W. E.; Rai, L.; Merritt, S. A.; Lu, K.; Linger, N. T.; Yu, K. C.

    2005-11-01

    The standard procedure for diagnosing lung cancer involves two stages. First, the physician evaluates a high-resolution three-dimensional (3D) computed-tomography (CT) chest image to produce a procedure plan. Next, the physician performs bronchoscopy on the patient, which involves navigating the the bronchoscope through the airways to planned biopsy sites. Unfortunately, the physician has no link between the 3D CT image data and the live video stream provided during bronchoscopy. In addition, these data sources differ greatly in what they physically give, and no true 3D planning tools exist for planning and guiding procedures. This makes it difficult for the physician to translate a CT-based procedure plan to the video domain of the bronchoscope. Thus, the physician must essentially perform biopsy blindly, and the skill levels between different physicians differ greatly. We describe a system that enables direct 3D CT-based procedure planning and provides direct 3D guidance during bronchoscopy. 3D CT-based information on biopsy sites is provided interactively as the physician moves the bronchoscope. Moreover, graphical information through a live fusion of the 3D CT data and bronchoscopic video is provided during the procedure. This information is coupled with a series of computer-graphics tools to give the physician a greatly augmented reality of the patient's interior anatomy during a procedure. Through a series of controlled tests and studies with human lung-cancer patients, we have found that the system not only reduces the variation in skill level between different physicians, but also increases biopsy success rate.

  5. The computation of steady 3-D separated flows over aerodynamic bodies at incidence and yaw

    NASA Technical Reports Server (NTRS)

    Pulliam, T. H.; Pan, D.

    1986-01-01

    This paper describes the implementation of a general purpose 3-D NS code and its application to simulated 3-D separated vortical flows over aerodynamic bodies. The thin-layer Reynolds-averaged NS equations are solved by an implicit approximate factorization scheme. The pencil data structure enables the code to run on very fine grids using only limited incore memories. Solutions of a low subsonic flow over an inclined ellipsoid are compared with experimental data to validate the code. Transonic flows over a yawed elliptical wing at incidence are computed and separations occurred at different yaw angles are discussed.

  6. Evaluation of a prototype 3D ultrasound system for multimodality imaging of cervical nodes for adaptive radiation therapy

    NASA Astrophysics Data System (ADS)

    Fraser, Danielle; Fava, Palma; Cury, Fabio; Vuong, Te; Falco, Tony; Verhaegen, Frank

    2007-03-01

    Sonography has good topographic accuracy for superficial lymph node assessment in patients with head and neck cancers. It is therefore an ideal non-invasive tool for precise inter-fraction volumetric analysis of enlarged cervical nodes. In addition, when registered with computed tomography (CT) images, ultrasound information may improve target volume delineation and facilitate image-guided adaptive radiation therapy. A feasibility study was developed to evaluate the use of a prototype ultrasound system capable of three dimensional visualization and multi-modality image fusion for cervical node geometry. A ceiling-mounted optical tracking camera recorded the position and orientation of a transducer in order to synchronize the transducer's position with respect to the room's coordinate system. Tracking systems were installed in both the CT-simulator and radiation therapy treatment rooms. Serial images were collected at the time of treatment planning and at subsequent treatment fractions. Volume reconstruction was performed by generating surfaces around contours. The quality of the spatial reconstruction and semi-automatic segmentation was highly dependent on the system's ability to track the transducer throughout each scan procedure. The ultrasound information provided enhanced soft tissue contrast and facilitated node delineation. Manual segmentation was the preferred method to contour structures due to their sonographic topography.

  7. Efficient 3D geometric and Zernike moments computation from unstructured surface meshes.

    PubMed

    Pozo, José María; Villa-Uriol, Maria-Cruz; Frangi, Alejandro F

    2011-03-01

    This paper introduces and evaluates a fast exact algorithm and a series of faster approximate algorithms for the computation of 3D geometric moments from an unstructured surface mesh of triangles. Being based on the object surface reduces the computational complexity of these algorithms with respect to volumetric grid-based algorithms. In contrast, it can only be applied for the computation of geometric moments of homogeneous objects. This advantage and restriction is shared with other proposed algorithms based on the object boundary. The proposed exact algorithm reduces the computational complexity for computing geometric moments up to order N with respect to previously proposed exact algorithms, from N(9) to N(6). The approximate series algorithm appears as a power series on the rate between triangle size and object size, which can be truncated at any desired degree. The higher the number and quality of the triangles, the better the approximation. This approximate algorithm reduces the computational complexity to N(3). In addition, the paper introduces a fast algorithm for the computation of 3D Zernike moments from the computed geometric moments, with a computational complexity N(4), while the previously proposed algorithm is of order N(6). The error introduced by the proposed approximate algorithms is evaluated in different shapes and the cost-benefit ratio in terms of error, and computational time is analyzed for different moment orders. PMID:20714011

  8. 3D Quantitative Assessment of Lesion Response to MR-guided High-Intensity Focused Ultrasound Treatment of Uterine Fibroids

    PubMed Central

    Savic, Lynn J.; Lin, MingDe; Duran, Rafael; Schernthaner, Rüdiger E.; Hamm, Bernd; Geschwind, Jean-François; Hong, Kelvin; Chapiro, Julius

    2015-01-01

    Rationale and Objectives To investigate the response after MR-guided high-intensity focused ultrasound (MRgHIFU) treatment of uterine fibroids (UF) using a 3D quantification of total and enhancing lesion volume (TLV, ELV) on contrast-enhanced MRI (ceMRI) scans. Methods and Materials In a total of 24 patients, ceMRI scans were obtained at baseline and 24 hrs, 6, 12 and 24 months after MRgHIFU treatment. The dominant lesion was assessed using a semi-automatic quantitative 3D segmentation technique. Agreement between software-assisted and manual measurements was then analyzed using a linear regression model. Patients were classified as responders (R) or non-responders (NR) based on their symptom report after 6 months. Statistical analysis included the paired t-test and Mann-Whitney-test. Results Preprocedurally, the median TLV and ELV were 263.74cm3 (30.45–689.56cm3) and 210.13cm3 (14.43–689.53cm3), respectively. The 6-month follow-up demonstrated a reduction of TLV in 21 patients (87.5%) with a median TLV of 171.7cm3 (8.5–791.2cm3) (p<.0001). TLV remained stable with significant differences compared to baseline (p<.001 and p=.047 after 12 and 24 months). A reduction of ELV was apparent in 16 patients (66.6%) with a median ELV of 158.91cm3 (8.55–779.61cm3) after 6 months (p=.065). 3D quantification and manual measurements showed strong intermethod-agreement for fibroid volumes (R2=.889 and R2=.917) but greater discrepancy for enhancement calculations (R2=.659 and R2=.419) at baseline and 6 mo. No significant differences in TLV or ELV were observed between clinical R (n=15) and NR (n=3). Conclusion The 3D assessment has proven feasible and accurate in the quantification of fibroid response to MRgHIFU. Contrary to ELV, changes in TLV may be representative of the clinical outcome. PMID:26160057

  9. Application of the ASP3D Computer Program to Unsteady Aerodynamic and Aeroelastic Analyses

    NASA Technical Reports Server (NTRS)

    Batina, John T.

    2006-01-01

    A new computer program has been developed called ASP3D (Advanced Small Perturbation - 3D), which solves the small perturbation potential flow equation in an advanced form including mass-consistent surface and trailing wake boundary conditions, and entropy, vorticity, and viscous effects. The purpose of the program is for unsteady aerodynamic and aeroelastic analyses, especially in the nonlinear transonic flight regime. The program exploits the simplicity of stationary Cartesian meshes with the movement or deformation of the configuration under consideration incorporated into the solution algorithm through a planar surface boundary condition. The paper presents unsteady aerodynamic and aeroelastic applications of ASP3D to assess the time dependent capability and demonstrate various features of the code.

  10. Organ printing: computer-aided jet-based 3D tissue engineering.

    PubMed

    Mironov, Vladimir; Boland, Thomas; Trusk, Thomas; Forgacs, Gabor; Markwald, Roger R

    2003-04-01

    Tissue engineering technology promises to solve the organ transplantation crisis. However, assembly of vascularized 3D soft organs remains a big challenge. Organ printing, which we define as computer-aided, jet-based 3D tissue-engineering of living human organs, offers a possible solution. Organ printing involves three sequential steps: pre-processing or development of "blueprints" for organs; processing or actual organ printing; and postprocessing or organ conditioning and accelerated organ maturation. A cell printer that can print gels, single cells and cell aggregates has been developed. Layer-by-layer sequentially placed and solidified thin layers of a thermo-reversible gel could serve as "printing paper". Combination of an engineering approach with the developmental biology concept of embryonic tissue fluidity enables the creation of a new rapid prototyping 3D organ printing technology, which will dramatically accelerate and optimize tissue and organ assembly. PMID:12679063

  11. Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive

    NASA Astrophysics Data System (ADS)

    Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.

    2012-03-01

    High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.

  12. Using the CAVE virtual-reality environment as an aid to 3-D electromagnetic field computation

    SciTech Connect

    Turner, L.R.; Levine, D.; Huang, M.; Papka, M; Kettunen, L.

    1995-08-01

    One of the major problems in three-dimensional (3-D) field computation is visualizing the resulting 3-D field distributions. A virtual-reality environment, such as the CAVE, (CAVE Automatic Virtual Environment) is helping to overcome this problem, thus making the results of computation more usable for designers and users of magnets and other electromagnetic devices. As a demonstration of the capabilities of the CAVE, the elliptical multipole wiggler (EMW), an insertion device being designed for the Advanced Photon Source (APS) now being commissioned at Argonne National Laboratory (ANL), wa made visible, along with its fields and beam orbits. Other uses of the CAVE in preprocessing and postprocessing computation for electromagnetic applications are also discussed.

  13. Synesthetic art through 3-D projection: The requirements of a computer-based supermedium

    NASA Technical Reports Server (NTRS)

    Mallary, Robert

    1989-01-01

    A computer-based form of multimedia art is proposed that uses the computer to fuse aspects of painting, sculpture, dance, music, film, and other media into a one-to-one synthesia of image and sound for spatially synchronous 3-D projection. Called synesthetic art, this conversion of many varied media into an aesthetically unitary experience determines the character and requirements of the system and its software. During the start-up phase, computer stereographic systems are unsuitable for software development. Eventually, a new type of illusory-projective supermedium will be required to achieve the needed combination of large-format projection and convincing real life presence, and to handle the vast amount of 3-D visual and acoustic information required. The influence of the concept on the author's research and creative work is illustrated through two examples.

  14. Computational optical-sectioning microscopy for 3D quantization of cell motion: results and challenges

    NASA Astrophysics Data System (ADS)

    McNally, James G.

    1994-09-01

    How cells move and navigate within a 3D tissue mass is of central importance in such diverse problems as embryonic development, wound healing and metastasis. This locomotion can now be visualized and quantified by using computation optical-sectioning microscopy. In this approach, a series of 2D images at different depths in a specimen are stacked to construct a 3D image, and then with a knowledge of the microscope's point-spread function, the actual distribution of fluorescent intensity in the specimen is estimated via computation. When coupled with wide-field optics and a cooled CCD camera, this approach permits non-destructive 3D imaging of living specimens over long time periods. With these techniques, we have observed a complex diversity of motile behaviors in a model embryonic system, the cellular slime mold Dictyostelium. To understand the mechanisms which control these various behaviors, we are examining motion in various Dictyostelium mutants with known defects in proteins thought to be essential for signal reception, cell-cell adhesion or locomotion. This application of computational techniques to analyze 3D cell locomotion raises several technical challenges. Image restoration techniques must be fast enough to process numerous 1 Gbyte time-lapse data sets (16 Mbytes per 3D image X 60 time points). Because some cells are weakly labeled and background intensity is often high due to unincorporated dye, the SNR in some of these images is poor. Currently, the images are processed by a regularized linear least- squares restoration method, and occasionally by a maximum-likelihood method. Also required for these studies are accurate automated- tracking procedures to generate both 3D trajectories for individual cells and 3D flows for a group of cells. Tracking is currently done independently for each cell, using a cell's image as a template to search for a similar image at the next time point. Finally, sophisticated visualization techniques are needed to view the

  15. 3D unsteady computer modeling of industrial scale Ky and Cz sapphire crystal growth

    NASA Astrophysics Data System (ADS)

    Demina, S. E.; Kalaev, V. V.

    2011-04-01

    In the present work, 3D features of melt convection during sapphire growth of 100 mm diameter Cz and of 200 mm diameter Ky crystals are studied. The approach accounting for radiative heat exchange with absorption and a specular reflection in the crystal, which we applied in 2D modeling [1-3], has been extended to 3D computational domains and coupled to 3D heat transfer in the melt, crystal, and crucible. 3D melt unsteady convection together with crystallization front formation are taken into account within the Direct Numerical Simulation (DNS) approach. Results of 3D modeling are discussed in detail and quantitatively compared to the previously reported data of 2D modeling and experiments [2,3]. It has been found that the features of unsteady melt convection during the "before seeding", "seeding", and "shouldering" growth stages are quite different from each other, which necessitates a flexible control of the radial and vertical temperature gradients in the crucible to provide optimal conditions for stable growth of high quality sapphire crystals.

  16. Analysis of 3-D images of dental imprints using computer vision

    NASA Astrophysics Data System (ADS)

    Aubin, Michele; Cote, Jean; Laurendeau, Denis; Poussart, Denis

    1992-05-01

    This paper addressed two important aspects of dental analysis: (1) location and (2) identification of the types of teeth by means of 3-D image acquisition and segmentation. The 3-D images of both maxillaries are acquired using a wax wafer as support. The interstices between teeth are detected by non-linear filtering of the 3-D and grey-level data. Two operators are presented: one for the detection of the interstices between incisors, canines, and premolars and one for those between molars. Teeth are then identified by mapping the imprint under analysis on the computer model of an 'ideal' imprint. For the mapping to be valid, a set of three reference points is detected on the imprint. Then, the points are put in correspondence with similar points on the model. Two such points are chosen based on a least-squares fit of a second-order polynomial of the 3-D data in the area of canines. This area is of particular interest since the canines show a very characteristic shape and are easily detected on the imprint. The mapping technique is described in detail in the paper as well as pre-processing of the 3-D profiles. Experimental results are presented for different imprints.

  17. Automatic short axis orientation of the left ventricle in 3D ultrasound recordings

    NASA Astrophysics Data System (ADS)

    Pedrosa, João.; Heyde, Brecht; Heeren, Laurens; Engvall, Jan; Zamorano, Jose; Papachristidis, Alexandros; Edvardsen, Thor; Claus, Piet; D'hooge, Jan

    2016-04-01

    The recent advent of three-dimensional echocardiography has led to an increased interest from the scientific community in left ventricle segmentation frameworks for cardiac volume and function assessment. An automatic orientation of the segmented left ventricular mesh is an important step to obtain a point-to-point correspondence between the mesh and the cardiac anatomy. Furthermore, this would allow for an automatic division of the left ventricle into the standard 17 segments and, thus, fully automatic per-segment analysis, e.g. regional strain assessment. In this work, a method for fully automatic short axis orientation of the segmented left ventricle is presented. The proposed framework aims at detecting the inferior right ventricular insertion point. 211 three-dimensional echocardiographic images were used to validate this framework by comparison to manual annotation of the inferior right ventricular insertion point. A mean unsigned error of 8, 05° +/- 18, 50° was found, whereas the mean signed error was 1, 09°. Large deviations between the manual and automatic annotations (> 30°) only occurred in 3, 79% of cases. The average computation time was 666ms in a non-optimized MATLAB environment, which potentiates real-time application. In conclusion, a successful automatic real-time method for orientation of the segmented left ventricle is proposed.

  18. Position tracking of moving liver lesion based on real-time registration between 2D ultrasound and 3D preoperative images

    SciTech Connect

    Weon, Chijun; Hyun Nam, Woo; Lee, Duhgoon; Ra, Jong Beom; Lee, Jae Young

    2015-01-15

    Purpose: Registration between 2D ultrasound (US) and 3D preoperative magnetic resonance (MR) (or computed tomography, CT) images has been studied recently for US-guided intervention. However, the existing techniques have some limits, either in the registration speed or the performance. The purpose of this work is to develop a real-time and fully automatic registration system between two intermodal images of the liver, and subsequently an indirect lesion positioning/tracking algorithm based on the registration result, for image-guided interventions. Methods: The proposed position tracking system consists of three stages. In the preoperative stage, the authors acquire several 3D preoperative MR (or CT) images at different respiratory phases. Based on the transformations obtained from nonrigid registration of the acquired 3D images, they then generate a 4D preoperative image along the respiratory phase. In the intraoperative preparatory stage, they properly attach a 3D US transducer to the patient’s body and fix its pose using a holding mechanism. They then acquire a couple of respiratory-controlled 3D US images. Via the rigid registration of these US images to the 3D preoperative images in the 4D image, the pose information of the fixed-pose 3D US transducer is determined with respect to the preoperative image coordinates. As feature(s) to use for the rigid registration, they may choose either internal liver vessels or the inferior vena cava. Since the latter is especially useful in patients with a diffuse liver disease, the authors newly propose using it. In the intraoperative real-time stage, they acquire 2D US images in real-time from the fixed-pose transducer. For each US image, they select candidates for its corresponding 2D preoperative slice from the 4D preoperative MR (or CT) image, based on the predetermined pose information of the transducer. The correct corresponding image is then found among those candidates via real-time 2D registration based on a

  19. Visualization of anthropometric measures of workers in computer 3D modeling of work place.

    PubMed

    Mijović, B; Ujević, D; Baksa, S

    2001-12-01

    In this work, 3D visualization of a work place by means of a computer-made 3D-machine model and computer animation of a worker have been performed. By visualization of 3D characters in inverse kinematic and dynamic relation with the operating part of a machine, the biomechanic characteristics of worker's body have been determined. The dimensions of a machine have been determined by an inspection of technical documentation as well as by direct measurements and recordings of the machine by camera. On the basis of measured body height of workers all relevant anthropometric measures have been determined by a computer program developed by the authors. By knowing the anthropometric measures, the vision fields and the scope zones while forming work places, exact postures of workers while performing technological procedures were determined. The minimal and maximal rotation angles and the translation of upper and lower arm which are basis for the analysis of worker burdening were analyzed. The dimensions of the seized space of a body are obtained by computer anthropometric analysis of movement, e.g. range of arms, position of legs, head, back. The influence of forming of a work place on correct postures of workers during work has been reconsidered and thus the consumption of energy and fatigue can be reduced to a minimum. PMID:11811295

  20. User's guide to the NOZL3D and NOZLIC computer programs

    NASA Technical Reports Server (NTRS)

    Thomas, P. D.

    1980-01-01

    Complete FORTRAN listings and running instructions are given for a set of computer programs that perform an implicit numerical solution to the unsteady Navier-Stokes equations to predict the flow characteristics and performance of nonaxisymmetric nozzles. The set includes the NOZL3D program, which performs the flow computations; the NOZLIC program, which sets up the flow field initial conditions for general nozzle configurations, and also generates the computational grid for simple two dimensional and axisymmetric configurations; and the RGRIDD program, which generates the computational grid for complicated three dimensional configurations. The programs are designed specifically for the NASA-Langley CYBER 175 computer, and employ auxiliary disk files for primary data storage. Input instructions and computed results are given for four test cases that include two dimensional, three dimensional, and axisymmetric configurations.

  1. An algorithm to correct 2D near-infrared fluorescence signals using 3D intravascular ultrasound architectural information

    NASA Astrophysics Data System (ADS)

    Mallas, Georgios; Brooks, Dana H.; Rosenthal, Amir; Vinegoni, Claudio; Calfon, Marcella A.; Razansky, R. Nika; Jaffer, Farouc A.; Ntziachristos, Vasilis

    2011-03-01

    Intravascular Near-Infrared Fluorescence (NIRF) imaging is a promising imaging modality to image vessel biology and high-risk plaques in vivo. We have developed a NIRF fiber optic catheter and have presented the ability to image atherosclerotic plaques in vivo, using appropriate NIR fluorescent probes. Our catheter consists of a 100/140 μm core/clad diameter housed in polyethylene tubing, emitting NIR laser light at a 90 degree angle compared to the fiber's axis. The system utilizes a rotational and a translational motor for true 2D imaging and operates in conjunction with a coaxial intravascular ultrasound (IVUS) device. IVUS datasets provide 3D images of the internal structure of arteries and are used in our system for anatomical mapping. Using the IVUS images, we are building an accurate hybrid fluorescence-IVUS data inversion scheme that takes into account photon propagation through the blood filled lumen. This hybrid imaging approach can then correct for the non-linear dependence of light intensity on the distance of the fluorescence region from the fiber tip, leading to quantitative imaging. The experimental and algorithmic developments will be presented and the effectiveness of the algorithm showcased with experimental results in both saline and blood-like preparations. The combined structural and molecular information obtained from these two imaging modalities are positioned to enable the accurate diagnosis of biologically high-risk atherosclerotic plaques in the coronary arteries that are responsible for heart attacks.

  2. Progress in Ring Array Transducers for Real-Time 3D Ultrasound Guidance of Cardiac Interventional Devices

    PubMed Central

    Light, Edward D.; Lieu, Victor; Suhocki, Paul; Wolf, Patrick D.; Smith, Stephen W.

