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Sample records for automated 3-d voxel

  1. Evaluation of brain perfusion in specific Brodmann areas in Frontotemporal dementia and Alzheimer disease using automated 3-D voxel based analysis

    NASA Astrophysics Data System (ADS)

    Valotassiou, V.; Papatriantafyllou, J.; Sifakis, N.; Karageorgiou, C.; Tsougos, I.; Tzavara, C.; Zerva, C.; Georgoulias, P.

    2009-05-01

    Introduction. Brain perfusion studies with single-photon emission computed tomography (SPECT) have been applied in demented patients to provide better discrimination between frontotemporal dementia (FTD) and Alzheimer's disease (AD). Aim. To assess the perfusion of specific Brodmann (Br) areas of the brain cortex in FTD and AD patients, using NeuroGam processing program to provide 3D voxel-by-voxel cerebral SPECT analysis. Material and methods. We studied 34 consecutive patients. We used the established criteria for the diagnosis of dementia and the specific established criteria for the diagnosis of FTD and AD. All the patients had a neuropsychological evaluation with a battery of tests including the mini-mental state examination (MMSE).Twenty-six patients (16 males, 10 females, mean age 68.76±6.51 years, education 11.81±4.25 years, MMSE 16.69±9.89) received the diagnosis of FTD and 8 patients (all females, mean age 71.25±10.48 years, education 10±4.6 years, MMSE 12.5±3.89) the diagnosis of AD. All the patients underwent a brain SPECT. We applied the NeuroGam Software for the evaluation of brain perfusion in specific Br areas in the left (L) and right (R) hemispheres. Results. Statistically significant hypoperfusion in FTD compared to AD patients, was found in the following Br areas: 11L (p<0.0001), 11R, 20L, 20R, 32L, 38L, 38R, 44L (p<0.001), 32R, 36L, 36R, 45L, 45R, 47R (p<0.01), 9L, 21L, 39R, 44R, 46R, 47L (p<0.05). On the contrary, AD patients presented significant (p<0.05) hypoperfusion in 7R and 39R Br areas. Conclusion. NeuroGam processing program of brain perfusion SPECT could result in enhanced accuracy for the differential diagnosis between AD and FTD patients.

  2. Visualization using 3D voxelization of full lidar waveforms

    NASA Astrophysics Data System (ADS)

    Park, Joong Yong; Ramnath, Vinod; Feygels, Victor

    2014-11-01

    Airborne bathymetric lidar (Light Detection and Ranging) systems measure photoelectrons on the optical path (range and angle) at the photocathode of a returned laser pulse at high rates, such as every nanosecond. The collected measurement of a single pulse in a time series is called a waveform. Based on the calibration of the lidar system, the return signal is converted into units of received power. This converted value from the lidar waveform data is used to compute an estimate of the reflectance from the returned backscatter, which contains environmental information from along the optical path. This concept led us to develop a novel tool to visualize lidar data in terms of the returned backscatter, and to use this as a data analysis and editing tool. The full lidar waveforms along the optical path, from laser points collected in the region of interest (ROI), are voxelized into a 3D image cube. This allows lidar measurements to be analyzed in three orthogonal directions simultaneously. The laser pulse return (reflection) from the seafloor is visible in the waveform as a pronounced "bump" above the volume backscatter. Floating or submerged objects in the water may also be visible. Similarly, forest canopies and tree branches can be identified in the 3D voxelization. This paper discusses the possibility of using this unique three-orthogonal volume visualizing tool to extract environmental information for carrying out rapid environmental assessments over forests and water.

  3. 3D-Printed Microfluidic Automation

    PubMed Central

    Au, Anthony K.; Bhattacharjee, Nirveek; Horowitz, Lisa F.; Chang, Tim C.; Folch, Albert

    2015-01-01

    Microfluidic automation – the automated routing, dispensing, mixing, and/or separation of fluids through microchannels – generally remains a slowly-spreading technology because device fabrication requires sophisticated facilities and the technology’s use demands expert operators. Integrating microfluidic automation in devices has involved specialized multi-layering and bonding approaches. Stereolithography is an assembly-free, 3D-printing technique that is emerging as an efficient alternative for rapid prototyping of biomedical devices. Here we describe fluidic valves and pumps that can be stereolithographically printed in optically-clear, biocompatible plastic and integrated within microfluidic devices at low cost. User-friendly fluid automation devices can be printed and used by non-engineers as replacement for costly robotic pipettors or tedious manual pipetting. Engineers can manipulate the designs as digital modules into new devices of expanded functionality. Printing these devices only requires the digital file and electronic access to a printer. PMID:25738695

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

    NASA Astrophysics Data System (ADS)

    Hosoi, F.

    2014-12-01

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

  5. Calculation of Dose Deposition in 3D Voxels by Heavy Ions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2010-01-01

    The biological response to high-LET radiation is very different from low-LET radiation, and can be partly attributed to the energy deposition by the radiation. Several experiments, notably detection of gamma-H2AX foci by immunofluorescence, has revealed important differences in the nature and in the spatial distribution of double-strand breaks (DSB) induced by low- and high-LET radiations. Many calculations, most of which are based on amorphous track models with radial dose, have been combined with chromosome models to calculate the number and distribution of DSB within nuclei and chromosome aberrations. In this work, the Monte-Carlo track structure simulation code RITRACKS have been used to calculate directly the energy deposition in voxels (3D pixels). A cubic volume of 5 micrometers of side was irradiated by 1) 450 (1)H+ ions of 300 MeV (LET is approximately 0.3 keV/micrometer) and 2) by 1 (56)Fe26+ ion of 1 GeV/amu (LET is approximately 150 keV/micrometer). In both cases, the dose deposited in the volume is approximately 1 Gy. All energy deposition events are recorded and dose is calculated in voxels of 20 micrometers of side. The voxels are then visualized in 3D by using a color scale to represent the intensity of the dose in a voxel. This simple approach has revealed several important points which may help understand experimental observations. In both simulations, voxels which receive low dose are the most numerous, and those corresponding to electron track ends received a dose which is in the higher range. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. The distribution of the voxels shows major differences for the (56)Fe26+ ion. The track structure can still be seen, and voxels with much higher dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and may be responsible for DSB that are more difficult to

  6. Automated robust generation of compact 3D statistical shape models

    NASA Astrophysics Data System (ADS)

    Vrtovec, Tomaz; Likar, Bostjan; Tomazevic, Dejan; Pernus, Franjo

    2004-05-01

    Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.

  7. 3D dose distribution calculation in a voxelized human phantom by means of Monte Carlo method.

    PubMed

    Abella, V; Miró, R; Juste, B; Verdú, G

    2010-01-01

    The aim of this work is to provide the reconstruction of a real human voxelized phantom by means of a MatLab program and the simulation of the irradiation of such phantom with the photon beam generated in a Theratron 780 (MDS Nordion) (60)Co radiotherapy unit, by using the Monte Carlo transport code MCNP (Monte Carlo N-Particle), version 5. The project results in 3D dose mapping calculations inside the voxelized antropomorphic head phantom. The program provides the voxelization by first processing the CT slices; the process follows a two-dimensional pixel and material identification algorithm on each slice and three-dimensional interpolation in order to describe the phantom geometry via small cubic cells, resulting in an MCNP input deck format output. Dose rates are calculated by using the MCNP5 tool FMESH, superimposed mesh tally, which gives the track length estimation of the particle flux in units of particles/cm(2). Furthermore, the particle flux is converted into dose by using the conversion coefficients extracted from the NIST Physical Reference Data. The voxelization using a three-dimensional interpolation technique in combination with the use of the FMESH tool of the MCNP Monte Carlo code offers an optimal simulation which results in 3D dose mapping calculations inside anthropomorphic phantoms. This tool is very useful in radiation treatment assessments, in which voxelized phantoms are widely utilized. PMID:19892556

  8. 3D sensitive voxel detector of ionizing radiation based on Timepix device

    NASA Astrophysics Data System (ADS)

    Soukup, P.; Jakubek, J.; Vykydal, Z.

    2011-01-01

    Position sensitive detectors are evolving towards higher segmentation geometries from 0D (single pad) over 1D (strip) to 2D (pixel) detectors. Each step has brought up substantial expansion in the field of applications. The next logical step in this evolution is to design a 3D, i.e. voxel detector. The voxel detector can be constructed from 2D volume element detectors arranged in layers forming a 3D matrix of sensitive elements — voxels. Such detectors can effectively record tracks of energetic particles. By proper analysis of these tracks it is possible to determine the type, direction and energy of the primary particle. One of the prominent applications of such device is in the localization and identification of gamma and neutron sources in the environment. It can be also used for emission and transmission radiography in many fields where standard imagers are currently utilized. The qualitative properties of current imagers such as: spatial resolution, efficiency, directional sensitivity, energy sensitivity and selectivity (background suppression) can be improved. The first prototype of a voxel detector was built using a number of Timepix devices. Timepix is hybrid semiconductor detector consisting of a segmented semiconductor sensor bump-bonded to a readout chip. Each sensor contains 256x256 square pixels of 55 μm size. The voxel detector prototype was successfully tested to prove the concept functionality. The detector has a modular architecture with a daisy chain connection of the individual detector layers. This permits easy rearrangement due to its modularity, while keeping a single readout system for a variable number of detector layers. A limitation of this approach is the relatively large inter-layer distance (4 mm) compared to the pixel thickness (0.3 mm). Therefore the next step in the design is to decrease the space between the 2D detectors.

  9. Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

    PubMed

    Nourian, Pirouz; Gonçalves, Romulo; Zlatanova, Sisi; Ohori, Ken Arroyo; Vu Vo, Anh

    2016-01-01

    Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency. PMID:27408832

  10. Automated 3D vascular segmentation in CT hepatic venography

    NASA Astrophysics Data System (ADS)

    Fetita, Catalin; Lucidarme, Olivier; Preteux, Francoise

    2005-08-01

    In the framework of preoperative evaluation of the hepatic venous anatomy in living-donor liver transplantation or oncologic rejections, this paper proposes an automated approach for the 3D segmentation of the liver vascular structure from 3D CT hepatic venography data. The developed segmentation approach takes into account the specificities of anatomical structures in terms of spatial location, connectivity and morphometric properties. It implements basic and advanced morphological operators (closing, geodesic dilation, gray-level reconstruction, sup-constrained connection cost) in mono- and multi-resolution filtering schemes in order to achieve an automated 3D reconstruction of the opacified hepatic vessels. A thorough investigation of the venous anatomy including morphometric parameter estimation is then possible via computer-vision 3D rendering, interaction and navigation capabilities.

  11. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    PubMed Central

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  12. Improving automated 3D reconstruction methods via vision metrology

    NASA Astrophysics Data System (ADS)

    Toschi, Isabella; Nocerino, Erica; Hess, Mona; Menna, Fabio; Sargeant, Ben; MacDonald, Lindsay; Remondino, Fabio; Robson, Stuart

    2015-05-01

    This paper aims to provide a procedure for improving automated 3D reconstruction methods via vision metrology. The 3D reconstruction problem is generally addressed using two different approaches. On the one hand, vision metrology (VM) systems try to accurately derive 3D coordinates of few sparse object points for industrial measurement and inspection applications; on the other, recent dense image matching (DIM) algorithms are designed to produce dense point clouds for surface representations and analyses. This paper strives to demonstrate a step towards narrowing the gap between traditional VM and DIM approaches. Efforts are therefore intended to (i) test the metric performance of the automated photogrammetric 3D reconstruction procedure, (ii) enhance the accuracy of the final results and (iii) obtain statistical indicators of the quality achieved in the orientation step. VM tools are exploited to integrate their main functionalities (centroid measurement, photogrammetric network adjustment, precision assessment, etc.) into the pipeline of 3D dense reconstruction. Finally, geometric analyses and accuracy evaluations are performed on the raw output of the matching (i.e. the point clouds) by adopting a metrological approach. The latter is based on the use of known geometric shapes and quality parameters derived from VDI/VDE guidelines. Tests are carried out by imaging the calibrated Portable Metric Test Object, designed and built at University College London (UCL), UK. It allows assessment of the performance of the image orientation and matching procedures within a typical industrial scenario, characterised by poor texture and known 3D/2D shapes.

  13. An Automated 3d Indoor Topological Navigation Network Modelling

    NASA Astrophysics Data System (ADS)

    Jamali, A.; Rahman, A. A.; Boguslawski, P.; Gold, C. M.

    2015-10-01

    Indoor navigation is important for various applications such as disaster management and safety analysis. In the last decade, indoor environment has been a focus of wide research; that includes developing techniques for acquiring indoor data (e.g. Terrestrial laser scanning), 3D indoor modelling and 3D indoor navigation models. In this paper, an automated 3D topological indoor network generated from inaccurate 3D building models is proposed. In a normal scenario, 3D indoor navigation network derivation needs accurate 3D models with no errors (e.g. gap, intersect) and two cells (e.g. rooms, corridors) should touch each other to build their connections. The presented 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. For reducing time and cost of indoor building data acquisition process, Trimble LaserAce 1000 as surveying instrument is used. The modelling results were validated against an accurate geometry of indoor building environment which was acquired using Trimble M3 total station.

  14. 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

  15. Automated building of organometallic complexes from 3D fragments.

    PubMed

    Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

    2014-07-28

    A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry. PMID:24998944

  16. Computerized method for automated measurement of thickness of cerebral cortex for 3-D MR images

    NASA Astrophysics Data System (ADS)

    Arimura, Hidetaka; Yoshiura, Takashi; Kumazawa, Seiji; Koga, Hiroshi; Sakai, Shuji; Mihara, Futoshi; Honda, Hiroshi; Ohki, Masafumi; Toyofuku, Fukai; Higashida, Yoshiharu

    2006-03-01

    Alzheimer's disease (AD) is associated with the degeneration of cerebral cortex, which results in focal volume change or thinning in the cerebral cortex in magnetic resonance imaging (MRI). Therefore, the measurement of the cortical thickness is important for detection of the atrophy related to AD. Our purpose was to develop a computerized method for automated measurement of the cortical thickness for three-dimensional (3-D) MRI. The cortical thickness was measured with normal vectors from white matter surface to cortical gray matter surface on a voxel-by-voxel basis. First, a head region was segmented by use of an automatic thresholding technique, and then the head region was separated into the cranium region and brain region by means of a multiple gray level thresholding with monitoring the ratio of the first maximum volume to the second one. Next, a fine white matter region was determined based on a level set method as a seed region of the rough white matter region extracted from the brain region. Finally, the cortical thickness was measured by extending normal vectors from the white matter surface to gray matter surface (brain surface) on a voxel-by-voxel basis. We applied the computerized method to high-resolution 3-D T1-weighted images of the whole brains from 7 clinically diagnosed AD patients and 8 healthy subjects. The average cortical thicknesses in the upper slices for AD patients were thinner than those for non-AD subjects, whereas the average cortical thicknesses in the lower slices for most AD patients were slightly thinner. Our preliminary results suggest that the MRI-based computerized measurement of gray matter atrophy is promising for detecting AD.

  17. Fully automated 2D-3D registration and verification.

    PubMed

    Varnavas, Andreas; Carrell, Tom; Penney, Graeme

    2015-12-01

    Clinical application of 2D-3D registration technology often requires a significant amount of human interaction during initialisation and result verification. This is one of the main barriers to more widespread clinical use of this technology. We propose novel techniques for automated initial pose estimation of the 3D data and verification of the registration result, and show how these techniques can be combined to enable fully automated 2D-3D registration, particularly in the case of a vertebra based system. The initialisation method is based on preoperative computation of 2D templates over a wide range of 3D poses. These templates are used to apply the Generalised Hough Transform to the intraoperative 2D image and the sought 3D pose is selected with the combined use of the generated accumulator arrays and a Gradient Difference Similarity Measure. On the verification side, two algorithms are proposed: one using normalised features based on the similarity value and the other based on the pose agreement between multiple vertebra based registrations. The proposed methods are employed here for CT to fluoroscopy registration and are trained and tested with data from 31 clinical procedures with 417 low dose, i.e. low quality, high noise interventional fluoroscopy images. When similarity value based verification is used, the fully automated system achieves a 95.73% correct registration rate, whereas a no registration result is produced for the remaining 4.27% of cases (i.e. incorrect registration rate is 0%). The system also automatically detects input images outside its operating range. PMID:26387052

  18. Determining correspondence in 3-D MR brain images using attribute vectors as morphological signatures of voxels.

    PubMed

    Xue, Zhong; Shen, Dinggang; Davatzikos, Christos

    2004-10-01

    Finding point correspondence in anatomical images is a key step in shape analysis and deformable registration. This paper proposes an automatic correspondence detection algorithm for intramodality MR brain images of different subjects using wavelet-based attribute vectors (WAVs) defined on every image voxel. The attribute vector (AV) is extracted from the wavelet subimages and reflects the image structure in a large neighborhood around the respective voxel in a multiscale fashion. It plays the role of a morphological signature for each voxel, and our goal is, therefore, to make it distinctive of the respective voxel. Correspondence is then determined from similarities of AVs. By incorporating the prior knowledge of the spatial relationship among voxels, the ability of the proposed algorithm to find anatomical correspondence is further improved. Experiments with MR images of human brains show that the algorithm performs similarly to experts, even for complex cortical structures. PMID:15493695

  19. Automated Identification of Fiducial Points on 3D Torso Images

    PubMed Central

    Kawale, Manas M; Reece, Gregory P; Crosby, Melissa A; Beahm, Elisabeth K; Fingeret, Michelle C; Markey, Mia K; Merchant, Fatima A

    2013-01-01

    Breast reconstruction is an important part of the breast cancer treatment process for many women. Recently, 2D and 3D images have been used by plastic surgeons for evaluating surgical outcomes. Distances between different fiducial points are frequently used as quantitative measures for characterizing breast morphology. Fiducial points can be directly marked on subjects for direct anthropometry, or can be manually marked on images. This paper introduces novel algorithms to automate the identification of fiducial points in 3D images. Automating the process will make measurements of breast morphology more reliable, reducing the inter- and intra-observer bias. Algorithms to identify three fiducial points, the nipples, sternal notch, and umbilicus, are described. The algorithms used for localization of these fiducial points are formulated using a combination of surface curvature and 2D color information. Comparison of the 3D co-ordinates of automatically detected fiducial points and those identified manually, and geodesic distances between the fiducial points are used to validate algorithm performance. The algorithms reliably identified the location of all three of the fiducial points. We dedicate this article to our late colleague and friend, Dr. Elisabeth K. Beahm. Elisabeth was both a talented plastic surgeon and physician-scientist; we deeply miss her insight and her fellowship. PMID:25288903

  20. Automated multilayer segmentation and characterization in 3D spectral-domain optical coherence tomography images

    NASA Astrophysics Data System (ADS)

    Hu, Zhihong; Wu, Xiaodong; Hariri, Amirhossein; Sadda, SriniVas R.

    2013-03-01

    Spectral-domain optical coherence tomography (SD-OCT) is a 3-D imaging technique, allowing direct visualization of retinal morphology and architecture. The various layers of the retina may be affected differentially by various diseases. In this study, an automated graph-based multilayer approach was developed to sequentially segment eleven retinal surfaces including the inner retinal bands to the outer retinal bands in normal SD-OCT volume scans at three different stages. For stage 1, the four most detectable and/or distinct surfaces were identified in the four-times-downsampled images and were used as a priori positional information to limit the graph search for other surfaces at stage 2. Eleven surfaces were then detected in the two-times-downsampled images at stage 2, and refined in the original image space at stage 3 using the graph search integrating the estimated morphological shape models. Twenty macular SD-OCT (Heidelberg Spectralis) volume scans from 20 normal subjects (one eye per subject) were used in this study. The overall mean and absolute mean differences in border positions between the automated and manual segmentation for all 11 segmented surfaces were -0.20 +/- 0.53 voxels (-0.76 +/- 2.06 μm) and 0.82 +/- 0.64 voxels (3.19 +/- 2.46 μm). Intensity and thickness properties in the resultant retinal layers were investigated. This investigation in normal subjects may provide a comparative reference for subsequent investigations in eyes with disease.

  1. Automation of 3D scan data capturing and processing

    NASA Astrophysics Data System (ADS)

    Sitnik, Robert; Karaszewski, Maciej; Załuski, Wojciech; Rutkiewicz, Jan

    2010-02-01

    In this paper a fully automated 3D shape measurement and processing method is presented. It assumes that positioning of measurement head in relation to measured object can be realized by specialized computer-controlled manipulator. On the base of existing 3D scans, the proposed method calculates "next best view" position for measurement head. All 3D data processing (filtering, ICP based fitting and final views integration) is performed automatically. Final 3D model is created on the base of user specified parameters like accuracy of surface representation or density of surface sampling. Exemplary system that implements all mentioned functionalities will be presented. The goal of this system is to automatically (without any user attention) and rapidly (from days and weeks to hours) measure whole object with some limitations to its properties: maximum measurement volume is described as a cylinder with 2,5m height and 1m radius, maximum object's weight is 2 tons. Measurement head is automatically calibrated by the system and its possible working volume starts from 120mm x 80mm x 60mm and ends up to 1,2m x 0,8m x 0,6m. Exemplary measurement result is presented.

  2. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  3. AUTOMATED, HIGHLY ACCURATE VERIFICATION OF RELAP5-3D

    SciTech Connect

    George L Mesina; David Aumiller; Francis Buschman

    2014-07-01

    Computer programs that analyze light water reactor safety solve complex systems of governing, closure and special process equations to model the underlying physics. In addition, these programs incorporate many other features and are quite large. RELAP5-3D[1] has over 300,000 lines of coding for physics, input, output, data management, user-interaction, and post-processing. For software quality assurance, the code must be verified and validated before being released to users. Verification ensures that a program is built right by checking that it meets its design specifications. Recently, there has been an increased importance on the development of automated verification processes that compare coding against its documented algorithms and equations and compares its calculations against analytical solutions and the method of manufactured solutions[2]. For the first time, the ability exists to ensure that the data transfer operations associated with timestep advancement/repeating and writing/reading a solution to a file have no unintended consequences. To ensure that the code performs as intended over its extensive list of applications, an automated and highly accurate verification method has been modified and applied to RELAP5-3D. Furthermore, mathematical analysis of the adequacy of the checks used in the comparisons is provided.

  4. An automated 3D reconstruction method of UAV images

    NASA Astrophysics Data System (ADS)

    Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

    2015-10-01

    In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

  5. Retrieving Leaf Area Index and Foliage Profiles Through Voxelized 3-D Forest Reconstruction Using Terrestrial Full-Waveform and Dual-Wavelength Echidna Lidars

    NASA Astrophysics Data System (ADS)

    Strahler, A. H.; Yang, X.; Li, Z.; Schaaf, C.; Wang, Z.; Yao, T.; Zhao, F.; Saenz, E.; Paynter, I.; Douglas, E. S.; Chakrabarti, S.; Cook, T.; Martel, J.; Howe, G.; Hewawasam, K.; Jupp, D.; Culvenor, D.; Newnham, G.; Lowell, J.

    2013-12-01

    Measuring and monitoring canopy biophysical parameters provide a baseline for carbon flux studies related to deforestation and disturbance in forest ecosystems. Terrestrial full-waveform lidar systems, such as the Echidna Validation Instrument (EVI) and its successor Dual-Wavelength Echidna Lidar (DWEL), offer rapid, accurate, and automated characterization of forest structure. In this study, we apply a methodology based on voxelized 3-D forest reconstructions built from EVI and DWEL scans to directly estimate two important biophysical parameters: Leaf Area Index (LAI) and foliage profile. Gap probability, apparent reflectance, and volume associated with the laser pulse footprint at the observed range are assigned to the foliage scattering events in the reconstructed point cloud. Leaf angle distribution is accommodated with a simple model based on gap probability with zenith angle as observed in individual scans of the stand. The DWEL instrument, which emits simultaneous laser pulses at 1064 nm and 1548 nm wavelengths, provides a better capability to separate trunk and branch hits from foliage hits due to water absorption by leaf cellular contents at 1548 nm band. We generate voxel datasets of foliage points using a classification methodology solely based on pulse shape for scans collected by EVI and with pulse shape and band ratio for scans collected by DWEL. We then compare the LAIs and foliage profiles retrieved from the voxel datasets of the two instruments at the same red fir site in Sierra National Forest, CA, with each other and with observations from airborne and field measurements. This study further tests the voxelization methodology in obtaining LAI and foliage profiles that are largely free of clumping effects and returns from woody materials in the canopy. These retrievals can provide a valuable 'ground-truth' validation data source for large-footprint spaceborne or airborne lidar systems retrievals.

  6. Automated 3D renal segmentation based on image partitioning

    NASA Astrophysics Data System (ADS)

    Yeghiazaryan, Varduhi; Voiculescu, Irina D.

    2016-03-01

    Despite several decades of research into segmentation techniques, automated medical image segmentation is barely usable in a clinical context, and still at vast user time expense. This paper illustrates unsupervised organ segmentation through the use of a novel automated labelling approximation algorithm followed by a hypersurface front propagation method. The approximation stage relies on a pre-computed image partition forest obtained directly from CT scan data. We have implemented all procedures to operate directly on 3D volumes, rather than slice-by-slice, because our algorithms are dimensionality-independent. The results picture segmentations which identify kidneys, but can easily be extrapolated to other body parts. Quantitative analysis of our automated segmentation compared against hand-segmented gold standards indicates an average Dice similarity coefficient of 90%. Results were obtained over volumes of CT data with 9 kidneys, computing both volume-based similarity measures (such as the Dice and Jaccard coefficients, true positive volume fraction) and size-based measures (such as the relative volume difference). The analysis considered both healthy and diseased kidneys, although extreme pathological cases were excluded from the overall count. Such cases are difficult to segment both manually and automatically due to the large amplitude of Hounsfield unit distribution in the scan, and the wide spread of the tumorous tissue inside the abdomen. In the case of kidneys that have maintained their shape, the similarity range lies around the values obtained for inter-operator variability. Whilst the procedure is fully automated, our tools also provide a light level of manual editing.

  7. Automated full-3D shape measurement of cultural heritage objects

    NASA Astrophysics Data System (ADS)

    Sitnik, Robert; Karaszewski, Maciej; Zaluski, Wojciech; Bolewicki, Pawel

    2009-07-01

    In this paper a fully automated 3D shape measurement system is presented. It consists of rotary stage for cultural heritage objects placement, vertical linear stage with mounted robot arm (with six degrees of freedom) and structured light measurement set-up mounted to its head. All these manipulation devices are automatically controlled by collision detection and next-best-view calculation modules. The goal of whole system is to automatically (without any user attention) and rapidly (from days and weeks to hours) measure whole object. Measurement head is automatically calibrated by the system and its possible working volume starts from centimeters and ends up to one meter. We present some measurement results with different working scenarios along with discussion about its possible applications.

  8. Automated 3D measurement with the DCS200 digital camera

    NASA Astrophysics Data System (ADS)

    Van den Heuvel, Frank A.

    1994-03-01

    A digital photogrammetric system for automated 3D coordinate measurement in a production environment has been developed. For the image acquisition the Kodak DCS200 digital camera is used. This camera is based on a standard 35-mm camera. The results of the radiometric and geometric calibration of the DCS200 camera show the potential of this camera for photogrammetric applications. The software part of the system performs the detection, identification, and measurement of artificial targets present in digital images. These artificial targets are designed for automatic detection in images of a complex scene. For the identification of the targets a circular bar code is read by the image processing software. The least squares template matching method is implemented for the target image measurement. A precision better than 2% of a pixel was obtained for the target location. The 3D coordinate computation is performed by Geodelta's bundle adjustment package BINAER. It includes extensive statistical testing to assess the accuracy of the results. Tests with the DCS200 camera show a repeatability of 18 micrometer standard deviation on a test field 60 X 50 X 30 centimeter. The achieved precision is in the order of 2 (DOT) 10-5.

  9. Automated curved planar reformation of 3D spine images

    NASA Astrophysics Data System (ADS)

    Vrtovec, Tomaz; Likar, Bostjan; Pernus, Franjo

    2005-10-01

    Traditional techniques for visualizing anatomical structures are based on planar cross-sections from volume images, such as images obtained by computed tomography (CT) or magnetic resonance imaging (MRI). However, planar cross-sections taken in the coordinate system of the 3D image often do not provide sufficient or qualitative enough diagnostic information, because planar cross-sections cannot follow curved anatomical structures (e.g. arteries, colon, spine, etc). Therefore, not all of the important details can be shown simultaneously in any planar cross-section. To overcome this problem, reformatted images in the coordinate system of the inspected structure must be created. This operation is usually referred to as curved planar reformation (CPR). In this paper we propose an automated method for CPR of 3D spine images, which is based on the image transformation from the standard image-based to a novel spine-based coordinate system. The axes of the proposed spine-based coordinate system are determined on the curve that represents the vertebral column, and the rotation of the vertebrae around the spine curve, both of which are described by polynomial models. The optimal polynomial parameters are obtained in an image analysis based optimization framework. The proposed method was qualitatively and quantitatively evaluated on five CT spine images. The method performed well on both normal and pathological cases and was consistent with manually obtained ground truth data. The proposed spine-based CPR benefits from reduced structural complexity in favour of improved feature perception of the spine. The reformatted images are diagnostically valuable and enable easier navigation, manipulation and orientation in 3D space. Moreover, reformatted images may prove useful for segmentation and other image analysis tasks.

  10. Automated Rapid Prototyping of 3D Ceramic Parts

    NASA Technical Reports Server (NTRS)

    McMillin, Scott G.; Griffin, Eugene A.; Griffin, Curtis W.; Coles, Peter W. H.; Engle, James D.

    2005-01-01

    An automated system of manufacturing equipment produces three-dimensional (3D) ceramic parts specified by computational models of the parts. The system implements an advanced, automated version of a generic rapid-prototyping process in which the fabrication of an object having a possibly complex 3D shape includes stacking of thin sheets, the outlines of which closely approximate the horizontal cross sections of the object at their respective heights. In this process, the thin sheets are made of a ceramic precursor material, and the stack is subsequently heated to transform it into a unitary ceramic object. In addition to the computer used to generate the computational model of the part to be fabricated, the equipment used in this process includes: 1) A commercially available laminated-object-manufacturing machine that was originally designed for building woodlike 3D objects from paper and was modified to accept sheets of ceramic precursor material, and 2) A machine designed specifically to feed single sheets of ceramic precursor material to the laminated-object-manufacturing machine. Like other rapid-prototyping processes that utilize stacking of thin sheets, this process begins with generation of the computational model of the part to be fabricated, followed by computational sectioning of the part into layers of predetermined thickness that collectively define the shape of the part. Information about each layer is transmitted to rapid-prototyping equipment, where the part is built layer by layer. What distinguishes this process from other rapid-prototyping processes that utilize stacking of thin sheets are the details of the machines and the actions that they perform. In this process, flexible sheets of ceramic precursor material (called "green" ceramic sheets) suitable for lamination are produced by tape casting. The binder used in the tape casting is specially formulated to enable lamination of layers with little or no applied heat or pressure. The tape is cut

  11. Automated Recognition of 3D Features in GPIR Images

    NASA Technical Reports Server (NTRS)

    Park, Han; Stough, Timothy; Fijany, Amir

    2007-01-01

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

  12. From pixel to voxel: a deeper view of biological tissue by 3D mass spectral imaging

    PubMed Central

    Ye, Hui; Greer, Tyler; Li, Lingjun

    2011-01-01

    Three dimensional mass spectral imaging (3D MSI) is an exciting field that grants the ability to study a broad mass range of molecular species ranging from small molecules to large proteins by creating lateral and vertical distribution maps of select compounds. Although the general premise behind 3D MSI is simple, factors such as choice of ionization method, sample handling, software considerations and many others must be taken into account for the successful design of a 3D MSI experiment. This review provides a brief overview of ionization methods, sample preparation, software types and technological advancements driving 3D MSI research of a wide range of low- to high-mass analytes. Future perspectives in this field are also provided to conclude that the positive and promises ever-growing applications in the biomedical field with continuous developments of this powerful analytical tool. PMID:21320052

  13. Shallow subsurface control on earthquake damage patterns: first results from a 3D geological voxel model study (Tokyo Lowland, Japan)

    NASA Astrophysics Data System (ADS)

    Stafleu, Jan; Busschers, Freek; Tanabe, Susumu

    2016-04-01

    The Tokyo Lowland is situated in a Neogene sedimentary basin near the triple junction of the North American, Pacific, and Philippine tectonic plates. The basin is filled with Neogene and Quaternary sediments up to a thickness of 3 km. In the upper 70 m of the basin, thick sequences of soft Holocene sediments occur which are assumed to have played a key role in the spatial variation of damage intensity during the 1923 Kanto earthquake (Magnitude 7.9 to 8.3). Historical records show this earthquake destroyed large parts of the Tokyo urban area which in that time was largely made up by wooden houses. Although the epicentre was 70 km to the southwest of Tokyo, severe damage occurred north of the city centre, presumably due to ground motion amplification in the soft Holocene sediments in the shallow subsurface. In order to assess the presumed relation between the damage pattern of the 1923 earthquake and the occurrence of soft Holocene sediments in the shallow subsurface, we constructed a 3D geological voxel model of the central part of the Tokyo Lowland. The model was constructed using a methodology originally developed for the lowlands of the Netherlands. The modelling workflow basically consists of three steps. First, some 10,000 borehole descriptions (gathered for geomechanical purposes), were subdivided into geological units that have uniform sediment characteristics, using both lithological and geomechanical (N-value) criteria. Second, 2D bounding surfaces were constructed, representing tops and bases of the geological units. These surfaces were used to place each voxel (100 by 100 by 1 m) within the correct geological unit. The N-values and lithological units in the borehole descriptions were subsequently used to perform a 3D stochastic interpolation of N-value and lithological class within each geological unit. Using a vertical voxel stack analysis, we were able to create a map showing the accumulated thickness of soft muds in the Holocene succession. A

  14. Cognitive 3D geological voxel modelling based on AEM and seismic data - a case from the southern part of Denmark

    NASA Astrophysics Data System (ADS)

    Jørgensen, Flemming; Møller, Rasmus R.; Sandersen, Peter B. E.; Høyer, Anne-Sophie

    2013-04-01

    high quality sediment samples and down-hole geophysical logs. A comprehensive geological overview and understanding of the area is gained by integrated and cognitive interpretation of the geophysical and geological data enabling a detailed and reliable 3D geological model to be built. The model covers the area on the Danish side of the border. In order to address the detailed information from the SkyTEM data, the model has been constructed as a voxel model combined with surfaces representing layer boundaries and unconformities. Lithofacies and interpretation uncertainty attributes have been added to each voxel. Geostatistic inversion has been used to distribute lithological parameters to voxels in the most complicated areas of the model (areas with glaciotectonism). Experiments with octree modelling giving a high resolution with a limited number of voxels have also been performed. The final 3D model is primarily intended to serve as an input for groundwater flow modelling. The voxel model will therefore be supplemented by another attribute, hydraulic conductivity.

