A Low-Cost Approach to Automatically Obtain Accurate 3D Models of Woody Crops

PubMed Central

Andújar, Dionisio; Sanchez-Sardana, Francisco L.; Cantuña, Karla

2017-01-01

Crop monitoring is an essential practice within the field of precision agriculture since it is based on observing, measuring and properly responding to inter- and intra-field variability. In particular, “on ground crop inspection” potentially allows early detection of certain crop problems or precision treatment to be carried out simultaneously with pest detection. “On ground monitoring” is also of great interest for woody crops. This paper explores the development of a low-cost crop monitoring system that can automatically create accurate 3D models (clouds of coloured points) of woody crop rows. The system consists of a mobile platform that allows the easy acquisition of information in the field at an average speed of 3 km/h. The platform, among others, integrates an RGB-D sensor that provides RGB information as well as an array with the distances to the objects closest to the sensor. The RGB-D information plus the geographical positions of relevant points, such as the starting and the ending points of the row, allow the generation of a 3D reconstruction of a woody crop row in which all the points of the cloud have a geographical location as well as the RGB colour values. The proposed approach for the automatic 3D reconstruction is not limited by the size of the sampled space and includes a method for the removal of the drift that appears in the reconstruction of large crop rows. PMID:29295536

SU-E-T-362: Automatic Catheter Reconstruction of Flap Applicators in HDR Surface Brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buzurovic, I; Devlin, P; Hansen, J

2014-06-01

Purpose: Catheter reconstruction is crucial for the accurate delivery of radiation dose in HDR brachytherapy. The process becomes complicated and time-consuming for large superficial clinical targets with a complex topology. A novel method for the automatic catheter reconstruction of flap applicators is proposed in this study. Methods: We have developed a program package capable of image manipulation, using C++class libraries of The-Visualization-Toolkit(VTK) software system. The workflow for automatic catheter reconstruction is: a)an anchor point is placed in 3D or in the axial view of the first slice at the tip of the first, last and middle points for the curvedmore » surface; b)similar points are placed on the last slice of the image set; c)the surface detection algorithm automatically registers the points to the images and applies the surface reconstruction filter; d)then a structured grid surface is generated through the center of the treatment catheters placed at a distance of 5mm from the patient's skin. As a result, a mesh-style plane is generated with the reconstructed catheters placed 10mm apart. To demonstrate automatic catheter reconstruction, we used CT images of patients diagnosed with cutaneous T-cell-lymphoma and imaged with Freiburg-Flap-Applicators (Nucletron™-Elekta, Netherlands). The coordinates for each catheter were generated and compared to the control points selected during the manual reconstruction for 16catheters and 368control point Results: The variation of the catheter tip positions between the automatically and manually reconstructed catheters was 0.17mm(SD=0.23mm). The position difference between the manually selected catheter control points and the corresponding points obtained automatically was 0.17mm in the x-direction (SD=0.23mm), 0.13mm in the y-direction (SD=0.22mm), and 0.14mm in the z-direction (SD=0.24mm). Conclusion: This study shows the feasibility of the automatic catheter reconstruction of flap applicators with a high level of positioning accuracy. Implementation of this technique has potential to decrease the planning time and may improve overall quality in superficial brachytherapy.« less

Reverse engineering physical models employing a sensor integration between 3D stereo detection and contact digitization

NASA Astrophysics Data System (ADS)

Chen, Liang-Chia; Lin, Grier C. I.

1997-12-01

A vision-drive automatic digitization process for free-form surface reconstruction has been developed, with a coordinate measurement machine (CMM) equipped with a touch-triggered probe and a CCD camera, in reverse engineering physical models. The process integrates 3D stereo detection, data filtering, Delaunay triangulation, adaptive surface digitization into a single process of surface reconstruction. By using this innovative approach, surface reconstruction can be implemented automatically and accurately. Least-squares B- spline surface models with the controlled accuracy of digitization can be generated for further application in product design and manufacturing processes. One industrial application indicates that this approach is feasible, and the processing time required in reverse engineering process can be significantly reduced up to more than 85%.

Automatic 3D power line reconstruction of multi-angular imaging power line inspection system

NASA Astrophysics Data System (ADS)

Zhang, Wuming; Yan, Guangjian; Wang, Ning; Li, Qiaozhi; Zhao, Wei

2007-06-01

We develop a multi-angular imaging power line inspection system. Its main objective is to monitor the relative distance between high voltage power line and around objects, and alert if the warning threshold is exceeded. Our multi-angular imaging power line inspection system generates DSM of the power line passage, which comprises ground surface and ground objects, for example trees and houses, etc. For the purpose of revealing the dangerous regions, where ground objects are too close to the power line, 3D power line information should be extracted at the same time. In order to improve the automation level of extraction, reduce labour costs and human errors, an automatic 3D power line reconstruction method is proposed and implemented. It can be achieved by using epipolar constraint and prior knowledge of pole tower's height. After that, the proper 3D power line information can be obtained by space intersection using found homologous projections. The flight experiment result shows that the proposed method can successfully reconstruct 3D power line, and the measurement accuracy of the relative distance satisfies the user requirement of 0.5m.

3D Reconstruction of the Retinal Arterial Tree Using Subject-Specific Fundus Images

NASA Astrophysics Data System (ADS)

Liu, D.; Wood, N. B.; Xu, X. Y.; Witt, N.; Hughes, A. D.; Samcg, Thom

Systemic diseases, such as hypertension and diabetes, are associated with changes in the retinal microvasculature. Although a number of studies have been performed on the quantitative assessment of the geometrical patterns of the retinal vasculature, previous work has been confined to 2 dimensional (2D) analyses. In this paper, we present an approach to obtain a 3D reconstruction of the retinal arteries from a pair of 2D retinal images acquired in vivo. A simple essential matrix based self-calibration approach was employed for the "fundus camera-eye" system. Vessel segmentation was performed using a semi-automatic approach and correspondence between points from different images was calculated. The results of 3D reconstruction show the centreline of retinal vessels and their 3D curvature clearly. Three-dimensional reconstruction of the retinal vessels is feasible and may be useful in future studies of the retinal vasculature in disease.

NASAL-Geom, a free upper respiratory tract 3D model reconstruction software

NASA Astrophysics Data System (ADS)

Cercos-Pita, J. L.; Cal, I. R.; Duque, D.; de Moreta, G. Sanjuán

2018-02-01

The tool NASAL-Geom, a free upper respiratory tract 3D model reconstruction software, is here described. As a free software, researchers and professionals are welcome to obtain, analyze, improve and redistribute it, potentially increasing the rate of development, and reducing at the same time ethical conflicts regarding medical applications which cannot be analyzed. Additionally, the tool has been optimized for the specific task of reading upper respiratory tract Computerized Tomography scans, and producing 3D geometries. The reconstruction process is divided into three stages: preprocessing (including Metal Artifact Reduction, noise removal, and feature enhancement), segmentation (where the nasal cavity is identified), and 3D geometry reconstruction. The tool has been automatized (i.e. no human intervention is required) a critical feature to avoid bias in the reconstructed geometries. The applied methodology is discussed, as well as the program robustness and precision.

Magnetically guided left ventricular lead implantation based on a virtual three-dimensional reconstructed image of the coronary sinus

PubMed Central

Rivero-Ayerza, Máximo; Jessurun, Emil; Ramcharitar, Steve; van Belle, Yves; Serruys, Patrick W.; Jordaens, Luc

2008-01-01

Aims Left ventricular (LV) lead implantation is feasible using remote magnetic navigation of a guidewire (Stereotaxis, St Louis, MO, USA). A novel software that performs a three-dimensional (3D) reconstruction of vessels based on two or more angiographic views has been developed recently (CardiOp-B system™, Paeion Inc., Haifa, Israel). The objective of this paper is to evaluate: (i) the performance of the 3D reconstruction software which reproduce the anatomy of the coronary sinus (CS) and (ii) the efficacy of remotely navigating a magnetic guidewire within the CS based on this reconstruction. Methods and results In patients undergoing cardiac resynchronization therapy implantation, a 3D reconstruction of the CS was performed using the CardiOp-B™ system. Accuracy of the reconstruction was evaluated by comparing with the CS angiogram. This reconstruction was imported into the Stereotaxis system. On the basis of the reconstruction, magnetic vectors were automatically selected to navigate within the CS and manually adjusted if required. Feasibility of deploying the guidewire and LV lead into the selected side branch (SB), fluoroscopy time (FT) required for cannulation of the target SB, and total FT were also evaluated. Sixteen patients were included. In one case, the software could not reconstruct the CS. The quality of the reconstruction was graded as good in 13 and poor in 2. In 10 cases, manual adjustments to the traced edges of the CS were required to perform the 3D reconstruction, and in 5, no adjustments were required. In 13 patients, the target SB was engaged on the basis of the automatically selected vectors. In two cases, manual modification of the vector was required. Mean total FT was 23 ± 14 min and the FT required to cannulate the target SB was 1.7 ± 1.3 min. Conclusion A 3D reconstruction of the CS can be accurately performed using two angiographic views. This reconstruction allows precise magnetic navigation of a guidewire within the CS. PMID:18587136

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

PubMed

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

2007-03-01

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

A semi-automatic method for positioning a femoral bone reconstruction for strict view generation.

PubMed

Milano, Federico; Ritacco, Lucas; Gomez, Adrian; Gonzalez Bernaldo de Quiros, Fernan; Risk, Marcelo

2010-01-01

In this paper we present a semi-automatic method for femoral bone positioning after 3D image reconstruction from Computed Tomography images. This serves as grounding for the definition of strict axial, longitudinal and anterior-posterior views, overcoming the problem of patient positioning biases in 2D femoral bone measuring methods. After the bone reconstruction is aligned to a standard reference frame, new tomographic slices can be generated, on which unbiased measures may be taken. This could allow not only accurate inter-patient comparisons but also intra-patient comparisons, i.e., comparisons of images of the same patient taken at different times. This method could enable medical doctors to diagnose and follow up several bone deformities more easily.

Moving metal artifact reduction in cone-beam CT scans with implanted cylindrical gold markers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toftegaard, Jakob, E-mail: jaktofte@rm.dk; Fledelius, Walther; Worm, Esben S.

2014-12-15

Purpose: Implanted gold markers for image-guided radiotherapy lead to streaking artifacts in cone-beam CT (CBCT) scans. Several methods for metal artifact reduction (MAR) have been published, but they all fail in scans with large motion. Here the authors propose and investigate a method for automatic moving metal artifact reduction (MMAR) in CBCT scans with cylindrical gold markers. Methods: The MMAR CBCT reconstruction method has six steps. (1) Automatic segmentation of the cylindrical markers in the CBCT projections. (2) Removal of each marker in the projections by replacing the pixels within a masked area with interpolated values. (3) Reconstruction of amore » marker-free CBCT volume from the manipulated CBCT projections. (4) Reconstruction of a standard CBCT volume with metal artifacts from the original CBCT projections. (5) Estimation of the three-dimensional (3D) trajectory during CBCT acquisition for each marker based on the segmentation in Step 1, and identification of the smallest ellipsoidal volume that encompasses 95% of the visited 3D positions. (6) Generation of the final MMAR CBCT reconstruction from the marker-free CBCT volume of Step 3 by replacing the voxels in the 95% ellipsoid with the corresponding voxels of the standard CBCT volume of Step 4. The MMAR reconstruction was performed retrospectively using a half-fan CBCT scan for 29 consecutive stereotactic body radiation therapy patients with 2–3 gold markers implanted in the liver. The metal artifacts of the MMAR reconstructions were scored and compared with a standard MAR reconstruction by counting the streaks and by calculating the standard deviation of the Hounsfield units in a region around each marker. Results: The markers were found with the same autosegmentation settings in 27 CBCT scans, while two scans needed slightly changed settings to find all markers automatically in Step 1 of the MMAR method. MMAR resulted in 15 scans with no streaking artifacts, 11 scans with 1–4 streaks, and 3 scans with severe streaking artifacts. The corresponding numbers for MAR were 8 (no streaks), 1 (1–4 streaks), and 20 (severe streaking artifacts). The MMAR method was superior to MAR in scans with more than 8 mm 3D marker motion and comparable to MAR for scans with less than 8 mm motion. In addition, the MMAR method was tested on a 4D CBCT reconstruction for which it worked equally well as for the 3D case. The markers in the 4D case had very low motion blur. Conclusions: An automatic method for MMAR in CBCT scans was proposed and shown to effectively remove almost all streaking artifacts in a large set of clinical CBCT scans with implanted gold markers in the liver. Residual streaking artifacts observed in three CBCT scans may be removed with better marker segmentation.« less

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

Weakly supervised automatic segmentation and 3D modeling of the knee joint from MR images

NASA Astrophysics Data System (ADS)

Amami, Amal; Ben Azouz, Zouhour

2013-12-01

Automatic segmentation and 3D modeling of the knee joint from MR images, is a challenging task. Most of the existing techniques require the tedious manual segmentation of a training set of MRIs. We present an approach that necessitates the manual segmentation of one MR image. It is based on a volumetric active appearance model. First, a dense tetrahedral mesh is automatically created on a reference MR image that is arbitrary selected. Second, a pairwise non-rigid registration between each MRI from a training set and the reference MRI is computed. The non-rigid registration is based on a piece-wise affine deformation using the created tetrahedral mesh. The minimum description length is then used to bring all the MR images into a correspondence. An average image and tetrahedral mesh, as well as a set of main modes of variations, are generated using the established correspondence. Any manual segmentation of the average MRI can be mapped to other MR images using the AAM. The proposed approach has the advantage of simultaneously generating 3D reconstructions of the surface as well as a 3D solid model of the knee joint. The generated surfaces and tetrahedral meshes present the interesting property of fulfilling a correspondence between different MR images. This paper shows preliminary results of the proposed approach. It demonstrates the automatic segmentation and 3D reconstruction of a knee joint obtained by mapping a manual segmentation of a reference image.