    2012-01-01

    As a treatment for aortic stenosis, several companies have recently introduced prosthetic heart valves designed to be deployed through a catheter using an intravenous or trans-apical approach. This procedure can either take the place of open heart surgery with some of the devices, or delay it with others. Real-time 3D ultrasound could enable continuous monitoring of these structures before, during and after deployment. We have developed a 2D ring array integrated with a 30 French catheter that is used for trans-apical prosthetic heart valve implantation. The transducer array was built using three 46 cm long flex circuits from MicroConnex (Snoqualmie, WA) which terminate in an interconnect that plugs directly into our system cable, thus no cable soldering is required. This transducer consists of 210 elements at .157 mm inter-element spacing and operates at 5 MHz. Average measured element bandwidth was 26% and average round-trip 50 Ohm insertion loss was -81.1 dB. The transducer were wrapped around the 1 cm diameter lumen of a heart valve deployment catheter. Prosthetic heart valve images were obtained in water tank studies. PMID:21842583

  3. Gust Acoustics Computation with a Space-Time CE/SE Parallel 3D Solver

    NASA Technical Reports Server (NTRS)

    Wang, X. Y.; Himansu, A.; Chang, S. C.; Jorgenson, P. C. E.; Reddy, D. R. (Technical Monitor)

    2002-01-01

    The benchmark Problem 2 in Category 3 of the Third Computational Aero-Acoustics (CAA) Workshop is solved using the space-time conservation element and solution element (CE/SE) method. This problem concerns the unsteady response of an isolated finite-span swept flat-plate airfoil bounded by two parallel walls to an incident gust. The acoustic field generated by the interaction of the gust with the flat-plate airfoil is computed by solving the 3D (three-dimensional) Euler equations in the time domain using a parallel version of a 3D CE/SE solver. The effect of the gust orientation on the far-field directivity is studied. Numerical solutions are presented and compared with analytical solutions, showing a reasonable agreement.

  4. Significant acceleration of 2D-3D registration-based fusion of ultrasound and x-ray images by mesh-based DRR rendering

    NASA Astrophysics Data System (ADS)

    Kaiser, Markus; John, Matthias; Borsdorf, Anja; Mountney, Peter; Ionasec, Razvan; Nöttling, Alois; Kiefer, Philipp; Seeburger, Jörg; Neumuth, Thomas

    2013-03-01

    For transcatheter-based minimally invasive procedures in structural heart disease ultrasound and X-ray are the two enabling imaging modalities. A live fusion of both real-time modalities can potentially improve the workflow and the catheter navigation by combining the excellent instrument imaging of X-ray with the high-quality soft tissue imaging of ultrasound. A recently published approach to fuse X-ray fluoroscopy with trans-esophageal echo (TEE) registers the ultrasound probe to X-ray images by a 2D-3D registration method which inherently provides a registration of ultrasound images to X-ray images. In this paper, we significantly accelerate the 2D-3D registration method in this context. The main novelty is to generate the projection images (DRR) of the 3D object not via volume ray-casting but instead via a fast rendering of triangular meshes. This is possible, because in the setting for TEE/X-ray fusion the 3D geometry of the ultrasound probe is known in advance and their main components can be described by triangular meshes. We show that the new approach can achieve a speedup factor up to 65 and does not affect the registration accuracy when used in conjunction with the gradient correlation similarity measure. The improvement is independent of the underlying registration optimizer. Based on the results, a TEE/X-ray fusion could be performed with a higher frame rate and a shorter time lag towards real-time registration performance. The approach could potentially accelerate other applications of 2D-3D registrations, e.g. the registration of implant models with X-ray images.

  5. Computed Tomography and its Application for the 3D Characterization of Coarse Grained Meteorites

    NASA Technical Reports Server (NTRS)

    Gillies, Donald C.; Engel, H. P.; Carpenter, P. K.

    2004-01-01

    With judicious selection of parameters, computed tomography can provide high precision density data. Such data can lead to a non-destructive determination of the phases and phase distribution within large solid objects. Of particular interest is the structure of the Mundrabilla meteorite, which has 25 volumes, percent of a sulfide within a metallic meteorite. 3D digital imaging has enabled a quantitative evaluation of the distribution and contiguity of the phases to be determined.

  6. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  7. 3D animation of facial plastic surgery based on computer graphics

    NASA Astrophysics Data System (ADS)

    Zhang, Zonghua; Zhao, Yan

    2013-12-01

    More and more people, especial women, are getting desired to be more beautiful than ever. To some extent, it becomes true because the plastic surgery of face was capable in the early 20th and even earlier as doctors just dealing with war injures of face. However, the effect of post-operation is not always satisfying since no animation could be seen by the patients beforehand. In this paper, by combining plastic surgery of face and computer graphics, a novel method of simulated appearance of post-operation will be given to demonstrate the modified face from different viewpoints. The 3D human face data are obtained by using 3D fringe pattern imaging systems and CT imaging systems and then converted into STL (STereo Lithography) file format. STL file is made up of small 3D triangular primitives. The triangular mesh can be reconstructed by using hash function. Top triangular meshes in depth out of numbers of triangles must be picked up by ray-casting technique. Mesh deformation is based on the front triangular mesh in the process of simulation, which deforms interest area instead of control points. Experiments on face model show that the proposed 3D animation facial plastic surgery can effectively demonstrate the simulated appearance of post-operation.

  8. Computer assisted 3D pre-operative planning tool for femur fracture orthopedic surgery

    NASA Astrophysics Data System (ADS)

    Gamage, Pavan; Xie, Sheng Quan; Delmas, Patrice; Xu, Wei Liang

    2010-02-01

    Femur shaft fractures are caused by high impact injuries and can affect gait functionality if not treated correctly. Until recently, the pre-operative planning for femur fractures has relied on two-dimensional (2D) radiographs, light boxes, tracing paper, and transparent bone templates. The recent availability of digital radiographic equipment has to some extent improved the workflow for preoperative planning. Nevertheless, imaging is still in 2D X-rays and planning/simulation tools to support fragment manipulation and implant selection are still not available. Direct three-dimensional (3D) imaging modalities such as Computed Tomography (CT) are also still restricted to a minority of complex orthopedic procedures. This paper proposes a software tool which allows orthopedic surgeons to visualize, diagnose, plan and simulate femur shaft fracture reduction procedures in 3D. The tool utilizes frontal and lateral 2D radiographs to model the fracture surface, separate a generic bone into the two fractured fragments, identify the pose of each fragment, and automatically customize the shape of the bone. The use of 3D imaging allows full spatial inspection of the fracture providing different views through the manipulation of the interactively reconstructed 3D model, and ultimately better pre-operative planning.

  9. CELSS-3D: a broad computer model simulating a controlled ecological life support system.

    PubMed

    Schneegurt, M A; Sherman, L A

    1997-01-01

    CELSS-3D is a dynamic, deterministic, and discrete computer simulation of a controlled ecological life support system (CELSS) focusing on biological issues. A series of linear difference equations within a graphic-based modeling environment, the IThink program, was used to describe a modular CELSS system. The overall model included submodels for crop growth chambers, food storage reservoirs, the human crew, a cyanobacterial growth chamber, a waste processor, fixed nitrogen reservoirs, and the atmospheric gases, CO, O2, and N2. The primary process variable was carbon, although oxygen and nitrogen flows were also modeled. Most of the input data used in CELSS-3D were from published sources. A separate linear optimization program, What'sBest!, was used to compare options for the crew's vegetarian diet. CELSS-3D simulations were run for the equivalent of 3 years with a 1-h time interval. Output from simulations run under nominal conditions was used to illustrate dynamic changes in the concentrations of atmospheric gases. The modular design of CELSS-3D will allow other configurations and various failure scenarios to be tested and compared. PMID:11540449

  10. Parallel computation of 3-D Navier-Stokes flowfields for supersonic vehicles

    NASA Technical Reports Server (NTRS)

    Ryan, James S.; Weeratunga, Sisira

    1993-01-01

    Multidisciplinary design optimization of aircraft will require unprecedented capabilities of both analysis software and computer hardware. The speed and accuracy of the analysis will depend heavily on the computational fluid dynamics (CFD) module which is used. A new CFD module has been developed to combine the robust accuracy of conventional codes with the ability to run on parallel architectures. This is achieved by parallelizing the ARC3D algorithm, a central-differenced Navier-Stokes method, on the Intel iPSC/860. The computed solutions are identical to those from conventional machines. Computational speed on 64 processors is comparable to the rate on one Cray Y-MP processor and will increase as new generations of parallel computers become available.

  11. Full 3-D OCT-based pseudophakic custom computer eye model.

    PubMed

    Sun, M; Pérez-Merino, P; Martinez-Enriquez, E; Velasco-Ocana, M; Marcos, S

    2016-03-01

    We compared measured wave aberrations in pseudophakic eyes implanted with aspheric intraocular lenses (IOLs) with simulated aberrations from numerical ray tracing on customized computer eye models, built using quantitative 3-D OCT-based patient-specific ocular geometry. Experimental and simulated aberrations show high correlation (R = 0.93; p<0.0001) and similarity (RMS for high order aberrations discrepancies within 23.58%). This study shows that full OCT-based pseudophakic custom computer eye models allow understanding the relative contribution of optical geometrical and surgically-related factors to image quality, and are an excellent tool for characterizing and improving cataract surgery. PMID:27231608

  12. Computation of an Underexpanded 3-D Rectangular Jet by the CE/SE Method

    NASA Technical Reports Server (NTRS)

    Loh, Ching Y.; Himansu, Ananda; Wang, Xiao Y.; Jorgenson, Philip C. E.

    2000-01-01

    Recently, an unstructured three-dimensional space-time conservation element and solution element (CE/SE) Euler solver was developed. Now it is also developed for parallel computation using METIS for domain decomposition and MPI (message passing interface). The method is employed here to numerically study the near-field of a typical 3-D rectangular under-expanded jet. For the computed case-a jet with Mach number Mj = 1.6. with a very modest grid of 1.7 million tetrahedrons, the flow features such as the shock-cell structures and the axis switching, are in good qualitative agreement with experimental results.

  13. The implementation of the upwind leapfrog scheme for 3D electromagnetic scattering on massively parallel computers

    SciTech Connect

    Nguyen, B.T.; Hutchinson, S.A.

    1995-07-01

    The upwind leapfrog scheme for electromagnetic scattering is briefly described. Its application to the 3D Maxwell`s time domain equations is shown in detail. The scheme`s use of upwind characteristic variables and a narrow stencil result in a smaller demand in communication overhead, making it ideal for implementation on distributed memory parallel computers. The algorithm`s implementation on two message passing computers, a 1024-processor nCUBE 2 and a 1840-processor Intel Paragon, is described. Performance evaluation demonstrates that the scheme performs well with both good scaling qualities and high efficiencies on these machines.

  14. Full 3-D OCT-based pseudophakic custom computer eye model

    PubMed Central

    Sun, M.; Pérez-Merino, P.; Martinez-Enriquez, E.; Velasco-Ocana, M.; Marcos, S.

    2016-01-01

    We compared measured wave aberrations in pseudophakic eyes implanted with aspheric intraocular lenses (IOLs) with simulated aberrations from numerical ray tracing on customized computer eye models, built using quantitative 3-D OCT-based patient-specific ocular geometry. Experimental and simulated aberrations show high correlation (R = 0.93; p<0.0001) and similarity (RMS for high order aberrations discrepancies within 23.58%). This study shows that full OCT-based pseudophakic custom computer eye models allow understanding the relative contribution of optical geometrical and surgically-related factors to image quality, and are an excellent tool for characterizing and improving cataract surgery. PMID:27231608

  15. NOTE: Adaptation of a 3D prostate cancer atlas for transrectal ultrasound guided target-specific biopsy

    NASA Astrophysics Data System (ADS)

    Narayanan, R.; Werahera, P. N.; Barqawi, A.; Crawford, E. D.; Shinohara, K.; Simoneau, A. R.; Suri, J. S.

    2008-10-01

    Due to lack of imaging modalities to identify prostate cancer in vivo, current TRUS guided prostate biopsies are taken randomly. Consequently, many important cancers are missed during initial biopsies. The purpose of this study was to determine the potential clinical utility of a high-speed registration algorithm for a 3D prostate cancer atlas. This 3D prostate cancer atlas provides voxel-level likelihood of cancer and optimized biopsy locations on a template space (Zhan et al 2007). The atlas was constructed from 158 expert annotated, 3D reconstructed radical prostatectomy specimens outlined for cancers (Shen et al 2004). For successful clinical implementation, the prostate atlas needs to be registered to each patient's TRUS image with high registration accuracy in a time-efficient manner. This is implemented in a two-step procedure, the segmentation of the prostate gland from a patient's TRUS image followed by the registration of the prostate atlas. We have developed a fast registration algorithm suitable for clinical applications of this prostate cancer atlas. The registration algorithm was implemented on a graphical processing unit (GPU) to meet the critical processing speed requirements for atlas guided biopsy. A color overlay of the atlas superposed on the TRUS image was presented to help pick statistically likely regions known to harbor cancer. We validated our fast registration algorithm using computer simulations of two optimized 7- and 12-core biopsy protocols to maximize the overall detection rate. Using a GPU, patient's TRUS image segmentation and atlas registration took less than 12 s. The prostate cancer atlas guided 7- and 12-core biopsy protocols had cancer detection rates of 84.81% and 89.87% respectively when validated on the same set of data. Whereas the sextant biopsy approach without the utility of 3D cancer atlas detected only 70.5% of the cancers using the same histology data. We estimate 10-20% increase in prostate cancer detection rates

  16. A hybrid method for the computation of quasi-3D seismograms.

    NASA Astrophysics Data System (ADS)

    Masson, Yder; Romanowicz, Barbara

    2013-04-01

    The development of powerful computer clusters and efficient numerical computation methods, such as the Spectral Element Method (SEM) made possible the computation of seismic wave propagation in a heterogeneous 3D earth. However, the cost of theses computations is still problematic for global scale tomography that requires hundreds of such simulations. Part of the ongoing research effort is dedicated to the development of faster modeling methods based on the spectral element method. Capdeville et al. (2002) proposed to couple SEM simulations with normal modes calculation (C-SEM). Nissen-Meyer et al. (2007) used 2D SEM simulations to compute 3D seismograms in a 1D earth model. Thanks to these developments, and for the first time, Lekic et al. (2011) developed a 3D global model of the upper mantle using SEM simulations. At the local and continental scale, adjoint tomography that is using a lot of SEM simulation can be implemented on current computers (Tape, Liu et al. 2009). Due to their smaller size, these models offer higher resolution. They provide us with images of the crust and the upper part of the mantle. In an attempt to teleport such local adjoint tomographic inversions into the deep earth, we are developing a hybrid method where SEM computation are limited to a region of interest within the earth. That region can have an arbitrary shape and size. Outside this region, the seismic wavefield is extrapolated to obtain synthetic data at the Earth's surface. A key feature of the method is the use of a time reversal mirror to inject the wavefield induced by distant seismic source into the region of interest (Robertsson and Chapman 2000). We compute synthetic seismograms as follow: Inside the region of interest, we are using regional spectral element software RegSEM to compute wave propagation in 3D. Outside this region, the wavefield is extrapolated to the surface by convolution with the Green's functions from the mirror to the seismic stations. For now, these

  17. New solutions and applications of 3D computer tomography image processing

    NASA Astrophysics Data System (ADS)

    Effenberger, Ira; Kroll, Julia; Verl, Alexander

    2008-02-01

    As nowadays the industry aims at fast and high quality product development and manufacturing processes a modern and efficient quality inspection is essential. Compared to conventional measurement technologies, industrial computer tomography (CT) is a non-destructive technology for 3D-image data acquisition which helps to overcome their disadvantages by offering the possibility to scan complex parts with all outer and inner geometric features. In this paper new and optimized methods for 3D image processing, including innovative ways of surface reconstruction and automatic geometric feature detection of complex components, are presented, especially our work of developing smart online data processing and data handling methods, with an integrated intelligent online mesh reduction. Hereby the processing of huge and high resolution data sets is guaranteed. Besides, new approaches for surface reconstruction and segmentation based on statistical methods are demonstrated. On the extracted 3D point cloud or surface triangulation automated and precise algorithms for geometric inspection are deployed. All algorithms are applied to different real data sets generated by computer tomography in order to demonstrate the capabilities of the new tools. Since CT is an emerging technology for non-destructive testing and inspection more and more industrial application fields will use and profit from this new technology.

  18. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.

    PubMed

    Parlea, Lorena G; Sweeney, Blake A; Hosseini-Asanjan, Maryam; Zirbel, Craig L; Leontis, Neocles B

    2016-07-01

    RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs. PMID:27125735

  19. A Computational Model for Suspended Large Rigid Bodies in 3D Unsteady Viscous Flows

    NASA Astrophysics Data System (ADS)

    Xiao, Feng

    1999-11-01

    A 3D numerical model for computing large rigid objects suspended in fluid flow has been developed. Rather than calculating the surface pressure upon the solid body, we evaluate the net force and torque based on a volume force formulation. The total effective force is obtained by summing up the forces at the Eulerian grids occupied by the rigid body. The effects of the moving bodies are coupled to the fluid flow by imposing the velocity field of the bodies to the fluid. A Poisson equation is used to compute the pressure over the whole domain. The objects are identified by color functions and calculated by the PPM scheme and a tangent function transformation which scales the transition region of the computed interface to a compact thickness. The model is then implemented on a parallel computer of distributed memory and validated with Stokes and low Reynolds number flows.

  20. Integration of ultrasound-based registration with statistical shape models for computer-assisted orthopaedic surgery

    NASA Astrophysics Data System (ADS)

    Chan, Carolyn S. K.; Edwards, Philip J.; Hawkes, David J.

    2003-05-01

    We present the first use of ultrasound to instantiate and register a statistical shape model of bony structures. Our aim is to provide accurate image-guided total hip replacement without the need for a preoperative computed tomography (CT) scan. We propose novel methods to determine the location of the bone surface intraoperatively using percutaneous ultrasound and, with the aid of a statistical shape model, reconstruct a complete three-dimensional (3D) model of relevant anatomy. The centre of the femoral head is used as a further constraint to improve accuracy in regions not accessible to ultrasound. CT scans of the femur from a database were aligned to one target CT scan using a non-rigid registration algorithm. The femur surface from the target scan was then propagated to each of the subjects and used to produce a statistical shape model. A cadaveric femur not used in the shape model construction was scanned using freehand 3D ultrasound. The iterative closest point (ICP) algorithm was used to match points corresponding to the bone Surface derived from ultrasound with the statistical bone surface model. We used the mean shape and the first five modes of variation of the shape model. The resulting root mean square (RMS) point-to-surface distance from ICP was minimised to provide the best fit of the model to the ultrasound data.

  1. User's manual for PELE3D: a computer code for three-dimensional incompressible fluid dynamics

    SciTech Connect

    McMaster, W H

    1982-05-07

    The PELE3D code is a three-dimensional semi-implicit Eulerian hydrodynamics computer program for the solution of incompressible fluid flow coupled to a structure. The fluid and coupling algorithms have been adapted from the previously developed two-dimensional code PELE-IC. The PELE3D code is written in both plane and cylindrical coordinates. The coupling algorithm is general enough to handle a variety of structural shapes. The free surface algorithm is able to accommodate a top surface and several independent bubbles. The code is in a developmental status since all the intended options have not been fully implemented and tested. Development of this code ended in 1980 upon termination of the contract with the Nuclear Regulatory Commission.

  2. Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model

    NASA Astrophysics Data System (ADS)

    Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.

    2008-11-01

    Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.

  3. Effect of Random Geometric Uncertainty on the Computational Design of a 3-D Flexible Wing

    NASA Technical Reports Server (NTRS)

    Gumbert, C. R.; Newman, P. A.; Hou, G. J.-W.

    2002-01-01

    The effect of geometric uncertainty due to statistically independent, random, normally distributed shape parameters is demonstrated in the computational design of a 3-D flexible wing. A first-order second-moment statistical approximation method is used to propagate the assumed input uncertainty through coupled Euler CFD aerodynamic / finite element structural codes for both analysis and sensitivity analysis. First-order sensitivity derivatives obtained by automatic differentiation are used in the input uncertainty propagation. These propagated uncertainties are then used to perform a robust design of a simple 3-D flexible wing at supercritical flow conditions. The effect of the random input uncertainties is shown by comparison with conventional deterministic design results. Sample results are shown for wing planform, airfoil section, and structural sizing variables.

  4. Determining inter-fractional motion of the uterus using 3D ultrasound imaging during radiotherapy for cervical cancer

    NASA Astrophysics Data System (ADS)

    Baker, Mariwan; Jensen, Jørgen Arendt; Behrens, Claus F.

    2014-03-01

    Uterine positional changes can reduce the accuracy of radiotherapy for cervical cancer patients. The purpose of this study was to; 1) Quantify the inter-fractional uterine displacement using a novel 3D ultrasound (US) imaging system, and 2) Compare the result with the bone match shift determined by Cone- Beam CT (CBCT) imaging.Five cervical cancer patients were enrolled in the study. Three of them underwent weekly CBCT imaging prior to treatment and bone match shift was applied. After treatment delivery they underwent a weekly US scan. The transabdominal scans were conducted using a Clarity US system (Clarity® Model 310C00). Uterine positional shifts based on soft-tissue match using US was performed and compared to bone match shifts for the three directions. Mean value (+/-1 SD) of the US shifts were (mm); anterior-posterior (A/P): (3.8+/-5.5), superior-inferior (S/I) (-3.5+/-5.2), and left-right (L/R): (0.4+/-4.9). The variations were larger than the CBCT shifts. The largest inter-fractional displacement was from -2 mm to +14 mm in the AP-direction for patient 3. Thus, CBCT bone matching underestimates the uterine positional displacement due to neglecting internal uterine positional change to the bone structures. Since the US images were significantly better than the CBCT images in terms of soft-tissue visualization, the US system can provide an optional image-guided radiation therapy (IGRT) system. US imaging might be a better IGRT system than CBCT, despite difficulty in capturing the entire uterus. Uterine shifts based on US imaging contains relative uterus-bone displacement, which is not taken into consideration using CBCT bone match.

  5. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    NASA Technical Reports Server (NTRS)

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-01

    This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

  6. 3D object optonumerical acquisition methods for CAD/CAM and computer graphics systems

    NASA Astrophysics Data System (ADS)

    Sitnik, Robert; Kujawinska, Malgorzata; Pawlowski, Michal E.; Woznicki, Jerzy M.