  15. Automatic 3D image registration using voxel similarity measurements based on a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Huang, Wei; Sullivan, John M., Jr.; Kulkarni, Praveen; Murugavel, Murali

    2006-03-01

    An automatic 3D non-rigid body registration system based upon the genetic algorithm (GA) process is presented. The system has been successfully applied to 2D and 3D situations using both rigid-body and affine transformations. Conventional optimization techniques and gradient search strategies generally require a good initial start location. The GA approach avoids the local minima/maxima traps of conventional optimization techniques. Based on the principles of Darwinian natural selection (survival of the fittest), the genetic algorithm has two basic steps: 1. Randomly generate an initial population. 2. Repeated application of the natural selection operation until a termination measure is satisfied. The natural selection process selects individuals based on their fitness to participate in the genetic operations; and it creates new individuals by inheritance from both parents, genetic recombination (crossover) and mutation. Once the termination criteria are satisfied, the optimum is selected from the population. The algorithm was applied on 2D and 3D magnetic resonance images (MRI). It does not require any preprocessing such as threshold, smoothing, segmentation, or definition of base points or edges. To evaluate the performance of the GA registration, the results were compared with results of the Automatic Image Registration technique (AIR) and manual registration which was used as the gold standard. Results showed that our GA implementation was a robust algorithm and gives very close results to the gold standard. A pre-cropping strategy was also discussed as an efficient preprocessing step to enhance the registration accuracy.

  16. 3D Mandibular Superimposition: Comparison of Regions of Reference for Voxel-Based Registration

    PubMed Central

    Ruellas, Antonio Carlos de Oliveira; Yatabe, Marilia Sayako; Souki, Bernardo Quiroga; Benavides, Erika; Nguyen, Tung; Luiz, Ronir Raggio; Franchi, Lorenzo; Cevidanes, Lucia Helena Soares

    2016-01-01

    Introduction The aim was to evaluate three regions of reference (Björk, Modified Björk and mandibular Body) for mandibular registration testing them in a patients’ CBCT sample. Methods Mandibular 3D volumetric label maps were built from CBCTs taken before (T1) and after treatment (T2) in a sample of 16 growing subjects and labeled with eight landmarks. Registrations of T1 and T2 images relative to the different regions of reference were performed, and 3D surface models were generated. Seven mandibular dimensions were measured separately for each time-point (T1 and T2) in relation to a stable reference structure (lingual cortical of symphysis), and the T2-T1 differences were calculated. These differences were compared to differences measured between the superimposed T2 (generated from different regions of reference: Björk, Modified Björk and Mandibular Body) over T1 surface models. ICC and the Bland-Altman method tested the agreement of the changes obtained by nonsuperimposition measurements from the patients’ sample, and changes between the overlapped surfaces after registration using the different regions of reference. Results The Björk region of reference (or mask) did work properly only in 2 of 16 patients. Evaluating the two other masks (Modified Björk and Mandibular body) on patients’ scans registration, the concordance and agreement of the changes obtained from superimpositions (registered T2 over T1) compared to results obtained from non superimposed T1 and T2 separately, indicated that Mandibular Body mask displayed more consistent results. Conclusions The mandibular body mask (mandible without teeth, alveolar bone, rami and condyles) is a reliable reference for 3D regional registration. PMID:27336366

  17. Voxel-based 2-D/3-D registration of fluoroscopy images and CT scans for image-guided surgery.

    PubMed

    Weese, J; Penney, G P; Desmedt, P; Buzug, T M; Hill, D L; Hawkes, D J

    1997-12-01

    Registration of intraoperative fluoroscopy images with preoperative three-dimensional (3-D) CT images can be used for several purposes in image-guided surgery. On the one hand, it can be used to display the position of surgical instruments, which are being tracked by a localizer, in the preoperative CT scan. On the other hand, the registration result can be used to project preoperative planning information or important anatomical structures visible in the CT image onto the fluoroscopy image. For this registration task, a novel voxel-based method in combination with a new similarity measure (pattern intensity) has been developed. The basic concept of the method is explained at the example of two-dimensional (2-D)/3-D registration of a vertebra in an X-ray fluoroscopy image with a 3-D CT image. The registration method is described, and the results for a spine phantom are presented and discussed. Registration has been carried out repeatedly with different starting estimates to study the capture range. Information about registration accuracy has been obtained by comparing the registration results with a highly accurate "ground-truth" registration, which has been derived from fiducial markers attached to the phantom prior to imaging. In addition, registration results for different vertebrae have been compared. The results show that the rotation parameters and the shifts parallel to the projection plane can accurately be determined from a single projection. Because of the projection geometry, the accuracy of the height above the projection plane is significantly lower. PMID:11020832

  18. Measuring Complete 3D Vegetation Structure With Airborne Waveform Lidar: A Calibration and Validation With Terrestrial Lidar Derived Voxels

    NASA Astrophysics Data System (ADS)

    Hancock, S.; Anderson, K.; Disney, M.; Gaston, K. J.

    2015-12-01

    Accurate measurements of vegetation are vital to understand habitats and their provision of ecosystem services as well as having applications in satellite calibration, weather modelling and forestry. The majority of humans now live in urban areas and so understanding vegetation structure in these very heterogeneous areas is of importance. A number of previous studies have used airborne lidar (ALS) to characterise canopy height and canopy cover, but very few have fully characterised 3D vegetation, including understorey. Those that have either relied on leaf-off scans to allow unattenuated measurement of understorey or else did not validate. A method for creating a detailed voxel map of urban vegetation, in which the surface area of vegetation within a grid of cuboids (1.5m by 1.5m by 25 cm) is defined, from full-waveform ALS is presented. The ALS was processed with deconvolution and attenuation correction methods. The signal processing was calibrated and validated against synthetic waveforms generated from terrestrial laser scanning (TLS) data, taken as "truth". The TLS data was corrected for partial hits and attenuation using a voxel approach and these steps were validated and found to be accurate. The ALS results were benchmarked against the more common discrete return ALS products (produced automatically by the lidar manufacturer's algorithms) and Gaussian decomposition of full-waveform ALS. The true vegetation profile was accurately recreated by deconvolution. Far more detail was captured by the deconvolved waveform than either the discrete return or Gaussian decomposed ALS, particularly detail within the canopy; vital information for understanding habitats. In the paper, we will present the results with a focus on the methodological steps towards generating the voxel model, and the subsequent quantitative calibration and validation of the modelling approach using TLS. We will discuss the implications of the work for complete vegetation canopy descriptions in

  19. Probabilistic Voxel-Fe model for single cell motility in 3D

    PubMed Central

    Borau, Carlos; Polacheck, William J; Kamm, Roger D; García-Aznar, José Manuel

    2015-01-01

    Background Cells respond to a variety of external stimuli regulated by the environment conditions. Mechanical, chemical and biological factors are of great interest and have been deeply studied. Furthermore, mathematical and computational models have been rapidly growing over the past few years, permitting researches to run complex scenarios saving time and resources. Usually these models focus on specific features of cell migration, making them only suitable to study restricted phenomena. Methods Here we present a versatile finite element (FE) cell-scale 3D migration model based on probabilities depending in turn on ECM mechanical properties, chemical, fluid and boundary conditions. Results With this approach we are able to capture important outcomes of cell migration such as: velocities, trajectories, cell shape and aspect ratio, cell stress or ECM displacements. Conclusions The modular form of the model will allow us to constantly update and redefine it as advancements are made in clarifying how cellular events take place. PMID:26290806

  20. The Monte Carlo SRNA-VOX code for 3D proton dose distribution in voxelized geometry using CT data

    NASA Astrophysics Data System (ADS)

    Ilic, Radovan D.; Spasic-Jokic, Vesna; Belicev, Petar; Dragovic, Milos

    2005-03-01

    This paper describes the application of the SRNA Monte Carlo package for proton transport simulations in complex geometry and different material compositions. The SRNA package was developed for 3D dose distribution calculation in proton therapy and dosimetry and it was based on the theory of multiple scattering. The decay of proton induced compound nuclei was simulated by the Russian MSDM model and our own using ICRU 63 data. The developed package consists of two codes: the SRNA-2KG, which simulates proton transport in combinatorial geometry and the SRNA-VOX, which uses the voxelized geometry using the CT data and conversion of the Hounsfield's data to tissue elemental composition. Transition probabilities for both codes are prepared by the SRNADAT code. The simulation of the proton beam characterization by multi-layer Faraday cup, spatial distribution of positron emitters obtained by the SRNA-2KG code and intercomparison of computational codes in radiation dosimetry, indicate immediate application of the Monte Carlo techniques in clinical practice. In this paper, we briefly present the physical model implemented in the SRNA package, the ISTAR proton dose planning software, as well as the results of the numerical experiments with proton beams to obtain 3D dose distribution in the eye and breast tumour.

  1. The Monte Carlo SRNA-VOX code for 3D proton dose distribution in voxelized geometry using CT data.

    PubMed

    Ilić, Radovan D; Spasić-Jokić, Vesna; Belicev, Petar; Dragović, Milos

    2005-03-01

    This paper describes the application of the SRNA Monte Carlo package for proton transport simulations in complex geometry and different material compositions. The SRNA package was developed for 3D dose distribution calculation in proton therapy and dosimetry and it was based on the theory of multiple scattering. The decay of proton induced compound nuclei was simulated by the Russian MSDM model and our own using ICRU 63 data. The developed package consists of two codes: the SRNA-2KG, which simulates proton transport in combinatorial geometry and the SRNA-VOX, which uses the voxelized geometry using the CT data and conversion of the Hounsfield's data to tissue elemental composition. Transition probabilities for both codes are prepared by the SRNADAT code. The simulation of the proton beam characterization by multi-layer Faraday cup, spatial distribution of positron emitters obtained by the SRNA-2KG code and intercomparison of computational codes in radiation dosimetry, indicate immediate application of the Monte Carlo techniques in clinical practice. In this paper, we briefly present the physical model implemented in the SRNA package, the ISTAR proton dose planning software, as well as the results of the numerical experiments with proton beams to obtain 3D dose distribution in the eye and breast tumour. PMID:15798273

  2. Automated 3D reconstruction of interiors with multiple scan views

    NASA Astrophysics Data System (ADS)

    Sequeira, Vitor; Ng, Kia C.; Wolfart, Erik; Goncalves, Joao G. M.; Hogg, David C.

    1998-12-01

    This paper presents two integrated solutions for realistic 3D model acquisition and reconstruction; an early prototype, in the form of a push trolley, and a later prototype in the form of an autonomous robot. The systems encompass all hardware and software required, from laser and video data acquisition, processing and output of texture-mapped 3D models in VRML format, to batteries for power supply and wireless network communications. The autonomous version is also equipped with a mobile platform and other sensors for the purpose of automatic navigation. The applications for such a system range from real estate and tourism (e.g., showing a 3D computer model of a property to a potential buyer or tenant) or as tool for content creation (e.g., creating 3D models of heritage buildings or producing broadcast quality virtual studios). The system can also be used in industrial environments as a reverse engineering tool to update the design of a plant, or as a 3D photo-archive for insurance purposes. The system is Internet compatible: the photo-realistic models can be accessed via the Internet and manipulated interactively in 3D using a common Web browser with a VRML plug-in. Further information and example reconstructed models are available on- line via the RESOLV web-page at http://www.scs.leeds.ac.uk/resolv/.

  3. From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

    PubMed Central

    Tsai, Wen-Ting; Hassan, Ahmed; Sarkar, Purbasha; Correa, Joaquin; Metlagel, Zoltan; Jorgens, Danielle M.; Auer, Manfred

    2014-01-01

    Modern 3D electron microscopy approaches have recently allowed unprecedented insight into the 3D ultrastructural organization of cells and tissues, enabling the visualization of large macromolecular machines, such as adhesion complexes, as well as higher-order structures, such as the cytoskeleton and cellular organelles in their respective cell and tissue context. Given the inherent complexity of cellular volumes, it is essential to first extract the features of interest in order to allow visualization, quantification, and therefore comprehension of their 3D organization. Each data set is defined by distinct characteristics, e.g., signal-to-noise ratio, crispness (sharpness) of the data, heterogeneity of its features, crowdedness of features, presence or absence of characteristic shapes that allow for easy identification, and the percentage of the entire volume that a specific region of interest occupies. All these characteristics need to be considered when deciding on which approach to take for segmentation. The six different 3D ultrastructural data sets presented were obtained by three different imaging approaches: resin embedded stained electron tomography, focused ion beam- and serial block face- scanning electron microscopy (FIB-SEM, SBF-SEM) of mildly stained and heavily stained samples, respectively. For these data sets, four different segmentation approaches have been applied: (1) fully manual model building followed solely by visualization of the model, (2) manual tracing segmentation of the data followed by surface rendering, (3) semi-automated approaches followed by surface rendering, or (4) automated custom-designed segmentation algorithms followed by surface rendering and quantitative analysis. Depending on the combination of data set characteristics, it was found that typically one of these four categorical approaches outperforms the others, but depending on the exact sequence of criteria, more than one approach may be successful. Based on these data

  4. The 3D Euler solutions using automated Cartesian grid generation

    NASA Technical Reports Server (NTRS)

    Melton, John E.; Enomoto, Francis Y.; Berger, Marsha J.

    1993-01-01

    Viewgraphs on 3-dimensional Euler solutions using automated Cartesian grid generation are presented. Topics covered include: computational fluid dynamics (CFD) and the design cycle; Cartesian grid strategy; structured body fit; grid generation; prolate spheroid; and ONERA M6 wing.

  5. Automated reconstruction of 3D scenes from sequences of images

    NASA Astrophysics Data System (ADS)

    Pollefeys, M.; Koch, R.; Vergauwen, M.; Van Gool, L.

    Modelling of 3D objects from image sequences is a challenging problem and has been an important research topic in the areas of photogrammetry and computer vision for many years. In this paper, a system is presented which automatically extracts a textured 3D surface model from a sequence of images of a scene. The system can deal with unknown camera settings. In addition, the parameters of this camera are allowed to change during acquisition (e.g., by zooming or focusing). No prior knowledge about the scene is necessary to build the 3D models. Therefore, this system offers a high degree of flexibility. The system is based on state-of-the-art algorithms recently developed in computer vision. The 3D modelling task is decomposed into a number of successive steps. Gradually, more knowledge of the scene and the camera setup is retrieved. At this point, the obtained accuracy is not yet at the level required for most metrology applications, but the visual quality is very convincing. This system has been applied to a number of applications in archaeology. The Roman site of Sagalassos (southwest Turkey) was used as a test case to illustrate the potential of this new approach.

  6. 3D vision system for intelligent milking robot automation

    NASA Astrophysics Data System (ADS)

    Akhloufi, M. A.

    2013-12-01

    In a milking robot, the correct localization and positioning of milking teat cups is of very high importance. The milking robots technology has not changed since a decade and is based primarily on laser profiles for teats approximate positions estimation. This technology has reached its limit and does not allow optimal positioning of the milking cups. Also, in the presence of occlusions, the milking robot fails to milk the cow. These problems, have economic consequences for producers and animal health (e.g. development of mastitis). To overcome the limitations of current robots, we have developed a new system based on 3D vision, capable of efficiently positioning the milking cups. A prototype of an intelligent robot system based on 3D vision for real-time positioning of a milking robot has been built and tested under various conditions on a synthetic udder model (in static and moving scenarios). Experimental tests, were performed using 3D Time-Of-Flight (TOF) and RGBD cameras. The proposed algorithms permit the online segmentation of teats by combing 2D and 3D visual information. The obtained results permit the teat 3D position computation. This information is then sent to the milking robot for teat cups positioning. The vision system has a real-time performance and monitors the optimal positioning of the cups even in the presence of motion. The obtained results, with both TOF and RGBD cameras, show the good performance of the proposed system. The best performance was obtained with RGBD cameras. This latter technology will be used in future real life experimental tests.

  7. 3-D ion distribution and evolution in storm-time RC Retrieved from TWINS ENA by differential voxel CT technique

    NASA Astrophysics Data System (ADS)

    Ma, S.; Yan, W.; Xu, L.

    2013-12-01

    The quantitative retrieval of the 3-D spatial distribution of the parent energetic ions of ENA from a 2-D ENA image is a quite challenge task. The Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission of NASA is the first constellation to perform stereoscopic magnetospheric imaging of energetic neutral atoms (ENA) from a pair of spacecraft flying on two widely-separated Molniya orbits. TWINS provides a unique opportunity to retrieve the 3-D distribution of ions in the ring current (RC) by using a volumetric pixel (voxel) CT inversion method. In this study the voxel CT method is implemented for a series of differential ENA fluxes averaged over about 6 to 7 sweeps (corresponding to a time period of about 9 min.) at different energy levels ranging from 5 to 100 keV, obtained simultaneously by the two satellites during the main phase of a great magnetic storm with minimum Sym-H of -156 nT on 24-25 October 2011. The data were selected to span a period about 50 minutes during which a large substorm was undergoing its expansion phase first and then recovery. The ENA species of O and H are distinguished for some time-segments by analyzing the signals of pulse heights of second electrons emitted from the carbon foil and impacted on the MCP detector in the TWINS sensors. In order to eliminate the possible influence on retrieval induced by instrument bias error, a differential voxel CT technique is applied. The flux intensity of the ENAs' parent ions in the RC has been obtained as a function of energy, L value, MLT sector and latitude, along with their time evolution during the storm-time substorm expansion phase. Forward calculations proved the reliability of the retrieved results. It shows that the RC is highly asymmetric, with a major concentration in the midnight to dawn sector for equatorial latitudes. Halfway through the substorm expansion there occurred a large enhancement of equatorial ion flux at lower energy (5 keV) in the dusk sector, with narrow extent

  8. Context-driven automated target detection in 3D data

    NASA Astrophysics Data System (ADS)

    West, Karen F.; Webb, Brian N.; Lersch, James R.; Pothier, Steven; Triscari, Joseph M.; Iverson, A. E.

    2004-09-01

    This paper summarizes a system, and its component algorithms, for context-driven target vehicle detection in 3-D data that was developed under the Defense Advanced Research Projects Agency (DARPA) Exploitation of 3-D Data (E3D) Program. In order to determine the power of shape and geometry for the extraction of context objects and the detection of targets, our algorithm research and development concentrated on the geometric aspects of the problem and did not utilize intensity information. Processing begins with extraction of context information and initial target detection at reduced resolution, followed by a detailed, full-resolution analysis of candidate targets. Our reduced-resolution processing includes a probabilistic procedure for finding the ground that is effective even in rough terrain; a hierarchical, graph-based approach for the extraction of context objects and potential vehicle hide sites; and a target detection process that is driven by context-object and hide-site locations. Full-resolution processing includes statistical false alarm reduction and decoy mitigation. When results are available from previously collected data, we also perform object-level change detection, which affects the probabilities that objects are context objects or targets. Results are presented for both synthetic and collected LADAR data.

  9. Automated objective characterization of visual field defects in 3D

    NASA Technical Reports Server (NTRS)

    Fink, Wolfgang (Inventor)

    2006-01-01

    A method and apparatus for electronically performing a visual field test for a patient. A visual field test pattern is displayed to the patient on an electronic display device and the patient's responses to the visual field test pattern are recorded. A visual field representation is generated from the patient's responses. The visual field representation is then used as an input into a variety of automated diagnostic processes. In one process, the visual field representation is used to generate a statistical description of the rapidity of change of a patient's visual field at the boundary of a visual field defect. In another process, the area of a visual field defect is calculated using the visual field representation. In another process, the visual field representation is used to generate a statistical description of the volume of a patient's visual field defect.

  10. An automated voxelized dosimetry tool for radionuclide therapy based on serial quantitative SPECT/CT imaging

    SciTech Connect

    Jackson, Price A.; Kron, Tomas; Beauregard, Jean-Mathieu; Hofman, Michael S.; Hogg, Annette; Hicks, Rodney J.

    2013-11-15

    Purpose: To create an accurate map of the distribution of radiation dose deposition in healthy and target tissues during radionuclide therapy.Methods: Serial quantitative SPECT/CT images were acquired at 4, 24, and 72 h for 28 {sup 177}Lu-octreotate peptide receptor radionuclide therapy (PRRT) administrations in 17 patients with advanced neuroendocrine tumors. Deformable image registration was combined with an in-house programming algorithm to interpolate pharmacokinetic uptake and clearance at a voxel level. The resultant cumulated activity image series are comprised of values representing the total number of decays within each voxel's volume. For PRRT, cumulated activity was translated to absorbed dose based on Monte Carlo-determined voxel S-values at a combination of long and short ranges. These dosimetric image sets were compared for mean radiation absorbed dose to at-risk organs using a conventional MIRD protocol (OLINDA 1.1).Results: Absorbed dose values to solid organs (liver, kidneys, and spleen) were within 10% using both techniques. Dose estimates to marrow were greater using the voxelized protocol, attributed to the software incorporating crossfire effect from nearby tumor volumes.Conclusions: The technique presented offers an efficient, automated tool for PRRT dosimetry based on serial post-therapy imaging. Following retrospective analysis, this method of high-resolution dosimetry may allow physicians to prescribe activity based on required dose to tumor volume or radiation limits to healthy tissue in individual patients.

  11. Comparison of the effect of simple and complex acquisition trajectories on the 2D SPR and 3D voxelized differences for dedicated breast CT imaging

    NASA Astrophysics Data System (ADS)

    Shah, Jainil P.; Mann, Steve D.; McKinley, Randolph L.; Tornai, Martin P.

    2014-03-01

    The 2D scatter-to-primary (SPR) ratios and 3D voxelized difference volumes were characterized for a cone beam breast CT scanner capable of arbitrary (non-traditional) 3D trajectories. The CT system uses a 30x30cm2 flat panel imager with 197 micron pixellation and a rotating tungsten anode x-ray source with 0.3mm focal spot, with an SID of 70cm. Data were acquired for two cylindrical phantoms (12.5cm and 15cm diameter) filled with three different combinations of water and methanol yielding a range of uniform densities. Projections were acquired with two acquisition trajectories: 1) simple-circular azimuthal orbit with fixed tilt; and 2) saddle orbit following a +/-15° sinusoidal trajectory around the object. Projection data were acquired in 2x2 binned mode. Projections were scatter corrected using a beam stop array method, and the 2D SPR was measured on the projections. The scatter corrected and uncorrected data were then reconstructed individually using an iterative ordered subsets convex algorithm, and the 3D difference volumes were calculated as the absolute difference between the two. Results indicate that the 2D SPR is ~7-15% higher on projections with greatest tilt for the saddle orbit, due to the longer x-ray path length through the volume, compared to the 0° tilt projections. Additionally, the 2D SPR increases with object diameter as well as density. The 3D voxelized difference volumes are an estimate of the scatter contribution to the reconstructed attenuation coefficients on a voxel level. They help visualize minor deficiencies and artifacts in the volumes due to correction methods.

  12. Biomek Cell Workstation: A Flexible System for Automated 3D Cell Cultivation.

    PubMed

    Lehmann, R; Gallert, C; Roddelkopf, T; Junginger, S; Thurow, K

    2016-08-01

    The shift from 2D cultures to 3D cultures enables improvement in cell culture research due to better mimicking of in vivo cell behavior and environmental conditions. Different cell lines and applications require altered 3D constructs. The automation of the manufacturing and screening processes can advance the charge stability, quality, repeatability, and precision. In this study we integrated the automated production of three 3D cell constructs (alginate beads, spheroid cultures, pellet cultures) using the Biomek Cell Workstation and compared them with the traditional manual methods and their consequent bioscreening processes (proliferation, toxicity; days 14 and 35) using a high-throughput screening system. Moreover, the possible influence of antibiotics (penicillin/streptomycin) on the production and screening processes was investigated. The cytotoxicity of automatically produced 3D cell cultures (with and without antibiotics) was mainly decreased. The proliferation showed mainly similar or increased results for the automatically produced 3D constructs. We concluded that the traditional manual methods can be replaced by the automated processes. Furthermore, the formation, cultivation, and screenings can be performed without antibiotics to prevent possible effects. PMID:26203054

  13. 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.

  14. 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

  15. Automated Mosaicking of Multiple 3d Point Clouds Generated from a Depth Camera

    NASA Astrophysics Data System (ADS)

    Kim, H.; Yoon, W.; Kim, T.

    2016-06-01

    In this paper, we propose a method for automated mosaicking of multiple 3D point clouds generated from a depth camera. A depth camera generates depth data by using ToF (Time of Flight) method and intensity data by using intensity of returned signal. The depth camera used in this paper was a SR4000 from MESA Imaging. This camera generates a depth map and intensity map of 176 x 44 pixels. Generated depth map saves physical depth data with mm of precision. Generated intensity map contains texture data with many noises. We used texture maps for extracting tiepoints and depth maps for assigning z coordinates to tiepoints and point cloud mosaicking. There are four steps in the proposed mosaicking method. In the first step, we acquired multiple 3D point clouds by rotating depth camera and capturing data per rotation. In the second step, we estimated 3D-3D transformation relationships between subsequent point clouds. For this, 2D tiepoints were extracted automatically from the corresponding two intensity maps. They were converted into 3D tiepoints using depth maps. We used a 3D similarity transformation model for estimating the 3D-3D transformation relationships. In the third step, we converted local 3D-3D transformations into a global transformation for all point clouds with respect to a reference one. In the last step, the extent of single depth map mosaic was calculated and depth values per mosaic pixel were determined by a ray tracing method. For experiments, 8 depth maps and intensity maps were used. After the four steps, an output mosaicked depth map of 454x144 was generated. It is expected that the proposed method would be useful for developing an effective 3D indoor mapping method in future.

  16. 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

  17. Fully automated 3D prostate central gland segmentation in MR images: a LOGISMOS based approach

    NASA Astrophysics Data System (ADS)

    Yin, Yin; Fotin, Sergei V.; Periaswamy, Senthil; Kunz, Justin; Haldankar, Hrishikesh; Muradyan, Naira; Turkbey, Baris; Choyke, Peter

    2012-02-01

    One widely accepted classification of a prostate is by a central gland (CG) and a peripheral zone (PZ). In some clinical applications, separating CG and PZ from the whole prostate is useful. For instance, in prostate cancer detection, radiologist wants to know in which zone the cancer occurs. Another application is for multiparametric MR tissue characterization. In prostate T2 MR images, due to the high intensity variation between CG and PZ, automated differentiation of CG and PZ is difficult. Previously, we developed an automated prostate boundary segmentation system, which tested on large datasets and showed good performance. Using the results of the pre-segmented prostate boundary, in this paper, we proposed an automated CG segmentation algorithm based on Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces (LOGISMOS). The designed LOGISMOS model contained both shape and topology information during deformation. We generated graph cost by training classifiers and used coarse-to-fine search. The LOGISMOS framework guarantees optimal solution regarding to cost and shape constraint. A five-fold cross-validation approach was applied to training dataset containing 261 images to optimize the system performance and compare with a voxel classification based reference approach. After the best parameter settings were found, the system was tested on a dataset containing another 261 images. The mean DSC of 0.81 for the test set indicates that our approach is promising for automated CG segmentation. Running time for the system is about 15 seconds.

  18. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  19. Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

    PubMed Central

    Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

    2014-01-01

    Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports

  20. Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data

    PubMed Central

    Khorshed, Reema A.; Hawkins, Edwin D.; Duarte, Delfim; Scott, Mark K.; Akinduro, Olufolake A.; Rashidi, Narges M.; Spitaler, Martin; Lo Celso, Cristina

    2015-01-01

    Summary Measuring three-dimensional (3D) localization of hematopoietic stem cells (HSCs) within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components. PMID:26120058

  1. Automated 3D Damaged Cavity Model Builder for Lower Surface Acreage Tile on Orbiter

    NASA Technical Reports Server (NTRS)

    Belknap, Shannon; Zhang, Michael

    2013-01-01

    The 3D Automated Thermal Tool for Damaged Acreage Tile Math Model builder was developed to perform quickly and accurately 3D thermal analyses on damaged lower surface acreage tiles and structures beneath the damaged locations on a Space Shuttle Orbiter. The 3D model builder created both TRASYS geometric math models (GMMs) and SINDA thermal math models (TMMs) to simulate an idealized damaged cavity in the damaged tile(s). The GMMs are processed in TRASYS to generate radiation conductors between the surfaces in the cavity. The radiation conductors are inserted into the TMMs, which are processed in SINDA to generate temperature histories for all of the nodes on each layer of the TMM. The invention allows a thermal analyst to create quickly and accurately a 3D model of a damaged lower surface tile on the orbiter. The 3D model builder can generate a GMM and the correspond ing TMM in one or two minutes, with the damaged cavity included in the tile material. A separate program creates a configuration file, which would take a couple of minutes to edit. This configuration file is read by the model builder program to determine the location of the damage, the correct tile type, tile thickness, structure thickness, and SIP thickness of the damage, so that the model builder program can build an accurate model at the specified location. Once the models are built, they are processed by the TRASYS and SINDA.