Optimizing the 3D-reconstruction technique for serial block-face scanning electron microscopy.

PubMed

Wernitznig, Stefan; Sele, Mariella; Urschler, Martin; Zankel, Armin; Pölt, Peter; Rind, F Claire; Leitinger, Gerd

2016-05-01

Elucidating the anatomy of neuronal circuits and localizing the synaptic connections between neurons, can give us important insights in how the neuronal circuits work. We are using serial block-face scanning electron microscopy (SBEM) to investigate the anatomy of a collision detection circuit including the Lobula Giant Movement Detector (LGMD) neuron in the locust, Locusta migratoria. For this, thousands of serial electron micrographs are produced that allow us to trace the neuronal branching pattern. The reconstruction of neurons was previously done manually by drawing cell outlines of each cell in each image separately. This approach was very time consuming and troublesome. To make the process more efficient a new interactive software was developed. It uses the contrast between the neuron under investigation and its surrounding for semi-automatic segmentation. For segmentation the user sets starting regions manually and the algorithm automatically selects a volume within the neuron until the edges corresponding to the neuronal outline are reached. Internally the algorithm optimizes a 3D active contour segmentation model formulated as a cost function taking the SEM image edges into account. This reduced the reconstruction time, while staying close to the manual reference segmentation result. Our algorithm is easy to use for a fast segmentation process, unlike previous methods it does not require image training nor an extended computing capacity. Our semi-automatic segmentation algorithm led to a dramatic reduction in processing time for the 3D-reconstruction of identified neurons. Copyright © 2016 Elsevier B.V. All rights reserved.

A Modular Hierarchical Approach to 3D Electron Microscopy Image Segmentation

PubMed Central

Liu, Ting; Jones, Cory; Seyedhosseini, Mojtaba; Tasdizen, Tolga

2014-01-01

The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy. PMID:24491638

Imaging Techniques for Dense 3D reconstruction of Swimming Aquatic Life using Multi-view Stereo

NASA Astrophysics Data System (ADS)

Daily, David; Kiser, Jillian; McQueen, Sarah

2016-11-01

Understanding the movement characteristics of how various species of fish swim is an important step to uncovering how they propel themselves through the water. Previous methods have focused on profile capture methods or sparse 3D manual feature point tracking. This research uses an array of 30 cameras to automatically track hundreds of points on a fish as they swim in 3D using multi-view stereo. Blacktip sharks, sting rays, puffer fish, turtles and more were imaged in collaboration with the National Aquarium in Baltimore, Maryland using the multi-view stereo technique. The processes for data collection, camera synchronization, feature point extraction, 3D reconstruction, 3D alignment, biological considerations, and lessons learned will be presented. Preliminary results of the 3D reconstructions will be shown and future research into mathematically characterizing various bio-locomotive maneuvers will be discussed.

Three-dimensional (3-D) model utilization for fracture reconstruction in oral and maxillofacial surgery: A case report

NASA Astrophysics Data System (ADS)

Damayanti, Ista; Lilies, Latief, Benny S.

2017-02-01

Three-dimensional (3-D) printing has been identified as an innovative manufacturing technology of functional parts. The 3-D model was produced based on CT-Scan using Osyrix software, where automatic segmentation was performed and convert into STL format. This STL format was then ready to be produced physically, layer-by-layer to create 3-D model.

Dynamic Human Body Modeling Using a Single RGB Camera.

PubMed

Zhu, Haiyu; Yu, Yao; Zhou, Yu; Du, Sidan

2016-03-18

In this paper, we present a novel automatic pipeline to build personalized parametric models of dynamic people using a single RGB camera. Compared to previous approaches that use monocular RGB images, our system can model a 3D human body automatically and incrementally, taking advantage of human motion. Based on coarse 2D and 3D poses estimated from image sequences, we first perform a kinematic classification of human body parts to refine the poses and obtain reconstructed body parts. Next, a personalized parametric human model is generated by driving a general template to fit the body parts and calculating the non-rigid deformation. Experimental results show that our shape estimation method achieves comparable accuracy with reconstructed models using depth cameras, yet requires neither user interaction nor any dedicated devices, leading to the feasibility of using this method on widely available smart phones.

Dynamic Human Body Modeling Using a Single RGB Camera

PubMed Central

Zhu, Haiyu; Yu, Yao; Zhou, Yu; Du, Sidan

2016-01-01

In this paper, we present a novel automatic pipeline to build personalized parametric models of dynamic people using a single RGB camera. Compared to previous approaches that use monocular RGB images, our system can model a 3D human body automatically and incrementally, taking advantage of human motion. Based on coarse 2D and 3D poses estimated from image sequences, we first perform a kinematic classification of human body parts to refine the poses and obtain reconstructed body parts. Next, a personalized parametric human model is generated by driving a general template to fit the body parts and calculating the non-rigid deformation. Experimental results show that our shape estimation method achieves comparable accuracy with reconstructed models using depth cameras, yet requires neither user interaction nor any dedicated devices, leading to the feasibility of using this method on widely available smart phones. PMID:26999159

Automatic 3D Building Detection and Modeling from Airborne LiDAR Point Clouds

ERIC Educational Resources Information Center

Sun, Shaohui

2013-01-01

Urban reconstruction, with an emphasis on man-made structure modeling, is an active research area with broad impact on several potential applications. Urban reconstruction combines photogrammetry, remote sensing, computer vision, and computer graphics. Even though there is a huge volume of work that has been done, many problems still remain…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmon, S; Jeraj, R; Galavis, P

Purpose: Sensitivity of PET-derived texture features to reconstruction methods has been reported for features extracted from axial planes; however, studies often utilize three dimensional techniques. This work aims to quantify the impact of multi-plane (3D) vs. single-plane (2D) feature extraction on radiomics-based analysis, including sensitivity to reconstruction parameters and potential loss of spatial information. Methods: Twenty-three patients with solid tumors underwent [{sup 18}F]FDG PET/CT scans under identical protocols. PET data were reconstructed using five sets of reconstruction parameters. Tumors were segmented using an automatic, in-house algorithm robust to reconstruction variations. 50 texture features were extracted using two Methods: 2D patchesmore » along axial planes and 3D patches. For each method, sensitivity of features to reconstruction parameters was calculated as percent difference relative to the average value across reconstructions. Correlations between feature values were compared when using 2D and 3D extraction. Results: 21/50 features showed significantly different sensitivity to reconstruction parameters when extracted in 2D vs 3D (wilcoxon α<0.05), assessed by overall range of variation, Rangevar(%). Eleven showed greater sensitivity to reconstruction in 2D extraction, primarily first-order and co-occurrence features (average Rangevar increase 83%). The remaining ten showed higher variation in 3D extraction (average Range{sub var}increase 27%), mainly co-occurence and greylevel run-length features. Correlation of feature value extracted in 2D and feature value extracted in 3D was poor (R<0.5) in 12/50 features, including eight co-occurrence features. Feature-to-feature correlations in 2D were marginally higher than 3D, ∣R∣>0.8 in 16% and 13% of all feature combinations, respectively. Larger sensitivity to reconstruction parameters were seen for inter-feature correlation in 2D(σ=6%) than 3D (σ<1%) extraction. Conclusion: Sensitivity and correlation of various texture features were shown to significantly differ between 2D and 3D extraction. Additionally, inter-feature correlations were more sensitive to reconstruction variation using single-plane extraction. This work highlights a need for standardized feature extraction/selection techniques in radiomics.« less

Three-Dimensional Assessment of Temporomandibular Joint Using MRI-CBCT Image Registration

PubMed Central

Lagravere, Manuel; Boulanger, Pierre; Jaremko, Jacob L.; Major, Paul W.

2017-01-01

Purpose To introduce a new approach to reconstruct a 3D model of the TMJ using magnetic resonance imaging (MRI) and cone-beam computed tomography (CBCT) registered images, and to evaluate the intra-examiner reproducibility values of reconstructing the 3D models of the TMJ. Methods MRI and CBCT images of five patients (10 TMJs) were obtained. Multiple MRIs and CBCT images were registered using a mutual information based algorithm. The articular disc, condylar head and glenoid fossa were segmented at two different occasions, at least one-week apart, by one investigator, and 3D models were reconstructed. Differences between the segmentation at two occasions were automatically measured using the surface contours (Average Perpendicular Distance) and the volume overlap (Dice Similarity Index) of the 3D models. Descriptive analysis of the changes at 2 occasions, including means and standard deviation (SD) were reported to describe the intra-examiner reproducibility. Results The automatic segmentation of the condyle revealed maximum distance change of 1.9±0.93 mm, similarity index of 98% and root mean squared distance of 0.1±0.08 mm, and the glenoid fossa revealed maximum distance change of 2±0.52 mm, similarity index of 96% and root mean squared distance of 0.2±0.04 mm. The manual segmentation of the articular disc revealed maximum distance change of 3.6±0.32 mm, similarity index of 80% and root mean squared distance of 0.3±0.1 mm. Conclusion The MRI-CBCT registration provides a reliable tool to reconstruct 3D models of the TMJ’s soft and hard tissues, allows quantification of the articular disc morphology and position changes with associated differences of the condylar head and glenoid fossa, and facilitates measuring tissue changes over time. PMID:28095486

Three-Dimensional Assessment of Temporomandibular Joint Using MRI-CBCT Image Registration.

PubMed

Al-Saleh, Mohammed A Q; Punithakumar, Kumaradevan; Lagravere, Manuel; Boulanger, Pierre; Jaremko, Jacob L; Major, Paul W

2017-01-01

To introduce a new approach to reconstruct a 3D model of the TMJ using magnetic resonance imaging (MRI) and cone-beam computed tomography (CBCT) registered images, and to evaluate the intra-examiner reproducibility values of reconstructing the 3D models of the TMJ. MRI and CBCT images of five patients (10 TMJs) were obtained. Multiple MRIs and CBCT images were registered using a mutual information based algorithm. The articular disc, condylar head and glenoid fossa were segmented at two different occasions, at least one-week apart, by one investigator, and 3D models were reconstructed. Differences between the segmentation at two occasions were automatically measured using the surface contours (Average Perpendicular Distance) and the volume overlap (Dice Similarity Index) of the 3D models. Descriptive analysis of the changes at 2 occasions, including means and standard deviation (SD) were reported to describe the intra-examiner reproducibility. The automatic segmentation of the condyle revealed maximum distance change of 1.9±0.93 mm, similarity index of 98% and root mean squared distance of 0.1±0.08 mm, and the glenoid fossa revealed maximum distance change of 2±0.52 mm, similarity index of 96% and root mean squared distance of 0.2±0.04 mm. The manual segmentation of the articular disc revealed maximum distance change of 3.6±0.32 mm, similarity index of 80% and root mean squared distance of 0.3±0.1 mm. The MRI-CBCT registration provides a reliable tool to reconstruct 3D models of the TMJ's soft and hard tissues, allows quantification of the articular disc morphology and position changes with associated differences of the condylar head and glenoid fossa, and facilitates measuring tissue changes over time.

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data

PubMed Central

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-01-01

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models. PMID:28335486

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data.

PubMed

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-03-19

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models.

A GUI visualization system for airborne lidar image data to reconstruct 3D city model

NASA Astrophysics Data System (ADS)

Kawata, Yoshiyuki; Koizumi, Kohei

2015-10-01

A visualization toolbox system with graphical user interfaces (GUIs) was developed for the analysis of LiDAR point cloud data, as a compound object oriented widget application in IDL (Interractive Data Language). The main features in our system include file input and output abilities, data conversion capability from ascii formatted LiDAR point cloud data to LiDAR image data whose pixel value corresponds the altitude measured by LiDAR, visualization of 2D/3D images in various processing steps and automatic reconstruction ability of 3D city model. The performance and advantages of our graphical user interface (GUI) visualization system for LiDAR data are demonstrated.

3D Lunar Terrain Reconstruction from Apollo Images

NASA Technical Reports Server (NTRS)

Broxton, Michael J.; Nefian, Ara V.; Moratto, Zachary; Kim, Taemin; Lundy, Michael; Segal, Alkeksandr V.