    1999-08-01

    The creation of a virtual object for CAD/CAM and computer graphics on the base of data gathered by full-field optical measurement of 3D object is presented. The experimental co- ordinates are alternatively obtained by combined fringe projection/photogrammetry based system or fringe projection/virtual markers setup. The new and fully automatic procedure which process the cloud of measured points into triangular mesh accepted by CAD/CAM and computer graphics systems is presented. Its applicability for various classes of objects is tested including the error analysis of virtual objects generated. The usefulness of the method is proved by applying the virtual object in rapid prototyping system and in computer graphics environment.

  7. Development of computer program NAS3D using Vector processing for geometric nonlinear analysis of structures

    NASA Technical Reports Server (NTRS)

    Mangalgiri, P. D.; Prabhakaran, R.

    1986-01-01

    An algorithm for vectorized computation of stiffness matrices of an 8 noded isoparametric hexahedron element for geometric nonlinear analysis was developed. This was used in conjunction with the earlier 2-D program GAMNAS to develop the new program NAS3D for geometric nonlinear analysis. A conventional, modified Newton-Raphson process is used for the nonlinear analysis. New schemes for the computation of stiffness and strain energy release rates is presented. The organization the program is explained and some results on four sample problems are given. The study of CPU times showed that savings by a factor of 11 to 13 were achieved when vectorized computation was used for the stiffness instead of the conventional scalar one. Finally, the scheme of inputting data is explained.

  8. A new method for real-time co-registration of 3D coronary angiography and intravascular ultrasound or optical coherence tomography.

    PubMed

    Carlier, Stéphane; Didday, Rich; Slots, Tristan; Kayaert, Peter; Sonck, Jeroen; El-Mourad, Mike; Preumont, Nicolas; Schoors, Dany; Van Camp, Guy

    2014-06-01

    We present a new clinically practical method for online co-registration of 3D quantitative coronary angiography (QCA) and intravascular ultrasound (IVUS) or optical coherence tomography (OCT). The workflow is based on two modified commercially available software packages. Reconstruction steps are explained and compared to previously available methods. The feasibility for different clinical scenarios is illustrated. The co-registration appears accurate, robust and induced a minimal delay on the normal cath lab activities. This new method is based on the 3D angiographic reconstruction of the catheter path and does not require operator's identification of landmarks to establish the image synchronization. PMID:24746102

  9. 3D cephalometric analysis obtained from computed tomography. Review of the literature

    PubMed Central

    Rossini, Giulia; Cavallini, Costanza; Cassetta, Michele; Barbato, Ersilia

    2012-01-01

    Summary Introduction The aim of this systematic review is to estimate accuracy and reproducibility of craniometric measurements and reliability of landmarks identified with computed tomography (CT) techniques in 3D cephalometric analysis. Methods Computerized and manual searches were conducted up to 2011 for studies that addressed these objectives. The selection criteria were: (1) the use of human specimen; (2) the comparison between 2D and 3D cephalometric analysis; (3) the assessment of accuracy, reproducibility of measurements and reliability of landmark identification with CT images compared with two-dimensional conventional radiographs. The Cochrane Handbook for Systematic Reviews of Interventions was used as the guideline for this article. Results Twenty-seven articles met the inclusion criteria. Most of them demonstrated high measurements accuracy and reproducibility, and landmarks reliability, but their cephalometric analysis methodology varied widely. Conclusion These differencies among the studies in making measurements don’t permit a direct comparison between them. The future developments in the knowledge of these techniques should provide a standardized method to conduct the 3D CT cephalometric analysis. PMID:22545187

  10. First direct 3D visualisation of microstructural evolutions during sintering through X-ray computed microtomography

    SciTech Connect

    Bernard, Dominique . E-mail: bernard@icmcb.u-bordeaux.fr; Gendron, Damien; Heintz, Jean-Marc; Bordere, Sylvie; Etourneau, Jean

    2005-01-03

    X-ray computed microtomography (XCMT) has been applied to ceramic samples of different materials to visualise, for the first time at this scale, real 3D microstructural evolutions during sintering. Using this technique, it has been possible to follow the whole sintering process of the same grains set. Two materials have been studied; a glass powder heat treated at 700 deg. C and a crystallised lithium borate (Li{sub 6}Gd(BO{sub 3}){sub 3}) powder heat treated at 720 deg. C. XCMT measurements have been done after different sintering times. For each material, a sub-volume was individualised and localised on the successive recordings and its 3D images numerically reconstructed. Description of the three-dimensional microstructures evolution is proposed. From the 3D experimental data, quantitative evolutions of parameters such as porosity and neck size are presented for the glass sample. Possibilities offered by this technique to study complex sintering processes, as for lithium borate, are illustrated.

  11. Traveltime computation and imaging from rugged topography in 3D TTI media

    NASA Astrophysics Data System (ADS)

    Liu, Shaoyong; Wang, Huazhong; Yang, Qinyong; Fang, Wubao

    2014-02-01

    Foothill areas with rugged topography are of great potential for oil and gas seismic exploration, but subsurface imaging in these areas is very challenging. Seismic acquisition with larger offset and wider azimuth is necessary for seismic imaging in complex areas. However, the scale anisotropy in this case must be taken into account. To generalize the pre-stack depth migration (PSDM) to 3D transversely isotropic media with vertical symmetry axes (VTI) and tilted symmetry axes (TTI) from rugged topography, a new dynamic programming approach for the first-arrival traveltime computation method is proposed. The first-arrival time on every uniform mesh point is calculated based on Fermat's principle with simple calculus techniques and a systematic mapping scheme. In order to calculate the minimum traveltime, a set of nonlinear equations is solved on each mesh point, where the group velocity is determined by the group angle. Based on the new first-arrival time calculation method, the corresponding PSDM and migration velocity analysis workflow for 3D anisotropic media from rugged surface is developed. Numerical tests demonstrate that the proposed traveltime calculation method is effective in both VTI and TTI media. The migration results for 3D field data show that it is necessary to choose a smooth datum to remove the high wavenumber move-out components for PSDM with rugged topography and take anisotropy into account to achieve better images.

  12. Hybrid system of optics and computer for 3-D object recognition

    NASA Astrophysics Data System (ADS)

    Li, Qun Z.; Miao, Peng C.; He, Anzhi

    1992-03-01

    In this paper, a hybrid system of optics and computer for 3D object recognition is presented. The system consists of a Twyman-Green interferometer, a He-Ne laser, a computer, a TV camera, and an image processor. The structured light produced by a Twyman-Green interferometer is split in and illuminates objects in two directions at the same time. Moire contour is formed on the surface of object. In order to delete unwanted patterns in moire contour, we don't utilize the moire contour on the surface of object. We place a TV camera in the middle of the angle between two illuminating directions and take two groups of deformed fringes on the surface of objects. Two groups of deformed fringes are processed using the digital image processing system controlled and operated by XOR logic in the computer, moire fringes are then extracted from the complicated environment. 3D coordinates of points of the object are obtained after moire fringe is followed, and points belonging to the same fringe are given the same altitude. The object is described by its projected drawings in three coordinate planes. The projected drawings in three coordinate planes of the known objects are stored in the library of judgment. The object can be recognized by inquiring the library of judgment.

  13. Radial subsampling for fast cost function computation in intensity-based 3D image registration

    NASA Astrophysics Data System (ADS)

    Boettger, Thomas; Wolf, Ivo; Meinzer, Hans-Peter; Celi, Juan Carlos

    2007-03-01

    Image registration is always a trade-off between accuracy and speed. Looking towards clinical scenarios the time for bringing two or more images into registration should be around a few seconds only. We present a new scheme for subsampling 3D-image data to allow for efficient computation of cost functions in intensity-based image registration. Starting from an arbitrary center point voxels are sampled along scan lines which do radially extend from the center point. We analyzed the characteristics of different cost functions computed on the sub-sampled data and compared them to known cost functions with respect to local optima. Results show the cost functions are smooth and give high peaks at the expected optima. Furthermore we investigated capture range of cost functions computed under the new subsampling scheme. Capture range was remarkably better for the new scheme compared to metrics using all voxels or different subsampling schemes and high registration accuracy was achieved as well. The most important result is the improvement in terms of speed making this scheme very interesting for clinical scenarios. We conclude using the new subsampling scheme intensity-based 3D image registration can be performed much faster than using other approaches while maintaining high accuracy. A variety of different extensions of the new approach is conceivable, e.g. non-regular distribution of the scan lines or not to let the scan lines start from a center point only, but from the surface of an organ model for example.

  14. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  15. Computing 3-D steady supersonic flow via a new Lagrangian approach

    NASA Technical Reports Server (NTRS)

    Loh, C. Y.; Liou, M.-S.

    1993-01-01

    The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.

  16. 3D rod-like copper oxide with nanowire hierarchical structure: Ultrasound assisted synthesis from Cu2(OH)3NO3 precursor, optical properties and formation mechanism

    NASA Astrophysics Data System (ADS)

    Ba, Ningning; Zhu, Lianjie; Li, Hongbin; Zhang, Guangzhi; Li, Jianfa; Sun, Jingfeng

    2016-03-01

    3-dimensional (3D) rod-like CuO with nanowire hierarchical structure has been synthesized successfully by a facile ultrasound assisted method combined with thermal conversion, using rouaite Cu2(OH)3NO3 as the precursor. The product was characterized by XRD, SEM, TEM, HRTEM and FT-IR spectrum. Its optical properties were studied by means of UV-Vis diffuse reflectance absorption spectroscopy and photoluminescence (PL) spectrum. Series of control experiments have been performed to explore influencing factors to the product morphologies and a possible formation mechanism has been proposed. The results show that each CuO rod assembled by tens of nanowires is 200-300 nm in diameter and about 1000 nm in length. Each nanowire contains many interconnected nanoparticles with sizes of about 15 nm. Particularly, ultrasound processing was found beneficial to the formation of the 3D rod-like CuO with nanowire hierarchical structure.

  17. Towards real time 2D to 3D registration for ultrasound-guided endoscopic and laparoscopic procedures

    PubMed Central

    Westin, Carl-Fredrik; Vosburgh, Kirby G.

    2010-01-01

    Purpose A method to register endoscopic and laparoscopic ultrasound (US) images in real time with pre-operative computed tomography (CT) data sets has been developed with the goal of improving diagnosis, biopsy guidance, and surgical interventions in the abdomen. Methods The technique, which has the potential to operate in real time, is based on a new phase correlation technique: LEPART, which specifies the location of a plane in the CT data which best corresponds to the US image. Validation of the method was carried out using an US phantom with cyst regions and with retrospective analysis of data sets from animal model experiments. Results The phantom validation study shows that local translation displacements can be recovered for each US frame with a root mean squared error of 1.56 ± 0.78 mm in less than 5 sec, using non-optimized algorithm implementations. Conclusion A new method for multimodality (preoperative CT and intraoperative US endoscopic images) registration to guide endoscopic interventions was developed and found to be efficient using clinically realistic datasets. The algorithm is inherently capable of being implemented in a parallel computing system so that full real time operation appears likely. PMID:20033331

  18. "Let's get physical": advantages of a physical model over 3D computer models and textbooks in learning imaging anatomy.

    PubMed

    Preece, Daniel; Williams, Sarah B; Lam, Richard; Weller, Renate

    2013-01-01

    Three-dimensional (3D) information plays an important part in medical and veterinary education. Appreciating complex 3D spatial relationships requires a strong foundational understanding of anatomy and mental 3D visualization skills. Novel learning resources have been introduced to anatomy training to achieve this. Objective evaluation of their comparative efficacies remains scarce in the literature. This study developed and evaluated the use of a physical model in demonstrating the complex spatial relationships of the equine foot. It was hypothesized that the newly developed physical model would be more effective for students to learn magnetic resonance imaging (MRI) anatomy of the foot than textbooks or computer-based 3D models. Third year veterinary medicine students were randomly assigned to one of three teaching aid groups (physical model; textbooks; 3D computer model). The comparative efficacies of the three teaching aids were assessed through students' abilities to identify anatomical structures on MR images. Overall mean MRI assessment scores were significantly higher in students utilizing the physical model (86.39%) compared with students using textbooks (62.61%) and the 3D computer model (63.68%) (P < 0.001), with no significant difference between the textbook and 3D computer model groups (P = 0.685). Student feedback was also more positive in the physical model group compared with both the textbook and 3D computer model groups. Our results suggest that physical models may hold a significant advantage over alternative learning resources in enhancing visuospatial and 3D understanding of complex anatomical architecture, and that 3D computer models have significant limitations with regards to 3D learning. PMID:23349117

  19. 3D virtual human atria: A computational platform for studying clinical atrial fibrillation.

    PubMed

    Aslanidi, Oleg V; Colman, Michael A; Stott, Jonathan; Dobrzynski, Halina; Boyett, Mark R; Holden, Arun V; Zhang, Henggui

    2011-10-01

    Despite a vast amount of experimental and clinical data on the underlying ionic, cellular and tissue substrates, the mechanisms of common atrial arrhythmias (such as atrial fibrillation, AF) arising from the functional interactions at the whole atria level remain unclear. Computational modelling provides a quantitative framework for integrating such multi-scale data and understanding the arrhythmogenic behaviour that emerges from the collective spatio-temporal dynamics in all parts of the heart. In this study, we have developed a multi-scale hierarchy of biophysically detailed computational models for the human atria--the 3D virtual human atria. Primarily, diffusion tensor MRI reconstruction of the tissue geometry and fibre orientation in the human sinoatrial node (SAN) and surrounding atrial muscle was integrated into the 3D model of the whole atria dissected from the Visible Human dataset. The anatomical models were combined with the heterogeneous atrial action potential (AP) models, and used to simulate the AP conduction in the human atria under various conditions: SAN pacemaking and atrial activation in the normal rhythm, break-down of regular AP wave-fronts during rapid atrial pacing, and the genesis of multiple re-entrant wavelets characteristic of AF. Contributions of different properties of the tissue to mechanisms of the normal rhythm and arrhythmogenesis were investigated. Primarily, the simulations showed that tissue heterogeneity caused the break-down of the normal AP wave-fronts at rapid pacing rates, which initiated a pair of re-entrant spiral waves; and tissue anisotropy resulted in a further break-down of the spiral waves into multiple meandering wavelets characteristic of AF. The 3D virtual atria model itself was incorporated into the torso model to simulate the body surface ECG patterns in the normal and arrhythmic conditions. Therefore, a state-of-the-art computational platform has been developed, which can be used for studying multi

  20. 3D modeling method for computer animate based on modified weak structured light method

    NASA Astrophysics Data System (ADS)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  1. Automatic pulmonary vessel segmentation in 3D computed tomographic pulmonary angiographic (CTPA) images

    NASA Astrophysics Data System (ADS)

    Zhou, Chuan; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Patel, Smita; Cascade, Philip N.; Sahiner, Berkman; Wei, Jun; Ge, Jun; Kazerooni, Ella A.

    2006-03-01

    Automatic and accurate segmentation of the pulmonary vessels in 3D computed tomographic angiographic images (CTPA) is an essential step for computerized detection of pulmonary embolism (PE) because PEs only occur inside the pulmonary arteries. We are developing an automated method to segment the pulmonary vessels in 3D CTPA images. The lung region is first extracted using thresholding and morphological operations. 3D multiscale filters in combination with a newly developed response function derived from the eigenvalues of Hessian matrices are used to enhance all vascular structures including the vessel bifurcations and suppress non-vessel structures such as the lymphoid tissues surrounding the vessels. At each scale, a volume of interest (VOI) containing the response function value at each voxel is defined. The voxels with a high response indicate that there is an enhanced vessel whose size matches the given filter scale. A hierarchical expectation-maximization (EM) estimation is then applied to the VOI to segment the vessel by extracting the high response voxels at this single scale. The vessel tree is finally reconstructed by combining the segmented vessels at all scales based on a "connected component" analysis. Two experienced thoracic radiologists provided the gold standard of pulmonary arteries by manually tracking the arterial tree and marking the center of the vessels using a computer graphical user interface. Two CTPA cases containing PEs were used to evaluate the performance. One of these two cases also contained other lung diseases. The accuracy of vessel tree segmentation was evaluated by the percentage of the "gold standard" vessel center points overlapping with the segmented vessels. The result shows that 97.3% (1868/1920) and 92.0% (2277/2476) of the manually marked center points overlapped with the segmented vessels for the cases without and with other lung disease, respectively. The results demonstrate that vessel segmentation using our method is

  2. Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals’ Behaviour

    PubMed Central

    Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola

    2016-01-01

    Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs’ behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals’ quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog’s shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non

  3. Quick, Accurate, Smart: 3D Computer Vision Technology Helps Assessing Confined Animals' Behaviour.

    PubMed

    Barnard, Shanis; Calderara, Simone; Pistocchi, Simone; Cucchiara, Rita; Podaliri-Vulpiani, Michele; Messori, Stefano; Ferri, Nicola

    2016-01-01

    Mankind directly controls the environment and lifestyles of several domestic species for purposes ranging from production and research to conservation and companionship. These environments and lifestyles may not offer these animals the best quality of life. Behaviour is a direct reflection of how the animal is coping with its environment. Behavioural indicators are thus among the preferred parameters to assess welfare. However, behavioural recording (usually from video) can be very time consuming and the accuracy and reliability of the output rely on the experience and background of the observers. The outburst of new video technology and computer image processing gives the basis for promising solutions. In this pilot study, we present a new prototype software able to automatically infer the behaviour of dogs housed in kennels from 3D visual data and through structured machine learning frameworks. Depth information acquired through 3D features, body part detection and training are the key elements that allow the machine to recognise postures, trajectories inside the kennel and patterns of movement that can be later labelled at convenience. The main innovation of the software is its ability to automatically cluster frequently observed temporal patterns of movement without any pre-set ethogram. Conversely, when common patterns are defined through training, a deviation from normal behaviour in time or between individuals could be assessed. The software accuracy in correctly detecting the dogs' behaviour was checked through a validation process. An automatic behaviour recognition system, independent from human subjectivity, could add scientific knowledge on animals' quality of life in confinement as well as saving time and resources. This 3D framework was designed to be invariant to the dog's shape and size and could be extended to farm, laboratory and zoo quadrupeds in artificial housing. The computer vision technique applied to this software is innovative in non

  4. Feasibility of Using Volumetric Contrast-Enhanced Ultrasound with a 3-D Transducer to Evaluate Therapeutic Response after Targeted Therapy in Rabbit Hepatic VX2 Carcinoma.

    PubMed

    Kim, Jeehyun; Kim, Jung Hoon; Yoon, Soon Ho; Choi, Won Seok; Kim, Young Jae; Han, Joon Koo; Choi, Byung-Ihn

    2015-12-01

    The aim of this study was to assess the feasibility of using dynamic contrast-enhanced ultrasound (DCE-US) with a 3-D transducer to evaluate therapeutic responses to targeted therapy. Rabbits with hepatic VX2 carcinomas, divided into a treatment group (n = 22, 30 mg/kg/d sorafenib) and a control group (n = 13), were evaluated with DCE-US using 2-D and 3-D transducers and computed tomography (CT) perfusion imaging at baseline and 1 d after the first treatment. Perfusion parameters were collected, and correlations between parameters were analyzed. In the treatment group, both volumetric and 2-D DCE-US perfusion parameters, including peak intensity (33.2 ± 19.9 vs. 16.6 ± 10.7, 63.7 ± 20.0 vs. 30.1 ± 19.8), slope (15.3 ± 12.4 vs. 5.7 ± 4.5, 37.3 ± 20.4 vs. 15.7 ± 13.0) and area under the curve (AUC; 1004.1 ± 560.3 vs. 611.4 ± 421.1, 1332.2 ± 708.3 vs. 670.4 ± 388.3), had significantly decreased 1 d after the first treatment (p = 0.00). In the control group, 2-D DCE-US revealed that peak intensity, time to peak and slope had significantly changed (p < 0.05); however, volumetric DCE-US revealed that peak intensity, time-intensity AUC, AUC during wash-in and AUC during wash-out had significantly changed (p = 0.00). CT perfusion imaging parameters, including blood flow, blood volume and permeability of the capillary vessel surface, had significantly decreased in the treatment group (p = 0.00); however, in the control group, peak intensity and blood volume had significantly increased (p = 0.00). It is feasible to use DCE-US with a 3-D transducer to predict early therapeutic response after targeted therapy because perfusion parameters, including peak intensity, slope and AUC, significantly decreased, which is similar to the trend observed for 2-D DCE-US and CT perfusion imaging parameters. PMID:26365926

  5. FaceWarehouse: a 3D facial expression database for visual computing.

    PubMed

    Cao, Chen; Weng, Yanlin; Zhou, Shun; Tong, Yiying; Zhou, Kun

    2014-03-01

    We present FaceWarehouse, a database of 3D facial expressions for visual computing applications. We use Kinect, an off-the-shelf RGBD camera, to capture 150 individuals aged 7-80 from various ethnic backgrounds. For each person, we captured the RGBD data of her different expressions, including the neutral expression and 19 other expressions such as mouth-opening, smile, kiss, etc. For every RGBD raw data record, a set of facial feature points on the color image such as eye corners, mouth contour, and the nose tip are automatically localized, and manually adjusted if better accuracy is required. We then deform a template facial mesh to fit the depth data as closely as possible while matching the feature points on the color image to their corresponding points on the mesh. Starting from these fitted face meshes, we construct a set of individual-specific expression blendshapes for each person. These meshes with consistent topology are assembled as a rank-3 tensor to build a bilinear face model with two attributes: identity and expression. Compared with previous 3D facial databases, for every person in our database, there is a much richer matching collection of expressions, enabling depiction of most human facial actions. We demonstrate the potential of FaceWarehouse for visual computing with four applications: facial image manipulation, face component transfer, real-time performance-based facial image animation, and facial animation retargeting from video to image. PMID:24434222

  6. High performance computing approaches for 3D reconstruction of complex biological specimens.

    PubMed

    da Silva, M Laura; Roca-Piera, Javier; Fernández, José-Jesús

    2010-01-01

    Knowledge of the structure of specimens is crucial to determine the role that they play in cellular and molecular biology. To yield the three-dimensional (3D) reconstruction by means of tomographic reconstruction algorithms, we need the use of large projection images and high processing time. Therefore, we propose the use of the high performance computing (HPC) to cope with the huge computational demands of this problem. We have implemented a HPC strategy where the distribution of tasks follows the master-slave paradigm. The master processor distributes a slab of slices, a piece of the final 3D structure to reconstruct, among the slave processors and receives reconstructed slices of the volume. We have evaluated the performance of our HPC approach using different sizes of the slab. We have observed that it is possible to find out an optimal size of the slab for the number of processor used that minimize communications time while maintaining a reasonable grain of parallelism to be exploited by the set of processors. PMID:20865517

  7. Using Computer-Aided Design Software and 3D Printers to Improve Spatial Visualization

    ERIC Educational Resources Information Center

    Katsio-Loudis, Petros; Jones, Millie

    2015-01-01

    Many articles have been published on the use of 3D printing technology. From prefabricated homes and outdoor structures to human organs, 3D printing technology has found a niche in many fields, but especially education. With the introduction of AutoCAD technical drawing programs and now 3D printing, learners can use 3D printed models to develop…

  8. A review of automated image understanding within 3D baggage computed tomography security screening.

    PubMed

    Mouton, Andre; Breckon, Toby P

    2015-01-01

    Baggage inspection is the principal safeguard against the transportation of prohibited and potentially dangerous materials at airport security checkpoints. Although traditionally performed by 2D X-ray based scanning, increasingly stringent security regulations have led to a growing demand for more advanced imaging technologies. The role of X-ray Computed Tomography is thus rapidly expanding beyond the traditional materials-based detection of explosives. The development of computer vision and image processing techniques for the automated understanding of 3D baggage-CT imagery is however, complicated by poor image resolutions, image clutter and high levels of noise and artefacts. We discuss the recent and most pertinent advancements and identify topics for future research within the challenging domain of automated image understanding for baggage security screening CT. PMID:26409422

  9. A new 3-D integral code for computation of accelerator magnets

    SciTech Connect

    Turner, L.R.; Kettunen, L.