  2. Design, fabrication, and implementation of voxel-based 3D printed textured phantoms for task-based image quality assessment in CT

    NASA Astrophysics Data System (ADS)

    Solomon, Justin; Ba, Alexandre; Diao, Andrew; Lo, Joseph; Bier, Elianna; Bochud, François; Gehm, Michael; Samei, Ehsan

    2016-03-01

    In x-ray computed tomography (CT), task-based image quality studies are typically performed using uniform background phantoms with low-contrast signals. Such studies may have limited clinical relevancy for modern non-linear CT systems due to possible influence of background texture on image quality. The purpose of this study was to design and implement anatomically informed textured phantoms for task-based assessment of low-contrast detection. Liver volumes were segmented from 23 abdominal CT cases. The volumes were characterized in terms of texture features from gray-level co-occurrence and run-length matrices. Using a 3D clustered lumpy background (CLB) model, a fitting technique based on a genetic optimization algorithm was used to find the CLB parameters that were most reflective of the liver textures, accounting for CT system factors of spatial blurring and noise. With the modeled background texture as a guide, a cylinder phantom (165 mm in diameter and 30 mm height) was designed, containing 20 low-contrast spherical signals (6 mm in diameter at targeted contrast levels of ~3.2, 5.2, 7.2, 10, and 14 HU, 4 repeats per signal). The phantom was voxelized and input into a commercial multi-material 3D printer (Object Connex 350), with custom software for voxel-based printing. Using principles of digital half-toning and dithering, the 3D printer was programmed to distribute two base materials (VeroWhite and TangoPlus, nominal voxel size of 42x84x30 microns) to achieve the targeted spatial distribution of x-ray attenuation properties. The phantom was used for task-based image quality assessment of a clinically available iterative reconstruction algorithm (Sinogram Affirmed Iterative Reconstruction, SAFIRE) using a channelized Hotelling observer paradigm. Images of the textured phantom and a corresponding uniform phantom were acquired at six dose levels and observer model performance was estimated for each condition (5 contrasts x 6 doses x 2 reconstructions x 2

  3. Differences in 3D dose distributions due to calculation method of voxel S-values and the influence of image blurring in SPECT

    NASA Astrophysics Data System (ADS)

    Pacilio, Massimiliano; Amato, Ernesto; Lanconelli, Nico; Basile, Chiara; Torres, Leonel Alberto; Botta, Francesca; Ferrari, Mahila; Cornejo Diaz, Nestor; Coca Perez, Marco; Fernández, María; Lassmann, Michael; Vergara Gil, Alex; Cremonesi, Marta

    2015-03-01

    This study compares 3D dose distributions obtained with voxel S values (VSVs) for soft tissue, calculated by several methods at their current state-of-the-art, varying the degree of image blurring. The methods were: 1) convolution of Dose Point Kernel (DPK) for water, using a scaling factor method; 2) an analytical model (AM), fitting the deposited energy as a function of the source-target distance; 3) a rescaling method (RSM) based on a set of high-resolution VSVs for each isotope; 4) local energy deposition (LED). VSVs calculated by direct Monte Carlo simulations were assumed as reference. Dose distributions were calculated considering spheroidal clusters with various sizes (251, 1237 and 4139 voxels of 3 mm size), uniformly filled with 131I, 177Lu, 188Re or 90Y. The activity distributions were blurred with Gaussian filters of various widths (6, 8 and 12 mm). Moreover, 3D-dosimetry was performed for 10 treatments with 90Y derivatives. Cumulative Dose Volume Histograms (cDVHs) were compared, studying the differences in D95%, D50% or Dmax (ΔD95%, ΔD50% and ΔDmax) and dose profiles. For unblurred spheroidal clusters, ΔD95%, ΔD50% and ΔDmax were mostly within some percents, slightly higher for 177Lu with DPK (8%) and RSM (12%) and considerably higher for LED (ΔD95% up to 59%). Increasing the blurring, differences decreased and also LED yielded very similar results, but D95% and D50% underestimations between 30-60% and 15-50%, respectively (with respect to 3D-dosimetry with unblurred distributions), were evidenced. Also for clinical images (affected by blurring as well), cDVHs differences for most methods were within few percents, except for slightly higher differences with LED, and almost systematic for dose profiles with DPK (-1.2%), AM (-3.0%) and RSM (4.5%), whereas showed an oscillating trend with LED. The major concern for 3D-dosimetry on clinical SPECT images is more strongly represented by image blurring than by differences among the VSVs

  4. Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing

    PubMed Central

    2014-01-01

    Background The zebrafish has been established as the main vertebrate model system for whole organism screening applications. However, the lack of consistent positioning of zebrafish embryos within wells of microtiter plates remains an obstacle for the comparative analysis of images acquired in automated screening assays. While technical solutions to the orientation problem exist, dissemination is often hindered by the lack of simple and inexpensive ways of distributing and duplicating tools. Results Here, we provide a cost effective method for the production of 96-well plate compatible zebrafish orientation tools using a desktop 3D printer. The printed tools enable the positioning and orientation of zebrafish embryos within cavities formed in agarose. Their applicability is demonstrated by acquiring lateral and dorsal views of zebrafish embryos arrayed within microtiter plates using an automated screening microscope. This enables the consistent visualization of morphological phenotypes and reporter gene expression patterns. Conclusions The designs are refined versions of previously demonstrated devices with added functionality and strongly reduced production costs. All corresponding 3D models are freely available and digital design can be easily shared electronically. In combination with the increasingly widespread usage of 3D printers, this provides access to the developed tools to a wide range of zebrafish users. Finally, the design files can serve as templates for other additive and subtractive fabrication methods. PMID:24886511

  5. Shear wave velocity for the upper 30 m: Combining a 3D voxel model and seismic CPTS for the Groningen gas field, the Netherlands.

    NASA Astrophysics Data System (ADS)

    Dambrink, Roula; Gunnink, Jan; Stafleu, Jan; de Lange, Ger; Kruiver, Pauline

    2016-04-01

    The Groningen gas field in the Netherlands is one of the largest gas fields of Europe and has been in production since the 1960's. Due to the progressive depletion of the reservoir, induced seismic activity has increased in recent years. In 2012, an earthquake of magnitude 3.6 initiated further research in prediction and management of risks related to man-induced earthquakes. Last year the government decided to reduce the gas extraction for this reason. One of the topics of concern is the large difference in earthquake-related damage to buildings which, in addition to the distance to the epicenter, appears to be also related to the composition of the shallow subsurface. To improve the spatial distribution of Shear Wave Velocities (Vs) in the shallow subsurface, used for hazard prediction, the Geological Survey of the Netherlands and Deltares constructed a Vs30 map of the upper 30 m of the gas field. In this map a high-resolution geological model (GeoTOP) is combined with seismic cone penetration tests (SCPT) from the area. The GeoTOP model is a 3D voxel model of the upper 50 m, in which each voxel (100x100x0.5 m) is attributed with lithostratigraphy and the most likely lithological class (peat, clay, fine sand, etc.). To obtain statistical distributions (with mean and standard deviation) of Vs for each combination of lithostratigraphical unit and lithoclass, 60 SCPTs were analyzed. In this way, it was possible to assign a specific Vs to each voxel in the model. For each voxel in the stack of voxels that covers the upper 30 m (i.e. 60 voxels), a Vs value was randomly drawn from the statistical distribution of the lithostratigraphical - lithoclass combination it belongs to. The Vs30 for each voxelstack is then calculated using the harmonic mean of the Vs of the 60 voxels. By repeating this procedure 100 times, an (average) Vs30 map and the uncertainty in Vs30 has been constructed. Using the procedure described above we were able to delineate zones with distinct Vs30

  6. Development of a 3D-based automated firearms evidence comparison system.

    PubMed

    Bachrach, Benjamin

    2002-11-01

    Since the early 1990's, the idea of automated systems for the comparison of microscopic firearms evidence has received considerable attention. The main objective of such systems is to enable the analysis of large amounts of evidence, therefore, transforming the comparison of firearms evidence from an evidence verification tool into a crime-fighting tool. Two such systems have been widely used in United States forensic laboratories: namely, the Integrated Ballistics Identification System (IBIS) (1) and DRUGFIRE (2). Both IBIS and DRUGFIRE have in common the fact that their characterization of a specimen is based on a two-dimensional (2D) representation of the specimen's surface. Although these systems have provided satisfactory results in the identification of cartridge cases, their performance in the identification of bullets has not yet met firearms examiner's expectations. This project was motivated by the premise that a better characterizations of the bullet's surface should translate into better performance of automated identification systems. A three-dimensional (3D) characterization of the bullet's surface is proposed as an alternative to a 2D characterization. This paper discusses the development and preliminary results obtained with SciClops, an automated microscopic comparison system based on the use of a 3D characterization of a bullet's surface. PMID:12455646

  7. Second generation anthropomorphic physical phantom for mammography and DBT: Incorporating voxelized 3D printing and inkjet printing of iodinated lesion inserts

    NASA Astrophysics Data System (ADS)

    Sikaria, Dhiraj; Musinsky, Stephanie; Sturgeon, Gregory M.; Solomon, Justin; Diao, Andrew; Gehm, Michael E.; Samei, Ehsan; Glick, Stephen J.; Lo, Joseph Y.

    2016-03-01

    Physical phantoms are needed for the evaluation and optimization of new digital breast tomosynthesis (DBT) systems. Previously, we developed an anthropomorphic phantom based on human subject breast CT data and fabricated using commercial 3D printing. We now present three key advancements: voxelized 3D printing, photopolymer material doping, and 2D inkjet printing of lesion inserts. First, we bypassed the printer's control software in order to print in voxelized form instead of conventional STL surfaces, thus improving resolution and allowing dithering to mix the two photopolymer materials into arbitrary proportions. We demonstrated ability to print details as small as 150μm, and dithering to combine VeroWhitePlus and TangoPlus in 10% increments. Second, to address the limited attenuation difference among commercial photopolymers, we evaluated a beta sample from Stratasys with increased TiO2 doping concentration up to 2.5%, which corresponded to 98% breast density. By spanning 36% to 98% breast density, this doubles our previous contrast. Third, using inkjet printers modified to print with iopamidol, we created 2D lesion patterns on paper that can be sandwiched into the phantom. Inkjet printing has advantages of being inexpensive and easy, and more contrast can be delivered through overprinting. Printing resolution was maintained at 210 μm horizontally and 330 μm vertically even after 10 overprints. Contrast increased linearly with overprinting at 0.7% per overprint. Together, these three new features provide the basis for creating a new anthropomorphic physical breast phantom with improved resolution and contrast, as well as the ability to insert 2D lesions for task-based assessment of performance.

  8. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  9. ON 3D, AUTOMATED, SELF-CONTAINED GRID GENERATION WITHIN THE RAGE CAMR HYDROCODE

    SciTech Connect

    Oakes, W.R.; Henning, P.J.; Gittings, M.L.; Weaver, R.P.

    2000-06-01

    We discuss using the inherent grid manipulation capability within a Continuously Adaptive Mesh Refinement hydrodynamics code, RAGE, to implement parallel, automated, self-contained grid generation. We show how arbitrarily complex 3D geometries specified in any unambiguous form can be used. The RAGE computational environment is any of several massively parallel computers being developed under the Department Of Energy's Accelerated Strategic Computing Initiative. A typical 3D RAGE analysis may contain 100 million cells and occupy 2000 processors for several weeks. RAGE grid generation is embarrassingly parallel. The RAGE computational grid is an octree decomposition of the model space. The problem domain is subdivided into as many subdomains as the number of processors assigned to the problem. The grid for each subdomain is then generated independently, except for occasional adjustments. Geometry used for initial grid generation includes CSG combinations of NURBS-based boundary representation models, stereo lithography (STL) files, implicit surfaces, and functionally perturbed surfaces.

  10. An automated tool for 3D tracking of single molecules in living cells

    NASA Astrophysics Data System (ADS)

    Gardini, L.; Capitanio, M.; Pavone, F. S.

    2015-03-01

    Since the behaviour of proteins and biological molecules is tightly related to cell's environment, more and more microscopy techniques are moving from in vitro to in living cells experiments. Looking at both diffusion and active transportation processes inside a cell requires three-dimensional localization over a few microns range, high SNR images and high temporal resolution. Since protein dynamics inside a cell involve all three dimensions, we developed an automated routine for 3D tracking of single fluorescent molecules inside living cells with nanometer accuracy, by exploiting the properties of the point-spread-function of out-of-focus Quantum Dots bound to the protein of interest.

  11. 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

  12. 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.

  13. a Semi-Automated Point Cloud Processing Methodology for 3d Cultural Heritage Documentation

    NASA Astrophysics Data System (ADS)

    Kıvılcım, C. Ö.; Duran, Z.

    2016-06-01

    The preliminary phase in any architectural heritage project is to obtain metric measurements and documentation of the building and its individual elements. On the other hand, conventional measurement techniques require tremendous resources and lengthy project completion times for architectural surveys and 3D model production. Over the past two decades, the widespread use of laser scanning and digital photogrammetry have significantly altered the heritage documentation process. Furthermore, advances in these technologies have enabled robust data collection and reduced user workload for generating various levels of products, from single buildings to expansive cityscapes. More recently, the use of procedural modelling methods and BIM relevant applications for historic building documentation purposes has become an active area of research, however fully automated systems in cultural heritage documentation still remains open. In this paper, we present a semi-automated methodology, for 3D façade modelling of cultural heritage assets based on parametric and procedural modelling techniques and using airborne and terrestrial laser scanning data. We present the contribution of our methodology, which we implemented in an open source software environment using the example project of a 16th century early classical era Ottoman structure, Sinan the Architect's Şehzade Mosque in Istanbul, Turkey.

  14. Automated Reconstruction of Walls from Airborne LIDAR Data for Complete 3d Building Modelling

    NASA Astrophysics Data System (ADS)

    He, Y.; Zhang, C.; Awrangjeb, M.; Fraser, C. S.

    2012-07-01

    Automated 3D building model generation continues to attract research interests in photogrammetry and computer vision. Airborne Light Detection and Ranging (LIDAR) data with increasing point density and accuracy has been recognized as a valuable source for automated 3D building reconstruction. While considerable achievements have been made in roof extraction, limited research has been carried out in modelling and reconstruction of walls, which constitute important components of a full building model. Low point density and irregular point distribution of LIDAR observations on vertical walls render this task complex. This paper develops a novel approach for wall reconstruction from airborne LIDAR data. The developed method commences with point cloud segmentation using a region growing approach. Seed points for planar segments are selected through principle component analysis, and points in the neighbourhood are collected and examined to form planar segments. Afterwards, segment-based classification is performed to identify roofs, walls and planar ground surfaces. For walls with sparse LIDAR observations, a search is conducted in the neighbourhood of each individual roof segment to collect wall points, and the walls are then reconstructed using geometrical and topological constraints. Finally, walls which were not illuminated by the LIDAR sensor are determined via both reconstructed roof data and neighbouring walls. This leads to the generation of topologically consistent and geometrically accurate and complete 3D building models. Experiments have been conducted in two test sites in the Netherlands and Australia to evaluate the performance of the proposed method. Results show that planar segments can be reliably extracted in the two reported test sites, which have different point density, and the building walls can be correctly reconstructed if the walls are illuminated by the LIDAR sensor.

  15. Automated three-dimensional choroidal vessel segmentation of 3D 1060 nm OCT retinal data

    PubMed Central

    Kajić, Vedran; Esmaeelpour, Marieh; Glittenberg, Carl; Kraus, Martin F.; Honegger, Joachim; Othara, Richu; Binder, Susanne; Fujimoto, James G.; Drexler, Wolfgang

    2012-01-01

    A fully automated, robust vessel segmentation algorithm has been developed for choroidal OCT, employing multiscale 3D edge filtering and projection of “probability cones” to determine the vessel “core”, even in the tomograms with low signal-to-noise ratio (SNR). Based on the ideal vessel response after registration and multiscale filtering, with computed depth related SNR, the vessel core estimate is dilated to quantify the full vessel diameter. As a consequence, various statistics can be computed using the 3D choroidal vessel information, such as ratios of inner (smaller) to outer (larger) choroidal vessels or the absolute/relative volume of choroid vessels. Choroidal vessel quantification can be displayed in various forms, focused and averaged within a special region of interest, or analyzed as the function of image depth. In this way, the proposed algorithm enables unique visualization of choroidal watershed zones, as well as the vessel size reduction when investigating the choroid from the sclera towards the retinal pigment epithelium (RPE). To the best of our knowledge, this is the first time that an automatic choroidal vessel segmentation algorithm is successfully applied to 1060 nm 3D OCT of healthy and diseased eyes. PMID:23304653

  16. Fast voxel-based 2D/3D registration algorithm using a volume rendering method based on the shear-warp factorization

    NASA Astrophysics Data System (ADS)

    Weese, Juergen; Goecke, Roland; Penney, Graeme P.; Desmedt, Paul; Buzug, Thorsten M.; Schumann, Heidrun

    1999-05-01

    2D/3D registration makes it possible to use pre-operative CT scans for navigation purposes during X-ray fluoroscopy guided interventions. We present a fast voxel-based method for this registration task, which uses a recently introduced similarity measure (pattern intensity). This measure is especially suitable for 2D/3D registration, because it is robust with respect to structures such as a stent visible in the X-ray fluoroscopy image but not in the CT scan. The method uses only a part of the CT scan for the generation of digitally reconstructed radiographs (DRRs) to accelerate their computation. Nevertheless, computation time is crucial for intra-operative application and a further speed-up is required, because numerous DRRs must be computed. For that reason, the suitability of different volume rendering methods for 2D/3D registration has been investigated. A method based on the shear-warp factorization of the viewing transformation turned out to be especially suitable and builds the basis of the registration algorithm. The algorithm has been applied to images of a spine phantom and to clinical images. For comparison, registration results have been calculated using ray-casting. The shear-warp factorization based rendering method accelerates registration by a factor of up to seven compared to ray-casting without degrading registration accuracy. Using a vertebra as feature for registration, computation time is in the range of 3-4s (Sun UltraSparc, 300 MHz) which is acceptable for intra-operative application.

  17. Automated torso organ segmentation from 3D CT images using structured perceptron and dual decomposition

    NASA Astrophysics Data System (ADS)

    Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Mori, Kensaku

    2015-03-01

    This paper presents a method for torso organ segmentation from abdominal CT images using structured perceptron and dual decomposition. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. This paper proposes an organ segmentation method using structured output learning. Our method utilizes a graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weights of the graphical model by structured perceptron and estimate the best organ label for a given image by dynamic programming and dual decomposition. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 4.4%. The DICE coefficients of left lung, right lung, heart, liver, spleen, pancreas, left kidney, right kidney, and gallbladder were 0.91, 0.95, 0.77, 0.81, 0.74, 0.08, 0.83, 0.84, and 0.03, respectively.

  18. An automated tool for 3D tracking of single molecules in living cells

    NASA Astrophysics Data System (ADS)

    Gardini, L.; Capitanio, M.; Pavone, F. S.

    2015-07-01

    Recently, tremendous improvements have been achieved in the precision of localization of single fluorescent molecules, allowing localization and tracking of biomolecules at the nm level. Since the behaviour of proteins and biological molecules is tightly influenced by the cell's environment, a growing number of microscopy techniques are moving from in vitro to live cell experiments. Looking at both diffusion and active transportation processes inside a cell requires three-dimensional localization over a few microns range, high SNR images and high temporal resolution (ms order of magnitude). To satisfy these requirements we developed an automated routine that allow 3D tracking of single fluorescent molecules in living cells with nanometer accuracy, by exploiting the properties of the point-spread-function of out-of-focus Quantum Dots bound to the protein of interest.

  19. Automated Segmentation of the Right Ventricle in 3D Echocardiography: A Kalman Filter State Estimation Approach.

    PubMed

    Bersvendsen, Jorn; Orderud, Fredrik; Massey, Richard John; Fosså, Kristian; Gerard, Olivier; Urheim, Stig; Samset, Eigil

    2016-01-01

    As the right ventricle's (RV) role in cardiovascular diseases is being more widely recognized, interest in RV imaging, function and quantification is growing. However, there are currently few RV quantification methods for 3D echocardiography presented in the literature or commercially available. In this paper we propose an automated RV segmentation method for 3D echocardiographic images. We represent the RV geometry by a Doo-Sabin subdivision surface with deformation modes derived from a training set of manual segmentations. The segmentation is then represented as a state estimation problem and solved with an extended Kalman filter by combining the RV geometry with a motion model and edge detection. Validation was performed by comparing surface-surface distances, volumes and ejection fractions in 17 patients with aortic insufficiency between the proposed method, magnetic resonance imaging (MRI), and a manual echocardiographic reference. The algorithm was efficient with a mean computation time of 2.0 s. The mean absolute distances between the proposed and manual segmentations were 3.6 ± 0.7 mm. Good agreements of end diastolic volume, end systolic volume and ejection fraction with respect to MRI ( -26±24 mL , -16±26 mL and 0 ± 10%, respectively) and a manual echocardiographic reference (7 ± 30 mL, 13 ± 17 mL and -5±7% , respectively) were observed. PMID:26168434

  20. 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.

  1. 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

  2. Automated bone segmentation from large field of view 3D MR images of the hip joint

    NASA Astrophysics Data System (ADS)

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S.; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

    2013-10-01

    Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation.

  3. Automated bone segmentation from large field of view 3D MR images of the hip joint.

    PubMed

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

    2013-10-21

    Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation. PMID:24077264

  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. A Neurocomputational Method for Fully Automated 3D Dendritic Spine Detection and Segmentation of Medium-sized Spiny Neurons

    PubMed Central

    Zhang, Yong; Chen, Kun; Baron, Matthew; Teylan, Merilee A.; Kim, Yong; Song, Zhihuan; Greengard, Paul

    2010-01-01

    Acquisition and quantitative analysis of high resolution images of dendritic spines are challenging tasks but are necessary for the study of animal models of neurological and psychiatric diseases. Currently available methods for automated dendritic spine detection are for the most part customized for 2D image slices, not volumetric 3D images. In this work, a fully automated method is proposed to detect and segment dendritic spines from 3D confocal microscopy images of medium-sized spiny neurons (MSNs). MSNs constitute a major neuronal population in striatum, and abnormalities in their function are associated with several neurological and psychiatric diseases. Such automated detection is critical for the development of new 3D neuronal assays which can be used for the screening of drugs and the studies of their therapeutic effects. The proposed method utilizes a generalized gradient vector flow (GGVF) with a new smoothing constraint and then detects feature points near the central regions of dendrites and spines. Then, the central regions are refined and separated based on eigen-analysis and multiple shape measurements. Finally, the spines are segmented in 3D space using the fast marching algorithm, taking the detected central regions of spines as initial points. The proposed method is compared with three popular existing methods for centerline extraction and also with manual results for dendritic spine detection in 3D space. The experimental results and comparisons show that the proposed method is able to automatically and accurately detect, segment, and quantitate dendritic spines in 3D images of MSNs. PMID:20100579

  7. Magnetic resonance virtual histology for embryos: 3D atlases for automated high-throughput phenotyping.

    PubMed

    Cleary, Jon O; Modat, Marc; Norris, Francesca C; Price, Anthony N; Jayakody, Sujatha A; Martinez-Barbera, Juan Pedro; Greene, Nicholas D E; Hawkes, David J; Ordidge, Roger J; Scambler, Peter J; Ourselin, Sebastien; Lythgoe, Mark F

    2011-01-15

    Ambitious international efforts are underway to produce gene-knockout mice for each of the 25,000 mouse genes, providing a new platform to study mammalian development and disease. Robust, large-scale methods for morphological assessment of prenatal mice will be essential to this work. Embryo phenotyping currently relies on histological techniques but these are not well suited to large volume screening. The qualitative nature of these approaches also limits the potential for detailed group analysis. Advances in non-invasive imaging techniques such as magnetic resonance imaging (MRI) may surmount these barriers. We present a high-throughput approach to generate detailed virtual histology of the whole embryo, combined with the novel use of a whole-embryo atlas for automated phenotypic assessment. Using individual 3D embryo MRI histology, we identified new pituitary phenotypes in Hesx1 mutant mice. Subsequently, we used advanced computational techniques to produce a whole-body embryo atlas from 6 CD-1 embryos, creating an average image with greatly enhanced anatomical detail, particularly in CNS structures. This methodology enabled unsupervised assessment of morphological differences between CD-1 embryos and Chd7 knockout mice (n=5 Chd7(+/+) and n=8 Chd7(+/-), C57BL/6 background). Using a new atlas generated from these three groups, quantitative organ volumes were automatically measured. We demonstrated a difference in mean brain volumes between Chd7(+/+) and Chd7(+/-) mice (42.0 vs. 39.1mm(3), p<0.05). Differences in whole-body, olfactory and normalised pituitary gland volumes were also found between CD-1 and Chd7(+/+) mice (C57BL/6 background). Our work demonstrates the feasibility of combining high-throughput embryo MRI with automated analysis techniques to distinguish novel mouse phenotypes. PMID:20656039

  8. TOBAGO — a semi-automated approach for the generation of 3-D building models

    NASA Astrophysics Data System (ADS)

    Gruen, Armin

    3-D city models are in increasing demand for a great number of applications. Photogrammetry is a relevant technology that can provide an abundance of geometric, topologic and semantic information concerning these models. The pressure to generate a large amount of data with high degree of accuracy and completeness poses a great challenge to phtogrammetry. The development of automated and semi-automated methods for the generation of those data sets is therefore a key issue in photogrammetric research. We present in this article a strategy and methodology for an efficient generation of even fairly complex building models. Within this concept we request the operator to measure the house roofs from a stereomodel in form of an unstructured point cloud. According to our experience this can be done very quickly. Even a non-experienced operator can measure several hundred roofs or roof units per day. In a second step we fit generic building models fully automatically to these point clouds. The structure information is inherently included in these building models. In such a way geometric, topologic and even semantic data can be handed over to a CAD-system, in our case AutoCad, for further visualization and manipulation. The structuring is achieved in three steps. In a first step a classifier is initiated which recognizes the class of houses a particular roof point cloud belongs to. This recognition step is primarily based on the analysis of the number of ridge points. In the second and third steps the concrete topological relations between roof points are investigated and generic building models are fitted to the point clouds. Based on the technique of constraint-based reasoning two geometrical parsers are solving this problem. We have tested the methodology under a variety of different conditions in several pilot projects. The results will indicate the good performance of our approach. In addition we will demonstrate how the results can be used for visualization (texture

  9. Automated analysis of barley organs using 3D laser scanning: an approach for high throughput phenotyping.

    PubMed

    Paulus, Stefan; Dupuis, Jan; Riedel, Sebastian; Kuhlmann, Heiner

    2014-01-01

    Due to the rise of laser scanning the 3D geometry of plant architecture is easy to acquire. Nevertheless, an automated interpretation and, finally, the segmentation into functional groups are still difficult to achieve. Two barley plants were scanned in a time course, and the organs were separated by applying a histogram-based classification algorithm. The leaf organs were represented by meshing algorithms, while the stem organs were parameterized by a least-squares cylinder approximation. We introduced surface feature histograms with an accuracy of 96% for the separation of the barley organs, leaf and stem. This enables growth monitoring in a time course for barley plants. Its reliability was demonstrated by a comparison with manually fitted parameters with a correlation R(2) = 0:99 for the leaf area and R(2) = 0:98 for the cumulated stem height. A proof of concept has been given for its applicability for the detection of water stress in barley, where the extension growth of an irrigated and a non-irrigated plant has been monitored. PMID:25029283

  10. A new method for automated discontinuity trace mapping on rock mass 3D surface model

    NASA Astrophysics Data System (ADS)

    Li, Xiaojun; Chen, Jianqin; Zhu, Hehua

    2016-04-01

    This paper presents an automated discontinuity trace mapping method on a 3D surface model of rock mass. Feature points of discontinuity traces are first detected using the Normal Tensor Voting Theory, which is robust to noisy point cloud data. Discontinuity traces are then extracted from feature points in four steps: (1) trace feature point grouping, (2) trace segment growth, (3) trace segment connection, and (4) redundant trace segment removal. A sensitivity analysis is conducted to identify optimal values for the parameters used in the proposed method. The optimal triangular mesh element size is between 5 cm and 6 cm; the angle threshold in the trace segment growth step is between 70° and 90°; the angle threshold in the trace segment connection step is between 50° and 70°, and the distance threshold should be at least 15 times the mean triangular mesh element size. The method is applied to the excavation face trace mapping of a drill-and-blast tunnel. The results show that the proposed discontinuity trace mapping method is fast and effective and could be used as a supplement to traditional direct measurement of discontinuity traces.

  11. pynoddy 1.0: an experimental platform for automated 3-D kinematic and potential field modelling

    NASA Astrophysics Data System (ADS)

    Florian Wellmann, J.; Thiele, Sam T.; Lindsay, Mark D.; Jessell, Mark W.

    2016-03-01

    We present a novel methodology for performing experiments with subsurface structural models using a set of flexible and extensible Python modules. We utilize the ability of kinematic modelling techniques to describe major deformational, tectonic, and magmatic events at low computational cost to develop experiments testing the interactions between multiple kinematic events, effect of uncertainty regarding event timing, and kinematic properties. These tests are simple to implement and perform, as they are automated within the Python scripting language, allowing the encapsulation of entire kinematic experiments within high-level class definitions and fully reproducible results. In addition, we provide a link to geophysical potential-field simulations to evaluate the effect of parameter uncertainties on maps of gravity and magnetics. We provide relevant fundamental information on kinematic modelling and our implementation, and showcase the application of our novel methods to investigate the interaction of multiple tectonic events on a pre-defined stratigraphy, the effect of changing kinematic parameters on simulated geophysical potential fields, and the distribution of uncertain areas in a full 3-D kinematic model, based on estimated uncertainties in kinematic input parameters. Additional possibilities for linking kinematic modelling to subsequent process simulations are discussed, as well as additional aspects of future research. Our modules are freely available on github, including documentation and tutorial examples, and we encourage the contribution to this project.

  12. pynoddy 1.0: an experimental platform for automated 3-D kinematic and potential field modelling

    NASA Astrophysics Data System (ADS)

    Wellmann, J. F.; Thiele, S. T.; Lindsay, M. D.; Jessell, M. W.

    2015-11-01

    We present a novel methodology for performing experiments with subsurface structural models using a set of flexible and extensible Python modules. We utilise the ability of kinematic modelling techniques to describe major deformational, tectonic, and magmatic events at low computational cost to develop experiments testing the interactions between multiple kinematic events, effect of uncertainty regarding event timing, and kinematic properties. These tests are simple to implement and perform, as they are automated within the Python scripting language, allowing the encapsulation of entire kinematic experiments within high-level class definitions and fully reproducible results. In addition, we provide a~link to geophysical potential-field simulations to evaluate the effect of parameter uncertainties on maps of gravity and magnetics. We provide relevant fundamental information on kinematic modelling and our implementation, and showcase the application of our novel methods to investigate the interaction of multiple tectonic events on a pre-defined stratigraphy, the effect of changing kinematic parameters on simulated geophysical potential-fields, and the distribution of uncertain areas in a full 3-D kinematic model, based on estimated uncertainties in kinematic input parameters. Additional possibilities for linking kinematic modelling to subsequent process simulations are discussed, as well as additional aspects of future research. Our modules are freely available on github, including documentation and tutorial examples, and we encourage the contribution to this project.

  13. 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

  14. Automated Foveola Localization in Retinal 3D-OCT Images Using Structural Support Vector Machine Prediction

    PubMed Central

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S.; Rehg, James M.

    2013-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark. PMID:23285565

  15. EFAB: low-cost automated electrochemical batch fabrication of arbitrary 3D microstructures

    NASA Astrophysics Data System (ADS)

    Cohen, Adam L.; Frodis, Uri; Tseng, Fan-Gang; Zhang, Gang; Mansfeld, Florian; Will, Peter M.

    1999-08-01

    EFAB is a new micromachining process promising to rapidly and automatically batch fabricate high-aspect-ratio microstructures with arbitrary 3D geometry using inexpensive equipment. Conventional microfabrication processes have so far produced fairly simple geometries, yet many MEMS could benefit if more sophisticated shapes could be manufactured. By using 'Instant Masking' (IM) - a novel in-situ micropatterning method - to simplify, accelerate, and automate through-mask electroplating, EFAB can produce extremely complex shapes by depositing hundreds-thousands of layers at high speed. While other processes of the do not allow integration with ICs, EFAB operates at less than 60 degrees C, making IC compatibility a possibility. Alternative processes require costly facilities and equipment; EFAB separates photolithography from device fabrication, requiring a cleanroom only for mask-making, then depositing all layers in a low-cost, self-contained machine. All IM required can be prepared simultaneously, without repeating the lithography on each layer. Selective electrodeposition requires simply mating the mask with the substrate and applying current; in this way we have patterned well-defined features as small as 20 X 20 micrometers . The procedures in EFAB are selective electrodeposition, blanket electrodeposition, and planarization. To date we have built metal structures with up to 12 layers consisting of independently-moving components.