2009-01-01

Generating accurate three dimensional planetary models is becoming increasingly important as NASA plans manned missions to return to the Moon in the next decade. This paper describes a 3D surface reconstruction system called the Ames Stereo Pipeline that is designed to produce such models automatically by processing orbital stereo imagery. We discuss two important core aspects of this system: (1) refinement of satellite station positions and pose estimates through least squares bundle adjustment; and (2) a stochastic plane fitting algorithm that generalizes the Lucas-Kanade method for optimal matching between stereo pair images.. These techniques allow us to automatically produce seamless, highly accurate digital elevation models from multiple stereo image pairs while significantly reducing the influence of image noise. Our technique is demonstrated on a set of 71 high resolution scanned images from the Apollo 15 mission

Evaluation of two 3D virtual computer reconstructions for comparison of cleft lip and palate to normal fetal microanatomy.

PubMed

Landes, Constantin A; Weichert, Frank; Geis, Philipp; Helga, Fritsch; Wagner, Mathias

2006-03-01

Cleft lip and palate reconstructive surgery requires thorough knowledge of normal and pathological labial, palatal, and velopharyngeal anatomy. This study compared two software algorithms and their 3D virtual anatomical reconstruction because exact 3D micromorphological reconstruction may improve learning, reveal spatial relationships, and provide data for mathematical modeling. Transverse and frontal serial sections of the midface of 18 fetal specimens (11th to 32nd gestational week) were used for two manual segmentation approaches. The first manual segmentation approach used bitmap images and either Windows-based or Mac-based SURFdriver commercial software that allowed manual contour matching, surface generation with average slice thickness, 3D triangulation, and real-time interactive virtual 3D reconstruction viewing. The second manual segmentation approach used tagged image format and platform-independent prototypical SeViSe software developed by one of the authors (F.W.). Distended or compressed structures were dynamically transformed. Registration was automatic but allowed manual correction, such as individual section thickness, surface generation, and interactive virtual 3D real-time viewing. SURFdriver permitted intuitive segmentation, easy manual offset correction, and the reconstruction showed complex spatial relationships in real time. However, frequent software crashes and erroneous landmarks appearing "out of the blue," requiring manual correction, were tedious. Individual section thickness, defined smoothing, and unlimited structure number could not be integrated. The reconstruction remained underdimensioned and not sufficiently accurate for this study's reconstruction problem. SeViSe permitted unlimited structure number, late addition of extra sections, and quantified smoothing and individual slice thickness; however, SeViSe required more elaborate work-up compared to SURFdriver, yet detailed and exact 3D reconstructions were created.

Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.

PubMed

Profico, Antonio; Schlager, Stefan; Valoriani, Veronica; Buzi, Costantino; Melchionna, Marina; Veneziano, Alessio; Raia, Pasquale; Moggi-Cecchi, Jacopo; Manzi, Giorgio

2018-04-21

We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities. We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available. The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus. Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists. © 2018 Wiley Periodicals, Inc.

An Automatic Registration Algorithm for 3D Maxillofacial Model

NASA Astrophysics Data System (ADS)

Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

2016-09-01

3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

ROOFN3D: Deep Learning Training Data for 3d Building Reconstruction

NASA Astrophysics Data System (ADS)

Wichmann, A.; Agoub, A.; Kada, M.

2018-05-01

Machine learning methods have gained in importance through the latest development of artificial intelligence and computer hardware. Particularly approaches based on deep learning have shown that they are able to provide state-of-the-art results for various tasks. However, the direct application of deep learning methods to improve the results of 3D building reconstruction is often not possible due, for example, to the lack of suitable training data. To address this issue, we present RoofN3D which provides a new 3D point cloud training dataset that can be used to train machine learning models for different tasks in the context of 3D building reconstruction. It can be used, among others, to train semantic segmentation networks or to learn the structure of buildings and the geometric model construction. Further details about RoofN3D and the developed data preparation framework, which enables the automatic derivation of training data, are described in this paper. Furthermore, we provide an overview of other available 3D point cloud training data and approaches from current literature in which solutions for the application of deep learning to unstructured and not gridded 3D point cloud data are presented.

Photogrammetric 3d Building Reconstruction from Thermal Images

NASA Astrophysics Data System (ADS)

Maset, E.; Fusiello, A.; Crosilla, F.; Toldo, R.; Zorzetto, D.

2017-08-01

This paper addresses the problem of 3D building reconstruction from thermal infrared (TIR) images. We show that a commercial Computer Vision software can be used to automatically orient sequences of TIR images taken from an Unmanned Aerial Vehicle (UAV) and to generate 3D point clouds, without requiring any GNSS/INS data about position and attitude of the images nor camera calibration parameters. Moreover, we propose a procedure based on Iterative Closest Point (ICP) algorithm to create a model that combines high resolution and geometric accuracy of RGB images with the thermal information deriving from TIR images. The process can be carried out entirely by the aforesaid software in a simple and efficient way.

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

PubMed Central

Kaltdorf, Kristin Verena; Schulze, Katja; Helmprobst, Frederik; Kollmannsberger, Philip; Stigloher, Christian

2017-01-01

Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial. PMID:28056033

SEM-microphotogrammetry, a new take on an old method for generating high-resolution 3D models from SEM images.

PubMed

Ball, A D; Job, P A; Walker, A E L

2017-08-01

The method we present here uses a scanning electron microscope programmed via macros to automatically capture dozens of images at suitable angles to generate accurate, detailed three-dimensional (3D) surface models with micron-scale resolution. We demonstrate that it is possible to use these Scanning Electron Microscope (SEM) images in conjunction with commercially available software originally developed for photogrammetry reconstructions from Digital Single Lens Reflex (DSLR) cameras and to reconstruct 3D models of the specimen. These 3D models can then be exported as polygon meshes and eventually 3D printed. This technique offers the potential to obtain data suitable to reconstruct very tiny features (e.g. diatoms, butterfly scales and mineral fabrics) at nanometre resolution. Ultimately, we foresee this as being a useful tool for better understanding spatial relationships at very high resolution. However, our motivation is also to use it to produce 3D models to be used in public outreach events and exhibitions, especially for the blind or partially sighted. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Left ventricular endocardial surface detection based on real-time 3D echocardiographic data

NASA Technical Reports Server (NTRS)

Corsi, C.; Borsari, M.; Consegnati, F.; Sarti, A.; Lamberti, C.; Travaglini, A.; Shiota, T.; Thomas, J. D.

2001-01-01

OBJECTIVE: A new computerized semi-automatic method for left ventricular (LV) chamber segmentation is presented. METHODS: The LV is imaged by real-time three-dimensional echocardiography (RT3DE). The surface detection model, based on level set techniques, is applied to RT3DE data for image analysis. The modified level set partial differential equation we use is solved by applying numerical methods for conservation laws. The initial conditions are manually established on some slices of the entire volume. The solution obtained for each slice is a contour line corresponding with the boundary between LV cavity and LV endocardium. RESULTS: The mathematical model has been applied to sequences of frames of human hearts (volume range: 34-109 ml) imaged by 2D and reconstructed off-line and RT3DE data. Volume estimation obtained by this new semi-automatic method shows an excellent correlation with those obtained by manual tracing (r = 0.992). Dynamic change of LV volume during the cardiac cycle is also obtained. CONCLUSION: The volume estimation method is accurate; edge based segmentation, image completion and volume reconstruction can be accomplished. The visualization technique also allows to navigate into the reconstructed volume and to display any section of the volume.

A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes

PubMed Central

2011-01-01

Background A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes. Methods We present a low-cost and flexible ultrasound imaging system that integrates several image processing components to allow for 3D reconstructions from limited numbers of 2D image planes and multiple acoustic views. Our approach is based on a 3D freehand ultrasound system that allows users to control the 2D acquisition imaging using conventional 2D probes. For reliable performance, we develop new methods for image segmentation and robust multi-view registration. We first present a new hybrid geometric level-set approach that provides reliable segmentation performance with relatively simple initializations and minimum edge leakage. Optimization of the segmentation model parameters and its effect on performance is carefully discussed. Second, using the segmented images, a new coarse to fine automatic multi-view registration method is introduced. The approach uses a 3D Hotelling transform to initialize an optimization search. Then, the fine scale feature-based registration is performed using a robust, non-linear least squares algorithm. The robustness of the multi-view registration system allows for accurate 3D reconstructions from sparse 2D image planes. Results Volume measurements from multi-view 3D reconstructions are found to be consistently and significantly more accurate than measurements from single view reconstructions. The volume error of multi-view reconstruction is measured to be less than 5% of the true volume. We show that volume reconstruction accuracy is a function of the total number of 2D image planes and the number of views for calibrated phantom. In clinical in-vivo cardiac experiments, we show that volume estimates of the left ventricle from multi-view reconstructions are found to be in better agreement with clinical measures than measures from single view reconstructions. Conclusions Multi-view 3D reconstruction from sparse 2D freehand B-mode images leads to more accurate volume quantification compared to single view systems. The flexibility and low-cost of the proposed system allow for fine control of the image acquisition planes for optimal 3D reconstructions from multiple views. PMID:21251284

A 3D freehand ultrasound system for multi-view reconstructions from sparse 2D scanning planes.

PubMed

Yu, Honggang; Pattichis, Marios S; Agurto, Carla; Beth Goens, M

2011-01-20

A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes. We present a low-cost and flexible ultrasound imaging system that integrates several image processing components to allow for 3D reconstructions from limited numbers of 2D image planes and multiple acoustic views. Our approach is based on a 3D freehand ultrasound system that allows users to control the 2D acquisition imaging using conventional 2D probes.For reliable performance, we develop new methods for image segmentation and robust multi-view registration. We first present a new hybrid geometric level-set approach that provides reliable segmentation performance with relatively simple initializations and minimum edge leakage. Optimization of the segmentation model parameters and its effect on performance is carefully discussed. Second, using the segmented images, a new coarse to fine automatic multi-view registration method is introduced. The approach uses a 3D Hotelling transform to initialize an optimization search. Then, the fine scale feature-based registration is performed using a robust, non-linear least squares algorithm. The robustness of the multi-view registration system allows for accurate 3D reconstructions from sparse 2D image planes. Volume measurements from multi-view 3D reconstructions are found to be consistently and significantly more accurate than measurements from single view reconstructions. The volume error of multi-view reconstruction is measured to be less than 5% of the true volume. We show that volume reconstruction accuracy is a function of the total number of 2D image planes and the number of views for calibrated phantom. In clinical in-vivo cardiac experiments, we show that volume estimates of the left ventricle from multi-view reconstructions are found to be in better agreement with clinical measures than measures from single view reconstructions. Multi-view 3D reconstruction from sparse 2D freehand B-mode images leads to more accurate volume quantification compared to single view systems. The flexibility and low-cost of the proposed system allow for fine control of the image acquisition planes for optimal 3D reconstructions from multiple views.

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.

D Reconstruction of AN Underwater Archaelogical Site: Comparison Between Low Cost Cameras

NASA Astrophysics Data System (ADS)

Capra, A.; Dubbini, M.; Bertacchini, E.; Castagnetti, C.; Mancini, F.

2015-04-01

The 3D reconstruction with a metric content of a submerged area, where objects and structures of archaeological interest are found, could play an important role in the research and study activities and even in the digitization of the cultural heritage. The reconstruction of 3D object, of interest for archaeologists, constitutes a starting point in the classification and description of object in digital format and for successive fruition by user after delivering through several media. The starting point is a metric evaluation of the site obtained with photogrammetric surveying and appropriate 3D restitution. The authors have been applying the underwater photogrammetric technique since several years using underwater digital cameras and, in this paper, digital low cost cameras (off-the-shelf). Results of tests made on submerged objects with three cameras are presented: Canon Power Shot G12, Intova Sport HD e GoPro HERO 2. The experimentation had the goal to evaluate the precision in self-calibration procedures, essential for multimedia underwater photogrammetry, and to analyze the quality of 3D restitution. Precisions obtained in the calibration and orientation procedures was assessed by using three cameras, and an homogeneous set control points. Data were processed with Agisoft Photoscan. Successively, 3D models were created and the comparison of the models derived from the use of different cameras was performed. Different potentialities of the used cameras are reported in the discussion section. The 3D restitution of objects and structures was integrated with sea bottom floor morphology in order to achieve a comprehensive description of the site. A possible methodology of survey and representation of submerged objects is therefore illustrated, considering an automatic and a semi-automatic approach.