    1991-01-01

    For computing accelerator magnets, integral codes have several advantages over finite element codes; far-field boundaries are treated automatically, and computed field in the bore region satisfy Maxwell's equations exactly. A new integral code employing edge elements rather than nodal elements has overcome the difficulties associated with earlier integral codes. By the use of field integrals (potential differences) as solution variables, the number of unknowns is reduced to one less than the number of nodes. Two examples, a hollow iron sphere and the dipole magnet of Advanced Photon Source injector synchrotron, show the capability of the code. The CPU time requirements are comparable to those of three-dimensional (3-D) finite-element codes. Experiments show that in practice it can realize much of the potential CPU time saving that parallel processing makes possible. 8 refs., 4 figs., 1 tab.

  10. Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

    NASA Technical Reports Server (NTRS)

    Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

    1989-01-01

    Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

  11. Evaluating the extent of cell death in 3D high frequency ultrasound by registration with whole-mount tumor histopathology

    SciTech Connect

    Vlad, Roxana M.; Kolios, Michael C.; Moseley, Joanne L.; Czarnota, Gregory J.; Brock, Kristy K.

    2010-08-15

    Purpose: High frequency ultrasound imaging, 10-30 MHz, has the capability to assess tumor response to radiotherapy in mouse tumors as early as 24 h after treatment administration. The advantage of this technique is that the image contrast is generated by changes in the physical properties of dying cells. Therefore, a subject can be imaged before and multiple times during the treatment without the requirement of injecting specialized contrast agents. This study is motivated by a need to provide metrics of comparison between the volume and localization of cell death, assessed from histology, with the volume and localization of cell death surrogate, assessed as regions with increased echogeneity from ultrasound images. Methods: The mice were exposed to radiation doses of 2, 4, and 8 Gy. Ultrasound images were collected from each tumor before and 24 h after exposure to radiation using a broadband 25 MHz center frequency transducer. After radiotherapy, tumors exhibited hyperechoic regions in ultrasound images that corresponded to areas of cell death in histology. The ultrasound and histological images were rigidly registered. The tumors and regions of cell death were manually outlined on histological images. Similarly, the tumors and hyperechoic regions were outlined on the ultrasound images. Each set of contours was converted to a volumetric mesh in order to compare the volumes and the localization of cell death in histological and ultrasound images. Results: A shrinkage factor of 17{+-}2% was calculated from the difference in the tumor volumes evaluated from histological and ultrasound images. This was used to correct the tumor and cell death volumes assessed from histology. After this correction, the average absolute difference between the volume of cell death assessed from ultrasound and histological images was 11{+-}14% and the volume overlap was 70{+-}12%. Conclusions: The method provided metrics of comparison between the volume of cell death assessed from

  12. The Effects of 3D Computer Modelling on Conceptual Change about Seasons and Phases of the Moon

    ERIC Educational Resources Information Center

    Kucukozer, Huseyin

    2008-01-01

    In this study, prospective science teachers' misconceptions about the seasons and the phases of the Moon were determined, and then the effects of 3D computer modelling on their conceptual changes were investigated. The topics were covered in two classes with a total of 76 students using a predict-observe-explain strategy supported by 3D computer…

  13. Infrared thermography and ultrasound C-scan for non-destructive evaluation of 3D carbon fiber materials: a comparative study

    NASA Astrophysics Data System (ADS)

    Zhang, Hai; Genest, Marc; Robitaille, Francois; Maldague, Xavier; West, Lucas; Joncas, Simon; Leduc, Catherine

    2015-05-01

    3D Carbon fiber polymer matrix composites (3D CF PMCs) are increasingly used for aircraft construction due to their exceptional stiffness and strength-to-mass ratios. However, defects are common in the 3D combining areas and are challenging to inspect. In this paper, Stitching is used to decrease these defects, but causes some new types of defects. Infrared NDT (non-destructive testing) and ultrasound NDT are used. In particular, a micro-laser line thermography technique (micro-LLT) and a micro-laser spot thermography (micro-LST) with locked-in technique are used to detect the micro-defects. In addition, a comparative study is conducted by using pulsed thermography (PT), vibrothermography (VT). In order to confirm the types of the defects, microscopic inspection is carried out before NDT work, after sectioning and polishing a small part of the sample..

  14. Image guided radiation therapy applications for head and neck, prostate, and breast cancers using 3D ultrasound imaging and Monte Carlo dose calculations

    NASA Astrophysics Data System (ADS)

    Fraser, Danielle

    In radiation therapy an uncertainty in the delivered dose always exists because anatomic changes are unpredictable and patient specific. Image guided radiation therapy (IGRT) relies on imaging in the treatment room to monitor the tumour and surrounding tissue to ensure their prescribed position in the radiation beam. The goal of this thesis was to determine the dosimetric impact on the misaligned radiation therapy target for three cancer sites due to common setup errors; organ motion, tumour tissue deformation, changes in body habitus, and treatment planning errors. For this purpose, a novel 3D ultrasound system (Restitu, Resonant Medical, Inc.) was used to acquire a reference image of the target in the computed tomography simulation room at the time of treatment planning, to acquire daily images in the treatment room at the time of treatment delivery, and to compare the daily images to the reference image. The measured differences in position and volume between daily and reference geometries were incorporated into Monte Carlo (MC) dose calculations. The EGSnrc (National Research Council, Canada) family of codes was used to model Varian linear accelerators and patient specific beam parameters, as well as to estimate the dose to the target and organs at risk under several different scenarios. After validating the necessity of MC dose calculations in the pelvic region, the impact of interfraction prostate motion, and subsequent patient realignment under the treatment beams, on the delivered dose was investigated. For 32 patients it is demonstrated that using 3D conformal radiation therapy techniques and a 7 mm margin, the prescribed dose to the prostate, rectum, and bladder is recovered within 0.5% of that planned when patient setup is corrected for prostate motion, despite the beams interacting with a new external surface and internal tissue boundaries. In collaboration with the manufacturer, the ultrasound system was adapted from transabdominal imaging to neck

  15. A brain-computer interface method combined with eye tracking for 3D interaction.

    PubMed

    Lee, Eui Chul; Woo, Jin Cheol; Kim, Jong Hwa; Whang, Mincheol; Park, Kang Ryoung

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI. PMID:20580646

  16. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  17. Using 3D infrared imaging to calibrate and refine computational fluid dynamic modeling for large computer and data centers

    NASA Astrophysics Data System (ADS)

    Stockton, Gregory R.

    2011-05-01

    Over the last 10 years, very large government, military, and commercial computer and data center operators have spent millions of dollars trying to optimally cool data centers as each rack has begun to consume as much as 10 times more power than just a few years ago. In fact, the maximum amount of data computation in a computer center is becoming limited by the amount of available power, space and cooling capacity at some data centers. Tens of millions of dollars and megawatts of power are being annually spent to keep data centers cool. The cooling and air flows dynamically change away from any predicted 3-D computational fluid dynamic modeling during construction and as time goes by, and the efficiency and effectiveness of the actual cooling rapidly departs even farther from predicted models. By using 3-D infrared (IR) thermal mapping and other techniques to calibrate and refine the computational fluid dynamic modeling and make appropriate corrections and repairs, the required power for data centers can be dramatically reduced which reduces costs and also improves reliability.

  18. Quality control of dose volume histogram computation characteristics of 3D treatment planning systems

    NASA Astrophysics Data System (ADS)

    Panitsa, E.; Rosenwald, J. C.; Kappas, C.

    1998-10-01

    Detailed quality control (QC) protocols are a necessity for modern radiotherapy departments. The established QC protocols for treatment planning systems (TPS) do not include recommendations on the advanced features of three-dimensional (3D) treatment planning, like the dose volume histograms (DVH). In this study, a test protocol for DVH characteristics was developed. The protocol assesses the consistency of the DVH computation to the dose distribution calculated by the same TPS by comparing DVH parameters with values obtained by the isodose distributions. The computation parameters (such as the dimension of the computation grid) that are applied to the TPS during the tests are not fixed but set by the user as if the test represents a typical clinical case. Six commercial TPS were examined with this protocol within the frame of the EC project Dynarad (Biomed I). The results of the intercomparison prove the consistency of the DVH results to the isodose values for most of the examined TPS. However, special attention should be paid when working with cases of adverse conditions such as high dose gradient regions. In these cases, higher errors are derived, especially when an insufficient number of dose calculation points are used for the DVH computation.

  19. Computational time analysis of the numerical solution of 3D electrostatic Poisson's equation

    NASA Astrophysics Data System (ADS)

    Kamboh, Shakeel Ahmed; Labadin, Jane; Rigit, Andrew Ragai Henri; Ling, Tech Chaw; Amur, Khuda Bux; Chaudhary, Muhammad Tayyab

    2015-05-01

    3D Poisson's equation is solved numerically to simulate the electric potential in a prototype design of electrohydrodynamic (EHD) ion-drag micropump. Finite difference method (FDM) is employed to discretize the governing equation. The system of linear equations resulting from FDM is solved iteratively by using the sequential Jacobi (SJ) and sequential Gauss-Seidel (SGS) methods, simulation results are also compared to examine the difference between the results. The main objective was to analyze the computational time required by both the methods with respect to different grid sizes and parallelize the Jacobi method to reduce the computational time. In common, the SGS method is faster than the SJ method but the data parallelism of Jacobi method may produce good speedup over SGS method. In this study, the feasibility of using parallel Jacobi (PJ) method is attempted in relation to SGS method. MATLAB Parallel/Distributed computing environment is used and a parallel code for SJ method is implemented. It was found that for small grid size the SGS method remains dominant over SJ method and PJ method while for large grid size both the sequential methods may take nearly too much processing time to converge. Yet, the PJ method reduces computational time to some extent for large grid sizes.

  20. Cloud4Psi: cloud computing for 3D protein structure similarity searching

    PubMed Central

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

    2014-01-01

    Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. Contact: dariusz.mrozek@polsl.pl PMID:24930141

  1. e-LEA3D: a computational-aided drug design web server

    PubMed Central

    Douguet, Dominique

    2010-01-01

    e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc.cnrs.fr/lea.html. PMID:20444867

  2. 3D robust Chan-Vese model for industrial computed tomography volume data segmentation

    NASA Astrophysics Data System (ADS)

    Liu, Linghui; Zeng, Li; Luan, Xiao

    2013-11-01

    Industrial computed tomography (CT) has been widely applied in many areas of non-destructive testing (NDT) and non-destructive evaluation (NDE). In practice, CT volume data to be dealt with may be corrupted by noise. This paper addresses the segmentation of noisy industrial CT volume data. Motivated by the research on the Chan-Vese (CV) model, we present a region-based active contour model that draws upon intensity information in local regions with a controllable scale. In the presence of noise, a local energy is firstly defined according to the intensity difference within a local neighborhood. Then a global energy is defined to integrate local energy with respect to all image points. In a level set formulation, this energy is represented by a variational level set function, where a surface evolution equation is derived for energy minimization. Comparative analysis with the CV model indicates the comparable performance of the 3D robust Chan-Vese (RCV) model. The quantitative evaluation also shows the segmentation accuracy of 3D RCV. In addition, the efficiency of our approach is validated under several types of noise, such as Poisson noise, Gaussian noise, salt-and-pepper noise and speckle noise.

  3. FaceWarehouse: A 3D Facial Expression Database for Visual Computing.

    PubMed

    Cao, Chen; Weng, Yanlin; Zhou, Shun; Tong, Yiying; Zhou, Kun

    2013-10-25

    We present FaceWarehouse, a database of 3D facial expressions for visual computing applications. We use Microsoft's Kinect system to capture 150 individuals from various ethnic backgrounds. For each person, we captured the RGBD data of her different expressions, including the neutral expression and 19 other expressions. For every raw data record, a set of facial feature points on the color image such as eye corners and mouth contour are automatically localized, and manually adjusted if better accuracy is required. We then deform a template facial mesh to fit the depth data as closely as possible while matching the feature points on the color image to their corresponding points on the mesh. Starting from these fitted face meshes, we construct a set of individual-specific expression blendshapes for each person. These meshes with consistent topology are assembled as a rank-three tensor to build a bilinear face model with two attributes, identity and expression. Compared with previous 3D facial databases, for every person in our database, there is a much richer matching collection of expressions, enabling depiction of most human facial actions. We demonstrate the potential of FaceWarehouse with four applications: facial image manipulation, face component transfer, real-time performance-based facial image animation, and facial animation retargeting from video to image. PMID:24166613

  4. Breast density measurement: 3D cone beam computed tomography (CBCT) images versus 2D digital mammograms

    NASA Astrophysics Data System (ADS)

    Han, Tao; Lai, Chao-Jen; Chen, Lingyun; Liu, Xinming; Shen, Youtao; Zhong, Yuncheng; Ge, Shuaiping; Yi, Ying; Wang, Tianpeng; Yang, Wei T.; Shaw, Chris C.

    2009-02-01

    Breast density has been recognized as one of the major risk factors for breast cancer. However, breast density is currently estimated using mammograms which are intrinsically 2D in nature and cannot accurately represent the real breast anatomy. In this study, a novel technique for measuring breast density based on the segmentation of 3D cone beam CT (CBCT) images was developed and the results were compared to those obtained from 2D digital mammograms. 16 mastectomy breast specimens were imaged with a bench top flat-panel based CBCT system. The reconstructed 3D CT images were corrected for the cupping artifacts and then filtered to reduce the noise level, followed by using threshold-based segmentation to separate the dense tissue from the adipose tissue. For each breast specimen, volumes of the dense tissue structures and the entire breast were computed and used to calculate the volumetric breast density. BI-RADS categories were derived from the measured breast densities and compared with those estimated from conventional digital mammograms. The results show that in 10 of 16 cases the BI-RADS categories derived from the CBCT images were lower than those derived from the mammograms by one category. Thus, breasts considered as dense in mammographic examinations may not be considered as dense with the CBCT images. This result indicates that the relation between breast cancer risk and true (volumetric) breast density needs to be further investigated.

  5. X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution

    PubMed Central

    Holler, M.; Diaz, A.; Guizar-Sicairos, M.; Karvinen, P.; Färm, Elina; Härkönen, Emma; Ritala, Mikko; Menzel, A.; Raabe, J.; Bunk, O.

    2014-01-01

    X-ray ptychography is a scanning variant of coherent diffractive imaging with the ability to image large fields of view at high resolution. It further allows imaging of non-isolated specimens and can produce quantitative mapping of the electron density distribution in 3D when combined with computed tomography. The method does not require imaging lenses, which makes it dose efficient and suitable to multi-keV X-rays, where efficient photon counting, pixelated detectors are available. Here we present the first highly resolved quantitative X-ray ptychographic tomography of an extended object yielding 16 nm isotropic 3D resolution recorded at 2 Å wavelength. This first-of-its-kind demonstration paves the way for ptychographic X-ray tomography to become a promising method for X-ray imaging of representative sample volumes at unmatched resolution, opening tremendous potential for characterizing samples in materials science and biology by filling the resolution gap between electron microscopy and other X-ray imaging techniques. PMID:24457289

  6. Computational Study of 3-D Hot-Spot Initiation in Shocked Insensitive High-Explosive

    NASA Astrophysics Data System (ADS)

    Najjar, F. M.; Howard, W. M.; Fried, L. E.

    2011-06-01

    High explosive shock sensitivity is controlled by a combination of mechanical response, thermal properties, and chemical properties. The interplay of these physical phenomena in realistic condensed energetic materials is currently lacking. A multiscale computational framework is developed investigating hot spot (void) ignition in a single crystal of an insensitive HE, TATB. Atomistic MD simulations are performed to provide the key chemical reactions and these reaction rates are used in 3-D multiphysics simulations. The multiphysics code, ALE3D, is linked to the chemistry software, Cheetah, and a three-way coupled approach is pursued including hydrodynamics, thermal and chemical analyses. A single spherical air bubble is embedded in the insensitive HE and its collapse due to shock initiation is evolved numerically in time; while the ignition processes due chemical reactions are studied. Our current predictions showcase several interesting features regarding hot spot dynamics including the formation of a ``secondary'' jet. Results obtained with hydro-thermo-chemical processes leading to ignition growth will be discussed for various pore sizes and different shock pressures. LLNL-ABS-471438. This work performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

  7. A 3-D Computational Study of a Variable Camber Continuous Trailing Edge Flap (VCCTEF) Spanwise Segment

    NASA Technical Reports Server (NTRS)

    Kaul, Upender K.; Nguyen, Nhan T.

    2015-01-01

    Results of a computational study carried out to explore the effects of various elastomer configurations joining spanwise contiguous Variable Camber Continuous Trailing Edge Flap (VCCTEF) segments are reported here. This research is carried out as a proof-of-concept study that will seek to push the flight envelope in cruise with drag optimization as the objective. The cruise conditions can be well off design such as caused by environmental conditions, maneuvering, etc. To handle these off-design conditions, flap deflection is used so when the flap is deflected in a given direction, the aircraft angle of attack changes accordingly to maintain a given lift. The angle of attack is also a design parameter along with the flap deflection. In a previous 2D study,1 the effect of camber was investigated and the results revealed some insight into the relative merit of various camber settings of the VCCTEF. The present state of the art has not advanced sufficiently to do a full 3-D viscous analysis of the whole NASA Generic Transport Model (GTM) wing with VCCTEF deployed with elastomers. Therefore, this study seeks to explore the local effects of three contiguous flap segments on lift and drag of a model devised here to determine possible trades among various flap deflections to achieve desired lift and drag results. Although this approach is an approximation, it provides new insights into the "local" effects of the relative deflections of the contiguous spanwise flap systems and various elastomer segment configurations. The present study is a natural extension of the 2-D study to assess these local 3-D effects. Design cruise condition at 36,000 feet at free stream Mach number of 0.797 and a mean aerodynamic chord (MAC) based Reynolds number of 30.734x10(exp 6) is simulated for an angle of attack (AoA) range of 0 to 6 deg. In the previous 2-D study, the calculations revealed that the parabolic arc camber (1x2x3) and circular arc camber (VCCTEF222) offered the best L

  8. Long-term viability and proliferation of alginate-encapsulated 3-D HepG2 aggregates formed in an ultrasound trap.

    PubMed

    Bazou, D; Coakley, W T; Hayes, A J; Jackson, S K

    2008-08-01

    We report proof of principle here of a gel encapsulation technique that departs from the minimum surface area to volume restriction of spherical microcapsules and allows gelation of preformed high-density (>or=2x10(4) cells/aggregate) 3-D HepG2 cell aggregates. The process involves forming a discoid 3-D cell aggregate in an ultrasound standing wave trap (USWT), which is subsequently recovered and encapsulated in alginate/CaCl2 hydrogel. The size of the ultrasound-formed aggregates was dependent upon the initial cell concentration, and was in the range of 0.4-2.6 mm in diameter (for cell concentrations ranging between 10(4) and 5x10(6)/ml). At low cell concentrations (or=10(6)/ml, 3-D aggregates were generated. Cells in non- and encapsulated 3-D HepG2 aggregates remained 70-80% viable over 10 days in culture. The proliferative activity of the aggregates resulted in the doubling of the aggregate cell number and a subsequent increase in the aggregate thickness, while albumin secretion levels in encapsulated aggregates was 4.5 times higher compared to non-encapsulated, control aggregates. The results reported here suggest that the ultrasound trap can provide an alternative, novel approach of hydrogel cell encapsulation and thus rapidly (within 5 min) produce in vitro models for hepatocyte functional studies (for example, toxicity studies particularly if primary hepatocytes are used) in a tissue-mimetic manner. PMID:18490133

  9. A comparative study for 2D and 3D computer-aided diagnosis methods for solitary pulmonary nodules.

    PubMed

    Yeh, Chinson; Wang, Jen-Feng; Wu, Ming-Ting; Yen, Chen-Wen; Nagurka, Mark L; Lin, Chen-Liang

    2008-06-01

    Many computer-aided diagnosis (CAD) methods, including 2D and 3D approaches, have been proposed for solitary pulmonary nodules (SPNs). However, the detection and diagnosis of SPNs remain challenging in many clinical circumstances. One goal of this work is to investigate the relative diagnostic accuracy of 2D and 3D methods. An additional goal is to develop a two-stage approach that combines the simplicity of 2D and the accuracy of 3D methods. The experimental results show statistically significant differences between the diagnostic accuracy of 2D and 3D methods. The results also show that with a very minor drop in diagnostic performance the two-stage approach can significantly reduce the number of nodules needed to be processed by the 3D method, streamlining the computational demand. PMID:18313899

  10. An improved version of NCOREL: A computer program for 3-D nonlinear supersonic potential flow computations

    NASA Technical Reports Server (NTRS)

    Siclari, Michael J.