  16. Automated Analysis of Barley Organs Using 3D Laser Scanning: An Approach for High Throughput Phenotyping

    PubMed Central

    Paulus, Stefan; Dupuis, Jan; Riedel, Sebastian; Kuhlmann, Heiner

    2014-01-01

    Due to the rise of laser scanning the 3D geometry of plant architecture is easy to acquire. Nevertheless, an automated interpretation and, finally, the segmentation into functional groups are still difficult to achieve. Two barley plants were scanned in a time course, and the organs were separated by applying a histogram-based classification algorithm. The leaf organs were represented by meshing algorithms, while the stem organs were parameterized by a least-squares cylinder approximation. We introduced surface feature histograms with an accuracy of 96% for the separation of the barley organs, leaf and stem. This enables growth monitoring in a time course for barley plants. Its reliability was demonstrated by a comparison with manually fitted parameters with a correlation R2 = 0.99 for the leaf area and R2 = 0.98 for the cumulated stem height. A proof of concept has been given for its applicability for the detection of water stress in barley, where the extension growth of an irrigated and a non-irrigated plant has been monitored. PMID:25029283

  17. Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

    NASA Astrophysics Data System (ADS)

    Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

    2012-12-01

    Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

  18. 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

  19. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.

    PubMed

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com . PMID:25261217

  20. Real-time automated 3D sensing, detection, and recognition of dynamic biological micro-organic events

    NASA Astrophysics Data System (ADS)

    Javidi, Bahram; Yeom, Seokwon; Moon, Inkyu; Daneshpanah, Mehdi

    2006-05-01

    In this paper, we present an overview of three-dimensional (3D) optical imaging techniques for real-time automated sensing, visualization, and recognition of dynamic biological microorganisms. Real time sensing and 3D reconstruction of the dynamic biological microscopic objects can be performed by single-exposure on-line (SEOL) digital holographic microscopy. A coherent 3D microscope-based interferometer is constructed to record digital holograms of dynamic micro biological events. Complex amplitude 3D images of the biological microorganisms are computationally reconstructed at different depths by digital signal processing. Bayesian segmentation algorithms are applied to identify regions of interest for further processing. A number of pattern recognition approaches are addressed to identify and recognize the microorganisms. One uses 3D morphology of the microorganisms by analyzing 3D geometrical shapes which is composed of magnitude and phase. Segmentation, feature extraction, graph matching, feature selection, and training and decision rules are used to recognize the biological microorganisms. In a different approach, 3D technique is used that are tolerant to the varying shapes of the non-rigid biological microorganisms. After segmentation, a number of sampling patches are arbitrarily extracted from the complex amplitudes of the reconstructed 3D biological microorganism. These patches are processed using a number of cost functions and statistical inference theory for the equality of means and equality of variances between the sampling segments. Also, we discuss the possibility of employing computational integral imaging for 3D sensing, visualization, and recognition of biological microorganisms illuminated under incoherent light. Experimental results with several biological microorganisms are presented to illustrate detection, segmentation, and identification of micro biological events.

  1. Automated 3d Road Sign Mapping with Stereovision-Based Mobile Mapping Exploiting Disparity Information from Dense Stereo Matching

    NASA Astrophysics Data System (ADS)

    Cavegn, S.; Nebiker, S.

    2012-07-01

    This paper presents algorithms and investigations on the automated detection, classification and mapping of road signs which systematically exploit depth information from stereo images. This approach was chosen due to recent progress in the development of stereo matching algorithms enabling the generation of accurate and dense depth maps. In comparison to mono imagery-based approaches, depth maps also allow 3D mapping of the objects. This is essential for efficient inventory and for future change detection purposes. Test measurements with the mobile mapping system by the Institute of Geomatics Engineering of the FHNW University of Applied Sciences and Arts Northwestern Switzerland demonstrated that the developed algorithms for the automated 3D road sign mapping perform well, even under difficult to poor lighting conditions. Approximately 90% of the relevant road signs with predominantly red, blue and yellow colors in Switzerland can be detected, and 85% can be classified correctly. Furthermore, fully automated mapping with a 3D accuracy of better than 10 cm is possible.

  2. Preliminary Results from the Application of Automated Adjoint Code Generation to CFL3D

    NASA Technical Reports Server (NTRS)

    Carle, Alan; Fagan, Mike; Green, Lawrence L.

    1998-01-01

    This report describes preliminary results obtained using an automated adjoint code generator for Fortran to augment a widely-used computational fluid dynamics flow solver to compute derivatives. These preliminary results with this augmented code suggest that, even in its infancy, the automated adjoint code generator can accurately and efficiently deliver derivatives for use in transonic Euler-based aerodynamic shape optimization problems with hundreds to thousands of independent design variables.

  3. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

    PubMed Central

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  4. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    PubMed

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  5. Automated generation of NC part programs for excimer laser ablation micromachining from known 3D surfaces

    NASA Astrophysics Data System (ADS)

    Mutapcic, Emir; Iovenitti, Pio G.; Hayes, Jason P.

    2002-11-01

    The purpose of this research project is to improve the capability of the laser micromachinning process, so that any desired 3D surface can be produced by taking the 3D information from a CAD system and automatically generating the NC part programs. In addition, surface quality should be able to be controlled by specifying optimised parameters. This paper presents the algorithms and a software system, which processes 3D geometry in an STL file format from a CAD system and produces the NC part program to mill the surface using the Excimer laser ablation process. Simple structures are used to demonstrate the prototype system's part programming capabilities, and an actual surface is machined.

  6. Automated Voxel Model from Point Clouds for Structural Analysis of Cultural Heritage

    NASA Astrophysics Data System (ADS)

    Bitelli, G.; Castellazzi, G.; D'Altri, A. M.; De Miranda, S.; Lambertini, A.; Selvaggi, I.

    2016-06-01

    In the context of cultural heritage, an accurate and comprehensive digital survey of a historical building is today essential in order to measure its geometry in detail for documentation or restoration purposes, for supporting special studies regarding materials and constructive characteristics, and finally for structural analysis. Some proven geomatic techniques, such as photogrammetry and terrestrial laser scanning, are increasingly used to survey buildings with different complexity and dimensions; one typical product is in form of point clouds. We developed a semi-automatic procedure to convert point clouds, acquired from laserscan or digital photogrammetry, to a filled volume model of the whole structure. The filled volume model, in a voxel format, can be useful for further analysis and also for the generation of a Finite Element Model (FEM) of the surveyed building. In this paper a new approach is presented with the aim to decrease operator intervention in the workflow and obtain a better description of the structure. In order to achieve this result a voxel model with variable resolution is produced. Different parameters are compared and different steps of the procedure are tested and validated in the case study of the North tower of the San Felice sul Panaro Fortress, a monumental historical building located in San Felice sul Panaro (Modena, Italy) that was hit by an earthquake in 2012.

  7. Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

    NASA Astrophysics Data System (ADS)

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

  8. Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue

    PubMed Central

    Bjornsson, Christopher S; Lin, Gang; Al-Kofahi, Yousef; Narayanaswamy, Arunachalam; Smith, Karen L; Shain, William; Roysam, Badrinath

    2009-01-01

    Brain structural complexity has confounded prior efforts to extract quantitative image-based measurements. We present a systematic ‘divide and conquer’ methodology for analyzing three-dimensional (3D) multi-parameter images of brain tissue to delineate and classify key structures, and compute quantitative associations among them. To demonstrate the method, thick (~100 μm) slices of rat brain tissue were labeled using 3 – 5 fluorescent signals, and imaged using spectral confocal microscopy and unmixing algorithms. Automated 3D segmentation and tracing algorithms were used to delineate cell nuclei, vasculature, and cell processes. From these segmentations, a set of 23 intrinsic and 8 associative image-based measurements was computed for each cell. These features were used to classify astrocytes, microglia, neurons, and endothelial cells. Associations among cells and between cells and vasculature were computed and represented as graphical networks to enable further analysis. The automated results were validated using a graphical interface that permits investigator inspection and corrective editing of each cell in 3D. Nuclear counting accuracy was >89%, and cell classification accuracy ranged from 81–92% depending on cell type. We present a software system named FARSIGHT implementing our methodology. Its output is a detailed XML file containing measurements that may be used for diverse quantitative hypothesis-driven and exploratory studies of the central nervous system. PMID:18294697

  9. A Comprehensive Automated 3D Approach for Building Extraction, Reconstruction, and Regularization from Airborne Laser Scanning Point Clouds

    PubMed Central

    Dorninger, Peter; Pfeifer, Norbert

    2008-01-01

    Three dimensional city models are necessary for supporting numerous management applications. For the determination of city models for visualization purposes, several standardized workflows do exist. They are either based on photogrammetry or on LiDAR or on a combination of both data acquisition techniques. However, the automated determination of reliable and highly accurate city models is still a challenging task, requiring a workflow comprising several processing steps. The most relevant are building detection, building outline generation, building modeling, and finally, building quality analysis. Commercial software tools for building modeling require, generally, a high degree of human interaction and most automated approaches described in literature stress the steps of such a workflow individually. In this article, we propose a comprehensive approach for automated determination of 3D city models from airborne acquired point cloud data. It is based on the assumption that individual buildings can be modeled properly by a composition of a set of planar faces. Hence, it is based on a reliable 3D segmentation algorithm, detecting planar faces in a point cloud. This segmentation is of crucial importance for the outline detection and for the modeling approach. We describe the theoretical background, the segmentation algorithm, the outline detection, and the modeling approach, and we present and discuss several actual projects.

  10. Automated 3D trajectory measuring of large numbers of moving particles.

    PubMed

    Wu, Hai Shan; Zhao, Qi; Zou, Danping; Chen, Yan Qiu

    2011-04-11

    Complex dynamics of natural particle systems, such as insect swarms, bird flocks, fish schools, has attracted great attention of scientists for years. Measuring 3D trajectory of each individual in a group is vital for quantitative study of their dynamic properties, yet such empirical data is rare mainly due to the challenges of maintaining the identities of large numbers of individuals with similar visual features and frequent occlusions. We here present an automatic and efficient algorithm to track 3D motion trajectories of large numbers of moving particles using two video cameras. Our method solves this problem by formulating it as three linear assignment problems (LAP). For each video sequence, the first LAP obtains 2D tracks of moving targets and is able to maintain target identities in the presence of occlusions; the second one matches the visually similar targets across two views via a novel technique named maximum epipolar co-motion length (MECL), which is not only able to effectively reduce matching ambiguity but also further diminish the influence of frequent occlusions; the last one links 3D track segments into complete trajectories via computing a globally optimal assignment based on temporal and kinematic cues. Experiment results on simulated particle swarms with various particle densities validated the accuracy and robustness of the proposed method. As real-world case, our method successfully acquired 3D flight paths of fruit fly (Drosophila melanogaster) group comprising hundreds of freely flying individuals. PMID:21503074

  11. Ultrasonic 3D imaging system for the automated application in milling machines

    NASA Astrophysics Data System (ADS)

    Schmitt, Robert; Hafner, Philip

    2007-04-01

    In order to meet the requirements of rising flexibility and an automated material inspection in a small batch production environment, an automatically changeable ultrasound sensor tool for milling machines has been developed. This system enables an automated ultrasonic inspection of varying parts to be carried out directly on a machining center and visualizes hidden geometries and material imperfections three-dimensionally. The sensor tool is based on commercialized ultrasonic squirter-probes, which are able to use the cooling lubricant for sound coupling. During the measurement recordings, the milling machine's axes move the sensor numerical-controlled across the workpiece. By this means, automated material inspection tasks can be performed very cost-effectively without setting up separate testing facilities. 4- or 5-axes kinematics capacitates the system to check even very complex-shaped parts.

  12. 3D camera assisted fully automated calibration of scanning laser Doppler vibrometers

    NASA Astrophysics Data System (ADS)

    Sels, Seppe; Ribbens, Bart; Mertens, Luc; Vanlanduit, Steve

    2016-06-01

    Scanning laser Doppler vibrometers (LDV) are used to measure full-field vibration shapes of products and structures. In most commercially available scanning laser Doppler vibrometer systems the user manually draws a grid of measurement locations on a 2D camera image of the product. The determination of the correct physical measurement locations can be a time consuming and diffcult task. In this paper we present a new methodology for product testing and quality control that integrates 3D imaging techniques with vibration measurements. This procedure allows to test prototypes in a shorter period because physical measurements locations will be located automatically. The proposed methodology uses a 3D time-of-flight camera to measure the location and orientation of the test-object. The 3D image of the time-of-flight camera is then matched with the 3D-CAD model of the object in which measurement locations are pre-defined. A time of flight camera operates strictly in the near infrared spectrum. To improve the signal to noise ratio in the time-of-flight measurement, a time-of-flight camera uses a band filter. As a result of this filter, the laser spot of most laser vibrometers is invisible in the time-of-flight image. Therefore a 2D RGB-camera is used to find the laser-spot of the vibrometer. The laser spot is matched to the 3D image obtained by the time-of-flight camera. Next an automatic calibration procedure is used to aim the laser at the (pre)defined locations. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. Secondly the orientation of the CAD model is known with respect to the laser beam. This information can be used to find the direction of the measured vibration relatively to the surface of the object. With this direction, the vibration measurements can be compared more precisely with numerical

  13. Automated 3D quantitative assessment and measurement of alpha angles from the femoral head-neck junction using MR imaging

    NASA Astrophysics Data System (ADS)

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S.; Walker, Duncan; Crozier, Stuart; Engstrom, Craig

    2015-10-01

    To develop an automated approach for 3D quantitative assessment and measurement of alpha angles from the femoral head-neck (FHN) junction using bone models derived from magnetic resonance (MR) images of the hip joint. Bilateral MR images of the hip joints were acquired from 30 male volunteers (healthy active individuals and high-performance athletes, aged 18-49 years) using a water-excited 3D dual echo steady state (DESS) sequence. In a subset of these subjects (18 water-polo players), additional True Fast Imaging with Steady-state Precession (TrueFISP) images were acquired from the right hip joint. For both MR image sets, an active shape model based algorithm was used to generate automated 3D bone reconstructions of the proximal femur. Subsequently, a local coordinate system of the femur was constructed to compute a 2D shape map to project femoral head sphericity for calculation of alpha angles around the FHN junction. To evaluate automated alpha angle measures, manual analyses were performed on anterosuperior and anterior radial MR slices from the FHN junction that were automatically reformatted using the constructed coordinate system. High intra- and inter-rater reliability (intra-class correlation coefficients  >  0.95) was found for manual alpha angle measurements from the auto-extracted anterosuperior and anterior radial slices. Strong correlations were observed between manual and automatic measures of alpha angles for anterosuperior (r  =  0.84) and anterior (r  =  0.92) FHN positions. For matched DESS and TrueFISP images, there were no significant differences between automated alpha angle measures obtained from the upper anterior quadrant of the FHN junction (two-way repeated measures ANOVA, F  <  0.01, p  =  0.98). Our automatic 3D method analysed MR images of the hip joints to generate alpha angle measures around the FHN junction circumference with very good reliability and reproducibility. This work has the

  14. Automated 3D quantitative assessment and measurement of alpha angles from the femoral head-neck junction using MR imaging.

    PubMed

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S; Walker, Duncan; Crozier, Stuart; Engstrom, Craig

    2015-10-01

    To develop an automated approach for 3D quantitative assessment and measurement of alpha angles from the femoral head-neck (FHN) junction using bone models derived from magnetic resonance (MR) images of the hip joint.Bilateral MR images of the hip joints were acquired from 30 male volunteers (healthy active individuals and high-performance athletes, aged 18–49 years) using a water-excited 3D dual echo steady state (DESS) sequence. In a subset of these subjects (18 water-polo players), additional True Fast Imaging with Steady-state Precession (TrueFISP) images were acquired from the right hip joint. For both MR image sets, an active shape model based algorithm was used to generate automated 3D bone reconstructions of the proximal femur. Subsequently, a local coordinate system of the femur was constructed to compute a 2D shape map to project femoral head sphericity for calculation of alpha angles around the FHN junction. To evaluate automated alpha angle measures, manual analyses were performed on anterosuperior and anterior radial MR slices from the FHN junction that were automatically reformatted using the constructed coordinate system.High intra- and inter-rater reliability (intra-class correlation coefficients  >  0.95) was found for manual alpha angle measurements from the auto-extracted anterosuperior and anterior radial slices. Strong correlations were observed between manual and automatic measures of alpha angles for anterosuperior (r  =  0.84) and anterior (r  =  0.92) FHN positions. For matched DESS and TrueFISP images, there were no significant differences between automated alpha angle measures obtained from the upper anterior quadrant of the FHN junction (two-way repeated measures ANOVA, F  <  0.01, p  =  0.98).Our automatic 3D method analysed MR images of the hip joints to generate alpha angle measures around the FHN junction circumference with very good reliability and reproducibility. This work has the

  15. Automated analysis of 3D morphology of human red blood cells via off-axis digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Moon, Inkyu

    2013-05-01

    In this paper we overview an automated method for the analysis of clinical parameters of human red blood cells (RBCs). The digital holograms of mature RBCs are recorded by CCD camera with off-axis interferometry setup and the quantitative phase images of RBCs are formed by a numerical reconstruction technique. For automated investigation of the 3D morphology and mean corpuscular hemoglobin of RBCs, the unnecessary background in the RBCs phase images are removed by marker-controlled watershed segmentation algorithm. Then, characteristic properties of each RBC such as projected cell surface, average phase, mean corpuscular hemoglobin (MCH) and (MCH) surface density is quantitatively measured. Finally, the equality of covariance matrixes and mean vectors of these features for different kinds of RBCs are experimentally analyzed using statistical test scheme. Results show that these characteristic parameters of RBCs can be used as feature pattern to discriminate between RBC populations that differ in shape and hemoglobin content.

  16. Automated and integrated mask generation from a CAD constructed 3D model.

    SciTech Connect

    Schiek, Richard Louis; Schmidt, Rodney Cannon

    2005-03-01

    We have developed and implemented a method which given a three-dimensional object can infer from topology the two-dimensional masks needed to produce that object with surface micromachining. This design tool calculates the two-dimensional mask set required to produce a given three-dimensional model by investigating the vertical topology to the model. The 3D model is first separated into bodies that are non-intersecting, made from different materials or only linked through a ground plane. Next, for each body unique horizontal cross sections are located and arranged into a tree based on their topological relationship. A branch-wise search of the tree uncovers locations where deposition boundaries must lie and identifies candidate masks creating a generic mask set for the 3D model. Finally, in the last step specific process requirements are considered that may constrain the generic mask set.

  17. Automated segmentation of necrotic femoral head from 3D MR data.

    PubMed

    Zoroofi, Reza A; Sato, Yoshinobu; Nishii, Takashi; Sugano, Nobuhiko; Yoshikawa, Hideki; Tamura, Shinichi

    2004-07-01

    Segmentation of diseased organs is an important topic in computer assisted medical image analysis. In particular, automatic segmentation of necrotic femoral head is of importance for various corresponding clinical tasks including visualization, quantitative assessment, early diagnosis and adequate management of patients suffering from avascular necrosis of the femoral head (ANFH). Early diagnosis and treatment of ANFH is crucial since the disease occurs in relatively young individuals with an average age of 20-50, and since treatment options for more advanced disease are frequently unsuccessful. The present paper describes several new techniques and software for automatic segmentation of necrotic femoral head based on clinically obtained multi-slice T1-weighted MR data. In vivo MR data sets of 50 actual patients are used in the study. An automatic method built up to manage the segmentation task according to image intensity of bone tissues, shape of the femoral head, and other characters. The processing scheme consisted of the following five steps. (1) Rough segmentation of non-necrotic lesions of the femur by applying a 3D gray morphological operation and a 3D region growing technique. (2) Fitting a 3D ellipse to the femoral head by a new approach utilizing the constraint of the shape of the femur, and employing a principle component analysis and a simulated annealing technique. (3) Estimating the femoral neck location, and also femoral head axis by integrating anatomical information of the femur and boundary of estimated 3D ellipse. (4) Removal of non-bony tissues around the femoral neck and femoral head ligament by utilizing the estimated femoral neck axis. (5) Classification of necrotic lesions inside the estimated femoral head by a k-means technique. The above method was implemented in a Microsoft Windows software package. The feasibility of this method was tested on the data sets of 50 clinical cases (3000 MR images). PMID:15249072

  18. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  19. Automated localization of implanted seeds in 3D TRUS images used for prostate brachytherapy

    SciTech Connect

    Wei Zhouping; Gardi, Lori; Downey, Donal B.; Fenster, Aaron

    2006-07-15

    An algorithm has been developed in this paper to localize implanted radioactive seeds in 3D ultrasound images for a dynamic intraoperative brachytherapy procedure. Segmentation of the seeds is difficult, due to their small size in relatively low quality of transrectal ultrasound (TRUS) images. In this paper, intraoperative seed segmentation in 3D TRUS images is achieved by performing a subtraction of the image before the needle has been inserted, and the image after the seeds have been implanted. The seeds are searched in a 'local' space determined by the needle position and orientation information, which are obtained from a needle segmentation algorithm. To test this approach, 3D TRUS images of the agar and chicken tissue phantoms were obtained. Within these phantoms, dummy seeds were implanted. The seed locations determined by the seed segmentation algorithm were compared with those obtained from a volumetric cone-beam flat-panel micro-CT scanner and human observers. Evaluation of the algorithm showed that the rms error in determining the seed locations using the seed segmentation algorithm was 0.98 mm in agar phantoms and 1.02 mm in chicken phantoms.

  20. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  1. A method for the evaluation of thousands of automated 3D stem cell segmentations.

    PubMed

    Bajcsy, P; Simon, M; Florczyk, S J; Simon, C G; Juba, D; Brady, M C

    2015-12-01

    There is no segmentation method that performs perfectly with any dataset in comparison to human segmentation. Evaluation procedures for segmentation algorithms become critical for their selection. The problems associated with segmentation performance evaluations and visual verification of segmentation results are exaggerated when dealing with thousands of three-dimensional (3D) image volumes because of the amount of computation and manual inputs needed. We address the problem of evaluating 3D segmentation performance when segmentation is applied to thousands of confocal microscopy images (z-stacks). Our approach is to incorporate experimental imaging and geometrical criteria, and map them into computationally efficient segmentation algorithms that can be applied to a very large number of z-stacks. This is an alternative approach to considering existing segmentation methods and evaluating most state-of-the-art algorithms. We designed a methodology for 3D segmentation performance characterization that consists of design, evaluation and verification steps. The characterization integrates manual inputs from projected surrogate 'ground truth' of statistically representative samples and from visual inspection into the evaluation. The novelty of the methodology lies in (1) designing candidate segmentation algorithms by mapping imaging and geometrical criteria into algorithmic steps, and constructing plausible segmentation algorithms with respect to the order of algorithmic steps and their parameters, (2) evaluating segmentation accuracy using samples drawn from probability distribution estimates of candidate segmentations and (3) minimizing human labour needed to create surrogate 'truth' by approximating z-stack segmentations with 2D contours from three orthogonal z-stack projections and by developing visual verification tools. We demonstrate the methodology by applying it to a dataset of 1253 mesenchymal stem cells. The cells reside on 10 different types of biomaterial

  2. LDRD final report: Automated planning and programming of assembly of fully 3D mechanisms

    SciTech Connect

    Kaufman, S.G.; Wilson, R.H.; Jones, R.E.; Calton, T.L.; Ames, A.L.

    1996-11-01

    This report describes the results of assembly planning research under the LDRD. The assembly planning problem is that of finding a sequence of assembly operations, starting from individual parts, that will result in complete assembly of a device specified as a CAD model. The automated assembly programming problem is that of automatically producing a robot program that will carry out a given assembly sequence. Given solutions to both of these problems, it is possible to automatically program a robot to assemble a mechanical device given as a CAD data file. This report describes the current state of our solutions to both of these problems, and a software system called Archimedes 2 we have constructed to automate these solutions. Because Archimedes 2 can input CAD data in several standard formats, we have been able to test it on a number of industrial assembly models more complex than any before attempted by automated assembly planning systems, some having over 100 parts. A complete path from a CAD model to an automatically generated robot program for assembling the device represented by the CAD model has also been demonstrated.

  3. Automated detection system for pulmonary emphysema on 3D chest CT images

    NASA Astrophysics Data System (ADS)

    Hara, Takeshi; Yamamoto, Akira; Zhou, Xiangrong; Iwano, Shingo; Itoh, Shigeki; Fujita, Hiroshi; Ishigaki, Takeo

    2004-05-01

    An automatic extraction of pulmonary emphysema area on 3-D chest CT images was performed using an adaptive thresholding technique. We proposed a method to estimate the ratio of the emphysema area to the whole lung volume. We employed 32 cases (15 normal and 17 abnormal) which had been already diagnosed by radiologists prior to the study. The ratio in all the normal cases was less than 0.02, and in abnormal cases, it ranged from 0.01 to 0.26. The effectiveness of our approach was confirmed through the results of the present study.

  4. Automated surface micro-machining mask creation from a 3D model.

    SciTech Connect

    Schiek, Richard Louis; Schmidt, Rodney Cannon

    2004-06-01

    We have developed and implemented a method, which given a three-dimensional object can infer from topology the two-dimensional masks needed to produce that object with surface micromachining. The masks produced by this design tool can be generic, process independent masks, or if given process constraints, specific for a target process. This design tool calculates the two-dimensional mask set required to produce a given three-dimensional model by investigating the vertical topology to the model. The 3D model is first separated into bodies that are non-intersecting, made from different materials or only linked through a ground plane. Next, for each body unique vertical cross sections are located and arranged into a tree based on their topological relationship. A branch-wise search of the tree uncovers locations where deposition boundaries must lie and identifies candidate masks creating a generic mask set for the 3D model. Finally, in the last step specific process requirements are considered that may constrain the generic mask set. Constraints can include the thickness or number of deposition layers, specific ordering of masks as required by a process and type of material used in a given layer. Candidate masks are reconciled with the process constraints through a constrained optimization.

  5. Using an Automated 3D-tracking System to Record Individual and Shoals of Adult Zebrafish

    PubMed Central

    Maaswinkel, Hans; Zhu, Liqun; Weng, Wei

    2013-01-01

    Like many aquatic animals, zebrafish (Danio rerio) moves in a 3D space. It is thus preferable to use a 3D recording system to study its behavior. The presented automatic video tracking system accomplishes this by using a mirror system and a calibration procedure that corrects for the considerable error introduced by the transition of light from water to air. With this system it is possible to record both single and groups of adult zebrafish. Before use, the system has to be calibrated. The system consists of three modules: Recording, Path Reconstruction, and Data Processing. The step-by-step protocols for calibration and using the three modules are presented. Depending on the experimental setup, the system can be used for testing neophobia, white aversion, social cohesion, motor impairments, novel object exploration etc. It is especially promising as a first-step tool to study the effects of drugs or mutations on basic behavioral patterns. The system provides information about vertical and horizontal distribution of the zebrafish, about the xyz-components of kinematic parameters (such as locomotion, velocity, acceleration, and turning angle) and it provides the data necessary to calculate parameters for social cohesions when testing shoals. PMID:24336189

  6. 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.

  7. Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images

    PubMed Central

    Schrader, Andrea; Hülskamp, Martin; Tresch, Achim

    2013-01-01

    Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons. PMID:23637587

  8. Automated extraction and analysis of rock discontinuity characteristics from 3D point clouds

    NASA Astrophysics Data System (ADS)

    Bianchetti, Matteo; Villa, Alberto; Agliardi, Federico; Crosta, Giovanni B.

    2016-04-01

    A reliable characterization of fractured rock masses requires an exhaustive geometrical description of discontinuities, including orientation, spacing, and size. These are required to describe discontinuum rock mass structure, perform Discrete Fracture Network and DEM modelling, or provide input for rock mass classification or equivalent continuum estimate of rock mass properties. Although several advanced methodologies have been developed in the last decades, a complete characterization of discontinuity geometry in practice is still challenging, due to scale-dependent variability of fracture patterns and difficult accessibility to large outcrops. Recent advances in remote survey techniques, such as terrestrial laser scanning and digital photogrammetry, allow a fast and accurate acquisition of dense 3D point clouds, which promoted the development of several semi-automatic approaches to extract discontinuity features. Nevertheless, these often need user supervision on algorithm parameters which can be difficult to assess. To overcome this problem, we developed an original Matlab tool, allowing fast, fully automatic extraction and analysis of discontinuity features with no requirements on point cloud accuracy, density and homogeneity. The tool consists of a set of algorithms which: (i) process raw 3D point clouds, (ii) automatically characterize discontinuity sets, (iii) identify individual discontinuity surfaces, and (iv) analyse their spacing and persistence. The tool operates in either a supervised or unsupervised mode, starting from an automatic preliminary exploration data analysis. The identification and geometrical characterization of discontinuity features is divided in steps. First, coplanar surfaces are identified in the whole point cloud using K-Nearest Neighbor and Principal Component Analysis algorithms optimized on point cloud accuracy and specified typical facet size. Then, discontinuity set orientation is calculated using Kernel Density Estimation and

  9. Automated 2D-3D registration of a radiograph and a cone beam CT using line-segment enhancement

    SciTech Connect

    Munbodh, Reshma; Jaffray, David A.; Moseley, Douglas J.; Chen Zhe; Knisely, Jonathan P.S.; Cathier, Pascal; Duncan, James S.

    2006-05-15

    The objective of this study was to develop a fully automated two-dimensional (2D)-three-dimensional (3D) registration framework to quantify setup deviations in prostate radiation therapy from cone beam CT (CBCT) data and a single AP radiograph. A kilovoltage CBCT image and kilovoltage AP radiograph of an anthropomorphic phantom of the pelvis were acquired at 14 accurately known positions. The shifts in the phantom position were subsequently estimated by registering digitally reconstructed radiographs (DRRs) from the 3D CBCT scan to the AP radiographs through the correlation of enhanced linear image features mainly representing bony ridges. Linear features were enhanced by filtering the images with ''sticks,'' short line segments which are varied in orientation to achieve the maximum projection value at every pixel in the image. The mean (and standard deviations) of the absolute errors in estimating translations along the three orthogonal axes in millimeters were 0.134 (0.096) AP(out-of-plane), 0.021 (0.023) ML and 0.020 (0.020) SI. The corresponding errors for rotations in degrees were 0.011 (0.009) AP, 0.029 (0.016) ML (out-of-plane), and 0.030 (0.028) SI (out-of-plane). Preliminary results with megavoltage patient data have also been reported. The results suggest that it may be possible to enhance anatomic features that are common to DRRs from a CBCT image and a single AP radiography of the pelvis for use in a completely automated and accurate 2D-3D registration framework for setup verification in prostate radiotherapy. This technique is theoretically applicable to other rigid bony structures such as the cranial vault or skull base and piecewise rigid structures such as the spine.