Three-dimensional curvilinear device reconstruction from two fluoroscopic views

NASA Astrophysics Data System (ADS)

Delmas, Charlotte; Berger, Marie-Odile; Kerrien, Erwan; Riddell, Cyril; Trousset, Yves; Anxionnat, René; Bracard, Serge

2015-03-01

In interventional radiology, navigating devices under the sole guidance of fluoroscopic images inside a complex architecture of tortuous and narrow vessels like the cerebral vascular tree is a difficult task. Visualizing the device in 3D could facilitate this navigation. For curvilinear devices such as guide-wires and catheters, a 3D reconstruction may be achieved using two simultaneous fluoroscopic views, as available on a biplane acquisition system. The purpose of this paper is to present a new automatic three-dimensional curve reconstruction method that has the potential to reconstruct complex 3D curves and does not require a perfect segmentation of the endovascular device. Using epipolar geometry, our algorithm translates the point correspondence problem into a segment correspondence problem. Candidate 3D curves can be formed and evaluated independently after identifying all possible combinations of compatible 3D segments. Correspondence is then inherently solved by looking in 3D space for the most coherent curve in terms of continuity and curvature. This problem can be cast into a graph problem where the most coherent curve corresponds to the shortest path of a weighted graph. We present quantitative results of curve reconstructions performed from numerically simulated projections of tortuous 3D curves extracted from cerebral vascular trees affected with brain arteriovenous malformations as well as fluoroscopic image pairs of a guide-wire from both phantom and clinical sets. Our method was able to select the correct 3D segments in 97.5% of simulated cases thus demonstrating its ability to handle complex 3D curves and can deal with imperfect 2D segmentation.

Reconstruction of measurable three-dimensional point cloud model based on large-scene archaeological excavation sites

NASA Astrophysics Data System (ADS)

Zhang, Chun-Sen; Zhang, Meng-Meng; Zhang, Wei-Xing

2017-01-01

This paper outlines a low-cost, user-friendly photogrammetric technique with nonmetric cameras to obtain excavation site digital sequence images, based on photogrammetry and computer vision. Digital camera calibration, automatic aerial triangulation, image feature extraction, image sequence matching, and dense digital differential rectification are used, combined with a certain number of global control points of the excavation site, to reconstruct the high precision of measured three-dimensional (3-D) models. Using the acrobatic figurines in the Qin Shi Huang mausoleum excavation as an example, our method solves the problems of little base-to-height ratio, high inclination, unstable altitudes, and significant ground elevation changes affecting image matching. Compared to 3-D laser scanning, the 3-D color point cloud obtained by this method can maintain the same visual result and has advantages of low project cost, simple data processing, and high accuracy. Structure-from-motion (SfM) is often used to reconstruct 3-D models of large scenes and has lower accuracy if it is a reconstructed 3-D model of a small scene at close range. Results indicate that this method quickly achieves 3-D reconstruction of large archaeological sites and produces heritage site distribution of orthophotos providing a scientific basis for accurate location of cultural relics, archaeological excavations, investigation, and site protection planning. This proposed method has a comprehensive application value.

Computer Reconstruction of Plant Growth and Chlorophyll Fluorescence Emission in Three Spatial Dimensions

PubMed Central

Bellasio, Chandra; Olejníčková, Julie; Tesař, Radek; Šebela, David; Nedbal, Ladislav

2012-01-01

Plant leaves grow and change their orientation as well their emission of chlorophyll fluorescence in time. All these dynamic plant properties can be semi-automatically monitored by a 3D imaging system that generates plant models by the method of coded light illumination, fluorescence imaging and computer 3D reconstruction. Here, we describe the essentials of the method, as well as the system hardware. We show that the technique can reconstruct, with a high fidelity, the leaf size, the leaf angle and the plant height. The method fails with wilted plants when leaves overlap obscuring their true area. This effect, naturally, also interferes when the method is applied to measure plant growth under water stress. The method is, however, very potent in capturing the plant dynamics under mild stress and without stress. The 3D reconstruction is also highly effective in correcting geometrical factors that distort measurements of chlorophyll fluorescence emission of naturally positioned plant leaves. PMID:22368511

Computer reconstruction of plant growth and chlorophyll fluorescence emission in three spatial dimensions.

PubMed

Bellasio, Chandra; Olejníčková, Julie; Tesař, Radek; Sebela, David; Nedbal, Ladislav

2012-01-01

Plant leaves grow and change their orientation as well their emission of chlorophyll fluorescence in time. All these dynamic plant properties can be semi-automatically monitored by a 3D imaging system that generates plant models by the method of coded light illumination, fluorescence imaging and computer 3D reconstruction. Here, we describe the essentials of the method, as well as the system hardware. We show that the technique can reconstruct, with a high fidelity, the leaf size, the leaf angle and the plant height. The method fails with wilted plants when leaves overlap obscuring their true area. This effect, naturally, also interferes when the method is applied to measure plant growth under water stress. The method is, however, very potent in capturing the plant dynamics under mild stress and without stress. The 3D reconstruction is also highly effective in correcting geometrical factors that distort measurements of chlorophyll fluorescence emission of naturally positioned plant leaves.

The One to Multiple Automatic High Accuracy Registration of Terrestrial LIDAR and Optical Images

NASA Astrophysics Data System (ADS)

Wang, Y.; Hu, C.; Xia, G.; Xue, H.

2018-04-01

The registration of ground laser point cloud and close-range image is the key content of high-precision 3D reconstruction of cultural relic object. In view of the requirement of high texture resolution in the field of cultural relic at present, The registration of point cloud and image data in object reconstruction will result in the problem of point cloud to multiple images. In the current commercial software, the two pairs of registration of the two kinds of data are realized by manually dividing point cloud data, manual matching point cloud and image data, manually selecting a two - dimensional point of the same name of the image and the point cloud, and the process not only greatly reduces the working efficiency, but also affects the precision of the registration of the two, and causes the problem of the color point cloud texture joint. In order to solve the above problems, this paper takes the whole object image as the intermediate data, and uses the matching technology to realize the automatic one-to-one correspondence between the point cloud and multiple images. The matching of point cloud center projection reflection intensity image and optical image is applied to realize the automatic matching of the same name feature points, and the Rodrigo matrix spatial similarity transformation model and weight selection iteration are used to realize the automatic registration of the two kinds of data with high accuracy. This method is expected to serve for the high precision and high efficiency automatic 3D reconstruction of cultural relic objects, which has certain scientific research value and practical significance.

Stochastic Surface Mesh Reconstruction

NASA Astrophysics Data System (ADS)

Ozendi, M.; Akca, D.; Topan, H.

2018-05-01

A generic and practical methodology is presented for 3D surface mesh reconstruction from the terrestrial laser scanner (TLS) derived point clouds. It has two main steps. The first step deals with developing an anisotropic point error model, which is capable of computing the theoretical precisions of 3D coordinates of each individual point in the point cloud. The magnitude and direction of the errors are represented in the form of error ellipsoids. The following second step is focused on the stochastic surface mesh reconstruction. It exploits the previously determined error ellipsoids by computing a point-wise quality measure, which takes into account the semi-diagonal axis length of the error ellipsoid. The points only with the least errors are used in the surface triangulation. The remaining ones are automatically discarded.

Micro-tomography based Geometry Modeling of Three-Dimensional Braided Composites

NASA Astrophysics Data System (ADS)

Fang, Guodong; Chen, Chenghua; Yuan, Shenggang; Meng, Songhe; Liang, Jun

2018-06-01

A tracking and recognizing algorithm is proposed to automatically generate irregular cross-sections and central path of braid yarn within the 3D braided composites by using sets of high resolution tomography images. Only the initial cross-sections of braid yarns in a tomography image after treatment are required to be calibrated manually as searching cross-section template. The virtual geometry of 3D braided composites including some detailed geometry information, such as the braid yarn squeezing deformation, braid yarn distortion and braid yarn path deviation etc., can be reconstructed. The reconstructed geometry model can reflect the change of braid configurations during solidification process. The geometry configurations and mechanical properties of the braided composites are analyzed by using the reconstructed geometry model.

Validation of a rapid, semiautomatic image analysis tool for measurement of gastric accommodation and emptying by magnetic resonance imaging

PubMed Central

Dixit, Sudeepa; Fox, Mark; Pal, Anupam

2014-01-01

Magnetic resonance imaging (MRI) has advantages for the assessment of gastrointestinal structures and functions; however, processing MRI data is time consuming and this has limited uptake to a few specialist centers. This study introduces a semiautomatic image processing system for rapid analysis of gastrointestinal MRI. For assessment of simpler regions of interest (ROI) such as the stomach, the system generates virtual images along arbitrary planes that intersect the ROI edges in the original images. This generates seed points that are joined automatically to form contours on each adjacent two-dimensional image and reconstructed in three dimensions (3D). An alternative thresholding approach is available for rapid assessment of complex structures like the small intestine. For assessment of dynamic gastrointestinal function, such as gastric accommodation and emptying, the initial 3D reconstruction is used as reference to process adjacent image stacks automatically. This generates four-dimensional (4D) reconstructions of dynamic volume change over time. Compared with manual processing, this semiautomatic system reduced the user input required to analyze a MRI gastric emptying study (estimated 100 vs. 10,000 mouse clicks). This analysis was not subject to variation in volume measurements seen between three human observers. In conclusion, the image processing platform presented processed large volumes of MRI data, such as that produced by gastric accommodation and emptying studies, with minimal user input. 3D and 4D reconstructions of the stomach and, potentially, other gastrointestinal organs are produced faster and more accurately than manual methods. This system will facilitate the application of MRI in gastrointestinal research and clinical practice. PMID:25540229

D Reconstruction of Cultural Tourism Attractions from Indoor to Outdoor Based on Portable Four-Camera Stereo Vision System

NASA Astrophysics Data System (ADS)

Shao, Z.; Li, C.; Zhong, S.; Liu, B.; Jiang, H.; Wen, X.

2015-05-01

Building the fine 3D model from outdoor to indoor is becoming a necessity for protecting the cultural tourism resources. However, the existing 3D modelling technologies mainly focus on outdoor areas. Actually, a 3D model should contain detailed descriptions of both its appearance and its internal structure, including architectural components. In this paper, a portable four-camera stereo photographic measurement system is developed, which can provide a professional solution for fast 3D data acquisition, processing, integration, reconstruction and visualization. Given a specific scene or object, it can directly collect physical geometric information such as positions, sizes and shapes of an object or a scene, as well as physical property information such as the materials and textures. On the basis of the information, 3D model can be automatically constructed. The system has been applied to the indooroutdoor seamless modelling of distinctive architecture existing in two typical cultural tourism zones, that is, Tibetan and Qiang ethnic minority villages in Sichuan Jiuzhaigou Scenic Area and Tujia ethnic minority villages in Hubei Shennongjia Nature Reserve, providing a new method and platform for protection of minority cultural characteristics, 3D reconstruction and cultural tourism.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons.

PubMed

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3-4 and 8-9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

PubMed Central

Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M.; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X.; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

2015-01-01

The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner. PMID:26052271

Online fully automated three-dimensional surface reconstruction of unknown objects

NASA Astrophysics Data System (ADS)

Khalfaoui, Souhaiel; Aigueperse, Antoine; Fougerolle, Yohan; Seulin, Ralph; Fofi, David

2015-04-01

This paper presents a novel scheme for automatic and intelligent 3D digitization using robotic cells. The advantage of our procedure is that it is generic since it is not performed for a specific scanning technology. Moreover, it is not dependent on the methods used to perform the tasks associated with each elementary process. The comparison of results between manual and automatic scanning of complex objects shows that our digitization strategy is very efficient and faster than trained experts. The 3D models of the different objects are obtained with a strongly reduced number of acquisitions while moving efficiently the ranging device.

Data-Driven Neural Network Model for Robust Reconstruction of Automobile Casting

NASA Astrophysics Data System (ADS)

Lin, Jinhua; Wang, Yanjie; Li, Xin; Wang, Lu

2017-09-01

In computer vision system, it is a challenging task to robustly reconstruct complex 3D geometries of automobile castings. However, 3D scanning data is usually interfered by noises, the scanning resolution is low, these effects normally lead to incomplete matching and drift phenomenon. In order to solve these problems, a data-driven local geometric learning model is proposed to achieve robust reconstruction of automobile casting. In order to relieve the interference of sensor noise and to be compatible with incomplete scanning data, a 3D convolution neural network is established to match the local geometric features of automobile casting. The proposed neural network combines the geometric feature representation with the correlation metric function to robustly match the local correspondence. We use the truncated distance field(TDF) around the key point to represent the 3D surface of casting geometry, so that the model can be directly embedded into the 3D space to learn the geometric feature representation; Finally, the training labels is automatically generated for depth learning based on the existing RGB-D reconstruction algorithm, which accesses to the same global key matching descriptor. The experimental results show that the matching accuracy of our network is 92.2% for automobile castings, the closed loop rate is about 74.0% when the matching tolerance threshold τ is 0.2. The matching descriptors performed well and retained 81.6% matching accuracy at 95% closed loop. For the sparse geometric castings with initial matching failure, the 3D matching object can be reconstructed robustly by training the key descriptors. Our method performs 3D reconstruction robustly for complex automobile castings.

Hybrid Automatic Building Interpretation System

NASA Astrophysics Data System (ADS)

Pakzad, K.; Klink, A.; Müterthies, A.; Gröger, G.; Stroh, V.; Plümer, L.