    1988-01-01

    A computer code called NCOREL (for Nonconical Relaxation) has been developed to solve for supersonic full potential flows over complex geometries. The method first solves for the conical at the apex and then marches downstream in a spherical coordinate system. Implicit relaxation techniques are used to numerically solve the full potential equation at each subsequent crossflow plane. Many improvements have been made to the original code including more reliable numerics for computing wing-body flows with multiple embedded shocks, inlet flow through simulation, wake model and entropy corrections. Line relaxation or approximate factorization schemes are optionally available. Improved internal grid generation using analytic conformal mappings, supported by a simple geometric Harris wave drag input that was originally developed for panel methods and internal geometry package are some of the new features.

  11. Hyperspeed data acquisition for 3D computer vision metrology as applied to law enforcement

    NASA Astrophysics Data System (ADS)

    Altschuler, Bruce R.

    1997-02-01

    cycling at 1 millisecond, each pattern is projected and recorded in a cycle time of 1/500th second. An entire set of patterns can then be recorded within 1/60th second. This pattern set contains all the information necessary to calculate a 3-D map. The use of hyper-speed parallel video cameras in conjunction with high speed modulators enables video data rate acquisition of all data necessary to calculate numerical digital 3-D metrological surface data. Thus a 3-D video camera can operate at the rate of a conventional 2-D video camera. The speed of actual 3-D output information is a function of the speed of the computer, a parallel processor being preferred for the task. With video rate 3-D data acquisition law enforcement could survey crime scenes, obtain evidence, watch and record people, packages, suitcases, and record disaster scenes very rapidly.

  12. The NCOREL computer program for 3D nonlinear supersonic potential flow computations

    NASA Technical Reports Server (NTRS)

    Siclari, M. J.

    1983-01-01

    An innovative computational technique (NCOREL) was established for the treatment of three dimensional supersonic flows. The method is nonlinear in that it solves the nonconservative finite difference analog of the full potential equation and can predict the formation of supercritical cross flow regions, embedded and bow shocks. The method implicitly computes a conical flow at the apex (R = 0) of a spherical coordinate system and uses a fully implicit marching technique to obtain three dimensional cross flow solutions. This implies that the radial Mach number must remain supersonic. The cross flow solutions are obtained by using type dependent transonic relaxation techniques with the type dependency linked to the character of the cross flow velocity (i.e., subsonic/supersonic). The spherical coordinate system and marching on spherical surfaces is ideally suited to the computation of wing flows at low supersonic Mach numbers due to the elimination of the subsonic axial Mach number problems that exist in other marching codes that utilize Cartesian transverse marching planes.

  13. Real-time computer-generated integral imaging and 3D image calibration for augmented reality surgical navigation.

    PubMed

    Wang, Junchen; Suenaga, Hideyuki; Liao, Hongen; Hoshi, Kazuto; Yang, Liangjing; Kobayashi, Etsuko; Sakuma, Ichiro

    2015-03-01

    Autostereoscopic 3D image overlay for augmented reality (AR) based surgical navigation has been studied and reported many times. For the purpose of surgical overlay, the 3D image is expected to have the same geometric shape as the original organ, and can be transformed to a specified location for image overlay. However, how to generate a 3D image with high geometric fidelity and quantitative evaluation of 3D image's geometric accuracy have not been addressed. This paper proposes a graphics processing unit (GPU) based computer-generated integral imaging pipeline for real-time autostereoscopic 3D display, and an automatic closed-loop 3D image calibration paradigm for displaying undistorted 3D images. Based on the proposed methods, a novel AR device for 3D image surgical overlay is presented, which mainly consists of a 3D display, an AR window, a stereo camera for 3D measurement, and a workstation for information processing. The evaluation on the 3D image rendering performance with 2560×1600 elemental image resolution shows the rendering speeds of 50-60 frames per second (fps) for surface models, and 5-8 fps for large medical volumes. The evaluation of the undistorted 3D image after the calibration yields sub-millimeter geometric accuracy. A phantom experiment simulating oral and maxillofacial surgery was also performed to evaluate the proposed AR overlay device in terms of the image registration accuracy, 3D image overlay accuracy, and the visual effects of the overlay. The experimental results show satisfactory image registration and image overlay accuracy, and confirm the system usability. PMID:25465067

  14. Fast and Robust Sixth Order Multigrid Computation for 3D Convection Diffusion Equation.

    PubMed

    Wang, Yin; Zhang, Jun

    2010-10-15

    We present a sixth order explicit compact finite difference scheme to solve the three dimensional (3D) convection diffusion equation. We first use multiscale multigrid method to solve the linear systems arising from a 19-point fourth order discretization scheme to compute the fourth order solutions on both the coarse grid and the fine grid. Then an operator based interpolation scheme combined with an extrapolation technique is used to approximate the sixth order accurate solution on the fine grid. Since the multigrid method using a standard point relaxation smoother may fail to achieve the optimal grid independent convergence rate for solving convection diffusion equation with a high Reynolds number, we implement the plane relaxation smoother in the multigrid solver to achieve better grid independency. Supporting numerical results are presented to demonstrate the efficiency and accuracy of the sixth order compact scheme (SOC), compared with the previously published fourth order compact scheme (FOC). PMID:21151737

  15. A revised scheme to compute horizontal covariances in an oceanographic 3D-VAR assimilation system

    NASA Astrophysics Data System (ADS)

    Farina, R.; Dobricic, S.; Storto, A.; Masina, S.; Cuomo, S.

    2015-03-01

    We propose an improvement of an oceanographic three dimensional variational assimilation scheme (3D-VAR), named OceanVar, by introducing a recursive filter (RF) with the third order of accuracy (3rd-RF), instead of an RF with first order of accuracy (1st-RF), to approximate horizontal Gaussian covariances. An advantage of the proposed scheme is that the CPU's time can be substantially reduced with benefits on the large scale applications. Experiments estimating the impact of 3rd-RF are performed by assimilating oceanographic data in two realistic oceanographic applications. The results evince benefits in terms of assimilation process computational time, accuracy of the Gaussian correlation modeling, and show that the 3rd-RF is a suitable tool for operational data assimilation.

  16. An accurate quadrature technique for the contact boundary in 3D finite element computations

    NASA Astrophysics Data System (ADS)

    Duong, Thang X.; Sauer, Roger A.

    2015-01-01

    This paper presents a new numerical integration technique for 3D contact finite element implementations, focusing on a remedy for the inaccurate integration due to discontinuities at the boundary of contact surfaces. The method is based on the adaptive refinement of the integration domain along the boundary of the contact surface, and is accordingly denoted RBQ for refined boundary quadrature. It can be used for common element types of any order, e.g. Lagrange, NURBS, or T-Spline elements. In terms of both computational speed and accuracy, RBQ exhibits great advantages over a naive increase of the number of quadrature points. Also, the RBQ method is shown to remain accurate for large deformations. Furthermore, since the sharp boundary of the contact surface is determined, it can be used for various purposes like the accurate post-processing of the contact pressure. Several examples are presented to illustrate the new technique.

  17. Modular Approaches to Earth Science Scientific Computing: 3D Electromagnetic Induction Modeling as an Example

    NASA Astrophysics Data System (ADS)

    Tandon, K.; Egbert, G.; Siripunvaraporn, W.

    2003-12-01

    We are developing a modular system for three-dimensional inversion of electromagnetic (EM) induction data, using an object oriented programming approach. This approach allows us to modify the individual components of the inversion scheme proposed, and also reuse the components for variety of problems in earth science computing howsoever diverse they might be. In particular, the modularity allows us to (a) change modeling codes independently of inversion algorithm details; (b) experiment with new inversion algorithms; and (c) modify the way prior information is imposed in the inversion to test competing hypothesis and techniques required to solve an earth science problem. Our initial code development is for EM induction equations on a staggered grid, using iterative solution techniques in 3D. An example illustrated here is an experiment with the sensitivity of 3D magnetotelluric inversion to uncertainties in the boundary conditions required for regional induction problems. These boundary conditions should reflect the large-scale geoelectric structure of the study area, which is usually poorly constrained. In general for inversion of MT data, one fixes boundary conditions at the edge of the model domain, and adjusts the earth?s conductivity structure within the modeling domain. Allowing for errors in specification of the open boundary values is simple in principle, but no existing inversion codes that we are aware of have this feature. Adding a feature such as this is straightforward within the context of the modular approach. More generally, a modular approach provides an efficient methodology for setting up earth science computing problems to test various ideas. As a concrete illustration relevant to EM induction problems, we investigate the sensitivity of MT data near San Andreas Fault at Parkfield (California) to uncertainties in the regional geoelectric structure.

  18. Analysis of bite marks in foodstuffs by computer tomography (cone beam CT)--3D reconstruction.

    PubMed

    Marques, Jeidson; Musse, Jamilly; Caetano, Catarina; Corte-Real, Francisco; Corte-Real, Ana Teresa

    2013-12-01

    The use of three-dimensional (3D) analysis of forensic evidence is highlighted in comparison with traditional methods. This three-dimensional analysis is based on the registration of the surface from a bitten object. The authors propose to use Cone Beam Computed Tomography (CBCT), which is used in dental practice, in order to study the surface and interior of bitten objects and dental casts of suspects. In this study, CBCT is applied to the analysis of bite marks in foodstuffs, which may be found in a forensic case scenario. 6 different types of foodstuffs were used: chocolate, cheese, apple, chewing gum, pizza and tart (flaky pastry and custard). The food was bitten into and dental casts of the possible suspects were made. The dental casts and bitten objects were registered using an x-ray source and the CBCT equipment iCAT® (Pennsylvania, EUA). The software InVivo5® (Anatomage Inc, EUA) was used to visualize and analyze the tomographic slices and 3D reconstructions of the objects. For each material an estimate of its density was assessed by two methods: HU values and specific gravity. All the used materials were successfully reconstructed as good quality 3D images. The relative densities of the materials in study were compared. Amongst the foodstuffs, the chocolate had the highest density (median value 100.5 HU and 1,36 g/cm(3)), while the pizza showed to have the lowest (median value -775 HU and 0,39 g/cm(3)), on both scales. Through tomographic slices and three-dimensional reconstructions it was possible to perform the metric analysis of the bite marks in all the foodstuffs, except for the pizza. These measurements could also be obtained from the dental casts. The depth of the bite mark was also successfully determined in all the foodstuffs except for the pizza. Cone Beam Computed Tomography has the potential to become an important tool for forensic sciences, namely for the registration and analysis of bite marks in foodstuffs that may be found in a crime

  19. FURN3D: A computer code for radiative heat transfer in pulverized coal furnaces

    SciTech Connect

    Ahluwalia, R.K.; Im, K.H.

    1992-08-01

    A computer code FURN3D has been developed for assessing the impact of burning different coals on heat absorption pattern in pulverized coal furnaces. The code is unique in its ability to conduct detailed spectral calculations of radiation transport in furnaces fully accounting for the size distributions of char, soot and ash particles, ash content, and ash composition. The code uses a hybrid technique of solving the three-dimensional radiation transport equation for absorbing, emitting and anisotropically scattering media. The technique achieves an optimal mix of computational speed and accuracy by combining the discrete ordinate method (S[sub 4]), modified differential approximation (MDA) and P, approximation in different range of optical thicknesses. The code uses spectroscopic data for estimating the absorption coefficients of participating gases C0[sub 2], H[sub 2]0 and CO. It invokes Mie theory for determining the extinction and scattering coefficients of combustion particulates. The optical constants of char, soot and ash are obtained from dispersion relations derived from reflectivity, transmissivity and extinction measurements. A control-volume formulation is adopted for determining the temperature field inside the furnace. A simple char burnout model is employed for estimating heat release and evolution of particle size distribution. The code is written in Fortran 77, has modular form, and is machine-independent. The computer memory required by the code depends upon the number of grid points specified and whether the transport calculations are performed on spectral or gray basis.

  20. FURN3D: A computer code for radiative heat transfer in pulverized coal furnaces

    SciTech Connect

    Ahluwalia, R.K.; Im, K.H.

    1992-08-01

    A computer code FURN3D has been developed for assessing the impact of burning different coals on heat absorption pattern in pulverized coal furnaces. The code is unique in its ability to conduct detailed spectral calculations of radiation transport in furnaces fully accounting for the size distributions of char, soot and ash particles, ash content, and ash composition. The code uses a hybrid technique of solving the three-dimensional radiation transport equation for absorbing, emitting and anisotropically scattering media. The technique achieves an optimal mix of computational speed and accuracy by combining the discrete ordinate method (S{sub 4}), modified differential approximation (MDA) and P, approximation in different range of optical thicknesses. The code uses spectroscopic data for estimating the absorption coefficients of participating gases C0{sub 2}, H{sub 2}0 and CO. It invokes Mie theory for determining the extinction and scattering coefficients of combustion particulates. The optical constants of char, soot and ash are obtained from dispersion relations derived from reflectivity, transmissivity and extinction measurements. A control-volume formulation is adopted for determining the temperature field inside the furnace. A simple char burnout model is employed for estimating heat release and evolution of particle size distribution. The code is written in Fortran 77, has modular form, and is machine-independent. The computer memory required by the code depends upon the number of grid points specified and whether the transport calculations are performed on spectral or gray basis.

  1. Enabling 3D-Liver Perfusion Mapping from MR-DCE Imaging Using Distributed Computing

    PubMed Central

    Leporq, Benjamin; Camarasu-Pop, Sorina; Davila-Serrano, Eduardo E.; Pilleul, Frank; Beuf, Olivier

    2013-01-01

    An MR acquisition protocol and a processing method using distributed computing on the European Grid Infrastructure (EGI) to allow 3D liver perfusion parametric mapping after Magnetic Resonance Dynamic Contrast Enhanced (MR-DCE) imaging are presented. Seven patients (one healthy control and six with chronic liver diseases) were prospectively enrolled after liver biopsy. MR-dynamic acquisition was continuously performed in free-breathing during two minutes after simultaneous intravascular contrast agent (MS-325 blood pool agent) injection. Hepatic capillary system was modeled by a 3-parameters one-compartment pharmacokinetic model. The processing step was parallelized and executed on the EGI. It was modeled and implemented as a grid workflow using the Gwendia language and the MOTEUR workflow engine. Results showed good reproducibility in repeated processing on the grid. The results obtained from the grid were well correlated with ROI-based reference method ran locally on a personal computer. The speed-up range was 71 to 242 with an average value of 126. In conclusion, distributed computing applied to perfusion mapping brings significant speed-up to quantification step to be used for further clinical studies in a research context. Accuracy would be improved with higher image SNR accessible on the latest 3T MR systems available today. PMID:27006915

  2. Automated Lung Segmentation and Image Quality Assessment for Clinical 3-D/4-D-Computed Tomography

    PubMed Central

    Li, Guang

    2014-01-01

    4-D-computed tomography (4DCT) provides not only a new dimension of patient-specific information for radiation therapy planning and treatment, but also a challenging scale of data volume to process and analyze. Manual analysis using existing 3-D tools is unable to keep up with vastly increased 4-D data volume, automated processing and analysis are thus needed to process 4DCT data effectively and efficiently. In this paper, we applied ideas and algorithms from image/signal processing, computer vision, and machine learning to 4DCT lung data so that lungs can be reliably segmented in a fully automated manner, lung features can be visualized and measured on the fly via user interactions, and data quality classifications can be computed in a robust manner. Comparisons of our results with an established treatment planning system and calculation by experts demonstrated negligible discrepancies (within ±2%) for volume assessment but one to two orders of magnitude performance enhancement. An empirical Fourier-analysis-based quality measure-delivered performances closely emulating human experts. Three machine learners are inspected to justify the viability of machine learning techniques used to robustly identify data quality of 4DCT images in the scalable manner. The resultant system provides a toolkit that speeds up 4-D tasks in the clinic and facilitates clinical research to improve current clinical practice. PMID:25621194

  3. Ultrasound

    MedlinePlus

    ... please enable JavaScript. Ultrasound uses high-frequency sound waves to make images of organs and structures inside ... examined. The machine sends out high-frequency sound waves, which reflect off body structures. A computer receives ...

  4. Multiple capture locations for 3D ultrasound-guided robotic retrieval of moving bodies from a beating heart

    NASA Astrophysics Data System (ADS)

    Thienphrapa, Paul; Ramachandran, Bharat; Elhawary, Haytham; Taylor, Russell H.; Popovic, Aleksandra

    2012-02-01

    Free moving bodies in the heart pose a serious health risk as they may be released in the arteries causing blood flow disruption. These bodies may be the result of various medical conditions and trauma. The conventional approach to removing these objects involves open surgery with sternotomy, the use of cardiopulmonary bypass, and a wide resection of the heart muscle. We advocate a minimally invasive surgical approach using a flexible robotic end effector guided by 3D transesophageal echocardiography. In a phantom study, we track a moving body in a beating heart using a modified normalized cross-correlation method, with mean RMS errors of 2.3 mm. We previously found the foreign body motion to be fast and abrupt, rendering infeasible a retrieval method based on direct tracking. We proposed a strategy based on guiding a robot to the most spatially probable location of the fragment and securing it upon its reentry to said location. To improve efficacy in the context of a robotic retrieval system, we extend this approach by exploring multiple candidate capture locations. Salient locations are identified based on spatial probability, dwell time, and visit frequency; secondary locations are also examined. Aggregate results indicate that the location of highest spatial probability (50% occupancy) is distinct from the longest-dwelled location (0.84 seconds). Such metrics are vital in informing the design of a retrieval system and capture strategies, and they can be computed intraoperatively to select the best capture location based on constraints such as workspace, time, and device manipulability. Given the complex nature of fragment motion, the ability to analyze multiple capture locations is a desirable capability in an interventional system.

  5. Potential hazards of viewing 3-D stereoscopic television, cinema and computer games: a review.

    PubMed

    Howarth, Peter A

    2011-03-01

    The visual stimulus provided by a 3-D stereoscopic display differs from that of the real world because the image provided to each eye is produced on a flat surface. The distance from the screen to the eye remains fixed, providing a single focal distance, but the introduction of disparity between the images allows objects to be located geometrically in front of, or behind, the screen. Unlike in the real world, the stimulus to accommodation and the stimulus to convergence do not match. Although this mismatch is used positively in some forms of Orthoptic treatment, a number of authors have suggested that it could negatively lead to the development of asthenopic symptoms. From knowledge of the zone of clear, comfortable, single binocular vision one can predict that, for people with normal binocular vision, adverse symptoms will not be present if the discrepancy is small, but are likely if it is large, and that what constitutes 'large' and 'small' are idiosyncratic to the individual. The accommodation-convergence mismatch is not, however, the only difference between the natural and the artificial stimuli. In the former case, an object located in front of, or behind, a fixated object will not only be perceived as double if the images fall outside Panum's fusional areas, but it will also be defocused and blurred. In the latter case, however, it is usual for the producers of cinema, TV or computer game content to provide an image that is in focus over the whole of the display, and as a consequence diplopic images will be sharply in focus. The size of Panum's fusional area is spatial frequency-dependent, and because of this the high spatial frequencies present in the diplopic 3-D image will provide a different stimulus to the fusion system from that found naturally. PMID:21309798

  6. Projection-based metal-artifact reduction for industrial 3D X-ray computed tomography.

    PubMed

    Amirkhanov, Artem; Heinzl, Christoph; Reiter, Michael; Kastner, Johann; Gröller, M Eduard

    2011-12-01

    Multi-material components, which contain metal parts surrounded by plastic materials, are highly interesting for inspection using industrial 3D X-ray computed tomography (3DXCT). Examples of this application scenario are connectors or housings with metal inlays in the electronic or automotive industry. A major problem of this type of components is the presence of metal, which causes streaking artifacts and distorts the surrounding media in the reconstructed volume. Streaking artifacts and dark-band artifacts around metal components significantly influence the material characterization (especially for the plastic components). In specific cases these artifacts even prevent a further analysis. Due to the nature and the different characteristics of artifacts, the development of an efficient artifact-reduction technique in reconstruction-space is rather complicated. In this paper we present a projection-space pipeline for metal-artifacts reduction. The proposed technique first segments the metal in the spatial domain of the reconstructed volume in order to separate it from the other materials. Then metal parts are forward-projected on the set of projections in a way that metal-projection regions are treated as voids. Subsequently the voids, which are left by the removed metal, are interpolated in the 2D projections. Finally, the metal is inserted back into the reconstructed 3D volume during the fusion stage. We present a visual analysis tool, allowing for interactive parameter estimation of the metal segmentation. The results of the proposed artifact-reduction technique are demonstrated on a test part as well as on real world components. For these specimens we achieve a significant reduction of metal artifacts, allowing an enhanced material characterization. PMID:22034338

  7. Toward virtual anatomy: a stereoscopic 3-D interactive multimedia computer program for cranial osteology.

    PubMed

    Trelease, R B

    1996-01-01

    Advances in computer visualization and user interface technologies have enabled development of "virtual reality" programs that allow users to perceive and to interact with objects in artificial three-dimensional environments. Such technologies were used to create an image database and program for studying the human skull, a specimen that has become increasingly expensive and scarce. Stereoscopic image pairs of a museum-quality skull were digitized from multiple views. For each view, the stereo pairs were interlaced into a single, field-sequential stereoscopic picture using an image processing program. The resulting interlaced image files are organized in an interactive multimedia program. At run-time, gray-scale 3-D images are displayed on a large-screen computer monitor and observed through liquid-crystal shutter goggles. Users can then control the program and change views with a mouse and cursor to point-and-click on screen-level control words ("buttons"). For each view of the skull, an ID control button can be used to overlay pointers and captions for important structures. Pointing and clicking on "hidden buttons" overlying certain structures triggers digitized audio spoken word descriptions or mini lectures. PMID:8793223

  8. Ultrasound-assisted fabrication of a new nano-rods 3D copper(II)-organic coordination supramolecular compound.

    PubMed

    Hanifehpour, Younes; Safarifard, Vahid; Morsali, Ali; Mirtamizdoust, Babak; Joo, Sang Woo

    2016-07-01

    High-energy ultrasound irradiation has been used for the synthesis of a new copper(II) coordination supramolecular compound, [Cu2(μ-O2CCH3)2(μ-OOCCH3)(phen)2](BF4) (1), ("phen" is 1,10-phenanthroline) with nano-rods morphology. The new nano-structure was characterized by scanning electron microscopy (SEM), X-ray powder diffraction (XRPD), FT-IR spectroscopy and elemental analyses. Compound 1 was structurally characterized by single crystal X-ray diffraction. The utilization of high intensity ultrasound has found as a facile, environmentally friendly, and versatile synthetic tool for the supramolecular coordination compounds. PMID:26964941

  9. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  10. Memory usage reduction and intensity modulation for 3D holographic display using non-uniformly sampled computer-generated holograms

    NASA Astrophysics Data System (ADS)

    Zhang, Zhao; Liu, Juan; Jia, Jia; Li, Xin; Pan, Yijie; Han, Jian; Hu, Bin; Wang, Yongtian

    2013-12-01

    The real-time holographic display encounters heavy computational load of computer-generated holograms and precisely intensity modulation of 3D images reconstructed by phase-only holograms. In this study, we demonstrate a method for reducing memory usage and modulating the intensity in 3D holographic display. The proposed method can eliminate the redundant information of holograms by employing the non-uniform sampling technique. By combining with the novel look-up table method, 70% reduction in the storage amount can be reached. The gray-scale modulation of 3D images reconstructed by phase-only holograms can be extended either. We perform both numerical simulations and optical experiments to verify the practicability of this method, and the results match well with each other. It is believed that the proposed method can be used in 3D dynamic holographic display and design of the diffractive phase elements.