  10. The Bubble Box: Towards an Automated Visual Sensor for 3D Analysis and Characterization of Marine Gas Release Sites

    PubMed Central

    Jordt, Anne; Zelenka, Claudius; Schneider von Deimling, Jens; Koch, Reinhard; Köser, Kevin

    2015-01-01

    Several acoustic and optical techniques have been used for characterizing natural and anthropogenic gas leaks (carbon dioxide, methane) from the ocean floor. Here, single-camera based methods for bubble stream observation have become an important tool, as they help estimating flux and bubble sizes under certain assumptions. However, they record only a projection of a bubble into the camera and therefore cannot capture the full 3D shape, which is particularly important for larger, non-spherical bubbles. The unknown distance of the bubble to the camera (making it appear larger or smaller than expected) as well as refraction at the camera interface introduce extra uncertainties. In this article, we introduce our wide baseline stereo-camera deep-sea sensor bubble box that overcomes these limitations, as it observes bubbles from two orthogonal directions using calibrated cameras. Besides the setup and the hardware of the system, we discuss appropriate calibration and the different automated processing steps deblurring, detection, tracking, and 3D fitting that are crucial to arrive at a 3D ellipsoidal shape and rise speed of each bubble. The obtained values for single bubbles can be aggregated into statistical bubble size distributions or fluxes for extrapolation based on diffusion and dissolution models and large scale acoustic surveys. We demonstrate and evaluate the wide baseline stereo measurement model using a controlled test setup with ground truth information. PMID:26690168

  11. The Bubble Box: Towards an Automated Visual Sensor for 3D Analysis and Characterization of Marine Gas Release Sites.

    PubMed

    Jordt, Anne; Zelenka, Claudius; von Deimling, Jens Schneider; Koch, Reinhard; Köser, Kevin

    2015-01-01

    Several acoustic and optical techniques have been used for characterizing natural and anthropogenic gas leaks (carbon dioxide, methane) from the ocean floor. Here, single-camera based methods for bubble stream observation have become an important tool, as they help estimating flux and bubble sizes under certain assumptions. However, they record only a projection of a bubble into the camera and therefore cannot capture the full 3D shape, which is particularly important for larger, non-spherical bubbles. The unknown distance of the bubble to the camera (making it appear larger or smaller than expected) as well as refraction at the camera interface introduce extra uncertainties. In this article, we introduce our wide baseline stereo-camera deep-sea sensor bubble box that overcomes these limitations, as it observes bubbles from two orthogonal directions using calibrated cameras. Besides the setup and the hardware of the system, we discuss appropriate calibration and the different automated processing steps deblurring, detection, tracking, and 3D fitting that are crucial to arrive at a 3D ellipsoidal shape and rise speed of each bubble. The obtained values for single bubbles can be aggregated into statistical bubble size distributions or fluxes for extrapolation based on diffusion and dissolution models and large scale acoustic surveys. We demonstrate and evaluate the wide baseline stereo measurement model using a controlled test setup with ground truth information. PMID:26690168

  12. Automated scoring of regional lung perfusion in children from contrast enhanced 3D MRI

    NASA Astrophysics Data System (ADS)

    Heimann, Tobias; Eichinger, Monika; Bauman, Grzegorz; Bischoff, Arved; Puderbach, Michael; Meinzer, Hans-Peter

    2012-03-01

    MRI perfusion images give information about regional lung function and can be used to detect pulmonary pathologies in cystic fibrosis (CF) children. However, manual assessment of the percentage of pathologic tissue in defined lung subvolumes features large inter- and intra-observer variation, making it difficult to determine disease progression consistently. We present an automated method to calculate a regional score for this purpose. First, lungs are located based on thresholding and morphological operations. Second, statistical shape models of left and right children's lungs are initialized at the determined locations and used to precisely segment morphological images. Segmentation results are transferred to perfusion maps and employed as masks to calculate perfusion statistics. An automated threshold to determine pathologic tissue is calculated and used to determine accurate regional scores. We evaluated the method on 10 MRI images and achieved an average surface distance of less than 1.5 mm compared to manual reference segmentations. Pathologic tissue was detected correctly in 9 cases. The approach seems suitable for detecting early signs of CF and monitoring response to therapy.

  13. Analyzing the relevance of shape descriptors in automated recognition of facial gestures in 3D images

    NASA Astrophysics Data System (ADS)

    Rodriguez A., Julian S.; Prieto, Flavio

    2013-03-01

    The present document shows and explains the results from analyzing shape descriptors (DESIRE and Spherical Spin Image) for facial recognition of 3D images. DESIRE is a descriptor made of depth images, silhouettes and rays extended from a polygonal mesh; whereas the Spherical Spin Image (SSI) associated to a polygonal mesh point, is a 2D histogram built from neighboring points by using the position information that captures features of the local shape. The database used contains images of facial expressions which in average were recognized 88.16% using a neuronal network and 91.11% with a Bayesian classifier in the case of the first descriptor; in contrast, the second descriptor only recognizes in average 32% and 23,6% using the same mentioned classifiers respectively.

  14. Automated 3-D tracking of centrosomes in sequences of confocal image stacks.

    PubMed

    Kerekes, Ryan A; Gleason, Shaun S; Trivedi, Niraj; Solecki, David J

    2009-01-01

    In order to facilitate the study of neuron migration, we propose a method for 3-D detection and tracking of centrosomes in time-lapse confocal image stacks of live neuron cells. We combine Laplacian-based blob detection, adaptive thresholding, and the extraction of scale and roundness features to find centrosome-like objects in each frame. We link these detections using the joint probabilistic data association filter (JPDAF) tracking algorithm with a Newtonian state-space model tailored to the motion characteristics of centrosomes in live neurons. We apply our algorithm to image sequences containing multiple cells, some of which had been treated with motion-inhibiting drugs. We provide qualitative results and quantitative comparisons to manual segmentation and tracking results showing that our average motion estimates agree to within 13% of those computed manually by neurobiologists. PMID:19964725

  15. Automated segmentation of breast in 3-D MR images using a robust atlas.

    PubMed

    Khalvati, Farzad; Gallego-Ortiz, Cristina; Balasingham, Sharmila; Martel, Anne L

    2015-01-01

    This paper presents a robust atlas-based segmentation (ABS) algorithm for segmentation of the breast boundary in 3-D MR images. The proposed algorithm combines the well-known methodologies of ABS namely probabilistic atlas and atlas selection approaches into a single framework where two configurations are realized. The algorithm uses phase congruency maps to create an atlas which is robust to intensity variations. This allows an atlas derived from images acquired with one MR imaging sequence to be used to segment images acquired with a different MR imaging sequence and eliminates the need for intensity-based registration. Images acquired using a Dixon sequence were used to create an atlas which was used to segment both Dixon images (intra-sequence) and T1-weighted images (inter-sequence). In both cases, highly accurate results were achieved with the median Dice similarity coefficient values of 94% ±4% and 87 ±6.5%, respectively. PMID:25137725

  16. Acquisition and automated 3-D segmentation of respiratory/cardiac-gated PET transmission images

    SciTech Connect

    Reutter, B.W.; Klein, G.J.; Brennan, K.M.; Huesman, R.H. |

    1996-12-31

    To evaluate the impact of respiratory motion on attenuation correction of cardiac PET data, we acquired and automatically segmented gated transmission data for a dog breathing on its own under gas anesthesia. Data were acquired for 20 min on a CTI/Siemens ECAT EXACT HR (47-slice) scanner configured for 12 gates in a static study, Two respiratory gates were obtained using data from a pneumatic bellows placed around the dog`s chest, in conjunction with 6 cardiac gates from standard EKG gating. Both signals were directed to a LabVIEW-controlled Macintosh, which translated them into one of 12 gate addresses. The respiratory gating threshold was placed near end-expiration to acquire 6 cardiac-gated datasets at end-expiration and 6 cardiac-gated datasets during breaths. Breaths occurred about once every 10 sec and lasted about 1-1.5 sec. For each respiratory gate, data were summed over cardiac gates and torso and lung surfaces were segmented automatically using a differential 3-D edge detection algorithm. Three-dimensional visualizations showed that lung surfaces adjacent to the heart translated 9 mm inferiorly during breaths. Our results suggest that respiration-compensated attenuation correction is feasible with a modest amount of gated transmission data and is necessary for accurate quantitation of high-resolution gated cardiac PET data.

  17. Automated design of coupled RF cavities using 2-D and 3-D codes

    SciTech Connect

    Smith, Peter; Christiansen, D. W.; Greninger, P. T.; Spalek, G.

    2001-01-01

    Coupled RF cavities in the Accelerator Production of Tritium Project have been designed using a procedure in which a 2-D code (CCT) searches for a design that meets frequency and coupling requirements, while a 3-D code (HFSS) is used to obtain empirical factors used by CCT to characterize the coupling slot between cavities. Using assumed values of the empirical factors, CCT runs the Superfish code iteratively to solve for a trial cavity design that has a specified frequency and coupling. The frequency shifts and the coupling constant k of the slot are modeled in CCT using a perturbation theory, the results of which are adjusted using the empirical factors. Given a trial design, HFSS is run using periodic boundary conditions to obtain a mode spectrum. The mode spectrum is processed using the DISPER code to obtain values of the coupling and the frequencies with slots. These results are used to calculate a new set of empirical factors, which are fed back into CCT for another design iteration. Cold models have been fabricated and tested to validate the codes, and results will be presented.

  18. Automated tracing of filaments in 3D electron tomography reconstructions using Sculptor and Situs.

    PubMed

    Rusu, Mirabela; Starosolski, Zbigniew; Wahle, Manuel; Rigort, Alexander; Wriggers, Willy

    2012-05-01

    The molecular graphics program Sculptor and the command-line suite Situs are software packages for the integration of biophysical data across spatial resolution scales. Herein, we provide an overview of recently developed tools relevant to cryo-electron tomography (cryo-ET), with an emphasis on functionality supported by Situs 2.7.1 and Sculptor 2.1.1. We describe a work flow for automatically segmenting filaments in cryo-ET maps including denoising, local normalization, feature detection, and tracing. Tomograms of cellular actin networks exhibit both cross-linked and bundled filament densities. Such filamentous regions in cryo-ET data sets can then be segmented using a stochastic template-based search, VolTrac. The approach combines a genetic algorithm and a bidirectional expansion with a tabu search strategy to localize and characterize filamentous regions. The automated filament segmentation by VolTrac compares well to a manual one performed by expert users, and it allows an efficient and reproducible analysis of large data sets. The software is free, open source, and can be used on Linux, Macintosh or Windows computers. PMID:22433493

  19. An automated framework for 3D serous pigment epithelium detachment segmentation in SD-OCT images

    PubMed Central

    Sun, Zhuli; Chen, Haoyu; Shi, Fei; Wang, Lirong; Zhu, Weifang; Xiang, Dehui; Yan, Chenglin; Li, Liang; Chen, Xinjian

    2016-01-01

    Pigment epithelium detachment (PED) is an important clinical manifestation of multiple chorioretinal diseases, which can cause loss of central vision. In this paper, an automated framework is proposed to segment serous PED in SD-OCT images. The proposed framework consists of four main steps: first, a multi-scale graph search method is applied to segment abnormal retinal layers; second, an effective AdaBoost method is applied to refine the initial segmented regions based on 62 extracted features; third, a shape-constrained graph cut method is applied to segment serous PED, in which the foreground and background seeds are obtained automatically; finally, an adaptive structure elements based morphology method is applied to remove false positive segmented regions. The proposed framework was tested on 25 SD-OCT volumes from 25 patients diagnosed with serous PED. The average true positive volume fraction (TPVF), false positive volume fraction (FPVF), dice similarity coefficient (DSC) and positive predictive value (PPV) are 90.08%, 0.22%, 91.20% and 92.62%, respectively. The proposed framework can provide clinicians with accurate quantitative information, including shape, size and position of the PED region, which can assist clinical diagnosis and treatment. PMID:26899236

  20. Automated breast mass detection in 3D reconstructed tomosynthesis volumes: a featureless approach.

    PubMed

    Singh, Swatee; Tourassi, Georgia D; Baker, Jay A; Samei, Ehsan; Lo, Joseph Y

    2008-08-01

    The purpose of this study was to propose and implement a computer aided detection (CADe) tool for breast tomosynthesis. This task was accomplished in two stages-a highly sensitive mass detector followed by a false positive (FP) reduction stage. Breast tomosynthesis data from 100 human subject cases were used, of which 25 subjects had one or more mass lesions and the rest were normal. For stage 1, filter parameters were optimized via a grid search. The CADe identified suspicious locations were reconstructed to yield 3D CADe volumes of interest. The first stage yielded a maximum sensitivity of 93% with 7.7 FPs/breast volume. Unlike traditional CADe algorithms in which the second stage FP reduction is done via feature extraction and analysis, instead information theory principles were used with mutual information as a similarity metric. Three schemes were proposed, all using leave-one-case-out cross validation sampling. The three schemes, A, B, and C, differed in the composition of their knowledge base of regions of interest (ROIs). Scheme A's knowledge base was comprised of all the mass and FP ROIs generated by the first stage of the algorithm. Scheme B had a knowledge base that contained information from mass ROIs and randomly extracted normal ROIs. Scheme C had information from three sources of information-masses, FPs, and normal ROIs. Also, performance was assessed as a function of the composition of the knowledge base in terms of the number of FP or normal ROIs needed by the system to reach optimal performance. The results indicated that the knowledge base needed no more than 20 times as many FPs and 30 times as many normal ROIs as masses to attain maximal performance. The best overall system performance was 85% sensitivity with 2.4 FPs per breast volume for scheme A, 3.6 FPs per breast volume for scheme B, and 3 FPs per breast volume for scheme C. PMID:18777923

  1. Automated multimodality concurrent classification for segmenting vessels in 3D spectral OCT and color fundus images

    NASA Astrophysics Data System (ADS)

    Hu, Zhihong; Abràmoff, Michael D.; Niemeijer, Meindert; Garvin, Mona K.

    2011-03-01

    Segmenting vessels in spectral-domain optical coherence tomography (SD-OCT) volumes is particularly challenging in the region near and inside the neural canal opening (NCO). Furthermore, accurately segmenting them in color fundus photographs also presents a challenge near the projected NCO. However, both modalities also provide complementary information to help indicate vessels, such as a better NCO contrast from the NCO-aimed OCT projection image and a better vessel contrast inside the NCO from fundus photographs. We thus present a novel multimodal automated classification approach for simultaneously segmenting vessels in SD-OCT volumes and fundus photographs, with a particular focus on better segmenting vessels near and inside the NCO by using a combination of their complementary features. In particular, in each SD-OCT volume, the algorithm pre-segments the NCO using a graph-theoretic approach and then applies oriented Gabor wavelets with oriented NCO-based templates to generate OCT image features. After fundus-to-OCT registration, the fundus image features are computed using Gaussian filter banks and combined with OCT image features. A k-NN classifier is trained on 5 and tested on 10 randomly chosen independent image pairs of SD-OCT volumes and fundus images from 15 subjects with glaucoma. Using ROC analysis, we demonstrate an improvement over two closest previous works performed in single modal SD-OCT volumes with an area under the curve (AUC) of 0.87 (0.81 for our and 0.72 for Niemeijer's single modal approach) in the region around the NCO and 0.90 outside the NCO (0.84 for our and 0.81 for Niemeijer's single modal approach).

  2. A robust automated method to detect stent struts in 3D intravascular optical coherence tomographic image sequences

    NASA Astrophysics Data System (ADS)

    Wang, A.; Eggermont, J.; Dekker, N.; Garcia-Garcia, H. M.; Pawar, R.; Reiber, J. H. C.; Dijkstra, J.

    2012-03-01

    Intravascular optical coherence tomography (IVOCT) provides very high resolution cross-sectional image sequences of vessels. It has been rapidly accepted for stent implantation and its follow up evaluation. Given the large amount of stent struts in a single image sequence, only automated detection methods are feasible. In this paper, we present an automated stent strut detection technique which requires neither lumen nor vessel wall segmentation. To detect strut-pixel candidates, both global intensity histograms and local intensity profiles of the raw polar images are used. Gaussian smoothing is applied followed by specified Prewitt compass filters to detect the trailing shadow of each strut. The shadow edge positions assist the strut-pixel candidates clustering. In the end, a 3D guide wire filter is applied to remove the guide wire from the detection results. For validation, two experts marked 6738 struts in 1021 frames in 10 IVOCT image sequences from a one-year follow up study. The struts were labeled as malapposed, apposed or covered together with the image quality (high, medium, low). The inter-observer agreement was 96%. The algorithm was validated for different combinations of strut status and image quality. Compared to the manual results, 93% of the struts were correctly detected by the new method. For each combination, the lowest accuracy was 88%, which shows the robustness towards different situations. The presented method can detect struts automatically regardless of the strut status or the image quality, which can be used for quantitative measurement, 3D reconstruction and visualization of the implanted stents.

  3. Automated 3D Motion Tracking using Gabor Filter Bank, Robust Point Matching, and Deformable Models

    PubMed Central

    Wang, Xiaoxu; Chung, Sohae; Metaxas, Dimitris; Axel, Leon

    2013-01-01

    Tagged Magnetic Resonance Imaging (tagged MRI or tMRI) provides a means of directly and noninvasively displaying the internal motion of the myocardium. Reconstruction of the motion field is needed to quantify important clinical information, e.g., the myocardial strain, and detect regional heart functional loss. In this paper, we present a three-step method for this task. First, we use a Gabor filter bank to detect and locate tag intersections in the image frames, based on local phase analysis. Next, we use an improved version of the Robust Point Matching (RPM) method to sparsely track the motion of the myocardium, by establishing a transformation function and a one-to-one correspondence between grid tag intersections in different image frames. In particular, the RPM helps to minimize the impact on the motion tracking result of: 1) through-plane motion, and 2) relatively large deformation and/or relatively small tag spacing. In the final step, a meshless deformable model is initialized using the transformation function computed by RPM. The model refines the motion tracking and generates a dense displacement map, by deforming under the influence of image information, and is constrained by the displacement magnitude to retain its geometric structure. The 2D displacement maps in short and long axis image planes can be combined to drive a 3D deformable model, using the Moving Least Square method, constrained by the minimization of the residual error at tag intersections. The method has been tested on a numerical phantom, as well as on in vivo heart data from normal volunteers and heart disease patients. The experimental results show that the new method has a good performance on both synthetic and real data. Furthermore, the method has been used in an initial clinical study to assess the differences in myocardial strain distributions between heart disease (left ventricular hypertrophy) patients and the normal control group. The final results show that the proposed method

  4. Fully Automated One-Step Production of Functional 3D Tumor Spheroids for High-Content Screening.

    PubMed

    Monjaret, François; Fernandes, Mathieu; Duchemin-Pelletier, Eve; Argento, Amelie; Degot, Sébastien; Young, Joanne

    2016-04-01

    Adoption of spheroids within high-content screening (HCS) has lagged behind high-throughput screening (HTS) due to issues with running complex assays on large three-dimensional (3D) structures.To enable multiplexed imaging and analysis of spheroids, different cancer cell lines were grown in 3D on micropatterned 96-well plates with automated production of nine uniform spheroids per well. Spheroids achieve diameters of up to 600 µm, and reproducibility was experimentally validated (interwell and interplate CV(diameter) <5%). Biphoton imaging confirmed that micropatterned spheroids exhibit characteristic cell heterogeneity with distinct microregions. Furthermore, central necrosis appears at a consistent spheroid size, suggesting standardized growth.Using three reference compounds (fluorouracil, irinotecan, and staurosporine), we validated HT-29 micropatterned spheroids on an HCS platform, benchmarking against hanging-drop spheroids. Spheroid formation and imaging in a single plate accelerate assay workflow, and fixed positioning prevents structures from overlapping or sticking to the well wall, augmenting image processing reliability. Furthermore, multiple spheroids per well increase the statistical confidence sufficiently to discriminate compound mechanisms of action and generate EC50 values for endpoints of cell death, architectural change, and size within a single-pass read. Higher quality data and a more efficient HCS work chain should encourage integration of micropatterned spheroid models within fundamental research and drug discovery applications. PMID:26385905

  5. Fully automated measurement of field-dependent AMS using MFK1-FA Kappabridge equipped with 3D rotator

    NASA Astrophysics Data System (ADS)

    Chadima, Martin; Studynka, Jan

    2013-04-01

    Low-field magnetic susceptibility of paramagnetic and diamagnetic minerals is field-independent by definition being also field-independent in pure magnetite. On the other hand, in pyrrhotite, hematite and high-Ti titanomagnetite it may be clearly field-dependent. Consequently, the field-dependent AMS enables the magnetic fabric of the latter group of minerals to be separated from the whole-rock AMS. The methods for the determination of the field-dependent AMS consist of separate measurements of each specimen in several fields within the Rayleigh Law range and subsequent processing in which the field-independent and field-dependent AMS components are calculated. The disadvantage of this technique is that each specimen must be measured several times, which is relatively laborious and time consuming. Recently, a new 3D rotator was developed for the MFK1-FA Kappabridge, which rotates the specimen simultaneously about two axes with different velocities. The measurement is fully automated in such a way that, once the specimen is inserted into the rotator, it requires no additional manipulation to measure the full AMS tensor. Consequently, the 3D rotator enables to measure the AMS tensors in the pre-set field intensities without any operator interference. Whole procedure is controlled by newly developed Safyr5 software; once the measurements are finished, the acquired data are immediately processed and can be visualized in a standard way.

  6. Digitized crime scene forensics: automated trace separation of toolmarks on high-resolution 2D/3D CLSM surface data

    NASA Astrophysics Data System (ADS)

    Clausing, Eric; Vielhauer, Claus

    2015-03-01

    Locksmith forensics is an important and very challenging part of classic crime scene forensics. In prior work, we propose a partial transfer to the digital domain, to effectively support forensic experts and present approaches for a full process chain consisting of five steps: Trace positioning, 2D/3D acquisition with a confocal 3D laser scanning microscope, detection by segmentation, trace type determination, and determination of the opening method. In particular the step of trace segmentation on high-resolution 3D surfaces thereby turned out to be the part most difficult to implement. The reason for that is the highly structured and complex surfaces to be analyzed. These surfaces are cluttered with a high number of toolmarks, which overlap and distort each other. In Clausing et al., we present an improved approach for a reliable segmentation of relevant trace regions but without the possibility of separating single traces out of segmented trace regions. However, in our past research, especially features based on shape and dimension turned out to be highly relevant for a fully automated analysis and interpretation. In this paper, we consequently propose an approach for this separation. To achieve this goal, we use our segmentation approach and expand it with a combination of the watershed algorithm with a graph-based analysis. Found sub-regions are compared based on their surface character and are connected or divided depending on their similarity. We evaluate our approach with a test set of about 1,300 single traces on the exemplary locking cylinder component 'key pin' and thereby are able of showing the high suitability of our approach.

  7. Fully automated prostate segmentation in 3D MR based on normalized gradient fields cross-correlation initialization and LOGISMOS refinement

    NASA Astrophysics Data System (ADS)

    Yin, Yin; Fotin, Sergei V.; Periaswamy, Senthil; Kunz, Justin; Haldankar, Hrishikesh; Muradyan, Naira; Cornud, François; Turkbey, Baris; Choyke, Peter

    2012-02-01

    Manual delineation of the prostate is a challenging task for a clinician due to its complex and irregular shape. Furthermore, the need for precisely targeting the prostate boundary continues to grow. Planning for radiation therapy, MR-ultrasound fusion for image-guided biopsy, multi-parametric MRI tissue characterization, and context-based organ retrieval are examples where accurate prostate delineation can play a critical role in a successful patient outcome. Therefore, a robust automated full prostate segmentation system is desired. In this paper, we present an automated prostate segmentation system for 3D MR images. In this system, the prostate is segmented in two steps: the prostate displacement and size are first detected, and then the boundary is refined by a shape model. The detection approach is based on normalized gradient fields cross-correlation. This approach is fast, robust to intensity variation and provides good accuracy to initialize a prostate mean shape model. The refinement model is based on a graph-search based framework, which contains both shape and topology information during deformation. We generated the graph cost using trained classifiers and used coarse-to-fine search and region-specific classifier training. The proposed algorithm was developed using 261 training images and tested on another 290 cases. The segmentation performance using mean DSC ranging from 0.89 to 0.91 depending on the evaluation subset demonstrates state of the art performance. Running time for the system is about 20 to 40 seconds depending on image size and resolution.

  8. An open-source, automated platform for visualizing subdural electrodes using 3D CT-MRI coregistration

    PubMed Central

    Pearce, Allison; Krish, Veena T.; Wagenaar, Joost; Chen, Weixuan; Zheng, Yuanjie; Wang, Hongzhi; Lucas, Timothy H.; Gee, James C.; Litt, Brian; Davis, Kathryn A.

    2014-01-01

    Objective Visualizing implanted subdural electrodes in 3D space can greatly aid planning, executing, and validating resection in epilepsy surgery. Coregistration software is available, but cost, complexity, insufficient accuracy or validation limit adoption. We present a fully automated open-source application, based upon a novel method using post-implant CT and post-implant MR images, for accurately visualizing intracranial electrodes in 3D space. Methods CT-MR rigid brain coregistration, MR non-rigid registration, and prior-based segmentation were carried out on 7 subjects. Post-implant CT, post-implant MR, and an external labeled atlas were then aligned in the same space. The coregistration algorithm was validated by manually marking identical anatomical landmarks on the post-implant CT and post-implant MR images. Following coregistration, distances between the center of the landmark masks on the post-implant MR and the coregistered CT images were calculated for all subjects. Algorithms were implemented in open-source software and translated into a “drag and drop” desktop application for Apple Mac OS X. Results Despite post-operative brain deformation, the method was able to automatically align intra-subject multi-modal images and segment cortical subregions so that all electrodes could be visualized on the parcellated brain. Manual marking of anatomical landmarks validated the coregistration algorithm with a mean misalignment distance of 2.87 ± 0.58 mm between the landmarks. Software was easily used by operators without prior image processing experience. Significance We demonstrate an easy to use, novel platform for accurately visualizing subdural electrodes in 3D space on a parcellated brain. We rigorously validated this method using quantitative measures. The method is unique because it involves no pre-processing, is fully automated, and freely available worldwide. A desktop application, as well as the source code, are both available for download on the

  9. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    PubMed

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days. PMID:25190042

  10. Automated 3D detection and classification of Giardia lamblia cysts using digital holographic microscopy with partially coherent source

    NASA Astrophysics Data System (ADS)

    El Mallahi, A.; Detavernier, A.; Yourassowsky, C.; Dubois, F.

    2012-06-01

    Over the past century, monitoring of Giardia lamblia became a matter of concern for all drinking water suppliers worldwide. Indeed, this parasitic flagellated protozoan is responsible for giardiasis, a widespread diarrhoeal disease (200 million symptomatic individuals) that can lead immunocompromised individuals to death. The major difficulty raised by Giardia lamblia's cyst, its vegetative transmission form, is its ability to survive for long periods in harsh environments, including the chlorine concentrations and treatment duration used traditionally in water disinfection. Currently, there is a need for a reliable, inexpensive, and easy-to-use sensor for the identification and quantification of cysts in the incoming water. For this purpose, we investigated the use of a digital holographic microscope working with partially coherent spatial illumination that reduces the coherent noise. Digital holography allows one to numerically investigate a volume by refocusing the different plane of depth of a hologram. In this paper, we perform an automated 3D analysis that computes the complex amplitude of each hologram, detects all the particles present in the whole volume given by one hologram and refocuses them if there are out of focus using a refocusing criterion based on the integrated complex amplitude modulus and we obtain the (x,y,z) coordinates of each particle. Then the segmentation of the particles is processed and a set of morphological and textures features characteristic to Giardia lamblia cysts is computed in order to classify each particles in the right classes.

  11. Toward Automated FAÇADE Texture Generation for 3d Photorealistic City Modelling with Smartphones or Tablet Pcs

    NASA Astrophysics Data System (ADS)

    Wang, S.

    2012-07-01

    An automated model-image fitting algorithm is proposed in this paper for generating façade texture image from pictures taken by smartphones or tablet PCs. The façade texture generation requires tremendous labour work and thus, has been the bottleneck of 3D photo-realistic city modelling. With advanced developments of the micro electro mechanical system (MEMS), camera, global positioning system (GPS), and gyroscope (G-sensors) can all be integrated into a smartphone or a table PC. These sensors bring the possibility of direct-georeferencing for the pictures taken by smartphones or tablet PCs. Since the accuracy of these sensors cannot compared to the surveying instruments, the image position and orientation derived from these sensors are not capable of photogrammetric measurements. This paper adopted the least-squares model-image fitting (LSMIF) algorithm to iteratively improve the image's exterior orientation. The image position from GPS and the image orientation from gyroscope are treated as the initial values. By fitting the projection of the wireframe model to the extracted edge pixels on image, the image exterior orientation elements are solved when the optimal fitting achieved. With the exact exterior orientation elements, the wireframe model of the building can be correctly projected on the image and, therefore, the façade texture image can be extracted from the picture.

  12. Automated Quantification of DNA Demethylation Effects in Cells via 3D Mapping of Nuclear Signatures and Population Homogeneity Assessment1

    PubMed Central

    Gertych, Arkadiusz; Wawrowsky, Kolja A.; Lindsley, Erik; Vishnevsky, Eugene; Farkas, Daniel L.; Tajbakhsh, Jian

    2009-01-01

    Background Today’s advanced microscopic imaging applies to the preclinical stages of drug discovery that employ high-throughput and high-content three-dimensional (3D) analysis of cells to more efficiently screen candidate compounds. Drug efficacy can be assessed by measuring response homogeneity to treatment within a cell population. In this study topologically quantified nuclear patterns of methylated cytosine and global nuclear DNA are utilized as signatures of cellular response to the treatment of cultured cells with the demethylating anti-cancer agents: 5-azacytidine (5-AZA) and octreotide (OCT). Methods Mouse pituitary folliculostellate TtT-GF cells treated with 5-AZA and OCT for 48 hours, and untreated populations, were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei (n=163). Cell images were processed utilizing an automated 3D analysis software that we developed by combining seeded watershed segmentation to extract nuclear shells with measurements of Kullback-Leibler’s (K-L) divergence to analyze cell population homogeneity in the relative nuclear distribution patterns of MeC versus DAPI stained sites. Each cell was assigned to one of the four classes: similar, likely similar, unlikely similar and dissimilar. Results Evaluation of the different cell groups revealed a significantly higher number of cells with similar or likely similar MeC/DAPI patterns among untreated cells (~100%), 5-AZA-treated cells (90%), and a lower degree of same type of cells (64%) in the OCT-treated population. The latter group contained (28%) of unlikely similar or dissimilar (7%) cells. Conclusion Our approach was successful in the assessment of cellular behavior relevant to the biological impact of the applied drugs, i.e. the reorganization of MeC/DAPI distribution by demethylation. In a comparison with other metrics, K-L divergence has

  13. Automated extraction of aorta and pulmonary artery in mediastinum from 3D chest x-ray CT images without contrast medium

    NASA Astrophysics Data System (ADS)

    Kitasaka, Takayuki; Mori, Kensaku; Hasegawa, Jun-ichi; Toriwaki, Jun-ichiro; Katada, Kazuhiro

    2002-05-01

    This paper proposes a method for automated extraction of the aorta and pulmonary artery (PA) in the mediastinum of the chest from uncontrasted chest X-ray CT images. The proposed method employs a model fitting technique to use shape features of blood vessels for extraction. First, edge voxels are detected based on the standard deviation of CT values. A likelihood image, which shows the degree of likelihood on medial axes of vessels, are calculated by applying the Euclidean distance transformation to non-edge voxels. Second, the medial axis of each vessel is obtained by fitting the model. This is done by referring the likelihood image. Finally, the aorta and PA areas are recovered from the medial axes by executing the reverse Euclidean distance transformation. We applied the proposed method to seven cases of uncontrasted chest X-ray CT images and evaluated the results by calculating the coincidence index computed from the extracted regions and the regions manually traced. Experimental results showed that the extracted aorta and the PA areas coincides with manually input regions with the coincidence indexes values 90% and 80-90%,respectively.

  14. Spatio-temporal interpolation of soil moisture in 3D+T using automated sensor network data

    NASA Astrophysics Data System (ADS)

    Gasch, C.; Hengl, T.; Magney, T. S.; Brown, D. J.; Gräler, B.

    2014-12-01

    Soil sensor networks provide frequent in situ measurements of dynamic soil properties at fixed locations, producing data in 2- or 3-dimensions and through time (2D+T and 3D+T). Spatio-temporal interpolation of 3D+T point data produces continuous estimates that can then be used for prediction at unsampled times and locations, as input for process models, and can simply aid in visualization of properties through space and time. Regression-kriging with 3D and 2D+T data has successfully been implemented, but currently the field of geostatistics lacks an analytical framework for modeling 3D+T data. Our objective is to develop robust 3D+T models for mapping dynamic soil data that has been collected with high spatial and temporal resolution. For this analysis, we use data collected from a sensor network installed on the R.J. Cook Agronomy Farm (CAF), a 37-ha Long-Term Agro-Ecosystem Research (LTAR) site in Pullman, WA. For five years, the sensors have collected hourly measurements of soil volumetric water content at 42 locations and five depths. The CAF dataset also includes a digital elevation model and derivatives, a soil unit description map, crop rotations, electromagnetic induction surveys, daily meteorological data, and seasonal satellite imagery. The soil-water sensor data, combined with the spatial and temporal covariates, provide an ideal dataset for developing 3D+T models. The presentation will include preliminary results and address main implementation strategies.

  15. 3-D Autojuggie: Automating Deployment of Two-Dimensional Geophone Arrays for Efficient Ultra-Shallow Seismic-Reflection Surveys

    NASA Astrophysics Data System (ADS)

    Tsoflias, G. P.; Steeples, D. W.; Czarnecki, G.; Sloan, S. D.; Eslick, R.