2011-09-01

HABIS (Hybrid Automatic Building Interpretation System) is a system for an automatic reconstruction of building roofs used in virtual 3D building models. Unlike most of the commercially available systems, HABIS is able to work to a high degree automatically. The hybrid method uses different sources intending to exploit the advantages of the particular sources. 3D point clouds usually provide good height and surface data, whereas spatial high resolution aerial images provide important information for edges and detail information for roof objects like dormers or chimneys. The cadastral data provide important basis information about the building ground plans. The approach used in HABIS works with a multi-stage-process, which starts with a coarse roof classification based on 3D point clouds. After that it continues with an image based verification of these predicted roofs. In a further step a final classification and adjustment of the roofs is done. In addition some roof objects like dormers and chimneys are also extracted based on aerial images and added to the models. In this paper the used methods are described and some results are presented.

Comparison of 3d Reconstruction Services and Terrestrial Laser Scanning for Cultural Heritage Documentation

NASA Astrophysics Data System (ADS)

Rasztovits, S.; Dorninger, P.

2013-07-01

Terrestrial Laser Scanning (TLS) is an established method to reconstruct the geometrical surface of given objects. Current systems allow for fast and efficient determination of 3D models with high accuracy and richness in detail. Alternatively, 3D reconstruction services are using images to reconstruct the surface of an object. While the instrumental expenses for laser scanning systems are high, upcoming free software services as well as open source software packages enable the generation of 3D models using digital consumer cameras. In addition, processing TLS data still requires an experienced user while recent web-services operate completely automatically. An indisputable advantage of image based 3D modeling is its implicit capability for model texturing. However, the achievable accuracy and resolution of the 3D models is lower than those of laser scanning data. Within this contribution, we investigate the results of automated web-services for image based 3D model generation with respect to a TLS reference model. For this, a copper sculpture was acquired using a laser scanner and using image series of different digital cameras. Two different webservices, namely Arc3D and AutoDesk 123D Catch were used to process the image data. The geometric accuracy was compared for the entire model and for some highly structured details. The results are presented and interpreted based on difference models. Finally, an economical comparison of the generation of the models is given considering the interactive and processing time costs.

Topology reconstruction for B-Rep modeling from 3D mesh in reverse engineering applications

NASA Astrophysics Data System (ADS)

Bénière, Roseline; Subsol, Gérard; Gesquière, Gilles; Le Breton, François; Puech, William

2012-03-01

Nowadays, most of the manufactured objects are designed using CAD (Computer-Aided Design) software. Nevertheless, for visualization, data exchange or manufacturing applications, the geometric model has to be discretized into a 3D mesh composed of a finite number of vertices and edges. But, in some cases, the initial model may be lost or unavailable. In other cases, the 3D discrete representation may be modified, for example after a numerical simulation, and does not correspond anymore to the initial model. A reverse engineering method is then required to reconstruct a 3D continuous representation from the discrete one. In previous work, we have presented a new approach for 3D geometric primitive extraction. In this paper, to complete our automatic and comprehensive reverse engineering process, we propose a method to construct the topology of the retrieved object. To reconstruct a B-Rep model, a new formalism is now introduced to define the adjacency relations. Then a new process is used to construct the boundaries of the object. The whole process is tested on 3D industrial meshes and bring a solution to recover B-Rep models.

a Line-Based 3d Roof Model Reconstruction Algorithm: Tin-Merging and Reshaping (tmr)

NASA Astrophysics Data System (ADS)

Rau, J.-Y.

2012-07-01

Three-dimensional building model is one of the major components of a cyber-city and is vital for the realization of 3D GIS applications. In the last decade, the airborne laser scanning (ALS) data is widely used for 3D building model reconstruction and object extraction. Instead, based on 3D roof structural lines, this paper presents a novel algorithm for automatic roof models reconstruction. A line-based roof model reconstruction algorithm, called TIN-Merging and Reshaping (TMR), is proposed. The roof structural line, such as edges, eaves and ridges, can be measured manually from aerial stereo-pair, derived by feature line matching or inferred from ALS data. The originality of the TMR algorithm for 3D roof modelling is to perform geometric analysis and topology reconstruction among those unstructured lines and then reshapes the roof-type using elevation information from the 3D structural lines. For topology reconstruction, a line constrained Delaunay Triangulation algorithm is adopted where the input structural lines act as constraint and their vertex act as input points. Thus, the constructed TINs will not across the structural lines. Later at the stage of Merging, the shared edge between two TINs will be check if the original structural line exists. If not, those two TINs will be merged into a polygon. Iterative checking and merging of any two neighboured TINs/Polygons will result in roof polygons on the horizontal plane. Finally, at the Reshaping stage any two structural lines with fixed height will be used to adjust a planar function for the whole roof polygon. In case ALS data exist, the Reshaping stage can be simplified by adjusting the point cloud within the roof polygon. The proposed scheme reduces the complexity of 3D roof modelling and makes the modelling process easier. Five test datasets provided by ISPRS WG III/4 located at downtown Toronto, Canada and Vaihingen, Germany are used for experiment. The test sites cover high rise buildings and residential area with diverse roof type. For performance evaluation, the adopted roof structural lines are manually measured from the provided stereo-pair. Experimental results indicate a nearly 100% success rate for topology reconstruction was achieved provided that the 3D structural lines can be enclosed as polygons. On the other hand, the success rate at the Reshaping stage is dependent on the complexity of the rooftop structure. Thus, a visual inspection and semi-automatic adjustment of roof-type is suggested and implemented to complete the roof modelling. The results demonstrate that the proposed scheme is robust and reliable with a high degree of completeness, correctness, and quality, even when a group of connected buildings with multiple layers and mixed roof types is processed.

An image engineering system for the inspection of transparent construction materials

NASA Astrophysics Data System (ADS)

Hinz, S.; Stephani, M.; Schiemann, L.; Zeller, K.

This article presents a modular photogrammetric recording and image analysis system for inspecting the material characteristics of transparent foils, in particular Ethylen-TetraFluorEthylen-Copolymer (ETFE) foils. The foils are put under increasing air pressure and are observed by a stereo camera system. Determining the time-variable 3D shape of transparent material imposes a number of challenges: especially the automatic point transfer between stereo images and, in temporal domain, from one image pair to the next. We developed an automatic approach that accommodates for these particular circumstances and allows reconstruction of the 3D shape for each epoch as well as determining 3D translation vectors between epochs by feature tracking. Examples including numerical results and accuracy measures prove the applicability of the system.

Fuzzy B-spline optimization for urban slum three-dimensional reconstruction using ENVISAT satellite data

NASA Astrophysics Data System (ADS)

Marghany, Maged

2014-06-01

A critical challenges in urban aeras is slums. In fact, they are considered a source of crime and disease due to poor-quality housing, unsanitary conditions, poor infrastructures and occupancy security. The poor in the dense urban slums are the most vulnerable to infection due to (i) inadequate and restricted access to safety, drinking water and sufficient quantities of water for personal hygiene; (ii) the lack of removal and treatment of excreta; and (iii) the lack of removal of solid waste. This study aims to investigate the capability of ENVISAT ASAR satellite and Google Earth data for three-dimensional (3-D) slum urban reconstruction in developed countries such as Egypt. The main objective of this work is to utilize some 3-D automatic detection algorithm for urban slum in ENVISAT ASAR and Google Erath images were acquired in Cairo, Egypt using Fuzzy B-spline algorithm. The results show that the fuzzy algorithm is the best indicator for chaotic urban slum as it can discriminate between them from its surrounding environment. The combination of Fuzzy and B-spline then used to reconstruct 3-D of urban slum. The results show that urban slums, road network, and infrastructures are perfectly discriminated. It can therefore be concluded that the fuzzy algorithm is an appropriate algorithm for chaotic urban slum automatic detection in ENVSIAT ASAR and Google Earth data.

Automatic Pedestrian Crossing Detection and Impairment Analysis Based on Mobile Mapping System

NASA Astrophysics Data System (ADS)

Liu, X.; Zhang, Y.; Li, Q.

2017-09-01

Pedestrian crossing, as an important part of transportation infrastructures, serves to secure pedestrians' lives and possessions and keep traffic flow in order. As a prominent feature in the street scene, detection of pedestrian crossing contributes to 3D road marking reconstruction and diminishing the adverse impact of outliers in 3D street scene reconstruction. Since pedestrian crossing is subject to wearing and tearing from heavy traffic flow, it is of great imperative to monitor its status quo. On this account, an approach of automatic pedestrian crossing detection using images from vehicle-based Mobile Mapping System is put forward and its defilement and impairment are analyzed in this paper. Firstly, pedestrian crossing classifier is trained with low recall rate. Then initial detections are refined by utilizing projection filtering, contour information analysis, and monocular vision. Finally, a pedestrian crossing detection and analysis system with high recall rate, precision and robustness will be achieved. This system works for pedestrian crossing detection under different situations and light conditions. It can recognize defiled and impaired crossings automatically in the meanwhile, which facilitates monitoring and maintenance of traffic facilities, so as to reduce potential traffic safety problems and secure lives and property.

Large-scale building scenes reconstruction from close-range images based on line and plane feature

NASA Astrophysics Data System (ADS)

Ding, Yi; Zhang, Jianqing

2007-11-01

Automatic generate 3D models of buildings and other man-made structures from images has become a topic of increasing importance, those models may be in applications such as virtual reality, entertainment industry and urban planning. In this paper we address the main problems and available solution for the generation of 3D models from terrestrial images. We first generate a coarse planar model of the principal scene planes and then reconstruct windows to refine the building models. There are several points of novelty: first we reconstruct the coarse wire frame model use the line segments matching with epipolar geometry constraint; Secondly, we detect the position of all windows in the image and reconstruct the windows by established corner points correspondences between images, then add the windows to the coarse model to refine the building models. The strategy is illustrated on image triple of college building.

Automatic Generation of Boundary Conditions Using Demons Nonrigid Image Registration for Use in 3-D Modality-Independent Elastography

PubMed Central

Ou, Jao J.; Ong, Rowena E.; Miga, Michael I.

2013-01-01

Modality-independent elastography (MIE) is a method of elastography that reconstructs the elastic properties of tissue using images acquired under different loading conditions and a biomechanical model. Boundary conditions are a critical input to the algorithm and are often determined by time-consuming point correspondence methods requiring manual user input. This study presents a novel method of automatically generating boundary conditions by nonrigidly registering two image sets with a demons diffusion-based registration algorithm. The use of this method was successfully performed in silico using magnetic resonance and X-ray-computed tomography image data with known boundary conditions. These preliminary results produced boundary conditions with an accuracy of up to 80% compared to the known conditions. Demons-based boundary conditions were utilized within a 3-D MIE reconstruction to determine an elasticity contrast ratio between tumor and normal tissue. Two phantom experiments were then conducted to further test the accuracy of the demons boundary conditions and the MIE reconstruction arising from the use of these conditions. Preliminary results show a reasonable characterization of the material properties on this first attempt and a significant improvement in the automation level and viability of the method. PMID:21690002

Automatic generation of boundary conditions using demons nonrigid image registration for use in 3-D modality-independent elastography.

PubMed

Pheiffer, Thomas S; Ou, Jao J; Ong, Rowena E; Miga, Michael I

2011-09-01

Modality-independent elastography (MIE) is a method of elastography that reconstructs the elastic properties of tissue using images acquired under different loading conditions and a biomechanical model. Boundary conditions are a critical input to the algorithm and are often determined by time-consuming point correspondence methods requiring manual user input. This study presents a novel method of automatically generating boundary conditions by nonrigidly registering two image sets with a demons diffusion-based registration algorithm. The use of this method was successfully performed in silico using magnetic resonance and X-ray-computed tomography image data with known boundary conditions. These preliminary results produced boundary conditions with an accuracy of up to 80% compared to the known conditions. Demons-based boundary conditions were utilized within a 3-D MIE reconstruction to determine an elasticity contrast ratio between tumor and normal tissue. Two phantom experiments were then conducted to further test the accuracy of the demons boundary conditions and the MIE reconstruction arising from the use of these conditions. Preliminary results show a reasonable characterization of the material properties on this first attempt and a significant improvement in the automation level and viability of the method.

A new method of three-dimensional computer assisted reconstruction of the developing biliary tract.