  11. A new approach of building 3D visualization framework for multimodal medical images display and computed assisted diagnosis

    NASA Astrophysics Data System (ADS)

    Li, Zhenwei; Sun, Jianyong; Zhang, Jianguo

    2012-02-01

    As more and more CT/MR studies are scanning with larger volume of data sets, more and more radiologists and clinician would like using PACS WS to display and manipulate these larger data sets of images with 3D rendering features. In this paper, we proposed a design method and implantation strategy to develop 3D image display component not only with normal 3D display functions but also with multi-modal medical image fusion as well as compute-assisted diagnosis of coronary heart diseases. The 3D component has been integrated into the PACS display workstation of Shanghai Huadong Hospital, and the clinical practice showed that it is easy for radiologists and physicians to use these 3D functions such as multi-modalities' (e.g. CT, MRI, PET, SPECT) visualization, registration and fusion, and the lesion quantitative measurements. The users were satisfying with the rendering speeds and quality of 3D reconstruction. The advantages of the component include low requirements for computer hardware, easy integration, reliable performance and comfortable application experience. With this system, the radiologists and the clinicians can manipulate with 3D images easily, and use the advanced visualization tools to facilitate their work with a PACS display workstation at any time.

  12. Error propagation in the computation of volumes in 3D city models with the Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Biljecki, F.; Ledoux, H.; Stoter, J.

    2014-11-01

    This paper describes the analysis of the propagation of positional uncertainty in 3D city models to the uncertainty in the computation of their volumes. Current work related to error propagation in GIS is limited to 2D data and 2D GIS operations, especially of rasters. In this research we have (1) developed two engines, one that generates random 3D buildings in CityGML in multiple LODs, and one that simulates acquisition errors to the geometry; (2) performed an error propagation analysis on volume computation based on the Monte Carlo method; and (3) worked towards establishing a framework for investigating error propagation in 3D GIS. The results of the experiments show that a comparatively small error in the geometry of a 3D city model may cause significant discrepancies in the computation of its volume. This has consequences for several applications, such as in estimation of energy demand and property taxes. The contribution of this work is twofold: this is the first error propagation analysis in 3D city modelling, and the novel approach and the engines that we have created can be used for analysing most of 3D GIS operations, supporting related research efforts in the future.

  13. Detectability of hepatic tumors during 3D post-processed ultrafast cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Paul, Jijo; Vogl, Thomas J.; Chacko, Annamma

    2015-10-01

    To evaluate hepatic tumor detection using ultrafast cone-beam computed tomography (UCBCT) cross-sectional and 3D post-processed image datasets. 657 patients were examined using UCBCT during hepatic transarterial chemoembolization (TACE), and data were collected retrospectively from January 2012 to September 2014. Tumor detectability, diagnostic ability, detection accuracy and sensitivity were examined for different hepatic tumors using UCBCT cross-sectional, perfusion blood volume (PBV) and UCBCT-MRI (magnetic resonance imaging) fused image datasets. Appropriate statistical tests were used to compare collected sample data. Fused image data showed the significantly higher (all P  <  0.05) diagnostic ability for hepatic tumors compared to UCBCT or PBV image data. The detectability of small hepatic tumors (<5 mm) was significantly reduced (all P  <  0.05) using UCBCT cross-sectional images compared to MRI or fused image data; however, PBV improved tumor detectability using a color display. Fused image data produced 100% tumor sensitivity due to the simultaneous availability of MRI and UCBCT information during tumor diagnosis. Fused image data produced excellent hepatic tumor sensitivity, detectability and diagnostic ability compared to other datasets assessed. Fused image data is extremely reliable and useful compared to UCBCT cross-sectional or PBV image datasets to depict hepatic tumors during TACE. Partial anatomical visualization on cross-sectional images was compensated by fused image data during tumor diagnosis.

  14. GBM Volumetry using the 3D Slicer Medical Image Computing Platform

    PubMed Central

    Egger, Jan; Kapur, Tina; Fedorov, Andriy; Pieper, Steve; Miller, James V.; Veeraraghavan, Harini; Freisleben, Bernd; Golby, Alexandra J.; Nimsky, Christopher; Kikinis, Ron

    2013-01-01

    Volumetric change in glioblastoma multiforme (GBM) over time is a critical factor in treatment decisions. Typically, the tumor volume is computed on a slice-by-slice basis using MRI scans obtained at regular intervals. (3D)Slicer – a free platform for biomedical research – provides an alternative to this manual slice-by-slice segmentation process, which is significantly faster and requires less user interaction. In this study, 4 physicians segmented GBMs in 10 patients, once using the competitive region-growing based GrowCut segmentation module of Slicer, and once purely by drawing boundaries completely manually on a slice-by-slice basis. Furthermore, we provide a variability analysis for three physicians for 12 GBMs. The time required for GrowCut segmentation was on an average 61% of the time required for a pure manual segmentation. A comparison of Slicer-based segmentation with manual slice-by-slice segmentation resulted in a Dice Similarity Coefficient of 88.43 ± 5.23% and a Hausdorff Distance of 2.32 ± 5.23 mm. PMID:23455483

  15. High resolution 3D imaging of bump-bonds by means of synchrotron radiation computed laminography

    NASA Astrophysics Data System (ADS)

    Cecilia, A.; Hamann, E.; Koenig, T.; Xu, F.; Cheng, Y.; Helfen, L.; Ruat, M.; Scheel, M.; Zuber, M.; Baumbach, T.; Fauler, A.; Fiederle, M.

    2013-12-01

    During the flip-chip bonding process of a semiconductor sensor onto readout electronics, a formation of defects may take place, like solder joint displacements, voids, cracks, pores and bridges. This may result in blind spots on the detector, which are insensitive to photons and thus reduce the detector performance. In this work, the flip-chip interconnections of selected CdTe and GaAs Medipix detectors were investigated by synchrotron radiation computed laminography at a micrometer scale. The analysis of the volume rendering proved the presence of voids in the CdTe sensor flip-chip interconnections, with sizes between 3 μm and 9 μm. These voids can be harmful for the long term use of the device, because their presence weakens the adhesive strength between a contact and the readout electronics. Consequently, their formation needs to be avoided. The GaAs Medipix detectors investigated include two sensors that were produced with different flip-chip methods. The comparison of the 3D renderings of the bump-bond interconnections in the two GaAs sensors demonstrated the presence of a misalignment in the range of 5-12 μm between pixel passivation and bump-bonds in the detector produced with an older technique. In contrast to this, no misalignment was observed for the most recently produced detector. The only remarkable observation is the presence of ``satellites'' of solder that do not compromise the detector operation.

  16. Computed Tomography 3-D Imaging of the Metal Deformation Flow Path in Friction Stir Welding

    NASA Technical Reports Server (NTRS)

    Schneider, Judy; Beshears, Ronald; Nunes, Arthur C., Jr.

    2005-01-01

    In friction stir welding (FSW), a rotating threaded pin tool is inserted into a weld seam and literally stirs the edges of the seam together. To determine optimal processing parameters for producing a defect free weld, a better understanding of the resulting metal deformation flow path is required. Marker studies are the principal method of studying the metal deformation flow path around the FSW pin tool. In our study, we have used computed tomography (CT) scans to reveal the flow pattern of a lead wire embedded in a FSW weld seam. At the welding temperature of aluminum, the lead becomes molten and is carried with the macro-flow of the weld metal. By using CT images, a 3-dimensional (3D) image of the lead flow pattern can be reconstructed. CT imaging was found to be a convenient and comprehensive way of collecting and displaying tracer data. It marks an advance over previous more tedious and ambiguous radiographic/metallographic data collection methods.

  17. Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling

    PubMed Central

    Bates, Karl T.; Manning, Phillip L.; Hodgetts, David; Sellers, William I.

    2009-01-01

    Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future

  18. Estimating mass properties of dinosaurs using laser imaging and 3D computer modelling.

    PubMed

    Bates, Karl T; Manning, Phillip L; Hodgetts, David; Sellers, William I

    2009-01-01

    Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future

  19. Improved image guidance technique for minimally invasive mitral valve repair using real-time tracked 3D ultrasound

    NASA Astrophysics Data System (ADS)

    Rankin, Adam; Moore, John; Bainbridge, Daniel; Peters, Terry

    2016-03-01

    In the past ten years, numerous new surgical and interventional techniques have been developed for treating heart valve disease without the need for cardiopulmonary bypass. Heart valve repair is now being performed in a blood-filled environment, reinforcing the need for accurate and intuitive imaging techniques. Previous work has demonstrated how augmenting ultrasound with virtual representations of specific anatomical landmarks can greatly simplify interventional navigation challenges and increase patient safety. These techniques often complicate interventions by requiring additional steps taken to manually define and initialize virtual models. Furthermore, overlaying virtual elements into real-time image data can also obstruct the view of salient image information. To address these limitations, a system was developed that uses real-time volumetric ultrasound alongside magnetically tracked tools presented in an augmented virtuality environment to provide a streamlined navigation guidance platform. In phantom studies simulating a beating-heart navigation task, procedure duration and tool path metrics have achieved comparable performance to previous work in augmented virtuality techniques, and considerable improvement over standard of care ultrasound guidance.

  20. Auto-masked 2D/3D image registration and its validation with clinical cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Steininger, P.; Neuner, M.; Weichenberger, H.; Sharp, G. C.; Winey, B.; Kametriser, G.; Sedlmayer, F.; Deutschmann, H.

    2012-07-01

    Image-guided alignment procedures in radiotherapy aim at minimizing discrepancies between the planned and the real patient setup. For that purpose, we developed a 2D/3D approach which rigidly registers a computed tomography (CT) with two x-rays by maximizing the agreement in pixel intensity between the x-rays and the corresponding reconstructed radiographs from the CT. Moreover, the algorithm selects regions of interest (masks) in the x-rays based on 3D segmentations from the pre-planning stage. For validation, orthogonal x-ray pairs from different viewing directions of 80 pelvic cone-beam CT (CBCT) raw data sets were used. The 2D/3D results were compared to corresponding standard 3D/3D CBCT-to-CT alignments. Outcome over 8400 2D/3D experiments showed that parametric errors in root mean square were <0.18° (rotations) and <0.73 mm (translations), respectively, using rank correlation as intensity metric. This corresponds to a mean target registration error, related to the voxels of the lesser pelvis, of <2 mm in 94.1% of the cases. From the results we conclude that 2D/3D registration based on sequentially acquired orthogonal x-rays of the pelvis is a viable alternative to CBCT-based approaches if rigid alignment on bony anatomy is sufficient, no volumetric intra-interventional data set is required and the expected error range fits the individual treatment prescription.

  1. Auto-masked 2D/3D image registration and its validation with clinical cone-beam computed tomography.

    PubMed

    Steininger, P; Neuner, M; Weichenberger, H; Sharp, G C; Winey, B; Kametriser, G; Sedlmayer, F; Deutschmann, H

    2012-07-01

    Image-guided alignment procedures in radiotherapy aim at minimizing discrepancies between the planned and the real patient setup. For that purpose, we developed a 2D/3D approach which rigidly registers a computed tomography (CT) with two x-rays by maximizing the agreement in pixel intensity between the x-rays and the corresponding reconstructed radiographs from the CT. Moreover, the algorithm selects regions of interest (masks) in the x-rays based on 3D segmentations from the pre-planning stage. For validation, orthogonal x-ray pairs from different viewing directions of 80 pelvic cone-beam CT (CBCT) raw data sets were used. The 2D/3D results were compared to corresponding standard 3D/3D CBCT-to-CT alignments. Outcome over 8400 2D/3D experiments showed that parametric errors in root mean square were <0.18° (rotations) and <0.73 mm (translations), respectively, using rank correlation as intensity metric. This corresponds to a mean target registration error, related to the voxels of the lesser pelvis, of <2 mm in 94.1% of the cases. From the results we conclude that 2D/3D registration based on sequentially acquired orthogonal x-rays of the pelvis is a viable alternative to CBCT-based approaches if rigid alignment on bony anatomy is sufficient, no volumetric intra-interventional data set is required and the expected error range fits the individual treatment prescription. PMID:22705709

  2. Computation of neutron fluxes in clusters of fuel pins arranged in hexagonal assemblies (2D and 3D)

    SciTech Connect

    Prabha, H.; Marleau, G.

    2012-07-01

    For computations of fluxes, we have used Carvik's method of collision probabilities. This method requires tracking algorithms. An algorithm to compute tracks (in 2D and 3D) has been developed for seven hexagonal geometries with cluster of fuel pins. This has been implemented in the NXT module of the code DRAGON. The flux distribution in cluster of pins has been computed by using this code. For testing the results, they are compared when possible with the EXCELT module of the code DRAGON. Tracks are plotted in the NXT module by using MATLAB, these plots are also presented here. Results are presented with increasing number of lines to show the convergence of these results. We have numerically computed volumes, surface areas and the percentage errors in these computations. These results show that 2D results converge faster than 3D results. The accuracy on the computation of fluxes up to second decimal is achieved with fewer lines. (authors)

  3. Applications of airborne ultrasound in human-computer interaction.

    PubMed

    Dahl, Tobias; Ealo, Joao L; Bang, Hans J; Holm, Sverre; Khuri-Yakub, Pierre

    2014-09-01

    Airborne ultrasound is a rapidly developing subfield within human-computer interaction (HCI). Touchless ultrasonic interfaces and pen tracking systems are part of recent trends in HCI and are gaining industry momentum. This paper aims to provide the background and overview necessary to understand the capabilities of ultrasound and its potential future in human-computer interaction. The latest developments on the ultrasound transducer side are presented, focusing on capacitive micro-machined ultrasonic transducers, or CMUTs. Their introduction is an important step toward providing real, low-cost multi-sensor array and beam-forming options. We also provide a unified mathematical framework for understanding and analyzing algorithms used for ultrasound detection and tracking for some of the most relevant applications. PMID:24974162

  4. Postpartum translabial 2D and 3D ultrasound measurements of the anal sphincter complex in primiparous women delivering by vaginal birth versus Cesarean delivery

    PubMed Central

    Hall, Rebecca J.; Leeman, Lawrence M.; Migliaccio, Laura; Qualls, Clifford; Rogers, Rebecca G.

    2015-01-01

    Introduction and hypothesis Consensus on normal translabial ultrasound (TL-US) anal sphincter complex measurements for postpartum women is lacking. We aimed to evaluate normative measurements in 2D and 3D TL-US for the anal sphincter complex (ASC) at 6 months postpartum and compare these measurements in women who had a vaginal birth (VB) and in those who had a Cesarean delivery (CD). Methods A large, prospective cohort of primiparous women underwent 2D and 3D TL-US 6 months after their first delivery. For normative sphincter measurements, we excluded women with third- or fourth-degree lacerations or with sphincter interruption on TL-US. Measurements included the sphincter thickness at the 3, 6, 9, and 12 o'clock positions of the external anal sphincter (EAS) and the internal anal sphincter (IAS) at proximal, mid, and distal levels. We also measured the mean coronal diameter of the pubovisceralis muscle (PVM). Results 696 women consented to participate, and 433 women presented for ultrasound imaging 6 months later. Women who sustained a third- or fourth-degree laceration had significantly thicker EAS measurements at 12 o'clock. Sphincter asymmetry was common (69 %), but was not related to mode of delivery. Only IAS measurements at the proximal and distal 12 o'clock position were significantly thicker for CD patients. There were no significant differences in the EAS or PVM measurements between VB and CD women. Conclusions There appear to be few differences in normative sphincter ultrasound measurements between primiparous patients who had VB or CD. PMID:24105408

  5. A comparison of needle tip localization accuracy using 2D and 3D trans-rectal ultrasound for high-dose-rate prostate cancer brachytherapy treatment planning

    NASA Astrophysics Data System (ADS)

    Hrinivich, W. Thomas; Hoover, Douglas A.; Surry, Kathleen; Edirisinghe, Chandima; Montreuil, Jacques; D'Souza, David; Fenster, Aaron; Wong, Eugene

    2016-03-01

    Background: High-dose-rate brachytherapy (HDR-BT) is a prostate cancer treatment option involving the insertion of hollow needles into the gland through the perineum to deliver a radioactive source. Conventional needle imaging involves indexing a trans-rectal ultrasound (TRUS) probe in the superior/inferior (S/I) direction, using the axial transducer to produce an image set for organ segmentation. These images have limited resolution in the needle insertion direction (S/I), so the sagittal transducer is used to identify needle tips, requiring a manual registration with the axial view. This registration introduces a source of uncertainty in the final segmentations and subsequent treatment plan. Our lab has developed a device enabling 3D-TRUS guided insertions with high S/I spatial resolution, eliminating the need to align axial and sagittal views. Purpose: To compare HDR-BT needle tip localization accuracy between 2D and 3D-TRUS. Methods: 5 prostate cancer patients underwent conventional 2D TRUS guided HDR-BT, during which 3D images were also acquired for post-operative registration and segmentation. Needle end-length measurements were taken, providing a gold standard for insertion depths. Results: 73 needles were analyzed from all 5 patients. Needle tip position differences between imaging techniques was found to be largest in the S/I direction with mean+/-SD of -2.5+/-4.0 mm. End-length measurements indicated that 3D TRUS provided statistically significantly lower mean+/-SD insertion depth error of -0.2+/-3.4 mm versus 2.3+/-3.7 mm with 2D guidance (p < .001). Conclusions: 3D TRUS may provide more accurate HDR-BT needle localization than conventional 2D TRUS guidance for the majority of HDR-BT needles.

  6. Computer numerical control (CNC) lithography: light-motion synchronized UV-LED lithography for 3D microfabrication

    NASA Astrophysics Data System (ADS)

    Kim, Jungkwun; Yoon, Yong-Kyu; Allen, Mark G.

    2016-03-01

    This paper presents a computer-numerical-controlled ultraviolet light-emitting diode (CNC UV-LED) lithography scheme for three-dimensional (3D) microfabrication. The CNC lithography scheme utilizes sequential multi-angled UV light exposures along with a synchronized switchable UV light source to create arbitrary 3D light traces, which are transferred into the photosensitive resist. The system comprises a switchable, movable UV-LED array as a light source, a motorized tilt-rotational sample holder, and a computer-control unit. System operation is such that the tilt-rotational sample holder moves in a pre-programmed routine, and the UV-LED is illuminated only at desired positions of the sample holder during the desired time period, enabling the formation of complex 3D microstructures. This facilitates easy fabrication of complex 3D structures, which otherwise would have required multiple manual exposure steps as in the previous multidirectional 3D UV lithography approach. Since it is batch processed, processing time is far less than that of the 3D printing approach at the expense of some reduction in the degree of achievable 3D structure complexity. In order to produce uniform light intensity from the arrayed LED light source, the UV-LED array stage has been kept rotating during exposure. UV-LED 3D fabrication capability was demonstrated through a plurality of complex structures such as V-shaped micropillars, micropanels, a micro-‘hi’ structure, a micro-‘cat’s claw,’ a micro-‘horn,’ a micro-‘calla lily,’ a micro-‘cowboy’s hat,’ and a micro-‘table napkin’ array.