    2005-12-01

    Near-surface seismic reflection methods require dense spatial sampling of the wavefield. Seismic surveys imaging the top ten meters of the subsurface employ geophone spacing on the order of decimeters. Two-dimensional (2-D), ultra-shallow seismic reflection methods have increased in popularity. However, placement of geophones remains a labor-intensive deterrent to the acquisition of near-surface, 3-D seismic data. Although 3-D seismic imaging is a mature hydrocarbon-exploration technique, only a handful of 3-D shallow seismic surveys have been acquired over the last decade. We present the development and field-testing of instrumentation for automatic deployment of a 2-D array of 72 geophones for acquisition of ultra-shallow 3-D reflection seismic data, referred to as the 3-D Autojuggie. The main components of the instrumentation include: a) two vertically stacked rigid steel frames used for positioning, planting, and transporting an array of geophones; b) an hydraulically controlled mechanism for decoupling the geophones from the steel frames during seismic data recording; and c) a 2-D array of seventy-two 100 Hz Mark Products geophones with 20.32 cm long spikes, spaced 20 cm apart in the inline (12 geophones) and crossline (6 rows) orientation. Seismic noise testing (walkaways) conducted at The University of Kansas employing automatically planted 2-D geophone arrays next to conventional hand-planted geophones resulted in equivalent seismic imaging of the subsurface. The geophone planting instrumentation did not degrade the quality of the recorded wavefield. The efficiency of automatically placing a dense 2-D array of geophones on the ground and the ease of moving the array quickly to adjacent positions, along with the ability to acquire comparable quality data to conventional hand-planted geophones, indicate that the 3-D Autojuggie is a viable approach to ultra-shallow 3-D seismic acquisition. Conceptually, the design could accommodate an array of hundreds of

  16. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    PubMed Central

    2009-01-01

    Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625

  17. Optic disc boundary segmentation from diffeomorphic demons registration of monocular fundus image sequences versus 3D visualization of stereo fundus image pairs for automated early stage glaucoma assessment

    NASA Astrophysics Data System (ADS)

    Gatti, Vijay; Hill, Jason; Mitra, Sunanda; Nutter, Brian

    2014-03-01

    Despite the current availability in resource-rich regions of advanced technologies in scanning and 3-D imaging in current ophthalmology practice, world-wide screening tests for early detection and progression of glaucoma still consist of a variety of simple tools, including fundus image-based parameters such as CDR (cup to disc diameter ratio) and CAR (cup to disc area ratio), especially in resource -poor regions. Reliable automated computation of the relevant parameters from fundus image sequences requires robust non-rigid registration and segmentation techniques. Recent research work demonstrated that proper non-rigid registration of multi-view monocular fundus image sequences could result in acceptable segmentation of cup boundaries for automated computation of CAR and CDR. This research work introduces a composite diffeomorphic demons registration algorithm for segmentation of cup boundaries from a sequence of monocular images and compares the resulting CAR and CDR values with those computed manually by experts and from 3-D visualization of stereo pairs. Our preliminary results show that the automated computation of CDR and CAR from composite diffeomorphic segmentation of monocular image sequences yield values comparable with those from the other two techniques and thus may provide global healthcare with a cost-effective yet accurate tool for management of glaucoma in its early stage.

  18. A linear programming approach to reconstructing subcellular structures from confocal images for automated generation of representative 3D cellular models

    PubMed Central

    Wood, Scott T.; Dean, Brian C.; Dean, Delphine

    2013-01-01

    This paper presents a novel computer vision algorithm to analyze 3D stacks of confocal images of fluorescently stained single cells. The goal of the algorithm is to create representative in silico model structures that can be imported into finite element analysis software for mechanical characterization. Segmentation of cell and nucleus boundaries is accomplished via standard thresholding methods. Using novel linear programming methods, a representative actin stress fiber network is generated by computing a linear superposition of fibers having minimum discrepancy compared with an experimental 3D confocal image. Qualitative validation is performed through analysis of seven 3D confocal image stacks of adherent vascular smooth muscle cells (VSMCs) grown in 2D culture. The presented method is able to automatically generate 3D geometries of the cell's boundary, nucleus, and representative F-actin network based on standard cell microscopy data. These geometries can be used for direct importation and implementation in structural finite element models for analysis of the mechanics of a single cell to potentially speed discoveries in the fields of regenerative medicine, mechanobiology, and drug discovery. PMID:23395283

  19. 3D-catFISH: a system for automated quantitative three-dimensional compartmental analysis of temporal gene transcription activity imaged by fluorescence in situ hybridization.

    PubMed

    Chawla, Monica K; Lin, Gang; Olson, Kathy; Vazdarjanova, Almira; Burke, Sara N; McNaughton, Bruce L; Worley, Paul F; Guzowski, John F; Roysam, Badrinath; Barnes, Carol A

    2004-10-15

    Fluorescence in situ hybridization (FISH) of neural activity-regulated, immediate-early gene (IEG) expression provides a method of functional brain imaging with cellular resolution. This enables the identification, in one brain, of which specific principal neurons were active during each of two distinct behavioral epochs. The unprecedented potential of this differential method for large-scale analysis of functional neural circuits is limited, however, by the time-intensive nature of manual image analysis. A comprehensive software tool for processing three-dimensional, multi-spectral confocal image stacks is described which supports the automation of this analysis. Nuclei counterstained with conventional DNA dyes and FISH signals indicating the sub-cellular distribution of specific, IEG RNA species are imaged using different spectral channels. The DNA channel data are segmented into individual nuclei by a three-dimensional multi-step algorithm that corrects for depth-dependent attenuation, non-isotropic voxels, and imaging noise. Intra-nuclear and cytoplasmic FISH signals are associated spatially with the nuclear segmentation results to generate a detailed tabular/database and graphic representation. Here we present a comprehensive validation of data generated by the automated software against manual quantification by human experts on hippocampal and parietal cortical regions (96.5% concordance with multi-expert consensus). The high degree of reliability and accuracy suggests that the software will generalize well to multiple brain areas and eventually to large-scale brain analysis. PMID:15351517

  20. Automated quantitative analysis of 3D morphology and mean corpuscular hemoglobin in human red blood cells stored in different periods.

    PubMed

    Moon, Inkyu; Yi, Faliu; Lee, Yeon H; Javidi, Bahram; Boss, Daniel; Marquet, Pierre

    2013-12-16

    Quantitative phase (QP) images of red blood cells (RBCs), which are obtained by off-axis digital holographic microscopy, can provide quantitative information about three-dimensional (3D) morphology of human RBCs and the characteristic properties such as mean corpuscular hemoglobin (MCH) and MCH surface density (MCHSD). In this paper, we investigate modifications of the 3D morphology and MCH in RBCs induced by the period of storage time for the purpose of classification of RBCs with different periods of storage by using off-axis digital holographic microscopy. The classification of RBCs based on the duration of storage is highly relevant because a long storage of blood before transfusion may alter the functionality of RBCs and, therefore, cause complications in patients. To analyze any changes in the 3D morphology and MCH of RBCs due to storage, we use data sets from RBC samples stored for 8, 13, 16, 23, 27, 30, 34, 37, 40, 47, and 57 days, respectively. The data sets consist of more than 3,300 blood cells in eleven classes, with more than 300 blood cells per class. The classes indicate the storage period of RBCs and are listed in chronological order. Using the RBCs donated by healthy persons, the off-axis digital holographic microscopy reconstructs several quantitative phase images of RBC samples stored for eleven different periods. We employ marker-controlled watershed transform to remove the background in the RBC quantitative phase images obtained by the off-axis digital holographic microscopy. More than 300 single RBCs are extracted from the segmented quantitative phase images for each class. Such a large number of RBC samples enable us to obtain statistical distributions of the characteristic properties of RBCs after a specific period of storage. Experimental results show that the 3D morphology of the RBCs, in contrast to MCH, is essentially related to the aging of the RBCs. PMID:24514667

  1. Semi-automated extraction and delineation of 3D roads of street scene from mobile laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Yang, Bisheng; Fang, Lina; Li, Jonathan

    2013-05-01

    Accurate 3D road information is important for applications such as road maintenance and virtual 3D modeling. Mobile laser scanning (MLS) is an efficient technique for capturing dense point clouds that can be used to construct detailed road models for large areas. This paper presents a method for extracting and delineating roads from large-scale MLS point clouds. The proposed method partitions MLS point clouds into a set of consecutive "scanning lines", which each consists of a road cross section. A moving window operator is used to filter out non-ground points line by line, and curb points are detected based on curb patterns. The detected curb points are tracked and refined so that they are both globally consistent and locally similar. To evaluate the validity of the proposed method, experiments were conducted using two types of street-scene point clouds captured by Optech's Lynx Mobile Mapper System. The completeness, correctness, and quality of the extracted roads are over 94.42%, 91.13%, and 91.3%, respectively, which proves the proposed method is a promising solution for extracting 3D roads from MLS point clouds.

  2. Speeding up 3D speckle tracking using PatchMatch

    NASA Astrophysics Data System (ADS)

    Zontak, Maria; O'Donnell, Matthew

    2016-03-01

    Echocardiography provides valuable information to diagnose heart dysfunction. A typical exam records several minutes of real-time cardiac images. To enable complete analysis of 3D cardiac strains, 4-D (3-D+t) echocardiography is used. This results in a huge dataset and requires effective automated analysis. Ultrasound speckle tracking is an effective method for tissue motion analysis. It involves correlation of a 3D kernel (block) around a voxel with kernels in later frames. The search region is usually confined to a local neighborhood, due to biomechanical and computational constraints. For high strains and moderate frame-rates, however, this search region will remain large, leading to a considerable computational burden. Moreover, speckle decorrelation (due to high strains) leads to errors in tracking. To solve this, spatial motion coherency between adjacent voxels should be imposed, e.g., by averaging their correlation functions.1 This requires storing correlation functions for neighboring voxels, thus increasing memory demands. In this work, we propose an efficient search using PatchMatch, 2 a powerful method to find correspondences between images. Here we adopt PatchMatch for 3D volumes and radio-frequency signals. As opposed to an exact search, PatchMatch performs random sampling of the search region and propagates successive matches among neighboring voxels. We show that: 1) Inherently smooth offset propagation in PatchMatch contributes to spatial motion coherence without any additional processing or memory demand. 2) For typical scenarios, PatchMatch is at least 20 times faster than the exact search, while maintaining comparable tracking accuracy.

  3. Standard and fenestrated endograft sizing in EVAR planning: Description and validation of a semi-automated 3D software.

    PubMed

    Macía, Iván; de Blas, Mariano; Legarreta, Jon Haitz; Kabongo, Luis; Hernández, Óscar; Egaña, José María; Emparanza, José Ignacio; García-Familiar, Ainhoa; Graña, Manuel

    2016-06-01

    An abdominal aortic aneurysm (AAA) is a pathological dilation of the abdominal aorta that may lead to a rupture with fatal consequences. Endovascular aneurysm repair (EVAR) is a minimally invasive surgical procedure consisting of the deployment and fixation of a stent-graft that isolates the damaged vessel wall from blood circulation. The technique requires adequate endovascular device sizing, which may be performed by vascular analysis and quantification on Computerized Tomography Angiography (CTA) scans. This paper presents a novel 3D CTA image-based software for AAA inspection and EVAR sizing, eVida Vascular, which allows fast and accurate 3D endograft sizing for standard and fenestrated endografts. We provide a description of the system and its innovations, including the underlying vascular image analysis and visualization technology, functional modules and user interaction. Furthermore, an experimental validation of the tool is described, assessing the degree of agreement with a commercial, clinically validated software, when comparing measurements obtained for standard endograft sizing in a group of 14 patients. PMID:25747803

  4. A Multi-Resolution Approach for an Automated Fusion of Different Low-Cost 3D Sensors

    PubMed Central

    Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

    2014-01-01

    The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory. PMID:24763255

  5. Automated 3D architecture reconstruction from photogrammetric structure-and-motion: A case study of the One Pilla pagoda, Hanoi, Vienam

    NASA Astrophysics Data System (ADS)

    To, T.; Nguyen, D.; Tran, G.

    2015-04-01

    Heritage system of Vietnam has decline because of poor-conventional condition. For sustainable development, it is required a firmly control, space planning organization, and reasonable investment. Moreover, in the field of Cultural Heritage, the use of automated photogrammetric systems, based on Structure from Motion techniques (SfM), is widely used. With the potential of high-resolution, low-cost, large field of view, easiness, rapidity and completeness, the derivation of 3D metric information from Structure-and- Motion images is receiving great attention. In addition, heritage objects in form of 3D physical models are recorded not only for documentation issues, but also for historical interpretation, restoration, cultural and educational purposes. The study suggests the archaeological documentation of the "One Pilla" pagoda placed in Hanoi capital, Vietnam. The data acquired through digital camera Cannon EOS 550D, CMOS APS-C sensor 22.3 x 14.9 mm. Camera calibration and orientation were carried out by VisualSFM, CMPMVS (Multi-View Reconstruction) and SURE (Photogrammetric Surface Reconstruction from Imagery) software. The final result represents a scaled 3D model of the One Pilla Pagoda and displayed different views in MeshLab software.

  6. Automated real-time search and analysis algorithms for a non-contact 3D profiling system

    NASA Astrophysics Data System (ADS)

    Haynes, Mark; Wu, Chih-Hang John; Beck, B. Terry; Peterman, Robert J.

    2013-04-01

    The purpose of this research is to develop a new means of identifying and extracting geometrical feature statistics from a non-contact precision-measurement 3D profilometer. Autonomous algorithms have been developed to search through large-scale Cartesian point clouds to identify and extract geometrical features. These algorithms are developed with the intent of providing real-time production quality control of cold-rolled steel wires. The steel wires in question are prestressing steel reinforcement wires for concrete members. The geometry of the wire is critical in the performance of the overall concrete structure. For this research a custom 3D non-contact profilometry system has been developed that utilizes laser displacement sensors for submicron resolution surface profiling. Optimizations in the control and sensory system allow for data points to be collected at up to an approximate 400,000 points per second. In order to achieve geometrical feature extraction and tolerancing with this large volume of data, the algorithms employed are optimized for parsing large data quantities. The methods used provide a unique means of maintaining high resolution data of the surface profiles while keeping algorithm running times within practical bounds for industrial application. By a combination of regional sampling, iterative search, spatial filtering, frequency filtering, spatial clustering, and template matching a robust feature identification method has been developed. These algorithms provide an autonomous means of verifying tolerances in geometrical features. The key method of identifying the features is through a combination of downhill simplex and geometrical feature templates. By performing downhill simplex through several procedural programming layers of different search and filtering techniques, very specific geometrical features can be identified within the point cloud and analyzed for proper tolerancing. Being able to perform this quality control in real time

  7. In Situ 3D Segmentation of Individual Plant Leaves Using a RGB-D Camera for Agricultural Automation

    PubMed Central

    Xia, Chunlei; Wang, Longtan; Chung, Bu-Keun; Lee, Jang-Myung

    2015-01-01

    In this paper, we present a challenging task of 3D segmentation of individual plant leaves from occlusions in the complicated natural scene. Depth data of plant leaves is introduced to improve the robustness of plant leaf segmentation. The low cost RGB-D camera is utilized to capture depth and color image in fields. Mean shift clustering is applied to segment plant leaves in depth image. Plant leaves are extracted from the natural background by examining vegetation of the candidate segments produced by mean shift. Subsequently, individual leaves are segmented from occlusions by active contour models. Automatic initialization of the active contour models is implemented by calculating the center of divergence from the gradient vector field of depth image. The proposed segmentation scheme is tested through experiments under greenhouse conditions. The overall segmentation rate is 87.97% while segmentation rates for single and occluded leaves are 92.10% and 86.67%, respectively. Approximately half of the experimental results show segmentation rates of individual leaves higher than 90%. Nevertheless, the proposed method is able to segment individual leaves from heavy occlusions. PMID:26295395

  8. Active shape models for a fully automated 3D segmentation of the liver--an evaluation on clinical data.

    PubMed

    Heimann, Tobias; Wolf, Ivo; Meinzer, Hans-Peter

    2006-01-01

    This paper presents an evaluation of the performance of a three-dimensional Active Shape Model (ASM) to segment the liver in 48 clinical CT scans. The employed shape model is built from 32 samples using an optimization approach based on the minimum description length (MDL). Three different gray-value appearance models (plain intensity, gradient and normalized gradient profiles) are created to guide the search. The employed segmentation techniques are ASM search with 10 and 30 modes of variation and a deformable model coupled to a shape model with 10 modes of variation. To assess the segmentation performance, the obtained results are compared to manual segmentations with four different measures (overlap, average distance, RMS distance and ratio of deviations larger 5mm). The only appearance model delivering usable results is the normalized gradient profile. The deformable model search achieves the best results, followed by the ASM search with 30 modes. Overall, statistical shape modeling delivers very promising results for a fully automated segmentation of the liver. PMID:17354754

  9. Automated 3-D Segmentation of Lungs With Lung Cancer in CT Data Using a Novel Robust Active Shape Model Approach

    PubMed Central

    Sun, Shanhui; Bauer, Christian; Beichel, Reinhard

    2013-01-01

    Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of 0.975 ± 0.006 and a mean absolute surface distance error of 0.84 ± 0.23 mm, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models. PMID:21997248

  10. Use of short roll C-arm computed tomography and fully automated 3D analysis tools to guide transcatheter aortic valve replacement.

    PubMed

    Kim, Michael S; Bracken, John; Eshuis, Peter; Chen, S Y James; Fullerton, David; Cleveland, Joseph; Messenger, John C; Carroll, John D

    2016-07-01

    Determination of the coplanar view is a critical component of transcatheter aortic valve replacement (TAVR). The safety and accuracy of a novel reduced angular range C-arm computed tomography (CACT) approach coupled with a fully automated 3D analysis tool package to predict the coplanar view in TAVR was evaluated. Fifty-seven patients with severe symptomatic aortic stenosis deemed prohibitive-risk for surgery and who underwent TAVR were enrolled. Patients were randomized 2:1 to CACT vs. angiography (control) in estimating the coplanar view. These approaches to determine the coplanar view were compared quantitatively. Radiation doses needed to determine the coplanar view were recorded for both the CACT and control patients. Use of CACT offered good agreement with the actual angiographic view utilized during TAVR in 34 out of 41 cases in which a CACT scan was performed (83 %). For these 34 cases, the mean angular magnitude difference, taking into account both oblique and cranial/caudal angulation, was 1.3° ± 0.4°, while the maximum difference was 7.3°. There were no significant differences in the mean total radiation dose delivered to patients between the CACT and control groups as measured by either dose area product (207.8 ± 15.2 Gy cm(2) vs. 186.1 ± 25.3 Gy cm(2), P = 0.47) or air kerma (1287.6 ± 117.7 mGy vs. 1098.9 ± 143.8 mGy, P = 0.32). Use of reduced-angular range CACT coupled with fully automated 3D analysis tools is a safe, practical, and feasible method by which to determine the optimal angiographic deployment view for guiding TAVR procedures. PMID:27091735

  11. An Automated Treatment Plan Quality Control Tool for Intensity-Modulated Radiation Therapy Using a Voxel-Weighting Factor-Based Re-Optimization Algorithm.

    PubMed

    Song, Ting; Li, Nan; Zarepisheh, Masoud; Li, Yongbao; Gautier, Quentin; Zhou, Linghong; Mell, Loren; Jiang, Steve; Cerviño, Laura

    2016-01-01

    Intensity-modulated radiation therapy (IMRT) currently plays an important role in radiotherapy, but its treatment plan quality can vary significantly among institutions and planners. Treatment plan quality control (QC) is a necessary component for individual clinics to ensure that patients receive treatments with high therapeutic gain ratios. The voxel-weighting factor-based plan re-optimization mechanism has been proved able to explore a larger Pareto surface (solution domain) and therefore increase the possibility of finding an optimal treatment plan. In this study, we incorporated additional modules into an in-house developed voxel weighting factor-based re-optimization algorithm, which was enhanced as a highly automated and accurate IMRT plan QC tool (TPS-QC tool). After importing an under-assessment plan, the TPS-QC tool was able to generate a QC report within 2 minutes. This QC report contains the plan quality determination as well as information supporting the determination. Finally, the IMRT plan quality can be controlled by approving quality-passed plans and replacing quality-failed plans using the TPS-QC tool. The feasibility and accuracy of the proposed TPS-QC tool were evaluated using 25 clinically approved cervical cancer patient IMRT plans and 5 manually created poor-quality IMRT plans. The results showed high consistency between the QC report quality determinations and the actual plan quality. In the 25 clinically approved cases that the TPS-QC tool identified as passed, a greater difference could be observed for dosimetric endpoints for organs at risk (OAR) than for planning target volume (PTV), implying that better dose sparing could be achieved in OAR than in PTV. In addition, the dose-volume histogram (DVH) curves of the TPS-QC tool re-optimized plans satisfied the dosimetric criteria more frequently than did the under-assessment plans. In addition, the criteria for unsatisfied dosimetric endpoints in the 5 poor-quality plans could typically be

  12. An Automated Treatment Plan Quality Control Tool for Intensity-Modulated Radiation Therapy Using a Voxel-Weighting Factor-Based Re-Optimization Algorithm

    PubMed Central

    Song, Ting; Li, Nan; Zarepisheh, Masoud; Li, Yongbao; Gautier, Quentin; Zhou, Linghong; Mell, Loren; Jiang, Steve; Cerviño, Laura

    2016-01-01

    Intensity-modulated radiation therapy (IMRT) currently plays an important role in radiotherapy, but its treatment plan quality can vary significantly among institutions and planners. Treatment plan quality control (QC) is a necessary component for individual clinics to ensure that patients receive treatments with high therapeutic gain ratios. The voxel-weighting factor-based plan re-optimization mechanism has been proved able to explore a larger Pareto surface (solution domain) and therefore increase the possibility of finding an optimal treatment plan. In this study, we incorporated additional modules into an in-house developed voxel weighting factor-based re-optimization algorithm, which was enhanced as a highly automated and accurate IMRT plan QC tool (TPS-QC tool). After importing an under-assessment plan, the TPS-QC tool was able to generate a QC report within 2 minutes. This QC report contains the plan quality determination as well as information supporting the determination. Finally, the IMRT plan quality can be controlled by approving quality-passed plans and replacing quality-failed plans using the TPS-QC tool. The feasibility and accuracy of the proposed TPS-QC tool were evaluated using 25 clinically approved cervical cancer patient IMRT plans and 5 manually created poor-quality IMRT plans. The results showed high consistency between the QC report quality determinations and the actual plan quality. In the 25 clinically approved cases that the TPS-QC tool identified as passed, a greater difference could be observed for dosimetric endpoints for organs at risk (OAR) than for planning target volume (PTV), implying that better dose sparing could be achieved in OAR than in PTV. In addition, the dose-volume histogram (DVH) curves of the TPS-QC tool re-optimized plans satisfied the dosimetric criteria more frequently than did the under-assessment plans. In addition, the criteria for unsatisfied dosimetric endpoints in the 5 poor-quality plans could typically be

  13. Automating measurement of subtle changes in articular cartilage from MRI of the knee by combining 3D image registration and segmentation

    NASA Astrophysics Data System (ADS)

    Lynch, John A.; Zaim, Souhil; Zhao, Jenny; Peterfy, Charles G.; Genant, Harry K.

    2001-07-01

    In osteoarthritis, articular cartilage loses integrity and becomes thinned. This usually occurs at sites which bear weight during normal use. Measurement of such loss from MRI scans, requires precise and reproducible techniques, which can overcome the difficulties of patient repositioning within the scanner. In this study, we combine a previously described technique for segmentation of cartilage from MRI of the knee, with a technique for 3D image registration that matches localized regions of interest at followup and baseline. Two patients, who had recently undergone meniscal surgery, and developed lesions during the 12 month followup period were examined. Image registration matched regions of interest (ROI) between baseline and followup, and changes within the cartilage lesions were estimate to be about a 16% reduction in cartilage volume within each ROI. This was more than 5 times the reproducibility of the measurement, but only represented a change of between 1 and 2% in total femoral cartilage volume. Changes in total cartilage volume may be insensitive for quantifying changes in cartilage morphology. A combined used of automated image segmentation, with 3D image registration could be a useful tool for the precise and sensitive measurement of localized changes in cartilage from MRI of the knee.

  14. Fluid Lensing, Applications to High-Resolution 3D Subaqueous Imaging & Automated Remote Biosphere Assessment from Airborne and Space-borne Platforms

    NASA Astrophysics Data System (ADS)

    Chirayath, V.

    2014-12-01

    Fluid Lensing is a theoretical model and algorithm I present for fluid-optical interactions in turbulent flows as well as two-fluid surface boundaries that, when coupled with an unique computer vision and image-processing pipeline, may be used to significantly enhance the angular resolution of a remote sensing optical system with applicability to high-resolution 3D imaging of subaqueous regions and through turbulent fluid flows. This novel remote sensing technology has recently been implemented on a quadcopter-based UAS for imaging shallow benthic systems to create the first dataset of a biosphere with unprecedented sub-cm-level imagery in 3D over areas as large as 15 square kilometers. Perturbed two-fluid boundaries with different refractive indices, such as the surface between the ocean and air, may be exploited for use as lensing elements for imaging targets on either side of the interface with enhanced angular resolution. I present theoretical developments behind Fluid Lensing and experimental results from its recent implementation for the Reactive Reefs project to image shallow reef ecosystems at cm scales. Preliminary results from petabyte-scale aerial survey efforts using Fluid Lensing to image at-risk coral reefs in American Samoa (August, 2013) show broad applicability to large-scale automated species identification, morphology studies and reef ecosystem characterization for shallow marine environments and terrestrial biospheres, of crucial importance to understanding climate change's impact on coastal zones, global oxygen production and carbon sequestration.

  15. Towards automated firearm identification based on high resolution 3D data: rotation-invariant features for multiple line-profile-measurement of firing pin shapes

    NASA Astrophysics Data System (ADS)

    Fischer, Robert; Vielhauer, Claus

    2015-03-01

    Understanding and evaluation of potential evidence, as well as evaluation of automated systems for forensic examinations currently play an important role within the domain of digital crime scene analysis. The application of 3D sensing and pattern recognition systems for automatic extraction and comparison of firearm related tool marks is an evolving field of research within this domain. In this context, the design and evaluation of rotation-invariant features for use on topography data play a particular important role. In this work, we propose and evaluate a 3D imaging system along with two novel features based on topography data and multiple profile-measurement-lines for automatic matching of firing pin shapes. Our test set contains 72 cartridges of three manufactures shot by six different 9mm guns. The entire pattern recognition workflow is addressed. This includes the application of confocal microscopy for data acquisition, preprocessing covers outlier handling, data normalization, as well as necessary segmentation and registration. Feature extraction involves the two introduced features for automatic comparison and matching of 3D firing pin shapes. The introduced features are called `Multiple-Circle-Path' (MCP) and `Multiple-Angle-Path' (MAP). Basically both features are compositions of freely configurable amounts of circular or straight path-lines combined with statistical evaluations. During the first part of evaluation (E1), we examine how well it is possible to differentiate between two 9mm weapons of the same mark and model. During second part (E2), we evaluate the discrimination accuracy regarding the set of six different 9mm guns. During the third part (E3), we evaluate the performance of the features in consideration of different rotation angles. In terms of E1, the best correct classification rate is 100% and in terms of E2 the best result is 86%. The preliminary results for E3 indicate robustness of both features regarding rotation. However, in future

  16. Automation and validation of micronucleus detection in the 3D EpiDerm™ human reconstructed skin assay and correlation with 2D dose responses.

    PubMed

    Chapman, K E; Thomas, A D; Wills, J W; Pfuhler, S; Doak, S H; Jenkins, G J S

    2014-05-01

    Recent restrictions on the testing of cosmetic ingredients in animals have resulted in the need to test the genotoxic potential of chemicals exclusively in vitro prior to licensing. However, as current in vitro tests produce some misleading positive results, sole reliance on such tests could prevent some chemicals with safe or beneficial exposure levels from being marketed. The 3D human reconstructed skin micronucleus (RSMN) assay is a promising new in vitro approach designed to assess genotoxicity of dermally applied compounds. The assay utilises a highly differentiated in vitro model of the human epidermis. For the first time, we have applied automated micronucleus detection to this assay using MetaSystems Metafer Slide Scanning Platform (Metafer), demonstrating concordance with manual scoring. The RSMN assay's fixation protocol was found to be compatible with the Metafer, providing a considerably shorter alternative to the recommended Metafer protocol. Lowest observed genotoxic effect levels (LOGELs) were observed for mitomycin-C at 4.8 µg/ml and methyl methanesulfonate (MMS) at 1750 µg/ml when applied topically to the skin surface. In-medium dosing with MMS produced a LOGEL of 20 µg/ml, which was very similar to the topical LOGEL when considering the total mass of MMS added. Comparisons between 3D medium and 2D LOGELs resulted in a 7-fold difference in total mass of MMS applied to each system, suggesting a protective function of the 3D microarchitecture. Interestingly, hydrogen peroxide (H2O2), a positive clastogen in 2D systems, tested negative in this assay. A non-genotoxic carcinogen, methyl carbamate, produced negative results, as expected. We also demonstrated expression of the DNA repair protein N-methylpurine-DNA glycosylase in EpiDerm™. Our preliminary validation here demonstrates that the RSMN assay may be a valuable follow-up to the current in vitro test battery, and together with its automation, could contribute to minimising unnecessary in vivo

  17. Automation and validation of micronucleus detection in the 3D EpiDerm™ human reconstructed skin assay and correlation with 2D dose responses

    PubMed Central

    Chapman, K. E.; Thomas, A. D.; Jenkins, G. J. S.

    2014-01-01

    Recent restrictions on the testing of cosmetic ingredients in animals have resulted in the need to test the genotoxic potential of chemicals exclusively in vitro prior to licensing. However, as current in vitro tests produce some misleading positive results, sole reliance on such tests could prevent some chemicals with safe or beneficial exposure levels from being marketed. The 3D human reconstructed skin micronucleus (RSMN) assay is a promising new in vitro approach designed to assess genotoxicity of dermally applied compounds. The assay utilises a highly differentiated in vitro model of the human epidermis. For the first time, we have applied automated micronucleus detection to this assay using MetaSystems Metafer Slide Scanning Platform (Metafer), demonstrating concordance with manual scoring. The RSMN assay’s fixation protocol was found to be compatible with the Metafer, providing a considerably shorter alternative to the recommended Metafer protocol. Lowest observed genotoxic effect levels (LOGELs) were observed for mitomycin-C at 4.8 µg/ml and methyl methanesulfonate (MMS) at 1750 µg/ml when applied topically to the skin surface. In-medium dosing with MMS produced a LOGEL of 20 µg/ml, which was very similar to the topical LOGEL when considering the total mass of MMS added. Comparisons between 3D medium and 2D LOGELs resulted in a 7-fold difference in total mass of MMS applied to each system, suggesting a protective function of the 3D microarchitecture. Interestingly, hydrogen peroxide (H2O2), a positive clastogen in 2D systems, tested negative in this assay. A non-genotoxic carcinogen, methyl carbamate, produced negative results, as expected. We also demonstrated expression of the DNA repair protein N-methylpurine-DNA glycosylase in EpiDerm™. Our preliminary validation here demonstrates that the RSMN assay may be a valuable follow-up to the current in vitro test battery, and together with its automation, could contribute to minimising unnecessary in

  18. Automated 3D-2D registration of X-ray microcomputed tomography with histological sections for dental implants in bone using chamfer matching and simulated annealing.