PubMed

Prudhomme, M; Gaubert-Cristol, R; Jaeger, M; De Reffye, P; Godlewski, G

1999-01-01

A three-dimensional (3-D) computer assisted reconstruction of the biliary tract was performed in human and rat embryos at Carnegie stage 23 to describe and compare the biliary structures and to point out the anatomic relations between the structures of the hepatic pedicle. Light micrograph images from consecutive serial sagittal sections (diameter 7 mm) of one human and 16 rat embryos were directly digitalized with a CCD camera. The serial views were aligned automatically by software. The data were analysed following segmentation and thresholding, allowing automatic reconstruction. The main bile ducts ascended in the mesoderm of the hepatoduodenal ligament. The extrahepatic bile ducts: common bile duct (CD), cystic duct and gallbladder in the human, formed a compound system which could not be shown so clearly in histologic sections. The hepato-pancreatic ampulla was studied as visualised through the duodenum. The course of the CD was like a chicane. The gallbladder diameter and length were similar to those of the CD. Computer-assisted reconstruction permitted easy acquisition of the data by direct examination of the sections through the microscope. This method showed the relationships between the different structures of the hepatic pedicle and allowed estimation of the volume of the bile duct. These findings were not obvious in two-dimensional (2-D) views from histologic sections. Each embryonic stage could be rebuilt in 3-D, which could introduce the time as a fourth dimension, fundamental for the study of organogenesis.

A Computational/Experimental Platform for Investigating Three-Dimensional Puzzle Solving of Comminuted Articular Fractures

PubMed Central

Thomas, Thaddeus P.; Anderson, Donald D.; Willis, Andrew R.; Liu, Pengcheng; Frank, Matthew C.; Marsh, J. Lawrence; Brown, Thomas D.

2011-01-01

Reconstructing highly comminuted articular fractures poses a difficult surgical challenge, akin to solving a complicated three-dimensional (3D) puzzle. Pre-operative planning using CT is critically important, given the desirability of less invasive surgical approaches. The goal of this work is to advance 3D puzzle solving methods toward use as a pre-operative tool for reconstructing these complex fractures. Methodology for generating typical fragmentation/dispersal patterns was developed. Five identical replicas of human distal tibia anatomy, were machined from blocks of high-density polyetherurethane foam (bone fragmentation surrogate), and were fractured using an instrumented drop tower. Pre- and post-fracture geometries were obtained using laser scans and CT. A semi-automatic virtual reconstruction computer program aligned fragment native (non-fracture) surfaces to a pre-fracture template. The tibias were precisely reconstructed with alignment accuracies ranging from 0.03-0.4mm. This novel technology has potential to significantly enhance surgical techniques for reconstructing comminuted intra-articular fractures, as illustrated for a representative clinical case. PMID:20924863

Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX)

PubMed Central

Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

2015-01-01

Cache blocking is a technique widely used in scientific computing to minimize the exchange of information with main memory by reusing the data kept in cache memory. In tomographic reconstruction on standard computers using vector instructions, cache blocking turns out to be central to optimize performance. To this end, sinograms of the tilt-series and slices of the volumes to be reconstructed have to be divided into small blocks that fit into the different levels of cache memory. The code is then reorganized so as to operate with a block as much as possible before proceeding with another one. This data article is related to the research article titled Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction (Agulleiro and Fernandez, 2015) [1]. Here we present data of a thorough study of the performance of tomographic reconstruction by varying cache block sizes, which allows derivation of expressions for their automatic quasi-optimal tuning. PMID:26217710

Tuning the cache memory usage in tomographic reconstruction on standard computers with Advanced Vector eXtensions (AVX).

PubMed

Agulleiro, Jose-Ignacio; Fernandez, Jose-Jesus

2015-06-01

Cache blocking is a technique widely used in scientific computing to minimize the exchange of information with main memory by reusing the data kept in cache memory. In tomographic reconstruction on standard computers using vector instructions, cache blocking turns out to be central to optimize performance. To this end, sinograms of the tilt-series and slices of the volumes to be reconstructed have to be divided into small blocks that fit into the different levels of cache memory. The code is then reorganized so as to operate with a block as much as possible before proceeding with another one. This data article is related to the research article titled Tomo3D 2.0 - Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction (Agulleiro and Fernandez, 2015) [1]. Here we present data of a thorough study of the performance of tomographic reconstruction by varying cache block sizes, which allows derivation of expressions for their automatic quasi-optimal tuning.

Does semi-automatic bone-fragment segmentation improve the reproducibility of the Letournel acetabular fracture classification?

PubMed

Boudissa, M; Orfeuvre, B; Chabanas, M; Tonetti, J

2017-09-01

The Letournel classification of acetabular fracture shows poor reproducibility in inexperienced observers, despite the introduction of 3D imaging. We therefore developed a method of semi-automatic segmentation based on CT data. The present prospective study aimed to assess: (1) whether semi-automatic bone-fragment segmentation increased the rate of correct classification; (2) if so, in which fracture types; and (3) feasibility using the open-source itksnap 3.0 software package without incurring extra cost for users. Semi-automatic segmentation of acetabular fractures significantly increases the rate of correct classification by orthopedic surgery residents. Twelve orthopedic surgery residents classified 23 acetabular fractures. Six used conventional 3D reconstructions provided by the center's radiology department (conventional group) and 6 others used reconstructions obtained by semi-automatic segmentation using the open-source itksnap 3.0 software package (segmentation group). Bone fragments were identified by specific colors. Correct classification rates were compared between groups on Chi 2 test. Assessment was repeated 2 weeks later, to determine intra-observer reproducibility. Correct classification rates were significantly higher in the "segmentation" group: 114/138 (83%) versus 71/138 (52%); P<0.0001. The difference was greater for simple (36/36 (100%) versus 17/36 (47%); P<0.0001) than complex fractures (79/102 (77%) versus 54/102 (53%); P=0.0004). Mean segmentation time per fracture was 27±3min [range, 21-35min]. The segmentation group showed excellent intra-observer correlation coefficients, overall (ICC=0.88), and for simple (ICC=0.92) and complex fractures (ICC=0.84). Semi-automatic segmentation, identifying the various bone fragments, was effective in increasing the rate of correct acetabular fracture classification on the Letournel system by orthopedic surgery residents. It may be considered for routine use in education and training. III: prospective case-control study of a diagnostic procedure. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

First performance evaluation of software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine at CT.

PubMed

Scholtz, Jan-Erik; Wichmann, Julian L; Kaup, Moritz; Fischer, Sebastian; Kerl, J Matthias; Lehnert, Thomas; Vogl, Thomas J; Bauer, Ralf W

2015-03-01

To evaluate software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine on CT in terms of accuracy, potential for time savings and workflow improvement. 77 patients (28 women, 49 men, mean age 65.3±14.4 years) with known or suspected spinal disorders (degenerative spine disease n=32; disc herniation n=36; traumatic vertebral fractures n=9) underwent 64-slice MDCT with thin-slab reconstruction. Time for automatic labeling of the thoracolumbar spine and reconstruction of double-angulated axial images of the pathological vertebrae was compared with manually performed reconstruction of anatomical aligned axial images. Reformatted images of both reconstruction methods were assessed by two observers regarding accuracy of symmetric depiction of anatomical structures. In 33 cases double-angulated axial images were created in 1 vertebra, in 28 cases in 2 vertebrae and in 16 cases in 3 vertebrae. Correct automatic labeling was achieved in 72 of 77 patients (93.5%). Errors could be manually corrected in 4 cases. Automatic labeling required 1min in average. In cases where anatomical aligned axial images of 1 vertebra were created, reconstructions made by hand were significantly faster (p<0.05). Automatic reconstruction was time-saving in cases of 2 and more vertebrae (p<0.05). Both reconstruction methods revealed good image quality with excellent inter-observer agreement. The evaluated software for automatic labeling and anatomically aligned, double-angulated axial image reconstruction of the thoracolumbar spine on CT is time-saving when reconstructions of 2 and more vertebrae are performed. Checking results of automatic labeling is necessary to prevent errors in labeling. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quality Analysis on 3d Buidling Models Reconstructed from Uav Imagery

NASA Astrophysics Data System (ADS)

Jarzabek-Rychard, M.; Karpina, M.

2016-06-01

Recent developments in UAV technology and structure from motion techniques have effected that UAVs are becoming standard platforms for 3D data collection. Because of their flexibility and ability to reach inaccessible urban parts, drones appear as optimal solution for urban applications. Building reconstruction from the data collected with UAV has the important potential to reduce labour cost for fast update of already reconstructed 3D cities. However, especially for updating of existing scenes derived from different sensors (e.g. airborne laser scanning), a proper quality assessment is necessary. The objective of this paper is thus to evaluate the potential of UAV imagery as an information source for automatic 3D building modeling at LOD2. The investigation process is conducted threefold: (1) comparing generated SfM point cloud to ALS data; (2) computing internal consistency measures of the reconstruction process; (3) analysing the deviation of Check Points identified on building roofs and measured with a tacheometer. In order to gain deep insight in the modeling performance, various quality indicators are computed and analysed. The assessment performed according to the ground truth shows that the building models acquired with UAV-photogrammetry have the accuracy of less than 18 cm for the plannimetric position and about 15 cm for the height component.

Best-next-view algorithm for three-dimensional scene reconstruction using range images

NASA Astrophysics Data System (ADS)

Banta, J. E.; Zhien, Yu; Wang, X. Z.; Zhang, G.; Smith, M. T.; Abidi, Mongi A.

1995-10-01

The primary focus of the research detailed in this paper is to develop an intelligent sensing module capable of automatically determining the optimal next sensor position and orientation during scene reconstruction. To facilitate a solution to this problem, we have assembled a system for reconstructing a 3D model of an object or scene from a sequence of range images. Candidates for the best-next-view position are determined by detecting and measuring occlusions to the range camera's view in an image. Ultimately, the candidate which will reveal the greatest amount of unknown scene information is selected as the best-next-view position. Our algorithm uses ray tracing to determine how much new information a given sensor perspective will reveal. We have tested our algorithm successfully on several synthetic range data streams, and found the system's results to be consistent with an intuitive human search. The models recovered by our system from range data compared well with the ideal models. Essentially, we have proven that range information of physical objects can be employed to automatically reconstruct a satisfactory dynamic 3D computer model at a minimal computational expense. This has obvious implications in the contexts of robot navigation, manufacturing, and hazardous materials handling. The algorithm we developed takes advantage of no a priori information in finding the best-next-view position.

360° Fourier transform profilometry in surface reconstruction for fluorescence molecular tomography.

PubMed

Shi, Bi'er; Zhang, Bin; Liu, Fei; Luo, Jianwen; Bai, Jing

2013-05-01

Fluorescence molecular tomography (FMT) is an emerging tool in the observation of diseases. A fast and accurate surface reconstruction of the experimental object is needed as a boundary constraint for FMT reconstruction. In this paper, an automatic, noncontact, and 3-D surface reconstruction method named 360◦ Fourier transform profilometry (FTP) is proposed to reconstruct 3-D surface profiles for FMT system. This method can reconstruct 360◦ integrated surface profiles utilizing the single-frame FTP at different angles. Results show that the relative mean error of the surface reconstruction of this method is less than 1.4% in phantom experiments, and is no more than 2.9% in mouse experiments in vivo. Compared with the Radon transform method, the proposed method reduces the computation time by more than 90% with a minimal error increase. At last, a combined 360◦ FTP/FMT experiment is conducted on a nude mouse. Not only can the 360◦ FTP system operate with the FMT system simultaneously, but it can also help to monitor the status of animals. Moreover, the 360◦ FTP system is independent of FMT system and can be performed to reconstruct the surface by itself.

Cup Implant Planning Based on 2-D/3-D Radiographic Pelvis Reconstruction-First Clinical Results.

PubMed

Schumann, Steffen; Sato, Yoshinobu; Nakanishi, Yuki; Yokota, Futoshi; Takao, Masaki; Sugano, Nobuhiko; Zheng, Guoyan

2015-11-01

In the following, we will present a newly developed X-ray calibration phantom and its integration for 2-D/3-D pelvis reconstruction and subsequent automatic cup planning. Two different planning strategies were applied and evaluated with clinical data. Two different cup planning methods were investigated: The first planning strategy is based on a combined pelvis and cup statistical atlas. Thereby, the pelvis part of the combined atlas is matched to the reconstructed pelvis model, resulting in an optimized cup planning. The second planning strategy analyzes the morphology of the reconstructed pelvis model to determine the best fitting cup implant. The first planning strategy was compared to 3-D CT-based planning. Digitally reconstructed radiographs of THA patients with differently severe pathologies were used to evaluate the accuracy of predicting the cup size and position. Within a discrepancy of one cup size, the size was correctly identified in 100% of the cases for Crowe type I datasets and in 77.8% of the cases for Crowe type II, III, and IV datasets. The second planning strategy was analyzed with respect to the eventually implanted cup size. In seven patients, the estimated cup diameter was correct within one cup size, while the estimation for the remaining five patients differed by two cup sizes. While both planning strategies showed the same prediction rate with a discrepancy of one cup size (87.5%), the prediction of the exact cup size was increased for the statistical atlas-based strategy (56%) in contrast to the anatomically driven approach (37.5%). The proposed approach demonstrated the clinical validity of using 2-D/3-D reconstruction technique for cup planning.

Nearly automatic motion capture system for tracking octopus arm movements in 3D space.