  7. Conceptual detector development and Monte Carlo simulation of a novel 3D breast computed tomography system

    NASA Astrophysics Data System (ADS)

    Ziegle, Jens; Müller, Bernhard H.; Neumann, Bernd; Hoeschen, Christoph

    2016-03-01

    A new 3D breast computed tomography (CT) system is under development enabling imaging of microcalcifications in a fully uncompressed breast including posterior chest wall tissue. The system setup uses a steered electron beam impinging on small tungsten targets surrounding the breast to emit X-rays. A realization of the corresponding detector concept is presented in this work and it is modeled through Monte Carlo simulations in order to quantify first characteristics of transmission and secondary photons. The modeled system comprises a vertical alignment of linear detectors hold by a case that also hosts the breast. Detectors are separated by gaps to allow the passage of X-rays towards the breast volume. The detectors located directly on the opposite side of the gaps detect incident X-rays. Mechanically moving parts in an imaging system increase the duration of image acquisition and thus can cause motion artifacts. So, a major advantage of the presented system design is the combination of the fixed detectors and the fast steering electron beam which enable a greatly reduced scan time. Thereby potential motion artifacts are reduced so that the visualization of small structures such as microcalcifications is improved. The result of the simulation of a single projection shows high attenuation by parts of the detector electronics causing low count levels at the opposing detectors which would require a flat field correction, but it also shows a secondary to transmission ratio of all counted X-rays of less than 1 percent. Additionally, a single slice with details of various sizes was reconstructed using filtered backprojection. The smallest detail which was still visible in the reconstructed image has a size of 0.2mm.

  8. 3D printing of preclinical X-ray computed tomographic data sets.

    PubMed

    Doney, Evan; Krumdick, Lauren A; Diener, Justin M; Wathen, Connor A; Chapman, Sarah E; Stamile, Brian; Scott, Jeremiah E; Ravosa, Matthew J; Van Avermaete, Tony; Leevy, W Matthew

    2013-01-01

    Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.(1) However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.(2) These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. (3, 4) The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages. PMID:23542702

  9. Detection of bone erosions in early rheumatoid arthritis: 3D ultrasonography versus computed tomography.

    PubMed

    Peluso, G; Bosello, S L; Gremese, E; Mirone, L; Di Gregorio, F; Di Molfetta, V; Pirronti, T; Ferraccioli, G

    2015-07-01

    Three-dimensional (3D) volumetric ultrasonography (US) is an interesting tool that could improve the traditional approach to musculoskeletal US in rheumatology, due to its virtual operator independence and reduced examination time. The aim of this study was to investigate the performance of 3DUS in the detection of bone erosions in hand and wrist joints of early rheumatoid arthritis (ERA) patients, with computed tomography (CT) as the reference method. Twenty ERA patients without erosions on standard radiography of hands and wrists underwent 3DUS and CT evaluation of eleven joints: radiocarpal, intercarpal, ulnocarpal, second to fifth metacarpo-phalangeal (MCP), and second to fifth proximal interphalangeal (PIP) joints of dominant hand. Eleven (55.0%) patients were erosive with CT and ten of them were erosive also at 3DUS evaluation. In five patients, 3DUS identified cortical breaks that were not erosions at CT evaluation. Considering CT as the gold standard to identify erosive patients, the 3DUS sensitivity, specificity, PPV, and NPV were 0.9, 0.55, 0.71, and 0.83, respectively. A total of 32 erosions were detected with CT, 15 of them were also observed at the same sites with 3DUS, whereas 17 were not seen on 3DUS evaluation. The majority of these 3DUS false-negative erosions were in the wrist joints. Furthermore, 18 erosions recorded by 3DUS were false positive. The majority of these 3DUS false-positive erosions were located at PIP joints. This study underlines the limits of 3DUS in detecting individual bone erosion, mostly at the wrist, despite the good sensitivity in identifying erosive patients. PMID:26091903

  10. Development, Verification and Use of Gust Modeling in the NASA Computational Fluid Dynamics Code FUN3D

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.

    2012-01-01

    This paper presents the implementation of gust modeling capability in the CFD code FUN3D. The gust capability is verified by computing the response of an airfoil to a sharp edged gust. This result is compared with the theoretical result. The present simulations will be compared with other CFD gust simulations. This paper also serves as a users manual for FUN3D gust analyses using a variety of gust profiles. Finally, the development of an Auto-Regressive Moving-Average (ARMA) reduced order gust model using a gust with a Gaussian profile in the FUN3D code is presented. ARMA simulated results of a sequence of one-minus-cosine gusts is shown to compare well with the same gust profile computed with FUN3D. Proper Orthogonal Decomposition (POD) is combined with the ARMA modeling technique to predict the time varying pressure coefficient increment distribution due to a novel gust profile. The aeroelastic response of a pitch/plunge airfoil to a gust environment is computed with a reduced order model, and compared with a direct simulation of the system in the FUN3D code. The two results are found to agree very well.

  11. Development and validation of a multiecho computer simulation of ultrasound propagation through cancellous bone

    NASA Astrophysics Data System (ADS)

    Langton, Christian; Church, Luke

    2002-05-01

    Cancellous bone consists of a porous open-celled framework of trabeculae interspersed with marrow. Although the measurement of broadband ultrasound attenuation (BUA) has been shown to be sensitive to osteoporotic changes, the exact dependence on material and structural parameters has not been elucidated. A 3-D computer simulation of ultrasound propagation through cancellous bone has been developed, based upon simple reflective behavior at the multitude of trabecular/marrow interfaces. A cancellous bone framework is initially described by an array of bone and marrow elements. An ultrasound pulse is launched along each row of the model with partial reflection occurring at each bone/marrow interface. If a reverse direction wave hits an interface, a further forward (echo) wave is created, with phase inversion implemented if appropriate. This process is monitored for each wave within each row. The effective received signal is created by summing the time domain data, thus simulating detection by a phase-sensitive ultrasound transducer, as incorporated in clinical systems. The simulation has been validated on a hexagonal honeycomb design of variable mesh size, first against a commercial computer simulation solution (Wave 2000 Pro), and second, via experimental measurement of physical replicas produced by stereolithography.

  12. Programmer's Guide for Subroutine PRNT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PRNT3D is a subroutine package which generates a variety of printed plot displays. The displays…

  13. User's Guide for Subroutine PLOT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    This module is part of a series designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PLOT3D is a subroutine package which generates a variety of three dimensional hidden…

  14. Programmer's Guide for Subroutine PLOT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    This module is part of a series designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PLOT3D is a subroutine package which generates a variety of three-dimensional hidden…

  15. User's Guide for Subroutine PRNT3D. Physical Processes in Terrestrial and Aquatic Ecosystems, Computer Programs and Graphics Capabilities.

    ERIC Educational Resources Information Center

    Gales, Larry

    These materials were designed to be used by life science students for instruction in the application of physical theory to ecosystem operation. Most modules contain computer programs which are built around a particular application of a physical process. PRNT3D is a subroutine package which generates a variety of printer plot displays. The displays…

  16. DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROOVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

    EPA Science Inventory

    DEVELOPMENT OF 3-D COMPUTER MODELS OF HUMAN LUNG MORPHOLOGY FOR IMPROVED RISK ASSESSMENT OF INHALED PARTICULATE MATTER

    Jeffry D. Schroeter, Curriculum in Toxicology, University of North Carolina, Chapel Hill, NC 27599; Ted B. Martonen, ETD, NHEERL, USEPA, RTP, NC 27711; Do...

  17. Automatic ultrasound-MRI registration for neurosurgery using the 2D and 3D LC(2) Metric.

    PubMed

    Fuerst, Bernhard; Wein, Wolfgang; Müller, Markus; Navab, Nassir

    2014-12-01

    To enable image guided neurosurgery, the alignment of pre-interventional magnetic resonance imaging (MRI) and intra-operative ultrasound (US) is commonly required. We present two automatic image registration algorithms using the similarity measure Linear Correlation of Linear Combination (LC(2)) to align either freehand US slices or US volumes with MRI images. Both approaches allow an automatic and robust registration, while the three dimensional method yields a significantly improved percentage of optimally aligned registrations for randomly chosen clinically relevant initializations. This study presents a detailed description of the methodology and an extensive evaluation showing an accuracy of 2.51mm, precision of 0.85mm and capture range of 15mm (>95% convergence) using 14 clinical neurosurgical cases. PMID:24842859

  18. Effective Permeability of Fractured Rocks by Analytical Methods: A 3D Computational Study

    NASA Astrophysics Data System (ADS)

    Sævik, P. N.; Berre, I.; Jakobsen, M.; Lien, M.

    2013-12-01

    Analytical upscaling methods have been proposed in the literature to predict the effective hydraulic permeability of a fractured rock from its micro-scale parameters (fracture aperture, fracture orientation, fracture content, etc.). In this presentation, we put special emphasis on three effective medium methods (the symmetric and asymmetric self-consistent methods, and the differential method), and evaluate their accuracy for a wide range of parameter values. The analytical predictions are computed using our recently developed effective medium formulations, which are specifically adapted for fractured media. Compared to previous formulations, the new expressions have improved numerical stability properties, and require fewer input parameters. To assess their accuracy, the analytical predictions have been compared with 3D finite element simulations. Specifically, we generated realizations of several different fracture geometries, each consisting of 102 fractures within a unit cube. We applied unit potential difference on two opposing sides, and no-flux conditions on the remaining sides. A commercial finite-element solver was used to calculate the mean flux, from which the effective conductivity was found. This process was repeated for fracture densities up to ɛ = 1.0. Also, a wide range of fracture permeabilities was considered, from completely blocking to infinitely permeable fractures. The results were used to determine the range of applicability for each analytical method, which excels in different regions of the parameter space. For blocking fractures, the differential method is very accurate throughout the investigated parameter range. The symmetric self-consistent method also agrees well with the numerical results on sealed fractures, while the asymmetric self-consistent method is more unreliable. For permeable fractures, the performance of the methods depends on the dimensionless quantity λ = (Kfrac a)/(r Kmat ), describing the contrast between fracture and

  19. Accuracy and reliability of measurements obtained from computed tomography 3D volume rendered images.

    PubMed

    Stull, Kyra E; Tise, Meredith L; Ali, Zabiullah; Fowler, David R

    2014-05-01

    Forensic pathologists commonly use computed tomography (CT) images to assist in determining the cause and manner of death as well as for mass disaster operations. Even though the design of the CT machine does not inherently produce distortion, most techniques within anthropology rely on metric variables, thus concern exists regarding the accuracy of CT images reflecting an object's true dimensions. Numerous researchers have attempted to validate the use of CT images, however the comparisons have only been conducted on limited elements and/or comparisons were between measurements taken from a dry element and measurements taken from the 3D-CT image of the same dry element. A full-body CT scan was performed prior to autopsy at the Office of the Chief Medical Examiner for the State of Maryland. Following autopsy, the remains were processed to remove all soft tissues and the skeletal elements were subject to an additional CT scan. Percent differences and Bland-Altman plots were used to assess the accuracy between osteometric variables obtained from the dry skeletal elements and from CT images with and without soft tissues. An additional seven crania were scanned, measured by three observers, and the reliability was evaluated by technical error of measurement (TEM) and relative technical error of measurement (%TEM). Average percent differences between the measurements obtained from the three data sources ranged from 1.4% to 2.9%. Bland-Altman plots illustrated the two sets of measurements were generally within 2mm for each comparison between data sources. Intra-observer TEM and %TEM for three observers and all craniometric variables ranged between 0.46mm and 0.77mm and 0.56% and 1.06%, respectively. The three-way inter-observer TEM and %TEM for craniometric variables was 2.6mm and 2.26%, respectively. Variables that yielded high error rates were orbital height, orbital breadth, inter-orbital breadth and parietal chord. Overall, minimal differences were found among the

  20. 3D parallel computations of turbofan noise propagation using a spectral element method

    NASA Astrophysics Data System (ADS)

    Taghaddosi, Farzad

    2006-12-01

    A three-dimensional code has been developed for the simulation of tone noise generated by turbofan engine inlets using computational aeroacoustics. The governing equations are the linearized Euler equations, which are further simplified to a set of equations in terms of acoustic potential, using the irrotational flow assumption, and subsequently solved in the frequency domain. Due to the special nature of acoustic wave propagation, the spatial discretization is performed using a spectral element method, where a tensor product of the nth-degree polynomials based on Chebyshev orthogonal functions is used to approximate variations within hexahedral elements. Non-reflecting boundary conditions are imposed at the far-field using a damping layer concept. This is done by augmenting the continuity equation with an additional term without modifying the governing equations as in PML methods. Solution of the linear system of equations for the acoustic problem is based on the Schur complement method, which is a nonoverlapping domain decomposition technique. The Schur matrix is first solved using a matrix-free iterative method, whose convergence is accelerated with a novel local preconditioner. The solution in the entire domain is then obtained by finding solutions in smaller subdomains. The 3D code also contains a mean flow solver based on the full potential equation in order to take into account the effects of flow variations around the nacelle on the scattering of the radiated sound field. All aspects of numerical simulations, including building and assembling the coefficient matrices, implementation of the Schur complement method, and solution of the system of equations for both the acoustic and mean flow problems are performed on multiprocessors in parallel using the resources of the CLUMEQ Supercomputer Center. A large number of test cases are presented, ranging in size from 100 000-2 000 000 unknowns for which, depending on the size of the problem, between 8-48 CPU's are

  1. Computational Graph Model for 3D Cells Tracking in Zebra Fish Datasets

    NASA Astrophysics Data System (ADS)

    Zhang, Lelin; Xiong, Hongkai; Zhao, Yang; Zhang, Kai; Zhou, Xiaobo

    2007-11-01

    This paper leads to a novel technique for tracking and identification of zebra-fish cells in 3D image sequences, extending graph-based multi-objects tracking algorithm to 3D applications. As raised in previous work of 2D graph-based method, separated cells are modeled as vertices that connected by edges. Then the tracking work is simplified to that of vertices matching between graphs generated from consecutive frames. Graph-based tracking is composed of three steps: graph generation, initial source vertices selection and graph saturation. To satisfy demands in this work separated cell records are segmented from original datasets using 3D level-set algorithms. Besides, advancements are achieved in each of the step including graph regulations, multi restrictions on source vertices and enhanced flow quantifications. Those strategies make a good compensation for graph-based multi-objects tracking method in 2D space. Experiments are carried out in 3D datasets sampled from zebra fish, results of which shows that this enhanced method could be potentially applied to tracking of objects with diverse features.

  2. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator With Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel L.

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  3. Comparison of Computational Aeroacoustics Prediction of Acoustic Transmission Through a 3D Stator with Experiment

    NASA Technical Reports Server (NTRS)

    Hixon, Ray; Envia, Edmane; Dahl, Milo; Sutliff, Daniel

    2014-01-01

    In this paper, numerical predictions of acoustic transmission through a 3D stator obtained using the NASA BASS code are compared with experimentally measured data. The influence of vane count and stagger as well as frequency and mode order on the transmission loss is investigated. The data-theory comparisons indicate that BASS can predict all the important trends observed in the experimental data.

  4. TBIEM3D: A Computer Program for Predicting Ducted Fan Engine Noise. Version 1.1

    NASA Technical Reports Server (NTRS)

    Dunn, M. H.

    1997-01-01

    This document describes the usage of the ducted fan noise prediction program TBIEM3D (Thin duct - Boundary Integral Equation Method - 3 Dimensional). A scattering approach is adopted in which the acoustic pressure field is split into known incident and unknown scattered parts. The scattering of fan-generated noise by a finite length circular cylinder in a uniform flow field is considered. The fan noise is modeled by a collection of spinning point thrust dipoles. The program, based on a Boundary Integral Equation Method (BIEM), calculates circumferential modal coefficients of the acoustic pressure at user-specified field locations. The duct interior can be of the hard wall type or lined. The duct liner is axisymmetric, locally reactive, and can be uniform or axially segmented. TBIEM3D is written in the FORTRAN programming language. Input to TBIEM3D is minimal and consists of geometric and kinematic parameters. Discretization and numerical parameters are determined automatically by the code. Several examples are presented to demonstrate TBIEM3D capabilities.

  5. Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.

    2014-01-01

    Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.

  6. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  7. Numerical modeling of the 3D dynamics of ultrasound contrast agent microbubbles using the boundary integral method

    NASA Astrophysics Data System (ADS)

    Wang, Qianxi; Manmi, Kawa; Calvisi, Michael L.

    2015-02-01

    Ultrasound contrast agents (UCAs) are microbubbles stabilized with a shell typically of lipid, polymer, or protein and are emerging as a unique tool for noninvasive therapies ranging from gene delivery to tumor ablation. While various models have been developed to describe the spherical oscillations of contrast agents, the treatment of nonspherical behavior has received less attention. However, the nonspherical dynamics of contrast agents are thought to play an important role in therapeutic applications, for example, enhancing the uptake of therapeutic agents across cell membranes and tissue interfaces, and causing tissue ablation. In this paper, a model for nonspherical contrast agent dynamics based on the boundary integral method is described. The effects of the encapsulating shell are approximated by adapting Hoff's model for thin-shell, spherical contrast agents. A high-quality mesh of the bubble surface is maintained by implementing a hybrid approach of the Lagrangian method and elastic mesh technique. The numerical model agrees well with a modified Rayleigh-Plesset equation for encapsulated spherical bubbles. Numerical analyses of the dynamics of UCAs in an infinite liquid and near a rigid wall are performed in parameter regimes of clinical relevance. The oscillation amplitude and period decrease significantly due to the coating. A bubble jet forms when the amplitude of ultrasound is sufficiently large, as occurs for bubbles without a coating; however, the threshold amplitude required to incite jetting increases due to the coating. When a UCA is near a rigid boundary subject to acoustic forcing, the jet is directed towards the wall if the acoustic wave propagates perpendicular to the boundary. When the acoustic wave propagates parallel to the rigid boundary, the jet direction has components both along the wave direction and towards the boundary that depend mainly on the dimensionless standoff distance of the bubble from the boundary. In all cases, the jet

  8. Computer-aided diagnosis of pulmonary nodules on CT scans: Segmentation and classification using 3D active contours

    PubMed Central

    Way, Ted W.; Hadjiiski, Lubomir M.; Sahiner, Berkman; Chan, Heang-Ping; Cascade, Philip N.; Kazerooni, Ella A.; Bogot, Naama; Zhou, Chuan

    2009-01-01

    We are developing a computer-aided diagnosis (CAD) system to classify malignant and benign lung nodules found on CT scans. A fully automated system was designed to segment the nodule from its surrounding structured background in a local volume of interest (VOI) and to extract image features for classification. Image segmentation was performed with a three-dimensional (3D) active contour (AC) method. A data set of 96 lung nodules (44 malignant, 52 benign) from 58 patients was used in this study. The 3D AC model is based on two-dimensional AC with the addition of three new energy components to take advantage of 3D information: (1) 3D gradient, which guides the active contour to seek the object surface, (2) 3D curvature, which imposes a smoothness constraint in the z direction, and (3) mask energy, which penalizes contours that grow beyond the pleura or thoracic wall. The search for the best energy weights in the 3D AC model was guided by a simplex optimization method. Morphological and gray-level features were extracted from the segmented nodule. The rubber band straightening transform (RBST) was applied to the shell of voxels surrounding the nodule. Texture features based on run-length statistics were extracted from the RBST image. A linear discriminant analysis classifier with stepwise feature selection was designed using a second simplex optimization to select the most effective features. Leave-one-case-out resampling was used to train and test the CAD system. The system achieved a test area under the receiver operating characteristic curve (Az) of 0.83±0.04. Our preliminary results indicate that use of the 3D AC model and the 3D texture features surrounding the nodule is a promising approach to the segmentation and classification of lung nodules with CAD. The segmentation performance of the 3D AC model trained with our data set was evaluated with 23 nodules available in the Lung Image Database Consortium (LIDC). The lung nodule volumes segmented by the 3D AC

  9. High-Throughput, High-Frequency 3D Ultrasound for In Utero Analysis of Embryonic Mouse Brain Development

    PubMed Central

    Aristizábal, Orlando; Mamou, Jonathan; Ketterling, Jeffrey A.; Turnbull, Daniel H.

    2013-01-01

    With the emergence of the mouse as the predominant model system for studying mammalian brain development, in utero imaging methods are urgently required to analyze the dynamics of brain growth and patterning in mouse embryos. To address this need, we combined synthetic focusing with a high-frequency (38-MHz) annular-array ultrasound imaging system for extended depth-of-field, coded excitation for improved penetration, and respiratory-gated transmit-receive. This combination allowed noninvasive in utero acquisition of motion-free, three-dimensional data from individual embryos in approximately 2 minutes, and data from 4 or more embryos in a pregnant mouse in less than 30 minutes. Data were acquired from 148 embryos spanning 5 days of early-to-mid gestational stages of brain development. The results showed that brain anatomy and cerebral vasculature can be imaged with this system, and that quantitative analyses of segmented cerebral ventricles can be used to characterize volumetric changes associated with mouse brain development. PMID:24035625

  10. Generating 3D anatomically detailed models of the retina from OCT data sets: implications for computational modelling

    NASA Astrophysics Data System (ADS)

    Shalbaf, Farzaneh; Dokos, Socrates; Lovell, Nigel H.; Turuwhenua, Jason; Vaghefi, Ehsan

    2015-12-01

    Retinal prosthesis has been proposed to restore vision for those suffering from the retinal pathologies that mainly affect the photoreceptors layer but keep the inner retina intact. Prior to costly risky experimental studies computational modelling of the retina will help to optimize the device parameters and enhance the outcomes. Here, we developed an anatomically detailed computational model of the retina based on OCT data sets. The consecutive OCT images of individual were subsequently segmented to provide a 3D representation of retina in the form of finite elements. Thereafter, the electrical properties of the retina were modelled by implementing partial differential equation on the 3D mesh. Different electrode configurations, that is bipolar and hexapolar configurations, were implemented and the results were compared with the previous computational and experimental studies. Furthermore, the possible effects of the curvature of retinal layers on the current steering through the retina were proposed and linked to the clinical observations.