    PubMed

    Becker, Kathrin; Stauber, Martin; Schwarz, Frank; Beißbarth, Tim

    2015-09-01

    We propose a novel 3D-2D registration approach for micro-computed tomography (μCT) and histology (HI), constructed for dental implant biopsies, that finds the position and normal vector of the oblique slice from μCT that corresponds to HI. During image pre-processing, the implants and the bone tissue are segmented using a combination of thresholding, morphological filters and component labeling. After this, chamfer matching is employed to register the implant edges and fine registration of the bone tissues is achieved using simulated annealing. The method was tested on n=10 biopsies, obtained at 20 weeks after non-submerged healing in the canine mandible. The specimens were scanned with μCT 100 and processed for hard tissue sectioning. After registration, we assessed the agreement of bone to implant contact (BIC) using automated and manual measurements. Statistical analysis was conducted to test the agreement of the BIC measurements in the registered samples. Registration was successful for all specimens and agreement of the respective binary images was high (median: 0.90, 1.-3. Qu.: 0.89-0.91). Direct comparison of BIC yielded that automated (median 0.82, 1.-3. Qu.: 0.75-0.85) and manual (median 0.61, 1.-3. Qu.: 0.52-0.67) measures from μCT were significant positively correlated with HI (median 0.65, 1.-3. Qu.: 0.59-0.72) between μCT and HI groups (manual: R(2)=0.87, automated: R(2)=0.75, p<0.001). The results show that this method yields promising results and that μCT may become a valid alternative to assess osseointegration in three dimensions. PMID:26026659

  19. Intrathoracic tumour motion estimation from CT imaging using the 3D optical flow method

    NASA Astrophysics Data System (ADS)

    Guerrero, Thomas; Zhang, Geoffrey; Huang, Tzung-Chi; Lin, Kang-Ping

    2004-09-01

    The purpose of this work was to develop and validate an automated method for intrathoracic tumour motion estimation from breath-hold computed tomography (BH CT) imaging using the three-dimensional optical flow method (3D OFM). A modified 3D OFM algorithm provided 3D displacement vectors for each voxel which were used to map tumour voxels on expiration BH CT onto inspiration BH CT images. A thoracic phantom and simulated expiration/inspiration BH CT pairs were used for validation. The 3D OFM was applied to the measured inspiration and expiration BH CT images from one lung cancer and one oesophageal cancer patient. The resulting displacements were plotted in histogram format and analysed to provide insight regarding the tumour motion. The phantom tumour displacement was measured as 1.20 and 2.40 cm with full-width at tenth maximum (FWTM) for the distribution of displacement estimates of 0.008 and 0.006 cm, respectively. The maximum error of any single voxel's motion estimate was 1.1 mm along the z-dimension or approximately one-third of the z-dimension voxel size. The simulated BH CT pairs revealed an rms error of less than 0.25 mm. The displacement of the oesophageal tumours was nonuniform and up to 1.4 cm, this was a new finding. A lung tumour maximum displacement of 2.4 cm was found in the case evaluated. In conclusion, 3D OFM provided an accurate estimation of intrathoracic tumour motion, with estimated errors less than the voxel dimension in a simulated motion phantom study. Surprisingly, oesophageal tumour motion was large and nonuniform, with greatest motion occurring at the gastro-oesophageal junction. Presented at The IASTED Second International Conference on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 16-18 February 2004.

  20. Using semi-automated photogrammetry software to generate 3D surfaces from oblique and vertical photographs at Mount St. Helens, WA

    NASA Astrophysics Data System (ADS)

    Schilling, S.; Diefenbach, A. K.

    2012-12-01

    Photogrammetry has been used to generate contours and Digital Elevation Models (DEMs) to monitor change at Mount St. Helens, WA since the 1980 eruption. We continue to improve techniques to monitor topographic changes within the crater. During the 2004-2008 eruption, 26 DEMs were used to track volume and rates of growth of a lava dome and changes of Crater Glacier. These measurements constrained seismogenic extrusion models and were compared with geodetic deflation volume to constrain magma chamber behavior. We used photogrammetric software to collect irregularly spaced 3D points primarily by hand and, in reasonably flat areas, by automated algorithms, from commercial vertical aerial photographs. These models took days to months to complete and the areal extent of each surface was determined by visual inspection. Later in the eruption, we pioneered the use of different software to generate irregularly spaced 3D points manually from oblique images captured by a hand-held digital camera. In each case, the irregularly spaced points and intervening interpolated points formed regular arrays of cells or DEMs. Calculations using DEMs produced from the hand-held images duplicated volumetric and rate results gleaned from the vertical aerial photographs. This manual point capture technique from oblique hand-held photographs required only a few hours to generate a model over a focused area such as the lava dome, but would have taken perhaps days to capture data over the entire crater. Here, we present results from new photogrammetric software that uses robust image-matching algorithms to produce 3D surfaces automatically after inner, relative, and absolute orientations between overlapping photographs are completed. Measurements using scans of vertical aerial photographs taken August 10, 2005 produced dome volume estimates within two percent of those from a surface generated using the vertical aerial photograph manual method. The new August 10th orientations took less than 8

  1. 3D Actin Network Centerline Extraction with Multiple Active Contours

    PubMed Central

    Xu, Ting; Vavylonis, Dimitrios; Huang, Xiaolei

    2013-01-01

    Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels. PMID:24316442

  2. Combined registration of 3D tibia and femur implant models in 3D magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Englmeier, Karl-Hans; Siebert, Markus; von Eisenhart-Rothe, Ruediger; Graichen, Heiko

    2008-03-01

    The most frequent reasons for revision of total knee arthroplasty are loosening and abnormal axial alignment leading to an unphysiological kinematic of the knee implant. To get an idea about the postoperative kinematic of the implant, it is essential to determine the position and orientation of the tibial and femoral prosthesis. Therefore we developed a registration method for fitting 3D CAD-models of knee joint prostheses into an 3D MR image. This rigid registration is the basis for a quantitative analysis of the kinematics of knee implants. Firstly the surface data of the prostheses models are converted into a voxel representation; a recursive algorithm determines all boundary voxels of the original triangular surface data. Secondly an initial preconfiguration of the implants by the user is still necessary for the following step: The user has to perform a rough preconfiguration of both remaining prostheses models, so that the fine matching process gets a reasonable starting point. After that an automated gradient-based fine matching process determines the best absolute position and orientation: This iterative process changes all 6 parameters (3 rotational- and 3 translational parameters) of a model by a minimal amount until a maximum value of the matching function is reached. To examine the spread of the final solutions of the registration, the interobserver variability was measured in a group of testers. This variability, calculated by the relative standard deviation, improved from about 50% (pure manual registration) to 0.5% (rough manual preconfiguration and subsequent fine registration with the automatic fine matching process).

  3. A Voxel-Based Approach for Imaging Voids in Three-Dimensional Point Clouds

    NASA Astrophysics Data System (ADS)

    Salvaggio, Katie N.

    Geographically accurate scene models have enormous potential beyond that of just simple visualizations in regard to automated scene generation. In recent years, thanks to ever increasing computational efficiencies, there has been significant growth in both the computer vision and photogrammetry communities pertaining to automatic scene reconstruction from multiple-view imagery. The result of these algorithms is a three-dimensional (3D) point cloud which can be used to derive a final model using surface reconstruction techniques. However, the fidelity of these point clouds has not been well studied, and voids often exist within the point cloud. Voids exist in texturally difficult areas, as well as areas where multiple views were not obtained during collection, constant occlusion existed due to collection angles or overlapping scene geometry, or in regions that failed to triangulate accurately. It may be possible to fill in small voids in the scene using surface reconstruction or hole-filling techniques, but this is not the case with larger more complex voids, and attempting to reconstruct them using only the knowledge of the incomplete point cloud is neither accurate nor aesthetically pleasing. A method is presented for identifying voids in point clouds by using a voxel-based approach to partition the 3D space. By using collection geometry and information derived from the point cloud, it is possible to detect unsampled voxels such that voids can be identified. This analysis takes into account the location of the camera and the 3D points themselves to capitalize on the idea of free space, such that voxels that lie on the ray between the camera and point are devoid of obstruction, as a clear line of sight is a necessary requirement for reconstruction. Using this approach, voxels are classified into three categories: occupied (contains points from the point cloud), free (rays from the camera to the point passed through the voxel), and unsampled (does not contain points

  4. Quantitative analysis of two-phase 3D+time aortic MR images

    NASA Astrophysics Data System (ADS)

    Zhao, Fei; Zhang, Honghai; Walker, Nicholas E.; Yang, Fuxing; Olszewski, Mark E.; Wahle, Andreas; Scholz, Thomas; Sonka, Milan

    2006-03-01

    Automated and accurate segmentation of the aorta in 3D+time MR image data is important for early detection of connective tissue disorders leading to aortic aneurysms and dissections. A computer-aided diagnosis method is reported that allows the objective identification of subjects with connective tissue disorders from two-phase 3D+time aortic MR images. Our automated segmentation method combines level-set and optimal border detection. The resulting aortic lumen surface was registered with an aortic model followed by calculation of modal indices of aortic shape and motion. The modal indices reflect the differences of any individual aortic shape and motion from an average aortic behavior. The indices were input to a Support Vector Machine (SVM) classifier and a discrimination model was constructed. 3D+time MR image data sets acquired from 22 normal and connective tissue disorder subjects at end-diastole (R-wave peak) and at 45% of the R-R interval were used to evaluate the performance of our method. The automated 3D segmentation result produced accurate aortic surfaces covering the aorta from the left-ventricular outflow tract to the diaphragm and yielded subvoxel accuracy with signed surface positioning errors of -0.09+/-1.21 voxel (-0.15+/-2.11 mm). The computer aided diagnosis method distinguished between normal and connective tissue disorder subjects with a classification correctness of 90.1 %.

  5. Label free cell tracking in 3D tissue engineering constructs with high resolution imaging

    NASA Astrophysics Data System (ADS)

    Smith, W. A.; Lam, K.-P.; Dempsey, K. P.; Mazzocchi-Jones, D.; Richardson, J. B.; Yang, Y.

    2014-02-01

    Within the field of tissue engineering there is an emphasis on studying 3-D live tissue structures. Consequently, to investigate and identify cellular activities and phenotypes in a 3-D environment for all in vitro experiments, including shape, migration/proliferation and axon projection, it is necessary to adopt an optical imaging system that enables monitoring 3-D cellular activities and morphology through the thickness of the construct for an extended culture period without cell labeling. This paper describes a new 3-D tracking algorithm developed for Cell-IQ®, an automated cell imaging platform, which has been equipped with an environmental chamber optimized to enable capturing time-lapse sequences of live cell images over a long-term period without cell labeling. As an integral part of the algorithm, a novel auto-focusing procedure was developed for phase contrast microscopy equipped with 20x and 40x objectives, to provide a more accurate estimation of cell growth/trajectories by allowing 3-D voxels to be computed at high spatiotemporal resolution and cell density. A pilot study was carried out in a phantom system consisting of horizontally aligned nanofiber layers (with precise spacing between them), to mimic features well exemplified in cellular activities of neuronal growth in a 3-D environment. This was followed by detailed investigations concerning axonal projections and dendritic circuitry formation in a 3-D tissue engineering construct. Preliminary work on primary animal neuronal cells in response to chemoattractant and topographic cue within the scaffolds has produced encouraging results.

  6. Multilayered, Hyaluronic Acid-Based Hydrogel Formulations Suitable for Automated 3D High Throughput Drug Screening of Cancer-Stromal Cell Cocultures.

    PubMed

    Engel, Brian J; Constantinou, Pamela E; Sablatura, Lindsey K; Doty, Nathaniel J; Carson, Daniel D; Farach-Carson, Mary C; Harrington, Daniel A; Zarembinski, Thomas I

    2015-08-01

    Validation of a high-throughput compatible 3D hyaluronic acid hydrogel coculture of cancer cells with stromal cells. The multilayered hyaluronic acid hydrogels improve drug screening predictability as evaluated with a panel of clinically relevant chemotherapeutics in both prostate and endometrial cancer cell lines compared to 2D culture. PMID:26059746

  7. NIF Ignition Target 3D Point Design

    SciTech Connect

    Jones, O; Marinak, M; Milovich, J; Callahan, D

    2008-11-05

    We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

  8. Quality control of 3D Geological Models using an Attention Model based on Gaze

    NASA Astrophysics Data System (ADS)

    Busschers, Freek S.; van Maanen, Peter-Paul; Brouwer, Anne-Marie

    2014-05-01

    The Geological Survey of the Netherlands (GSN) produces 3D stochastic geological models of the upper 50 meters of the Dutch subsurface. The voxel models are regarded essential in answering subsurface questions on, for example, aggregate resources, groundwater flow, land subsidence studies and the planning of large-scale infrastructural works such as tunnels. GeoTOP is the most recent and detailed generation of 3D voxel models. This model describes 3D lithological variability up to a depth of 50 m using voxels of 100*100*0.5m. Due to the expected increase in data-flow, model output and user demands, the development of (semi-)automated quality control systems is getting more important in the near future. Besides numerical control systems, capturing model errors as seen from the expert geologist viewpoint is of increasing interest. We envision the use of eye gaze to support and speed up detection of errors in the geological voxel models. As a first step in this direction we explore gaze behavior of 12 geological experts from the GSN during quality control of part of the GeoTOP 3D geological model using an eye-tracker. Gaze is used as input of an attention model that results in 'attended areas' for each individual examined image of the GeoTOP model and each individual expert. We compared these attended areas to errors as marked by the experts using a mouse. Results show that: 1) attended areas as determined from experts' gaze data largely match with GeoTOP errors as indicated by the experts using a mouse, and 2) a substantial part of the match can be reached using only gaze data from the first few seconds of the time geologists spend to search for errors. These results open up the possibility of faster GeoTOP model control using gaze if geologists accept a small decrease of error detection accuracy. Attention data may also be used to make independent comparisons between different geologists varying in focus and expertise. This would facilitate a more effective use of

  9. Chest wall segmentation in automated 3D breast ultrasound using rib shadow enhancement and multi-plane cumulative probability enhanced map

    NASA Astrophysics Data System (ADS)

    Kim, Hyeonjin; Kim, Hannah; Hong, Helen

    2015-03-01

    We propose an automatic segmentation method of chest wall in 3D ABUS images using rib shadow enhancement and multi-planar cumulative probability enhanced map. For the identification of individual dark rib shadows, each rib shadow is enhanced using intensity transfer function and 3D sheet-like enhancement filtering. Then, wrongly enhanced intercostal regions and small fatty tissues are removed using coronal and sagittal cumulative probability enhanced maps. The large fatty tissues with globular and sheet-like shapes at the top of rib shadow are removed using shape and orientation analysis based on moment matrix. Detected chest walls are connected with cubic B-spline interpolation. Experimental results show that the Dice similarity coefficient of proposed method as comparison with two manually outlining results provides over 90% in average.

  10. Automated Voxel-Based Analysis of Volumetric Dynamic Contrast-Enhanced CT Data Improves Measurement of Serial Changes in Tumor Vascular Biomarkers

    SciTech Connect

    Coolens, Catherine; Driscoll, Brandon; Chung, Caroline; Shek, Tina; Gorjizadeh, Alborz; Ménard, Cynthia; Jaffray, David

    2015-01-01

    Objectives: Development of perfusion imaging as a biomarker requires more robust methodologies for quantification of tumor physiology that allow assessment of volumetric tumor heterogeneity over time. This study proposes a parametric method for automatically analyzing perfused tissue from volumetric dynamic contrast-enhanced (DCE) computed tomography (CT) scans and assesses whether this 4-dimensional (4D) DCE approach is more robust and accurate than conventional, region-of-interest (ROI)-based CT methods in quantifying tumor perfusion with preliminary evaluation in metastatic brain cancer. Methods and Materials: Functional parameter reproducibility and analysis of sensitivity to imaging resolution and arterial input function were evaluated in image sets acquired from a 320-slice CT with a controlled flow phantom and patients with brain metastases, whose treatments were planned for stereotactic radiation surgery and who consented to a research ethics board-approved prospective imaging biomarker study. A voxel-based temporal dynamic analysis (TDA) methodology was used at baseline, at day 7, and at day 20 after treatment. The ability to detect changes in kinetic parameter maps in clinical data sets was investigated for both 4D TDA and conventional 2D ROI-based analysis methods. Results: A total of 7 brain metastases in 3 patients were evaluated over the 3 time points. The 4D TDA method showed improved spatial efficacy and accuracy of perfusion parameters compared to ROI-based DCE analysis (P<.005), with a reproducibility error of less than 2% when tested with DCE phantom data. Clinically, changes in transfer constant from the blood plasma into the extracellular extravascular space (K{sub trans}) were seen when using TDA, with substantially smaller errors than the 2D method on both day 7 post radiation surgery (±13%; P<.05) and by day 20 (±12%; P<.04). Standard methods showed a decrease in K{sub trans} but with large uncertainty (111.6 ± 150.5) %. Conclusions

  11. 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.

  12. Novel 3D modeling methods for virtual fabrication and EDA compatible design of MEMS via parametric libraries

    NASA Astrophysics Data System (ADS)

    Schröpfer, Gerold; Lorenz, Gunar; Rouvillois, Stéphane; Breit, Stephen

    2010-06-01

    This paper provides a brief summary of the state-of-the-art of MEMS-specific modeling techniques and describes the validation of new models for a parametric component library. Two recently developed 3D modeling tools are described in more detail. The first one captures a methodology for designing MEMS devices and simulating them together with integrated electronics within a standard electronic design automation (EDA) environment. The MEMS designer can construct the MEMS model directly in a 3D view. The resulting 3D model differs from a typical feature-based 3D CAD modeling tool in that there is an underlying behavioral model and parametric layout associated with each MEMS component. The model of the complete MEMS device that is shared with the standard EDA environment can be fully parameterized with respect to manufacturing- and design-dependent variables. Another recent innovation is a process modeling tool that allows accurate and highly realistic visualization of the step-by-step creation of 3D micro-fabricated devices. The novelty of the tool lies in its use of voxels (3D pixels) rather than conventional 3D CAD techniques to represent the 3D geometry. Case studies for experimental devices are presented showing how the examination of these virtual prototypes can reveal design errors before mask tape out, support process development before actual fabrication and also enable failure analysis after manufacturing.

  13. Automated neurosphere sorting and plating by the COPAS large particle sorter is a suitable method for high-throughput 3D in vitro applications.

    PubMed

    Gassmann, K; Baumann, J; Giersiefer, S; Schuwald, J; Schreiber, T; Merk, H F; Fritsche, E

    2012-09-01

    Existing guidelines for testing developmental neurotoxicity (DNT) propose investigations in rodents, which are ethically questionable as well as time and cost intensive. Thus, there is international agreement that predictive in vitro methods are needed to increase efficiency of testing and limit the number of animals used. One of a variety of novel approaches for DNT testing utilizes neurospheres, three-dimensional aggregate cultures of primary normal neural progenitor cells (NPCs). Because sorting and plating of single neurospheres is one of the most time-consuming steps within the assay, the aim of this study was to evaluate if the complex object parametric analyzer and sorter (COPAS PLUS(TM), Union Biometrica Inc.) is a suitable tool for automated sorting and plating of neurospheres. The results of the comparison of NPC viability, proliferation, migration, differentiation and intracellular oxidative stress between manually and COPAS sorted and plated neurospheres of different species show that the automation by the COPAS instrument does not influence the basic performance of neurospheres. Therefore, we consider the COPAS instrument as a useful tool for higher throughput neurosphere research in toxicology, neuroregeneration, brain development, drug development and brain aging research. PMID:22579513

  14. Volumetric 3D Display System with Static Screen

    NASA Technical Reports Server (NTRS)

    Geng, Jason

    2011-01-01

    Current display technology has relied on flat, 2D screens that cannot truly convey the third dimension of visual information: depth. In contrast to conventional visualization that is primarily based on 2D flat screens, the volumetric 3D display possesses a true 3D display volume, and places physically each 3D voxel in displayed 3D images at the true 3D (x,y,z) spatial position. Each voxel, analogous to a pixel in a 2D image, emits light from that position to form a real 3D image in the eyes of the viewers. Such true volumetric 3D display technology provides both physiological (accommodation, convergence, binocular disparity, and motion parallax) and psychological (image size, linear perspective, shading, brightness, etc.) depth cues to human visual systems to help in the perception of 3D objects. In a volumetric 3D display, viewers can watch the displayed 3D images from a completely 360 view without using any special eyewear. The volumetric 3D display techniques may lead to a quantum leap in information display technology and can dramatically change the ways humans interact with computers, which can lead to significant improvements in the efficiency of learning and knowledge management processes. Within a block of glass, a large amount of tiny dots of voxels are created by using a recently available machining technique called laser subsurface engraving (LSE). The LSE is able to produce tiny physical crack points (as small as 0.05 mm in diameter) at any (x,y,z) location within the cube of transparent material. The crack dots, when illuminated by a light source, scatter the light around and form visible voxels within the 3D volume. The locations of these tiny voxels are strategically determined such that each can be illuminated by a light ray from a high-resolution digital mirror device (DMD) light engine. The distribution of these voxels occupies the full display volume within the static 3D glass screen. This design eliminates any moving screen seen in previous

  15. Voxel-Based LIDAR Analysis and Applications

    NASA Astrophysics Data System (ADS)

    Hagstrom, Shea T.

    One of the greatest recent changes in the field of remote sensing is the addition of high-quality Light Detection and Ranging (LIDAR) instruments. In particular, the past few decades have been greatly beneficial to these systems because of increases in data collection speed and accuracy, as well as a reduction in the costs of components. These improvements allow modern airborne instruments to resolve sub-meter details, making them ideal for a wide variety of applications. Because LIDAR uses active illumination to capture 3D information, its output is fundamentally different from other modalities. Despite this difference, LIDAR datasets are often processed using methods appropriate for 2D images and that do not take advantage of its primary virtue of 3-dimensional data. It is this problem we explore by using volumetric voxel modeling. Voxel-based analysis has been used in many applications, especially medical imaging, but rarely in traditional remote sensing. In part this is because the memory requirements are substantial when handling large areas, but with modern computing and storage this is no longer a significant impediment. Our reason for using voxels to model scenes from LIDAR data is that there are several advantages over standard triangle-based models, including better handling of overlapping surfaces and complex shapes. We show how incorporating system position information from early in the LIDAR point cloud generation process allows radiometrically-correct transmission and other novel voxel properties to be recovered. This voxelization technique is validated on simulated data using the Digital Imaging and Remote Sensing Image Generation (DIRSIG) software, a first-principles based ray-tracer developed at the Rochester Institute of Technology. Voxel-based modeling of LIDAR can be useful on its own, but we believe its primary advantage is when applied to problems where simpler surface-based 3D models conflict with the requirement of realistic geometry. To

  16. Automated Quantification of Human Brain Metabolites by Artificial Neural Network Analysis from in VivoSingle-Voxel 1H NMR Spectra

    NASA Astrophysics Data System (ADS)

    Kaartinen, Jouni; Mierisová, Šarka; Oja, Joni M. E.; Usenius, Jukka-Pekka; Kauppinen, Risto A.; Hiltunen, Yrjö

    1998-09-01

    A real-time automated way of quantifying metabolites fromin vivoNMR spectra using an artificial neural network (ANN) analysis is presented. The spectral training and test sets for ANN containing peaks at the chemical shift ranges resembling long echo time proton NMR spectra from human brain were simulated. The performance of the ANN constructed was compared with an established lineshape fitting (LF) analysis using both simulated and experimental spectral data as inputs. The correspondence between the ANN and LF analyses showed correlation coefficients of order of 0.915-0.997 for spectra with large variations in both signal-to-noise and peak areas. Water suppressed1H NMR spectra from 24 healthy subjects were collected and choline-containing compounds (Cho), total creatine (Cr), and N-acetyl aspartate (NAA) were quantified with both methods. The ANN quantified these spectra with an accuracy similar to LF analysis (correlation coefficients of 0.915-0.951). These results show that LF and ANN are equally good quantifiers; however, the ANN analyses are more easily automated than LF analyses.

  17. A rat brain MRI template with digital stereotaxic atlas of fine anatomical delineations in paxinos space and its automated application in voxel-wise analysis.

    PubMed

    Nie, Binbin; Chen, Kewei; Zhao, Shujun; Liu, Junhua; Gu, Xiaochun; Yao, Qunli; Hui, Jiaojie; Zhang, Zhijun; Teng, Gaojun; Zhao, Chunjie; Shan, Baoci

    2013-06-01

    This study constructs a rat brain T2 -weighted magnetic resonance imaging template including olfactory bulb and a compatible digital atlas. The atlas contains 624 carefully delineated brain structures based on the newest (2005) edition of rat brain atlas by Paxinos and Watson. An automated procedure, as an SPM toolbox, was introduced for spatially normalizing individual rat brains, conducting statistical analysis and visually localizing the results in the Atlas coordinate space. The brain template/atlas and the procedure were evaluated using functional images between rats with the right side middle cerebral artery occlusion (MCAO) and normal controls. The result shows that the brain region with significant signal decline in the MCAO rats was consistent with the occlusion position. PMID:22287270

  18. 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

  19. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  20. Rasterization and Voxelization of - and Three-Dimensional Space Partitionings

    NASA Astrophysics Data System (ADS)

    Gorte, Ben; Zlatanov, Sisi

    2016-06-01

    The paper presents a very straightforward and effective algorithm to convert a space partitioning, made up of polyhedral objects, into a 3D block of voxels, which is fully occupied, i.e. in which every voxel has a value. In addition to walls, floors, etc. there are 'air' voxels, which in turn may be distinguished as indoor and outdoor air. The method is a 3D extension of a 2D polygon-to-raster conversion algorithm. The input of the algorithm is a set of non-overlapping, closed polyhedra, which can be nested or touching. The air volume is not necessarily represented explicitly as a polyhedron (it can be treated as 'background', leading to the 'default' voxel value). The approach consists of two stages, the first being object (boundary) based, the second scan-line based. In addition to planar faces, other primitives, such as ellipsoids, can be accommodated in the first stage without affecting the second.

  1. Fine-Resolution Voxel S Values for Constructing Absorbed Dose Distributions at Variable Voxel Size

    PubMed Central

    Dieudonné, Arnaud; Hobbs, Robert F.; Bolch, Wesley E.; Sgouros, George; Gardin, Isabelle

    2010-01-01

    This article presents a revised voxel S values (VSVs) approach for dosimetry in targeted radiotherapy, allowing dose calculation for any voxel size and shape of a given SPECT or PET dataset. This approach represents an update to the methodology presented in MIRD pamphlet no. 17. Methods VSVs were generated in soft tissue with a fine spatial sampling using the Monte Carlo (MC) code MCNPX for particle emissions of 9 radionuclides: 18F, 90Y, 99mTc, 111In, 123I, 131I, 177Lu, 186Re, and 201Tl. A specific resampling algorithm was developed to compute VSVs for desired voxel dimensions. The dose calculation was performed by convolution via a fast Hartley transform. The fine VSVs were calculated for cubic voxels of 0.5 mm for electrons and 1.0 mm for photons. Validation studies were done for 90Y and 131I VSV sets by comparing the revised VSV approach to direct MC simulations. The first comparison included 20 spheres with different voxel sizes (3.8–7.7 mm) and radii (4–64 voxels) and the second comparison a hepatic tumor with cubic voxels of 3.8 mm. MC simulations were done with MCNPX for both. The third comparison was performed on 2 clinical patients with the 3D-RD (3-Dimensional Radiobiologic Dosimetry) software using the EGSnrc (Electron Gamma Shower National Research Council Canada)-based MC implementation, assuming a homogeneous tissue-density distribution. Results For the sphere model study, the mean relative difference in the average absorbed dose was 0.20% ± 0.41% for 90Y and −0.36% ± 0.51% for 131I (n = 20). For the hepatic tumor, the difference in the average absorbed dose to tumor was 0.33% for 90Y and −0.61% for 131I and the difference in average absorbed dose to the liver was 0.25% for 90Y and −1.35% for 131I. The comparison with the 3D-RD software showed an average voxel-to-voxel dose ratio between 0.991 and 0.996. The calculation time was below 10 s with the VSV approach and 50 and 15 h with 3D-RD for the 2 clinical patients. Conclusion This new

  2. Magmatic Systems in 3-D

    NASA Astrophysics Data System (ADS)

    Kent, G. M.; Harding, A. J.; Babcock, J. M.; Orcutt, J. A.; Bazin, S.; Singh, S.; Detrick, R. S.; Canales, J. P.; Carbotte, S. M.; Diebold, J.

    2002-12-01

    Multichannel seismic (MCS) images of crustal magma chambers are ideal targets for advanced visualization techniques. In the mid-ocean ridge environment, reflections originating at the melt-lens are well separated from other reflection boundaries, such as the seafloor, layer 2A and Moho, which enables the effective use of transparency filters. 3-D visualization of seismic reflectivity falls into two broad categories: volume and surface rendering. Volumetric-based visualization is an extremely powerful approach for the rapid exploration of very dense 3-D datasets. These 3-D datasets are divided into volume elements or voxels, which are individually color coded depending on the assigned datum value; the user can define an opacity filter to reject plotting certain voxels. This transparency allows the user to peer into the data volume, enabling an easy identification of patterns or relationships that might have geologic merit. Multiple image volumes can be co-registered to look at correlations between two different data types (e.g., amplitude variation with offsets studies), in a manner analogous to draping attributes onto a surface. In contrast, surface visualization of seismic reflectivity usually involves producing "fence" diagrams of 2-D seismic profiles that are complemented with seafloor topography, along with point class data, draped lines and vectors (e.g. fault scarps, earthquake locations and plate-motions). The overlying seafloor can be made partially transparent or see-through, enabling 3-D correlations between seafloor structure and seismic reflectivity. Exploration of 3-D datasets requires additional thought when constructing and manipulating these complex objects. As numbers of visual objects grow in a particular scene, there is a tendency to mask overlapping objects; this clutter can be managed through the effective use of total or partial transparency (i.e., alpha-channel). In this way, the co-variation between different datasets can be investigated

  3. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  4. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  5. Registration of 3D spectral OCT volumes using 3D SIFT feature point matching

    NASA Astrophysics Data System (ADS)

    Niemeijer, Meindert; Garvin, Mona K.; Lee, Kyungmoo; van Ginneken, Bram; Abràmoff, Michael D.; Sonka, Milan

    2009-02-01

    The recent introduction of next generation spectral OCT scanners has enabled routine acquisition of high resolution, 3D cross-sectional volumetric images of the retina. 3D OCT is used in the detection and management of serious eye diseases such as glaucoma and age-related macular degeneration. For follow-up studies, image registration is a vital tool to enable more precise, quantitative comparison of disease states. This work presents a registration method based on a recently introduced extension of the 2D Scale-Invariant Feature Transform (SIFT) framework1 to 3D.2 The SIFT feature extractor locates minima and maxima in the difference of Gaussian scale space to find salient feature points. It then uses histograms of the local gradient directions around each found extremum in 3D to characterize them in a 4096 element feature vector. Matching points are found by comparing the distance between feature vectors. We apply this method to the rigid registration of optic nerve head- (ONH) and macula-centered 3D OCT scans of the same patient that have only limited overlap. Three OCT data set pairs with known deformation were used for quantitative assessment of the method's robustness and accuracy when deformations of rotation and scaling were considered. Three-dimensional registration accuracy of 2.0+/-3.3 voxels was observed. The accuracy was assessed as average voxel distance error in N=1572 matched locations. The registration method was applied to 12 3D OCT scans (200 x 200 x 1024 voxels) of 6 normal eyes imaged in vivo to demonstrate the clinical utility and robustness of the method in a real-world environment.

  6. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  7. Voxel-Based Texture Analysis of the Brain

    PubMed Central

    Maani, Rouzbeh; Yang, Yee Hong; Kalra, Sanjay

    2015-01-01

    This paper presents a novel voxel-based method for texture analysis of brain images. Texture analysis is a powerful quantitative approach for analyzing voxel intensities and their interrelationships, but has been thus far limited to analyzing regions of interest. The proposed method provides a 3D statistical map comparing texture features on a voxel-by-voxel basis. The validity of the method was examined on artificially generated effects as well as on real MRI data in Alzheimer's Disease (AD). The artificially generated effects included hyperintense and hypointense signals added to T1-weighted brain MRIs from 30 healthy subjects. The AD dataset included 30 patients with AD and 30 age/sex matched healthy control subjects. The proposed method detected artificial effects with high accuracy and revealed statistically significant differences between the AD and control groups. This paper extends the usage of texture analysis beyond the current region of interest analysis to voxel-by-voxel 3D statistical mapping and provides a hypothesis-free analysis tool to study cerebral pathology in neurological diseases. PMID:25756621

  8. Voxel-based texture analysis of the brain.

    PubMed

    Maani, Rouzbeh; Yang, Yee Hong; Kalra, Sanjay

    2015-01-01

    This paper presents a novel voxel-based method for texture analysis of brain images. Texture analysis is a powerful quantitative approach for analyzing voxel intensities and their interrelationships, but has been thus far limited to analyzing regions of interest. The proposed method provides a 3D statistical map comparing texture features on a voxel-by-voxel basis. The validity of the method was examined on artificially generated effects as well as on real MRI data in Alzheimer's Disease (AD). The artificially generated effects included hyperintense and hypointense signals added to T1-weighted brain MRIs from 30 healthy subjects. The AD dataset included 30 patients with AD and 30 age/sex matched healthy control subjects. The proposed method detected artificial effects with high accuracy and revealed statistically significant differences between the AD and control groups. This paper extends the usage of texture analysis beyond the current region of interest analysis to voxel-by-voxel 3D statistical mapping and provides a hypothesis-free analysis tool to study cerebral pathology in neurological diseases. PMID:25756621

  9. Voxel-based morphometry and epilepsy.

    PubMed

    Yasuda, Clarissa Lin; Betting, Luiz Eduardo; Cendes, Fernando

    2010-06-01

    Voxel-based morphometry is an automated technique for MRI analyses, developed to study differences in brain morphology and frequently used to study patients with diverse disorders. In epilepsy, it has been used to investigate areas with reduction or increase of gray and white matter, in different syndromes (i.e., temporal lobe epilepsy, focal cortical dysplasia and generalized epilepsies). In temporal lobe epilepsy, voxel-based morphometry showed gray/white matter atrophy extending beyond the atrophic hippocampus. These widespread abnormalities have been associated with seizure frequency, epilepsy duration, incidence of precipitating factors, cognitive dysfunction and surgical outcome. In generalized epilepsies, gray matter abnormalities were identified mainly in the thalamus and frontal cortex, reinforcing the role of the thalamocortical network in the mechanisms of generalized seizures. PMID:20518612

  10. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

    TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.