PubMed

Zelman, Ido; Galun, Meirav; Akselrod-Ballin, Ayelet; Yekutieli, Yoram; Hochner, Binyamin; Flash, Tamar

2009-08-30

Tracking animal movements in 3D space is an essential part of many biomechanical studies. The most popular technique for human motion capture uses markers placed on the skin which are tracked by a dedicated system. However, this technique may be inadequate for tracking animal movements, especially when it is impossible to attach markers to the animal's body either because of its size or shape or because of the environment in which the animal performs its movements. Attaching markers to an animal's body may also alter its behavior. Here we present a nearly automatic markerless motion capture system that overcomes these problems and successfully tracks octopus arm movements in 3D space. The system is based on three successive tracking and processing stages. The first stage uses a recently presented segmentation algorithm to detect the movement in a pair of video sequences recorded by two calibrated cameras. In the second stage, the results of the first stage are processed to produce 2D skeletal representations of the moving arm. Finally, the 2D skeletons are used to reconstruct the octopus arm movement as a sequence of 3D curves varying in time. Motion tracking, segmentation and reconstruction are especially difficult problems in the case of octopus arm movements because of the deformable, non-rigid structure of the octopus arm and the underwater environment in which it moves. Our successful results suggest that the motion-tracking system presented here may be used for tracking other elongated objects.

Real-Time 3d Reconstruction from Images Taken from AN Uav

NASA Astrophysics Data System (ADS)

Zingoni, A.; Diani, M.; Corsini, G.; Masini, A.

2015-08-01

We designed a method for creating 3D models of objects and areas from two aerial images acquired from an UAV. The models are generated automatically and in real-time, and consist in dense and true-colour reconstructions of the considered areas, which give the impression to the operator to be physically present within the scene. The proposed method only needs a cheap compact camera, mounted on a small UAV. No additional instrumentation is necessary, so that the costs are very limited. The method consists of two main parts: the design of the acquisition system and the 3D reconstruction algorithm. In the first part, the choices for the acquisition geometry and for the camera parameters are optimized, in order to yield the best performance. In the second part, a reconstruction algorithm extracts the 3D model from the two acquired images, maximizing the accuracy under the real-time constraint. A test was performed in monitoring a construction yard, obtaining very promising results. Highly realistic and easy-to-interpret 3D models of objects and areas of interest were produced in less than one second, with an accuracy of about 0.5m. For its characteristics, the designed method is suitable for video-surveillance, remote sensing and monitoring, especially in those applications that require intuitive and reliable information quickly, as disasters monitoring, search and rescue and area surveillance.

Enhanced visualization of the retinal vasculature using depth information in OCT.

PubMed

de Moura, Joaquim; Novo, Jorge; Charlón, Pablo; Barreira, Noelia; Ortega, Marcos

2017-12-01

Retinal vessel tree extraction is a crucial step for analyzing the microcirculation, a frequently needed process in the study of relevant diseases. To date, this has normally been done by using 2D image capture paradigms, offering a restricted visualization of the real layout of the retinal vasculature. In this work, we propose a new approach that automatically segments and reconstructs the 3D retinal vessel tree by combining near-infrared reflectance retinography information with Optical Coherence Tomography (OCT) sections. Our proposal identifies the vessels, estimates their calibers, and obtains the depth at all the positions of the entire vessel tree, thereby enabling the reconstruction of the 3D layout of the complete arteriovenous tree for subsequent analysis. The method was tested using 991 OCT images combined with their corresponding near-infrared reflectance retinography. The different stages of the methodology were validated using the opinion of an expert as a reference. The tests offered accurate results, showing coherent reconstructions of the 3D vasculature that can be analyzed in the diagnosis of relevant diseases affecting the retinal microcirculation, such as hypertension or diabetes, among others.

Automated circumferential construction of first-order aqueous humor outflow pathways using spectral-domain optical coherence tomography

NASA Astrophysics Data System (ADS)

Huang, Alex S.; Belghith, Akram; Dastiridou, Anna; Chopra, Vikas; Zangwill, Linda M.; Weinreb, Robert N.

2017-06-01

The purpose was to create a three-dimensional (3-D) model of circumferential aqueous humor outflow (AHO) in a living human eye with an automated detection algorithm for Schlemm's canal (SC) and first-order collector channels (CC) applied to spectral-domain optical coherence tomography (SD-OCT). Anterior segment SD-OCT scans from a subject were acquired circumferentially around the limbus. A Bayesian Ridge method was used to approximate the location of the SC on infrared confocal laser scanning ophthalmoscopic images with a cross multiplication tool developed to initiate SC/CC detection automated through a fuzzy hidden Markov Chain approach. Automatic segmentation of SC and initial CC's was manually confirmed by two masked graders. Outflow pathways detected by the segmentation algorithm were reconstructed into a 3-D representation of AHO. Overall, only <1% of images (5114 total B-scans) were ungradable. Automatic segmentation algorithm performed well with SC detection 98.3% of the time and <0.1% false positive detection compared to expert grader consensus. CC was detected 84.2% of the time with 1.4% false positive detection. 3-D representation of AHO pathways demonstrated variably thicker and thinner SC with some clear CC roots. Circumferential (360 deg), automated, and validated AHO detection of angle structures in the living human eye with reconstruction was possible.

3D Reconstruction in the Presence of Glass and Mirrors by Acoustic and Visual Fusion.

PubMed

Zhang, Yu; Ye, Mao; Manocha, Dinesh; Yang, Ruigang

2017-07-06

We present a practical and inexpensive method to reconstruct 3D scenes that include transparent and mirror objects. Our work is motivated by the need for automatically generating 3D models of interior scenes, which commonly include glass. These large structures are often invisible to cameras. Existing 3D reconstruction methods for transparent objects are usually not applicable in such a room-sized reconstruction setting. Our simple hardware setup augments a regular depth camera with a single ultrasonic sensor, which is able to measure the distance to any object, including transparent surfaces. The key technical challenge is the sparse sampling rate from the acoustic sensor, which only takes one point measurement per frame. To address this challenge, we take advantage of the fact that the large scale glass structures in indoor environments are usually either piece-wise planar or simple parametric surfaces. Based on these assumptions, we have developed a novel sensor fusion algorithm that first segments the (hybrid) depth map into different categories such as opaque/transparent/infinity (e.g., too far to measure) and then updates the depth map based on the segmentation outcome. We validated our algorithms with a number of challenging cases, including multiple panes of glass, mirrors, and even a curved glass cabinet.

Three- and four-dimensional reconstruction of intra-cardiac anatomy from two-dimensional magnetic resonance images.

PubMed

Miquel, M E; Hill, D L G; Baker, E J; Qureshi, S A; Simon, R D B; Keevil, S F; Razavi, R S

2003-06-01

The present study was designed to evaluate the feasibility and clinical usefulness of three-dimensional (3D) reconstruction of intra-cardiac anatomy from a series of two-dimensional (2D) MR images using commercially available software. Sixteen patients (eight with structurally normal hearts but due to have catheter radio-frequency ablation of atrial tachyarrhythmias and eight with atrial septal defects (ASD) due for trans-catheter closure) and two volunteers were imaged at 1T. For each patient, a series of ECG-triggered images (5 mm thick slices, 2-3 mm apart) were acquired during breath holding. Depending on image quality, T1- or T2-weighted spin-echo images or gradient-echo cine images were used. The 3D reconstruction was performed off-line: the blood pools within cardiac chambers and great vessels were semi-automatically segmented, their outer surface was extracted using a marching cube algorithm and rendered. Intra- and inter-observer variability, effect of breath-hold position and differences between pulse sequences were assessed by imaging a volunteer. The 3D reconstructions were assessed by three cardiologists and compared with the 2D MR images and with 2D and 3D trans-esophagal and intra-cardiac echocardiography obtained during interventions. In every case, an anatomically detailed 3D volume was obtained. In the two patients where a 3 mm interval between slices was used, the resolution was not as good but it was still possible to visualize all the major anatomical structures. Spin-echo images lead to reconstructions more detailed than those obtained from gradient-echo images. However, gradient-echo images are easier to segment due to their greater contrast. Furthermore, because images were acquired at least at ten points in the cardiac cycles for every slice it was possible to reconstruct a cine loop and, for example, to visualize the evolution of the size and margins of the ASD during the cardiac cycle. 3D reconstruction proved to be an effective way to assess the relationship between the different parts of the cardiac anatomy. The technique was useful in planning interventions in these patients.

Biologically inspired EM image alignment and neural reconstruction.

PubMed

Knowles-Barley, Seymour; Butcher, Nancy J; Meinertzhagen, Ian A; Armstrong, J Douglas

2011-08-15

Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden. Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman-Wunsch and Smith-Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections. An open-source reference implementation is available in the Supplementary information. seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.uk Supplementary data are available at Bioinformatics online.

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/.

Automated Generation of 3D Volcanic Gas Plume Models for Geobrowsers

NASA Astrophysics Data System (ADS)

Wright, T. E.; Burton, M.; Pyle, D. M.

2007-12-01

A network of five UV spectrometers on Etna automatically gathers column amounts of SO2 during daylight hours. Near-simultaneous scans from adjacent spectrometers, comprising 210 column amounts in total, are then converted to 2D slices showing the spatial distribution of the gas by tomographic reconstruction. The trajectory of the plume is computed using an automatically-submitted query to NOAA's HYSPLIT Trajectory Model. This also provides local estimates of air temperature, which are used to determine the atmospheric stability and therefore the degree to which the plume is dispersed by turbulence. This information is sufficient to construct an animated sequence of models which show how the plume is advected and diffused over time. These models are automatically generated in the Collada Digital Asset Exchange format and combined into a single file which displays the evolution of the plume in Google Earth. These models are useful for visualising and predicting the shape and distribution of the plume for civil defence, to assist field campaigns and as a means of communicating some of the work of volcano observatories to the public. The Simultaneous Algebraic Reconstruction Technique is used to create the 2D slices. This is a well-known method, based on iteratively updating a forward model (from 2D distribution to column amounts). Because it is based on a forward model, it also provides a simple way to quantify errors.

[Application of computer-assisted 3D imaging simulation for surgery].

PubMed

Matsushita, S; Suzuki, N

1994-03-01

This article describes trends in application of various imaging technology in surgical planning, navigation, and computer aided surgery. Imaging information is essential factor for simulation in medicine. It includes three dimensional (3D) image reconstruction, neuro-surgical navigation, creating substantial model based on 3D imaging data and etc. These developments depend mostly on 3D imaging technique, which is much contributed by recent computer technology. 3D imaging can offer new intuitive information to physician and surgeon, and this method is suitable for mechanical control. By utilizing simulated results, we can obtain more precise surgical orientation, estimation, and operation. For more advancement, automatic and high speed recognition of medical imaging is being developed.

Efficient Semi-Automatic 3D Segmentation for Neuron Tracing in Electron Microscopy Images

PubMed Central

Jones, Cory; Liu, Ting; Cohan, Nathaniel Wood; Ellisman, Mark; Tasdizen, Tolga

2015-01-01

0.1. Background In the area of connectomics, there is a significant gap between the time required for data acquisition and dense reconstruction of the neural processes contained in the same dataset. Automatic methods are able to eliminate this timing gap, but the state-of-the-art accuracy so far is insufficient for use without user corrections. If completed naively, this process of correction can be tedious and time consuming. 0.2. New Method We present a new semi-automatic method that can be used to perform 3D segmentation of neurites in EM image stacks. It utilizes an automatic method that creates a hierarchical structure for recommended merges of superpixels. The user is then guided through each predicted region to quickly identify errors and establish correct links. 0.3. Results We tested our method on three datasets with both novice and expert users. Accuracy and timing were compared with published automatic, semi-automatic, and manual results. 0.4. Comparison with Existing Methods Post-automatic correction methods have also been used in [1] and [2]. These methods do not provide navigation or suggestions in the manner we present. Other semi-automatic methods require user input prior to the automatic segmentation such as [3] and [4] and are inherently different than our method. 0.5. Conclusion Using this method on the three datasets, novice users achieved accuracy exceeding state-of-the-art automatic results, and expert users achieved accuracy on par with full manual labeling but with a 70% time improvement when compared with other examples in publication. PMID:25769273

Pulmonary lobar volumetry using novel volumetric computer-aided diagnosis and computed tomography

PubMed Central

Iwano, Shingo; Kitano, Mariko; Matsuo, Keiji; Kawakami, Kenichi; Koike, Wataru; Kishimoto, Mariko; Inoue, Tsutomu; Li, Yuanzhong; Naganawa, Shinji

2013-01-01

OBJECTIVES To compare the accuracy of pulmonary lobar volumetry using the conventional number of segments method and novel volumetric computer-aided diagnosis using 3D computed tomography images. METHODS We acquired 50 consecutive preoperative 3D computed tomography examinations for lung tumours reconstructed at 1-mm slice thicknesses. We calculated the lobar volume and the emphysematous lobar volume < −950 HU of each lobe using (i) the slice-by-slice method (reference standard), (ii) number of segments method, and (iii) semi-automatic and (iv) automatic computer-aided diagnosis. We determined Pearson correlation coefficients between the reference standard and the three other methods for lobar volumes and emphysematous lobar volumes. We also compared the relative errors among the three measurement methods. RESULTS Both semi-automatic and automatic computer-aided diagnosis results were more strongly correlated with the reference standard than the number of segments method. The correlation coefficients for automatic computer-aided diagnosis were slightly lower than those for semi-automatic computer-aided diagnosis because there was one outlier among 50 cases (2%) in the right upper lobe and two outliers among 50 cases (4%) in the other lobes. The number of segments method relative error was significantly greater than those for semi-automatic and automatic computer-aided diagnosis (P < 0.001). The computational time for automatic computer-aided diagnosis was 1/2 to 2/3 than that of semi-automatic computer-aided diagnosis. CONCLUSIONS A novel lobar volumetry computer-aided diagnosis system could more precisely measure lobar volumes than the conventional number of segments method. Because semi-automatic computer-aided diagnosis and automatic computer-aided diagnosis were complementary, in clinical use, it would be more practical to first measure volumes by automatic computer-aided diagnosis, and then use semi-automatic measurements if automatic computer-aided diagnosis failed. PMID:23526418

Accuracy and reproducibility of novel echocardiographic three-dimensional automated software for the assessment of the aortic root in candidates for thanscatheter aortic valve replacement.