  11. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    NASA Astrophysics Data System (ADS)

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-02-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries.

  12. A computational model that recovers the 3D shape of an object from a single 2D retinal representation.

    PubMed

    Li, Yunfeng; Pizlo, Zygmunt; Steinman, Robert M

    2009-05-01

    Human beings perceive 3D shapes veridically, but the underlying mechanisms remain unknown. The problem of producing veridical shape percepts is computationally difficult because the 3D shapes have to be recovered from 2D retinal images. This paper describes a new model, based on a regularization approach, that does this very well. It uses a new simplicity principle composed of four shape constraints: viz., symmetry, planarity, maximum compactness and minimum surface. Maximum compactness and minimum surface have never been used before. The model was tested with random symmetrical polyhedra. It recovered their 3D shapes from a single randomly-chosen 2D image. Neither learning, nor depth perception, was required. The effectiveness of the maximum compactness and the minimum surface constraints were measured by how well the aspect ratio of the 3D shapes was recovered. These constraints were effective; they recovered the aspect ratio of the 3D shapes very well. Aspect ratios recovered by the model were compared to aspect ratios adjusted by four human observers. They also adjusted aspect ratios very well. In those rare cases, in which the human observers showed large errors in adjusted aspect ratios, their errors were very similar to the errors made by the model. PMID:18621410

  13. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs.

    PubMed

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  14. Use of micro computed-tomography and 3D printing for reverse engineering of mouse embryo nasal capsule

    NASA Astrophysics Data System (ADS)

    Tesařová, M.; Zikmund, T.; Kaucká, M.; Adameyko, I.; Jaroš, J.; Paloušek, D.; Škaroupka, D.; Kaiser, J.

    2016-03-01

    Imaging of increasingly complex cartilage in vertebrate embryos is one of the key tasks of developmental biology. This is especially important to study shape-organizing processes during initial skeletal formation and growth. Advanced imaging techniques that are reflecting biological needs give a powerful impulse to push the boundaries of biological visualization. Recently, techniques for contrasting tissues and organs have improved considerably, extending traditional 2D imaging approaches to 3D . X-ray micro computed tomography (μCT), which allows 3D imaging of biological objects including their internal structures with a resolution in the micrometer range, in combination with contrasting techniques seems to be the most suitable approach for non-destructive imaging of embryonic developing cartilage. Despite there are many software-based ways for visualization of 3D data sets, having a real solid model of the studied object might give novel opportunities to fully understand the shape-organizing processes in the developing body. In this feasibility study we demonstrated the full procedure of creating a real 3D object of mouse embryo nasal capsule, i.e. the staining, the μCT scanning combined by the advanced data processing and the 3D printing.

  15. Computer-aided multiple-head 3D printing system for printing of heterogeneous organ/tissue constructs

    PubMed Central

    Jung, Jin Woo; Lee, Jung-Seob; Cho, Dong-Woo

    2016-01-01

    Recently, much attention has focused on replacement or/and enhancement of biological tissues via the use of cell-laden hydrogel scaffolds with an architecture that mimics the tissue matrix, and with the desired three-dimensional (3D) external geometry. However, mimicking the heterogeneous tissues that most organs and tissues are formed of is challenging. Although multiple-head 3D printing systems have been proposed for fabricating heterogeneous cell-laden hydrogel scaffolds, to date only the simple exterior form has been realized. Here we describe a computer-aided design and manufacturing (CAD/CAM) system for this application. We aim to develop an algorithm to enable easy, intuitive design and fabrication of a heterogeneous cell-laden hydrogel scaffolds with a free-form 3D geometry. The printing paths of the scaffold are automatically generated from the 3D CAD model, and the scaffold is then printed by dispensing four materials; i.e., a frame, two kinds of cell-laden hydrogel and a support. We demonstrated printing of heterogeneous tissue models formed of hydrogel scaffolds using this approach, including the outer ear, kidney and tooth tissue. These results indicate that this approach is particularly promising for tissue engineering and 3D printing applications to regenerate heterogeneous organs and tissues with tailored geometries to treat specific defects or injuries. PMID:26899876

  16. Classification and quantification of pore shapes in sandstone reservoir rocks with 3-D X-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Halisch, M.; Müller, C.; Fernandes, C. P.

    2015-12-01

    Recent years have seen a growing interest in the characterization of the pore morphologies of reservoir rocks and how the spatial organization of pore traits affects the macro behaviour of rock-fluid systems. With the availability of 3-D high-resolution imaging (e.g. μ-CT), the detailed quantification of particle shapes has been facilitated by progress in computer science. Here, we show how the shapes of irregular rock particles (pores) can be classified and quantified based on binary 3-D images. The methodology requires the measurement of basic 3-D particle descriptors and a shape classification that involves the similarity of artificial objects, which is based on main pore network detachments and 3-D sample sizes. The results were validated for three sandstones (S1, S2 and S3) from distinct reservoirs, and most of the pore shapes were found to be plate- and cube-like. Furthermore, this study generalizes a practical way to correlate specific particle shapes, such as rods, blades, cuboids, plates and cubes, to characterize asymmetric particles of any material type with 3-D image analysis.

  17. A fully programmable computing architecture for medical ultrasound machines.

    PubMed

    Schneider, Fabio Kurt; Agarwal, Anup; Yoo, Yang Mo; Fukuoka, Tetsuya; Kim, Yongmin

    2010-03-01

    Application-specific ICs have been traditionally used to support the high computational and data rate requirements in medical ultrasound systems, particularly in receive beamforming. Utilizing the previously developed efficient front-end algorithms, in this paper, we present a simple programmable computing architecture, consisting of a field-programmable gate array (FPGA) and a digital signal processor (DSP), to support core ultrasound signal processing. It was found that 97.3% and 51.8% of the FPGA and DSP resources are, respectively, needed to support all the front-end and back-end processing for B-mode imaging with 64 channels and 120 scanlines per frame at 30 frames/s. These results indicate that this programmable architecture can meet the requirements of low- and medium-level ultrasound machines while providing a flexible platform for supporting the development and deployment of new algorithms and emerging clinical applications. PMID:19546045

  18. Ultrasound attenuation computed tomography assessment of PAGAT gel dose.

    PubMed

    Khoei, S; Trapp, J V; Langton, C M

    2014-08-01

    Ultrasound has been previously investigated as an alternative readout method for irradiated polymer gel dosimeters, with authors reporting varying dose responses. We extend previous work utilizing a new computed tomography ultrasound scanner comprising of two identical 5 MHz, 128-element linear-array ultrasound transducers, co-axially aligned and submerged in water as a coupling agent, with rotational of the gel dosimeter between the transducers facilitated by a robotic arm. We have investigated the dose-dependence of both ultrasound bulk attenuation and broadband ultrasound attenuation (BUA) for the PAGAT gel dosimeter. The ultrasound bulk attenuation dose sensitivity was found to be 1.46  ±  0.04 dB m( -1) Gy( -1), being in agreement with previously published results for PAG and MAGIC gels. BUA was also found to be dose dependent and was measured to be 0.024  ±  0.003 dB MHz( -1) Gy( -1); the advantage of BUA being its insensitivity to frequency-independent attenuation mechanisms including reflection and refraction, thereby minimizing image reconstruction artefacts. PMID:25049236

  19. Analyzing bone remodeling patterns after total hip arthroplasty using quantitative computed tomography and patient-specific 3D computational models

    PubMed Central

    Arachchi, Shanika; Pitto, Rocco P.; Anderson, Iain A.

    2015-01-01

    Background Computational models in the form of finite element analysis technique that incorporates bone remodeling theories along with DEXA scans has been extensively used in predicting bone remodeling patterns around the implant. However, majority of such studies used generic models. Therefore, the aim of this study is to develop patient-specific finite element models of total hip replacement patients using their quantitative computed tomography (QCT) scans and accurately analyse bone remodelling patterns after total hip arthroplasty (THA). Methods Patient-specific finite element models have been generated using the patients’ QCT scans from a previous clinical follow-up study. The femur was divided into five regions in proximal-distal direction and then further divided into four quadrants for detailed analysis of bone remodeling patterns. Two types of analysis were performed—inter-patient and intra patient to compare them and then the resulting bone remodeling patterns were quantitatively analyzed. Results Our results show that cortical bone density decrease is higher in diaphyseal region over time and the cancellous bone density decreases significantly in metaphyseal region over time. In metaphyseal region, posterior-medial (P-M) quadrant showed high bone loss while diaphyseal regions show high bone loss in anterior-lateral (A-L) quadrant. Conclusions Our study demonstrated that combining QCT with 3D patient-specific models has the ability of monitoring bone density change patterns after THA in much finer details. Future studies include using these findings for the development of a bone remodelling algorithm capable of predicting surgical outcomes for THA patients. PMID:26435921

  20. Development of transrectal diffuse optical tomography combined with 3D-transrectal ultrasound imaging to monitor the photocoagulation front during interstitial photothermal therapy of primary focal prostate cancer

    NASA Astrophysics Data System (ADS)

    He, Jie; Weersink, Robert; Veilleux, Israel; Mayo, Kenwrick; Zhang, Anqi; Piao, Daqing; Alam, Adeel; Trachtenberg, John; Wilson, Brian C.

    2013-03-01

    Interstitial near-infrared laser thermal therapy (LITT) is currently undergoing clinical trials as an alternative to watchful waiting or radical surgery in patients with low-risk focal prostate cancer. Currently, we use magnetic resonance image (MRI)-based thermography to monitor treatment delivery and determine indirectly the completeness of the target tissue destruction while avoiding damage to adjacent normal tissues, particularly the rectal wall. However, incomplete tumor destruction has occurred in a significant fraction of patients due to premature termination of treatment, since the photocoagulation zone is not directly observed. Hence, we are developing transrectal diffuse optical tomography (TRDOT), in combination with transrectal 3D ultrasound (3D-TRUS), to address his limitation. This is based on the large changes in optical scattering expected upon tissue coagulation. Here, we present forward simulations of a growing coagulated lesion with optical scattering contrast, using an established finite element analysis software platform (NIRFAST). The simulations were validated in tissue-simulating phantoms, with measurements acquired by a state-of-the-art continuous wave (CW) TRDOT system and a recently assembled bench-top CW-DOT system, with specific source-detector configurations. Two image reconstruction schemes were investigated and evaluated, specifically for the accurate delineation of the posterior boundary of the coagulation zone as the critical parameter for treatment guidance in this clinical application.

  1. The Relationship of 3D Translabial Ultrasound Anal Sphincter Complex Measurements to Postpartum Anal and Fecal Incontinence

    PubMed Central

    MERIWETHER, Kate V.; HALL, Rebecca J.; LEEMAN, Lawrence M.; MIGLIACCIO, Laura; QUALLS, Clifford; ROGERS, Rebecca G.

    2015-01-01

    Objective We aimed to determine whether ASC measurements on translabial ultrasound (TL-US) were related to anal incontinence (AI) or fecal incontinence (FI) symptoms six months postpartum. Methods A prospective cohort of primiparous women underwent TL-US six months after a vaginal birth (VB) or Cesarean delivery (CD). Muscle thickness was measured at 3, 6, 9, and 12 o’clock positions of the external sphincter (EAS), the same four quadrants of the internal sphincter (IAS) at proximal, mid, and distal levels, and at the bilateral pubovisceralis muscle (PVM). Measurements were correlated to AI and FI on the Wexner Fecal Incontinence Scale, with sub-analyses by mode of delivery. The odds ratio (OR) of symptoms was calculated for every one millimeter increase in muscle thickness (E1MIT). Results 423 women (299 VB, 124 CD) had TL-US six months postpartum. Decreased AI risk was associated with thicker measurements at the 6 o’clock (OR 0.74 E1MIT) and 9 o’clock proximal IAS (OR 0.71 E1MIT) in the entire cohort. For CD women, thicker measurements of the 9 o’clock proximal IAS were associated with decreased risk of AI (OR 0.56 E1MIT) and thicker distal 6 o’clock IAS measurements were related to a decreased risk of FI (OR 0.37 E1MIT). For VB women, no sphincter measurements were significantly related to symptoms, but thicker PVM measurements were associated with increased risk of AI (right side OR 1.32 E1MIT; left side OR 1.21 E1MIT). Conclusions ASC anatomy is associated with AI and FI in certain locations; these locations varybased on the patient’s mode of delivery. PMID:26085463

  2. Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

    PubMed Central

    Mourad, Raphaël; Cuvier, Olivier

    2016-01-01

    Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237

  3. A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery.

    PubMed

    Nowell, Mark; Rodionov, Roman; Zombori, Gergely; Sparks, Rachel; Rizzi, Michele; Ourselin, Sebastien; Miserocchi, Anna; McEvoy, Andrew; Duncan, John

    2016-01-01

    Epilepsy surgery is challenging and the use of 3D multimodality image integration (3DMMI) to aid presurgical planning is well-established. Multimodality image integration can be technically demanding, and is underutilised in clinical practice. We have developed a single software platform for image integration, 3D visualization and surgical planning. Here, our pipeline is described in step-by-step fashion, starting with image acquisition, proceeding through image co-registration, manual segmentation, brain and vessel extraction, 3D visualization and manual planning of stereoEEG (SEEG) implantations. With dissemination of the software this pipeline can be reproduced in other centres, allowing other groups to benefit from 3DMMI. We also describe the use of an automated, multi-trajectory planner to generate stereoEEG implantation plans. Preliminary studies suggest this is a rapid, safe and efficacious adjunct for planning SEEG implantations. Finally, a simple solution for the export of plans and models to commercial neuronavigation systems for implementation of plans in the operating theater is described. This software is a valuable tool that can support clinical decision making throughout the epilepsy surgery pathway. PMID:27286266

  4. A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery

    PubMed Central

    Nowell, Mark; Rodionov, Roman; Zombori, Gergely; Sparks, Rachel; Rizzi, Michele; Ourselin, Sebastien; Miserocchi, Anna; McEvoy, Andrew; Duncan, John

    2016-01-01

    Epilepsy surgery is challenging and the use of 3D multimodality image integration (3DMMI) to aid presurgical planning is well-established. Multimodality image integration can be technically demanding, and is underutilised in clinical practice. We have developed a single software platform for image integration, 3D visualization and surgical planning. Here, our pipeline is described in step-by-step fashion, starting with image acquisition, proceeding through image co-registration, manual segmentation, brain and vessel extraction, 3D visualization and manual planning of stereoEEG (SEEG) implantations. With dissemination of the software this pipeline can be reproduced in other centres, allowing other groups to benefit from 3DMMI. We also describe the use of an automated, multi-trajectory planner to generate stereoEEG implantation plans. Preliminary studies suggest this is a rapid, safe and efficacious adjunct for planning SEEG implantations. Finally, a simple solution for the export of plans and models to commercial neuronavigation systems for implementation of plans in the operating theater is described. This software is a valuable tool that can support clinical decision making throughout the epilepsy surgery pathway. PMID:27286266

  5. Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture

    PubMed Central

    Quaini, A.; Canic, S.; Glowinski, R.; Igo, S.; Hartley, C.J.; Zoghbi, W.; Little, S.

    2011-01-01

    This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194

  6. Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture.

    PubMed

    Quaini, A; Canic, S; Glowinski, R; Igo, S; Hartley, C J; Zoghbi, W; Little, S

    2012-01-10

    This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194

  7. Computer-aided segmentation and 3D analysis of in vivo MRI examinations of the human vocal tract during phonation

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; Behrends, Johannes; Hoole, Phil; Leinsinger, Gerda L.; Meyer-Baese, Anke; Reiser, Maximilian F.

    2008-03-01

    We developed, tested, and evaluated a 3D segmentation and analysis system for in vivo MRI examinations of the human vocal tract during phonation. For this purpose, six professionally trained speakers, age 22-34y, were examined using a standardized MRI protocol (1.5 T, T1w FLASH, ST 4mm, 23 slices, acq. time 21s). The volunteers performed a prolonged (>=21s) emission of sounds of the German phonemic inventory. Simultaneous audio tape recording was obtained to control correct utterance. Scans were made in axial, coronal, and sagittal planes each. Computer-aided quantitative 3D evaluation included (i) automated registration of the phoneme-specific data acquired in different slice orientations, (ii) semi-automated segmentation of oropharyngeal structures, (iii) computation of a curvilinear vocal tract midline in 3D by nonlinear PCA, (iv) computation of cross-sectional areas of the vocal tract perpendicular to this midline. For the vowels /a/,/e/,/i/,/o/,/ø/,/u/,/y/, the extracted area functions were used to synthesize phoneme sounds based on an articulatory-acoustic model. For quantitative analysis, recorded and synthesized phonemes were compared, where area functions extracted from 2D midsagittal slices were used as a reference. All vowels could be identified correctly based on the synthesized phoneme sounds. The comparison between synthesized and recorded vowel phonemes revealed that the quality of phoneme sound synthesis was improved for phonemes /a/ and /y/, if 3D instead of 2D data were used, as measured by the average relative frequency shift between recorded and synthesized vowel formants (p<0.05, one-sided Wilcoxon rank sum test). In summary, the combination of fast MRI followed by subsequent 3D segmentation and analysis is a novel approach to examine human phonation in vivo. It unveils functional anatomical findings that may be essential for realistic modelling of the human vocal tract during speech production.

  8. Implementation of Headtracking and 3D Stereo with Unity and VRPN for Computer Simulations

    NASA Technical Reports Server (NTRS)

    Noyes, Matthew A.

    2013-01-01

    This paper explores low-cost hardware and software methods to provide depth cues traditionally absent in monocular displays. The use of a VRPN server in conjunction with a Microsoft Kinect and/or Nintendo Wiimote to provide head tracking information to a Unity application, and NVIDIA 3D Vision for retinal disparity support, is discussed. Methods are suggested to implement this technology with NASA's EDGE simulation graphics package, along with potential caveats. Finally, future applications of this technology to astronaut crew training, particularly when combined with an omnidirectional treadmill for virtual locomotion and NASA's ARGOS system for reduced gravity simulation, are discussed.

  9. Isoparametric 3-D Finite Element Mesh Generation Using Interactive Computer Graphics

    NASA Technical Reports Server (NTRS)

    Kayrak, C.; Ozsoy, T.

    1985-01-01

    An isoparametric 3-D finite element mesh generator was developed with direct interface to an interactive geometric modeler program called POLYGON. POLYGON defines the model geometry in terms of boundaries and mesh regions for the mesh generator. The mesh generator controls the mesh flow through the 2-dimensional spans of regions by using the topological data and defines the connectivity between regions. The program is menu driven and the user has a control of element density and biasing through the spans and can also apply boundary conditions, loads interactively.

  10. Novel low-cost 2D/3D switchable autostereoscopic system for notebook computers and other portable devices

    NASA Astrophysics Data System (ADS)

    Eichenlaub, Jesse B.

    1995-03-01

    Mounting a lenticular lens in front of a flat panel display is a well known, inexpensive, and easy way to create an autostereoscopic system. Such a lens produces half resolution 3D images because half the pixels on the LCD are seen by the left eye and half by the right eye. This may be acceptable for graphics, but it makes full resolution text, as displayed by common software, nearly unreadable. Very fine alignment tolerances normally preclude the possibility of removing and replacing the lens in order to switch between 2D and 3D applications. Lenticular lens based displays are therefore limited to use as dedicated 3D devices. DTI has devised a technique which removes this limitation, allowing switching between full resolution 2D and half resolution 3D imaging modes. A second element, in the form of a concave lenticular lens array whose shape is exactly the negative of the first lens, is mounted on a hinge so that it can be swung down over the first lens array. When so positioned the two lenses cancel optically, allowing the user to see full resolution 2D for text or numerical applications. The two lenses, having complementary shapes, naturally tend to nestle together and snap into perfect alignment when pressed together--thus obviating any need for user operated alignment mechanisms. This system represents an ideal solution for laptop and notebook computer applications. It was devised to meet the stringent requirements of a laptop computer manufacturer including very compact size, very low cost, little impact on existing manufacturing or assembly procedures, and compatibility with existing full resolution 2D text- oriented software as well as 3D graphics. Similar requirements apply to high and electronic calculators, several models of which now use LCDs for the display of graphics.

  11. Classification and quantification of pore shapes in sandstone reservoir rocks with 3-D X-ray micro-computed tomography

    NASA Astrophysics Data System (ADS)

    Schmitt, Mayka; Halisch, Matthias; Müller, Cornelia; Peres Fernandes, Celso

    2016-02-01

    Recent years have seen a growing interest in the characterization of the pore morphologies of reservoir rocks and how the spatial organization of pore traits affects the macro behavior of rock-fluid systems. With the availability of 3-D high-resolution imaging, such as x-ray micro-computed tomography (µ-CT), the detailed quantification of particle shapes has been facilitated by progress in computer science. Here, we show how the shapes of irregular rock particles (pores) can be classified and quantified based on binary 3-D images. The methodology requires the measurement of basic 3-D particle descriptors (length, width, and thickness) and a shape classification that involves the similarity of artificial objects, which is based on main pore network detachments and 3-D sample sizes. Two main pore components were identified from the analyzed volumes: pore networks and residual pore ganglia. A watershed algorithm was applied to preserve the pore morphology after separating the main pore networks, which is essential for the pore shape characterization. The results were validated for three sandstones (S1, S2, and S3) from distinct reservoirs, and most of the pore shapes were found to be plate- and cube-like, ranging from 39.49 to 50.94 % and from 58.80 to 45.18 % when the Feret caliper descriptor was investigated in a 10003 voxel volume. Furthermore, this study generalizes a practical way to correlate specific particle shapes, such as rods, blades, cuboids, plates, and cubes to characterize asymmetric particles of any material type with 3-D image analysis.

  12. Compu