  11. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  12. Diaphragm dome surface segmentation in CT data sets: a 3D active appearance model approach

    NASA Astrophysics Data System (ADS)

    Beichel, Reinhard; Gotschuli, Georg; Sorantin, Erich; Leberl, Franz W.; Sonka, Milan

    2002-05-01

    Knowledge about the location of the diaphragm dome surface, which separates the lungs and the heart from the abdominal cavity, is of vital importance for applications like automated segmentation of adjacent organs (e.g., liver) or functional analysis of the respiratory cycle. We present a new 3D Active Appearance Model (AAM) approach to segmentation of the top layer of the diaphragm dome. The 3D AAM consists of three parts: a 2D closed curve (reference curve), an elevation image and texture layers. The first two parts combined represent 3D shape information and the third part image intensity of the diaphragm dome and the surrounding layers. Differences in height between dome voxels and a reference plane are stored in the elevation image. The reference curve is generated by a parallel projection of the diaphragm dome outline in the axial direction. Landmark point placement is only done on the (2D) reference curve, which can be seen as the bounding curve of the elevation image. Matching is based on a gradient-descent optimization process and uses image intensity appearance around the actual dome shape. Results achieved in 60 computer generated phantom data sets show a high degree of accuracy (positioning error -0.07+/-1.29 mm). Validation using real CT data sets yielded a positioning error of -0.16+/-2.95 mm. Additional training and testing on in-vivo CT image data is ongoing.

  13. Automatic generation of 3D coronary artery centerlines using rotational X-ray angiography.

    PubMed

    Jandt, Uwe; Schäfer, Dirk; Grass, Michael; Rasche, Volker

    2009-12-01

    A fully automated 3D centerline modeling algorithm for coronary arteries is presented. It utilizes a subset of standard rotational X-ray angiography projections that correspond to one single cardiac phase. The algorithm is based on a fast marching approach, which selects voxels in 3D space that belong to the vascular structure and introduces a hierarchical order. The local 3D propagation speed is determined by a combination of corresponding 2D projections filtered with a vessel enhancing kernel. The best achievable accuracy of the algorithm is evaluated on simulated projections of a virtual heart phantom, showing that it is capable of extracting coronary centerlines with an accuracy that is mainly limited by projection and volume quantization (0.25 mm). The algorithm is reasonably insensitive to residual motion, which means that it is able to cope with inconsistencies within the projection data set caused by limited gating accuracy and respiration. Its accuracy on clinical data is evaluated based on expert ratings of extracted models of 17 consecutive clinical cases (10 LCA, 7 RCA). A success rate of 93.5% (i.e. with no or slight deviations) is achieved compared to 58.8% success rate of semi-automatically extracted models. PMID:19713148

  14. A complete system for 3D reconstruction of roots for phenotypic analysis.

    PubMed

    Kumar, Pankaj; Cai, Jinhai; Miklavcic, Stanley J

    2015-01-01

    Here we present a complete system for 3D reconstruction of roots grown in a transparent gel medium or washed and suspended in water. The system is capable of being fully automated as it is self calibrating. The system starts with detection of root tips in root images from an image sequence generated by a turntable motion. Root tips are detected using the statistics of Zernike moments on image patches centred on high curvature points on root boundary and Bayes classification rule. The detected root tips are tracked in the image sequence using a multi-target tracking algorithm. Conics are fitted to the root tip trajectories using a novel ellipse fitting algorithm which weighs the data points by its eccentricity. The conics projected from the circular trajectory have a complex conjugate intersection which are image of the circular points. Circular points constraint the image of the absolute conics which are directly related to the internal parameters of the camera. The pose of the camera is computed from the image of the rotation axis and the horizon. The silhouettes of the roots and camera parameters are used to reconstruction the 3D voxel model of the roots. We show the results of real 3D reconstruction of roots which are detailed and realistic for phenotypic analysis. PMID:25381112

  15. New portable FELIX 3D display

    NASA Astrophysics Data System (ADS)

    Langhans, Knut; Bezecny, Daniel; Homann, Dennis; Bahr, Detlef; Vogt, Carsten; Blohm, Christian; Scharschmidt, Karl-Heinz

    1998-04-01

    An improved generation of our 'FELIX 3D Display' is presented. This system is compact, light, modular and easy to transport. The created volumetric images consist of many voxels, which are generated in a half-sphere display volume. In that way a spatial object can be displayed occupying a physical space with height, width and depth. The new FELIX generation uses a screen rotating with 20 revolutions per second. This target screen is mounted by an easy to change mechanism making it possible to use appropriate screens for the specific purpose of the display. An acousto-optic deflection unit with an integrated small diode pumped laser draws the images on the spinning screen. Images can consist of up to 10,000 voxels at a refresh rate of 20 Hz. Currently two different hardware systems are investigated. The first one is based on a standard PCMCIA digital/analog converter card as an interface and is controlled by a notebook. The developed software is provided with a graphical user interface enabling several animation features. The second, new prototype is designed to display images created by standard CAD applications. It includes the development of a new high speed hardware interface suitable for state-of-the- art fast and high resolution scanning devices, which require high data rates. A true 3D volume display as described will complement the broad range of 3D visualization tools, such as volume rendering packages, stereoscopic and virtual reality techniques, which have become widely available in recent years. Potential applications for the FELIX 3D display include imaging in the field so fair traffic control, medical imaging, computer aided design, science as well as entertainment.

  16. Plane Localization in 3-D Fetal Neurosonography for Longitudinal Analysis of the Developing Brain.

    PubMed

    Yaqub, Mohammad; Rueda, Sylvia; Kopuri, Anil; Melo, Pedro; Papageorghiou, A T; Sullivan, Peter B; McCormick, Kenneth; Noble, J Alison

    2016-07-01

    The parasagittal (PS) plane is a 2-D diagnostic plane used routinely in cranial ultrasonography of the neonatal brain. This paper develops a novel approach to find the PS plane in a 3-D fetal ultrasound scan to allow image-based biomarkers to be tracked from prebirth through the first weeks of postbirth life. We propose an accurate plane-finding solution based on regression forests (RF). The method initially localizes the fetal brain and its midline automatically. The midline on several axial slices is used to detect the midsagittal plane, which is used as a constraint in the proposed RF framework to detect the PS plane. The proposed learning algorithm guides the RF learning method in a novel way by: 1) using informative voxels and voxel informative strength as a weighting within the training stage objective function, and 2) introducing regularization of the RF by proposing a geometrical feature within the training stage. Results on clinical data indicate that the new automated method is more reproducible than manual plane finding obtained by two clinicians. PMID:26011873

  17. Multidimensional morphometric 3D MRI analyses for detecting brain abnormalities in children: impact of control population.

    PubMed

    Wilke, Marko; Rose, Douglas F; Holland, Scott K; Leach, James L

    2014-07-01

    Automated morphometric approaches are used to detect epileptogenic structural abnormalities in 3D MR images in adults, using the variance of a control population to obtain z-score maps in an individual patient. Due to the substantial changes the developing human brain undergoes, performing such analyses in children is challenging. This study investigated six features derived from high-resolution T1 datasets in four groups: normal children (1.5T or 3T data), normal clinical scans (3T data), and patients with structural brain lesions (3T data), with each n = 10. Normative control data were obtained from the NIH study on normal brain development (n = 401). We show that control group size substantially influences the captured variance, directly impacting the patient's z-scores. Interestingly, matching on gender does not seem to be beneficial, which was unexpected. Using data obtained at higher field scanners produces slightly different base rates of suprathreshold voxels, as does using clinically derived normal studies, suggesting a subtle but systematic effect of both factors. Two approaches for controlling suprathreshold voxels in a multidimensional approach (combining features and requiring a minimum cluster size) were shown to be substantial and effective in reducing this number. Finally, specific strengths and limitations of such an approach could be demonstrated in individual cases. PMID:25050423

  18. Uncertainty in 3D gel dosimetry

    NASA Astrophysics Data System (ADS)

    De Deene, Yves; Jirasek, Andrew

    2015-01-01

    Three-dimensional (3D) gel dosimetry has a unique role to play in safeguarding conformal radiotherapy treatments as the technique can cover the full treatment chain and provides the radiation oncologist with the integrated dose distribution in 3D. It can also be applied to benchmark new treatment strategies such as image guided and tracking radiotherapy techniques. A major obstacle that has hindered the wider dissemination of gel dosimetry in radiotherapy centres is a lack of confidence in the reliability of the measured dose distribution. Uncertainties in 3D dosimeters are attributed to both dosimeter properties and scanning performance. In polymer gel dosimetry with MRI readout, discrepancies in dose response of large polymer gel dosimeters versus small calibration phantoms have been reported which can lead to significant inaccuracies in the dose maps. The sources of error in polymer gel dosimetry with MRI readout are well understood and it has been demonstrated that with a carefully designed scanning protocol, the overall uncertainty in absolute dose that can currently be obtained falls within 5% on an individual voxel basis, for a minimum voxel size of 5 mm3. However, several research groups have chosen to use polymer gel dosimetry in a relative manner by normalizing the dose distribution towards an internal reference dose within the gel dosimeter phantom. 3D dosimetry with optical scanning has also been mostly applied in a relative way, although in principle absolute calibration is possible. As the optical absorption in 3D dosimeters is less dependent on temperature it can be expected that the achievable accuracy is higher with optical CT. The precision in optical scanning of 3D dosimeters depends to a large extend on the performance of the detector. 3D dosimetry with X-ray CT readout is a low contrast imaging modality for polymer gel dosimetry. Sources of error in x-ray CT polymer gel dosimetry (XCT) are currently under investigation and include inherent

  19. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  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. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-01

    We study the conformal bootstrap for a 4-point function of fermions < ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T . We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N . We also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  2. Voxel Based Representation of Full-Waveform Airborne Laser Scanner Data for Forestry Applications

    NASA Astrophysics Data System (ADS)

    Stelling, N.; Richter, K.

    2016-06-01

    The advantages of using airborne full-waveform laser scanner data in forest applications, e.g. for the description of the vertical vegetation structure or accurate biomass estimation, have been emphasized in many publications. To exploit the full potential offered by airborne full-waveform laser scanning data, the development of voxel based methods for data analysis is essential. In contrast to existing approaches based on the extraction of discrete 3D points by a Gaussian decomposition, it is very promising to derive the voxel attributes from the digitised waveform directly. For this purpose, the waveform data have to be transferred into a 3D voxel representation. This requires a series of radiometric and geometric transformations of the raw full-waveform laser scanner data. Thus, the paper deals with the geometric aspects and describes a processing chain from the raw waveform data to an attenuationcorrected volumetric forest stand reconstruction. The integration of attenuation-corrected waveform data into the voxel space is realised with an efficient parametric voxel traversal method operating on an octree data structure. The voxel attributes are derived from the amplitudes of the attenuation-corrected waveforms. Additionally, a new 3D filtering approach is presented to eliminate non-object voxel. Applying these methods to real full-waveform laser scanning data, a voxel based representation of a spruce was generated combining three flight strips from different viewing directions.

  3. 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.

  4. Digital breast tomosynthesis reconstruction with an adaptive voxel grid

    NASA Astrophysics Data System (ADS)

    Claus, Bernhard; Chan, Heang-Ping

    2014-03-01

    In digital breast tomosynthesis (DBT) volume datasets are typically reconstructed with an anisotropic voxel size, where the in-plane voxel size usually reflects the detector pixel size (e.g., 0.1 mm), and the slice separation is generally between 0.5-1.0 mm. Increasing the tomographic angle is expected to give better 3D image quality; however, the slice spacing in the reconstruction should be reduced, otherwise one may risk losing fine-scale image detail (e.g., small microcalcifications). An alternative strategy consists of reconstructing on an adaptive voxel grid, where the voxel height at each location is adapted based on the backprojected data at this location, with the goal to improve image quality for microcalcifications. In this paper we present an approach for generating such an adaptive voxel grid. This approach is based on an initial reconstruction step that is performed at a finer slice-spacing combined with a selection of an "optimal" height for each voxel. This initial step is followed by a (potentially iterative) reconstruction acting now on the adaptive grid only.

  5. Voxelated liquid crystal elastomers

    NASA Astrophysics Data System (ADS)

    Ware, Taylor H.; McConney, Michael E.; Wie, Jeong Jae; Tondiglia, Vincent P.; White, Timothy J.

    2015-02-01

    Dynamic control of shape can bring multifunctionality to devices. Soft materials capable of programmable shape change require localized control of the magnitude and directionality of a mechanical response. We report the preparation of soft, ordered materials referred to as liquid crystal elastomers. The direction of molecular order, known as the director, is written within local volume elements (voxels) as small as 0.0005 cubic millimeters. Locally, the director controls the inherent mechanical response (55% strain) within the material. In monoliths with spatially patterned director, thermal or chemical stimuli transform flat sheets into three-dimensional objects through controlled bending and stretching. The programmable mechanical response of these materials could yield monolithic multifunctional devices or serve as reconfigurable substrates for flexible devices in aerospace, medicine, or consumer goods.

  6. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

    In order to circumvent the fact that only one observer can view the image from a stereoscopic microscope, an attachment was devised for displaying the 3D microscopic image on a large LCD monitor for viewing by multiple observers in real time. The principle of operation, design, fabrication, and performance are presented, along with tolerance measurements relating to the properties of the cellophane half-wave plate used in the design.

  7. Fabricating 3D figurines with personalized faces.

    PubMed

    Tena, J Rafael; Mahler, Moshe; Beeler, Thabo; Grosse, Max; Hengchin Yeh; Matthews, Iain

    2013-01-01

    We present a semi-automated system for fabricating figurines with faces that are personalised to the individual likeness of the customer. The efficacy of the system has been demonstrated by commercial deployments at Walt Disney World Resort and Star Wars Celebration VI in Orlando Florida. Although the system is semi automated, human intervention is limited to a few simple tasks to maintain the high throughput and consistent quality required for commercial application. In contrast to existing systems that fabricate custom heads that are assembled to pre-fabricated plastic bodies, our system seamlessly integrates 3D facial data with a predefined figurine body into a unique and continuous object that is fabricated as a single piece. The combination of state-of-the-art 3D capture, modelling, and printing that are the core of our system provide the flexibility to fabricate figurines whose complexity is only limited by the creativity of the designer. PMID:24808129

  8. Volumetric 3D display using a DLP projection engine

    NASA Astrophysics Data System (ADS)

    Geng, Jason

    2012-03-01

    In this article, we describe a volumetric 3D display system based on the high speed DLPTM (Digital Light Processing) projection engine. Existing two-dimensional (2D) flat screen displays often lead to ambiguity and confusion in high-dimensional data/graphics presentation due to lack of true depth cues. Even with the help of powerful 3D rendering software, three-dimensional (3D) objects displayed on a 2D flat screen may still fail to provide spatial relationship or depth information correctly and effectively. Essentially, 2D displays have to rely upon capability of human brain to piece together a 3D representation from 2D images. Despite the impressive mental capability of human visual system, its visual perception is not reliable if certain depth cues are missing. In contrast, volumetric 3D display technologies to be discussed in this article are capable of displaying 3D volumetric images in true 3D space. Each "voxel" on a 3D image (analogous to a pixel in 2D image) locates physically at the spatial position where it is supposed to be, and emits light from that position toward omni-directions to form a real 3D image in 3D space. Such a volumetric 3D display provides both physiological depth cues and psychological depth cues to human visual system to truthfully perceive 3D objects. It yields a realistic spatial representation of 3D objects and simplifies our understanding to the complexity of 3D objects and spatial relationship among them.

  9. Laser printing of 3D metallic interconnects

    NASA Astrophysics Data System (ADS)

    Beniam, Iyoel; Mathews, Scott A.; Charipar, Nicholas A.; Auyeung, Raymond C. Y.; Piqué, Alberto

    2016-04-01

    The use of laser-induced forward transfer (LIFT) techniques for the printing of functional materials has been demonstrated for numerous applications. The printing gives rise to patterns, which can be used to fabricate planar interconnects. More recently, various groups have demonstrated electrical interconnects from laser-printed 3D structures. The laser printing of these interconnects takes place through aggregation of voxels of either molten metal or of pastes containing dispersed metallic particles. However, the generated 3D structures do not posses the same metallic conductivity as a bulk metal interconnect of the same cross-section and length as those formed by wire bonding or tab welding. An alternative is to laser transfer entire 3D structures using a technique known as lase-and-place. Lase-and-place is a LIFT process whereby whole components and parts can be transferred from a donor substrate onto a desired location with one single laser pulse. This paper will describe the use of LIFT to laser print freestanding, solid metal foils or beams precisely over the contact pads of discrete devices to interconnect them into fully functional circuits. Furthermore, this paper will also show how the same laser can be used to bend or fold the bulk metal foils prior to transfer, thus forming compliant 3D structures able to provide strain relief for the circuits under flexing or during motion from thermal mismatch. These interconnect "ridges" can span wide gaps (on the order of a millimeter) and accommodate height differences of tens of microns between adjacent devices. Examples of these laser printed 3D metallic bridges and their role in the development of next generation electronics by additive manufacturing will be presented.

  10. A combination of atlas-based and voxel-wise approaches to analyze metabolic changes in autoradiographic data from Alzheimer's mice.

    PubMed

    Lebenberg, J; Hérard, A-S; Dubois, A; Dhenain, M; Hantraye, P; Delzescaux, T

    2011-08-15

    Murine models are commonly used in neuroscience research to improve our knowledge of disease processes and to test drug effects. To accurately study brain glucose metabolism in these animals, ex vivo autoradiography remains the gold standard. The analysis of 3D-reconstructed autoradiographic volumes using a voxel-wise approach allows clusters of voxels representing metabolic differences between groups to be revealed. However, the spatial localization of these clusters requires careful visual identification by a neuroanatomist, a time-consuming task that is often subject to misinterpretation. Moreover, the large number of voxels to be computed in autoradiographic rodent images leads to many false positives. Here, we proposed an original automated indexation of the results of a voxel-wise approach using an MRI-based 3D digital atlas, followed by the restriction of the statistical analysis using atlas-based segmentation, thus taking advantage of the specific and complementary strengths of these two approaches. In a preliminary study of transgenic Alzheimer's mice (APP/PS1), and control littermates (PS1), we were able to achieve prompt and direct anatomical indexation of metabolic changes detected between the two groups, revealing both hypo- and hypermetabolism in the brain of APP/PS1 mice. Furthermore, statistical results were refined using atlas-based segmentation: most interesting results were obtained for the hippocampus. We thus confirmed and extended our previous results by identifying the brain structures affected in this pathological model and demonstrating modified glucose uptake in structures like the olfactory bulb. Our combined approach thus paves the way for a complete and accurate examination of functional data from cerebral structures involved in models of neurodegenerative diseases. PMID:21571077

  11. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  12. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

    Kostrzewski, Andrew A.; Aye, Tin M.; Kim, Dai Hyun; Esterkin, Vladimir; Savant, Gajendra D.

    1998-09-01

    Physical Optics Corporation has developed an advanced 3-D virtual reality system for use with simulation tools for training technical and military personnel. This system avoids such drawbacks of other virtual reality (VR) systems as eye fatigue, headaches, and alignment for each viewer, all of which are due to the need to wear special VR goggles. The new system is based on direct viewing of an interactive environment. This innovative holographic multiplexed screen technology makes it unnecessary for the viewer to wear special goggles.

  13. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  14. 3D Printed Multimaterial Microfluidic Valve

    PubMed Central

    Patrick, William G.; Sharma, Sunanda; Kong, David S.; Oxman, Neri

    2016-01-01

    We present a novel 3D printed multimaterial microfluidic proportional valve. The microfluidic valve is a fundamental primitive that enables the development of programmable, automated devices for controlling fluids in a precise manner. We discuss valve characterization results, as well as exploratory design variations in channel width, membrane thickness, and membrane stiffness. Compared to previous single material 3D printed valves that are stiff, these printed valves constrain fluidic deformation spatially, through combinations of stiff and flexible materials, to enable intricate geometries in an actuated, functionally graded device. Research presented marks a shift towards 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics. PMID:27525809

  15. 3D Printed Multimaterial Microfluidic Valve.

    PubMed

    Keating, Steven J; Gariboldi, Maria Isabella; Patrick, William G; Sharma, Sunanda; Kong, David S; Oxman, Neri

    2016-01-01

    We present a novel 3D printed multimaterial microfluidic proportional valve. The microfluidic valve is a fundamental primitive that enables the development of programmable, automated devices for controlling fluids in a precise manner. We discuss valve characterization results, as well as exploratory design variations in channel width, membrane thickness, and membrane stiffness. Compared to previous single material 3D printed valves that are stiff, these printed valves constrain fluidic deformation spatially, through combinations of stiff and flexible materials, to enable intricate geometries in an actuated, functionally graded device. Research presented marks a shift towards 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics. PMID:27525809

  16. Laser-induced forward transfer (LIFT) of congruent voxels

    NASA Astrophysics Data System (ADS)

    Piqué, Alberto; Kim, Heungsoo; Auyeung, Raymond C. Y.; Beniam, Iyoel; Breckenfeld, Eric

    2016-06-01

    Laser-induced forward transfer (LIFT) of functional materials offers unique advantages and capabilities for the rapid prototyping of electronic, optical and sensor elements. The use of LIFT for printing high viscosity metallic nano-inks and nano-pastes can be optimized for the transfer of voxels congruent with the shape of the laser pulse, forming thin film-like structures non-lithographically. These processes are capable of printing patterns with excellent lateral resolution and thickness uniformity typically found in 3-dimensional stacked assemblies, MEMS-like structures and free-standing interconnects. However, in order to achieve congruent voxel transfer with LIFT, the particle size and viscosity of the ink or paste suspensions must be adjusted to minimize variations due to wetting and drying effects. When LIFT is carried out with high-viscosity nano-suspensions, the printed voxel size and shape become controllable parameters, allowing the printing of thin-film like structures whose shape is determined by the spatial distribution of the laser pulse. The result is a new level of parallelization beyond current serial direct-write processes whereby the geometry of each printed voxel can be optimized according to the pattern design. This work shows how LIFT of congruent voxels can be applied to the fabrication of 2D and 3D microstructures by adjusting the viscosity of the nano-suspension and laser transfer parameters.

  17. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The Mars Exploration Rover Spirit took this 3-D navigation camera mosaic of the crater called 'Bonneville' after driving approximately 13 meters (42.7 feet) to get a better vantage point. Spirit's current position is close enough to the edge to see the interior of the crater, but high enough and far enough back to get a view of all of the walls. Because scientists and rover controllers are so pleased with this location, they will stay here for at least two more martian days, or sols, to take high resolution panoramic camera images of 'Bonneville' in its entirety. Just above the far crater rim, on the left side, is the rover's heatshield, which is visible as a tiny reflective speck.

  18. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  19. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

    From our previous definition of the indices of polarimetric purity for 3D light beams [J.J. Gil, J.M. Correas, P.A. Melero and C. Ferreira, Monogr. Semin. Mat. G. de Galdeano 31, 161 (2004)], an analysis of their geometric and physical interpretation is presented. It is found that, in agreement with previous results, the first parameter is a measure of the degree of polarization, whereas the second parameter (called the degree of directionality) is a measure of the mean angular aperture of the direction of propagation of the corresponding light beam. This pair of invariant, non-dimensional, indices of polarimetric purity contains complete information about the polarimetric purity of a light beam. The overall degree of polarimetric purity is obtained as a weighted quadratic average of the degree of polarization and the degree of directionality.

  20. Template-Free 3D Microprinting of Metals Using a Force-Controlled Nanopipette for Layer-by-Layer Electrodeposition.

    PubMed

    Hirt, Luca; Ihle, Stephan; Pan, Zhijian; Dorwling-Carter, Livie; Reiser, Alain; Wheeler, Jeffrey M; Spolenak, Ralph; Vörös, János; Zambelli, Tomaso

    2016-03-23

    A novel 3D printing method for voxel-by-voxel metal printing is presented. Hollow atomic force microscopy (AFM) cantilevers are used to locally supply metal ions in an electrochemical cell, enabling a localized electroplating reaction. By exploiting the deflection feedback of these probes, electrochemical 3D metal printing is, for the first time, demonstrated in a layer-by-layer fashion, enabling the fabrication of arbitrary-shaped geometries. PMID:26783090

  1. A visual LISP program for voxelizing AutoCAD solid models

    NASA Astrophysics Data System (ADS)

    Marschallinger, Robert; Jandrisevits, Carmen; Zobl, Fritz

    2015-01-01

    AutoCAD solid models are increasingly recognized in geological and geotechnical 3D modeling. In order to bridge the currently existing gap between AutoCAD solid models and the grid modeling realm, a Visual LISP program is presented that converts AutoCAD solid models into voxel arrays. Acad2Vox voxelizer works on a 3D-model that is made up of arbitrary non-overlapping 3D-solids. After definition of the target voxel array geometry, 3D-solids are scanned at grid positions and properties are streamed to an ASCII output file. Acad2Vox has a novel voxelization strategy that combines a hierarchical reduction of sampling dimensionality with an innovative use of AutoCAD-specific methods for a fast and memory-saving operation. Acad2Vox provides georeferenced, voxelized analogs of 3D design data that can act as regions-of-interest in later geostatistical modeling and simulation. The Supplement includes sample geological solid models with instructions for practical work with Acad2Vox.

  2. Miniaturized 3D microscope imaging system

    NASA Astrophysics Data System (ADS)

    Lan, Yung-Sung; Chang, Chir-Weei; Sung, Hsin-Yueh; Wang, Yen-Chang; Chang, Cheng-Yi

    2015-05-01

    We designed and assembled a portable 3-D miniature microscopic image system with the size of 35x35x105 mm3 . By integrating a microlens array (MLA) into the optical train of a handheld microscope, the biological specimen's image will be captured for ease of use in a single shot. With the light field raw data and program, the focal plane can be changed digitally and the 3-D image can be reconstructed after the image was taken. To localize an object in a 3-D volume, an automated data analysis algorithm to precisely distinguish profundity position is needed. The ability to create focal stacks from a single image allows moving or specimens to be recorded. Applying light field microscope algorithm to these focal stacks, a set of cross sections will be produced, which can be visualized using 3-D rendering. Furthermore, we have developed a series of design rules in order to enhance the pixel using efficiency and reduce the crosstalk between each microlens for obtain good image quality. In this paper, we demonstrate a handheld light field microscope (HLFM) to distinguish two different color fluorescence particles separated by a cover glass in a 600um range, show its focal stacks, and 3-D position.

  3. 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

  4. 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.

  5. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  6. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  7. Interactive 3D medical data cutting using closed curve with arbitrary shape.

    PubMed

    Ning, Hai; Yang, Rongqian; Ma, Amin; Wu, Xiaoming

    2015-03-01

    Interactive 3D cutting is widely used as a flexible manual segmentation tool to extract medical data on regions of interest. A novel method for clipping 3D medical data is proposed to reveal the interior of volumetric data. The 3D cutting method retains or clips away selected voxels projected inside an arbitrary-shaped closed curve which is clipping geometry constructed by interactive tool to make cutting operation more flexible. Transformation between the world and screen coordinate frames is studied to project voxels of medical data onto the screen frame and avoid computing intersection of clipping geometry and volumetric data in 3D space. For facilitating the decision on whether the voxels should be retained, voxels through coordinate transformation are all projected onto a binary mask image on screen frame which the closed curve is also projected onto to conveniently obtain the voxels of intersection. The paper pays special attention to optimization algorithm of cutting process. The optimization algorithm that mixes octree with quad-tree decomposition is introduced to reduce computation complexity, save computation time, and match real time. The paper presents results obtained from raw and segmented medical volume datasets and the process time of cutting operation. PMID:25456145

  8. Iterative Reconstruction of Volumetric Particle Distribution for 3D Velocimetry

    NASA Astrophysics Data System (ADS)

    Wieneke, Bernhard; Neal, Douglas

    2011-11-01

    A number of different volumetric flow measurement techniques exist for following the motion of illuminated particles. For experiments that have lower seeding densities, 3D-PTV uses recorded images from typically 3-4 cameras and then tracks the individual particles in space and time. This technique is effective in flows that have lower seeding densities. For flows that have a higher seeding density, tomographic PIV uses a tomographic reconstruction algorithm (e.g. MART) to reconstruct voxel intensities of the recorded volume followed by the cross-correlation of subvolumes to provide the instantaneous 3D vector fields on a regular grid. A new hybrid algorithm is presented which iteratively reconstructs the 3D-particle distribution directly using particles with certain imaging properties instead of voxels as base functions. It is shown with synthetic data that this method is capable of reconstructing densely seeded flows up to 0.05 particles per pixel (ppp) with the same or higher accuracy than 3D-PTV and tomographic PIV. Finally, this new method is validated using experimental data on a turbulent jet.

  9. Rapid three-dimensional quantification of voxel-wise collagen fiber orientation

    PubMed Central

    Liu, Zhiyi; Quinn, Kyle P.; Speroni, Lucia; Arendt, Lisa; Kuperwasser, Charlotte; Sonnenschein, Carlos; Soto, Ana M.; Georgakoudi, Irene

    2015-01-01

    Defining fiber orientation at each voxel within a 3D biomedical image stack is potentially useful for a variety of applications, including cancer, wound healing and tissue regeneration. Current methods are typically computationally intensive or inaccurate. Herein, we present a 3D weighted orientation vector summation algorithm, which is a generalization of a previously reported 2D vector summation technique aimed at quantifying collagen fiber orientations simultaneously at each voxel of an image stack. As a result, voxel-wise fiber orientation information with 4° to 5° accuracy can be determined, and the computational time required to analyze a typical stack with the size of 512x512x100 voxels is less than 5 min. Thus, this technique enables the practical extraction of voxel-specific orientation data for characterizing structural anisotropy in 3D specimens. As examples, we use this approach to characterize the fiber organization in an excised mouse mammary gland and a 3D breast tissue model. PMID:26203362

  10. Automatic Reconstruction of Spacecraft 3D Shape from Imagery

    NASA Astrophysics Data System (ADS)

    Poelman, C.; Radtke, R.; Voorhees, H.

    We describe a system that computes the three-dimensional (3D) shape of a spacecraft from a sequence of uncalibrated, two-dimensional images. While the mathematics of multi-view geometry is well understood, building a system that accurately recovers 3D shape from real imagery remains an art. A novel aspect of our approach is the combination of algorithms from computer vision, photogrammetry, and computer graphics. We demonstrate our system by computing spacecraft models from imagery taken by the Air Force Research Laboratory's XSS-10 satellite and DARPA's Orbital Express satellite. Using feature tie points (each identified in two or more images), we compute the relative motion of each frame and the 3D location of each feature using iterative linear factorization followed by non-linear bundle adjustment. The "point cloud" that results from this traditional shape-from-motion approach is typically too sparse to generate a detailed 3D model. Therefore, we use the computed motion solution as input to a volumetric silhouette-carving algorithm, which constructs a solid 3D model based on viewpoint consistency with the image frames. The resulting voxel model is then converted to a facet-based surface representation and is texture-mapped, yielding realistic images from arbitrary viewpoints. We also illustrate other applications of the algorithm, including 3D mensuration and stereoscopic 3D movie generation.