PubMed

García-Martín, Ana; Lázaro-Rivera, Carla; Fernández-Golfín, Covadonga; Salido-Tahoces, Luisa; Moya-Mur, Jose-Luis; Jiménez-Nacher, Jose-Julio; Casas-Rojo, Eduardo; Aquila, Iolanda; González-Gómez, Ariana; Hernández-Antolín, Rosana; Zamorano, José Luis

2016-07-01

A specialized three-dimensional transoesophageal echocardiography (3D-TOE) reconstruction tool has recently been introduced; the system automatically configures a geometric model of the aortic root from the images obtained by 3D-TOE and performs quantitative analysis of these structures. The aim of this study was to compare the measurements of the aortic annulus (AA) obtained by the new model to that obtained by 3D-TOE and multidetector computed tomography (MDCT) in candidates to transcatheter aortic valve implantation (TAVI) and to assess the reproducibility of this new method. We included 31 patients who underwent TAVI. The AA diameters and area were evaluated by the manual 3D-TOE method and by the automatic software. We showed an excellent correlation between the measurements obtained by both methods: intra-class correlation coefficient (ICC): 0.731 (0.508-0.862), r: 0.742 for AA diameter and ICC: 0.723 (0.662-0.923), r: 0.723 for the AA area, with no significant differences regardless of the method used. The interobserver variability was superior for the automatic measurements than for the manual ones. In a subgroup of 10 patients, we also found an excellent correlation between the automatic measurements and those obtained by MDCT, ICC: 0.941 (0.761-0.985), r: 0.901 for AA diameter and ICC: 0.853 (0.409-0.964), r: 0.744 for the AA area. The new automatic 3D-TOE software allows modelling and quantifying the aortic root from 3D-TOE data with high reproducibility. There is good correlation between the automated measurements and other 3D validated techniques. Our results support its use in clinical practice as an alternative to MDCT previous to TAVI. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

3D reconstruction of microminiature objects based on contour line

NASA Astrophysics Data System (ADS)

Li, Cailin; Wang, Qiang; Guo, Baoyun

2009-10-01

A new 3D automatic reconstruction method of micro solid of revolution is presented in this paper. In the implementation procedure of this method, image sequence of the solid of revolution of 360° is obtained, which rotation speed is controlled by motor precisely, in the rotate photographic mode of back light. Firstly, we need calibrate the height of turntable, the size of pixel and rotation axis of turntable. Then according to the calibration result of rotation axis, the height of turntable, rotation angle and the pixel size, the contour points of each image can be transformed into 3D points in the reference coordinate system to generate the point cloud model. Finally, the surface geometrical model of solid of revolution is obtained by using the relationship of two adjacent contours. Experimental results on real images are presented, which demonstrate the effectiveness of the Approach.

Automated Recovery of Three-Dimensional Models of Plant Shoots from Multiple Color Images1[C][W][OPEN

PubMed Central

Pound, Michael P.; French, Andrew P.; Murchie, Erik H.; Pridmore, Tony P.

2014-01-01

Increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. This includes a need for realistic three-dimensional (3D) representations of plant shoots for quantification and modeling. Previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level-set method, optimizing the model based on image information, curvature constraints, and the position of neighboring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed and, as such, is applicable to a wide variety of plant species and topologies and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on data sets of wheat (Triticum aestivum) and rice (Oryza sativa) plants as well as a unique virtual data set that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modeling applications in a format that can be imported in the majority of 3D graphics and software packages. PMID:25332504

Art care: A multi-modality coronary 3D reconstruction and hemodynamic status assessment software.

PubMed

Siogkas, Panagiotis K; Stefanou, Kostas A; Athanasiou, Lambros S; Papafaklis, Michail I; Michalis, Lampros K; Fotiadis, Dimitrios I

2018-01-01

Due to the incremental increase of clinical interest in the development of software that allows the 3-dimensional (3D) reconstruction and the functional assessment of the coronary vasculature, several software packages have been developed and are available today. Taking this into consideration, we have developed an innovative suite of software modules that perform 3D reconstruction of coronary arterial segments using different coronary imaging modalities such as IntraVascular UltraSound (IVUS) and invasive coronary angiography images (ICA), Optical Coherence Tomography (OCT) and ICA images, or plain ICA images and can safely and accurately assess the hemodynamic status of the artery of interest. The user can perform automated or manual segmentation of the IVUS or OCT images, visualize in 3D the reconstructed vessel and export it to formats, which are compatible with other Computer Aided Design (CAD) software systems. We employ finite elements to provide the capability to assess the hemodynamic functionality of the reconstructed vessels by calculating the virtual functional assessment index (vFAI), an index that corresponds and has been shown to correlate well to the actual fractional flow reserve (FFR) value. All the modules of the proposed system have been thoroughly validated. In brief, the 3D-QCA module, compared to a successful commercial software of the same genre, presented very good correlation using several validation metrics, with a Pearson's correlation coefficient (R) for the calculated volumes, vFAI, length and minimum lumen diameter of 0.99, 0.99, 0.99 and 0.88, respectively. Moreover, the automatic lumen detection modules for IVUS and OCT presented very high accuracy compared to the annotations by medical experts with the Pearson's correlation coefficient reaching the values of 0.94 and 0.99, respectively. In this study, we have presented a user-friendly software for the 3D reconstruction of coronary arterial segments and the accurate hemodynamic assessment of the severity of existing stenosis.

Reconstruction of vessel structures from serial whole slide sections of murine liver samples

NASA Astrophysics Data System (ADS)

Schwier, Michael; Hahn, Horst K.; Dahmen, Uta; Dirsch, Olaf

2013-03-01

Image-based analysis of the vascular structures of murine liver samples is an important tool for scientists to understand liver physiology and morphology. Typical assessment methods are MicroCT, which allows for acquiring images of the whole organ while lacking resolution for fine details, and confocal laser scanning microscopy, which allows detailed insights into fine structures while lacking the broader context. Imaging of histological serial whole slide sections is a recent technology able to fill this gap, since it provides a fine resolution up to the cellular level, but on a whole organ scale. However, whole slide imaging is a modality providing only 2D images. Therefore the challenge is to use stacks of serial sections from which to reconstruct the 3D vessel structures. In this paper we present a semi-automatic procedure to achieve this goal. We employ an automatic method that detects vessel structures based on continuity and shape characteristics. Furthermore it supports the user to perform manual corrections where required. With our methods we were able to successfully extract and reconstruct vessel structures from a stack of 100 and a stack of 397 serial sections of a mouse liver lobe, thus proving the potential of our approach.

Detection and 3D reconstruction of traffic signs from multiple view color images

NASA Astrophysics Data System (ADS)

Soheilian, Bahman; Paparoditis, Nicolas; Vallet, Bruno

2013-03-01

3D reconstruction of traffic signs is of great interest in many applications such as image-based localization and navigation. In order to reflect the reality, the reconstruction process should meet both accuracy and precision. In order to reach such a valid reconstruction from calibrated multi-view images, accurate and precise extraction of signs in every individual view is a must. This paper presents first an automatic pipeline for identifying and extracting the silhouette of signs in every individual image. Then, a multi-view constrained 3D reconstruction algorithm provides an optimum 3D silhouette for the detected signs. The first step called detection, tackles with a color-based segmentation to generate ROIs (Region of Interests) in image. The shape of every ROI is estimated by fitting an ellipse, a quadrilateral or a triangle to edge points. A ROI is rejected if none of the three shapes can be fitted sufficiently precisely. Thanks to the estimated shape the remained candidates ROIs are rectified to remove the perspective distortion and then matched with a set of reference signs using textural information. Poor matches are rejected and the types of remained ones are identified. The output of the detection algorithm is a set of identified road signs whose silhouette in image plane is represented by and ellipse, a quadrilateral or a triangle. The 3D reconstruction process is based on a hypothesis generation and verification. Hypotheses are generated by a stereo matching approach taking into account epipolar geometry and also the similarity of the categories. The hypotheses that are plausibly correspond to the same 3D road sign are identified and grouped during this process. Finally, all the hypotheses of the same group are merged to generate a unique 3D road sign by a multi-view algorithm integrating a priori knowledges about 3D shape of road signs as constraints. The algorithm is assessed on real and synthetic images and reached and average accuracy of 3.5cm for position and 4.5° for orientation.

The SF3M approach to 3-D photo-reconstruction for non-expert users: application to a gully network

NASA Astrophysics Data System (ADS)

Castillo, C.; James, M. R.; Redel-Macías, M. D.; Pérez, R.; Gómez, J. A.

2015-04-01

3-D photo-reconstruction (PR) techniques have been successfully used to produce high resolution elevation models for different applications and over different spatial scales. However, innovative approaches are required to overcome some limitations that this technique may present in challenging scenarios. Here, we evaluate SF3M, a new graphical user interface for implementing a complete PR workflow based on freely available software (including external calls to VisualSFM and CloudCompare), in combination with a low-cost survey design for the reconstruction of a several-hundred-meters-long gully network. SF3M provided a semi-automated workflow for 3-D reconstruction requiring ~ 49 h (of which only 17% required operator assistance) for obtaining a final gully network model of > 17 million points over a gully plan area of 4230 m2. We show that a walking itinerary along the gully perimeter using two light-weight automatic cameras (1 s time-lapse mode) and a 6 m-long pole is an efficient method for 3-D monitoring of gullies, at a low cost (about EUR 1000 budget for the field equipment) and time requirements (~ 90 min for image collection). A mean error of 6.9 cm at the ground control points was found, mainly due to model deformations derived from the linear geometry of the gully and residual errors in camera calibration. The straightforward image collection and processing approach can be of great benefit for non-expert users working on gully erosion assessment.

A new strategic neurosurgical planning tool for brainstem cavernous malformations using interactive computer graphics with multimodal fusion images.

PubMed

Kin, Taichi; Nakatomi, Hirofumi; Shojima, Masaaki; Tanaka, Minoru; Ino, Kenji; Mori, Harushi; Kunimatsu, Akira; Oyama, Hiroshi; Saito, Nobuhito

2012-07-01

In this study, the authors used preoperative simulation employing 3D computer graphics (interactive computer graphics) to fuse all imaging data for brainstem cavernous malformations. The authors evaluated whether interactive computer graphics or 2D imaging correlated better with the actual operative field, particularly in identifying a developmental venous anomaly (DVA). The study population consisted of 10 patients scheduled for surgical treatment of brainstem cavernous malformations. Data from preoperative imaging (MRI, CT, and 3D rotational angiography) were automatically fused using a normalized mutual information method, and then reconstructed by a hybrid method combining surface rendering and volume rendering methods. With surface rendering, multimodality and multithreshold techniques for 1 tissue were applied. The completed interactive computer graphics were used for simulation of surgical approaches and assumed surgical fields. Preoperative diagnostic rates for a DVA associated with brainstem cavernous malformation were compared between conventional 2D imaging and interactive computer graphics employing receiver operating characteristic (ROC) analysis. The time required for reconstruction of 3D images was 3-6 hours for interactive computer graphics. Observation in interactive mode required approximately 15 minutes. Detailed anatomical information for operative procedures, from the craniotomy to microsurgical operations, could be visualized and simulated three-dimensionally as 1 computer graphic using interactive computer graphics. Virtual surgical views were consistent with actual operative views. This technique was very useful for examining various surgical approaches. Mean (±SEM) area under the ROC curve for rate of DVA diagnosis was significantly better for interactive computer graphics (1.000±0.000) than for 2D imaging (0.766±0.091; p<0.001, Mann-Whitney U-test). The authors report a new method for automatic registration of preoperative imaging data from CT, MRI, and 3D rotational angiography for reconstruction into 1 computer graphic. The diagnostic rate of DVA associated with brainstem cavernous malformation was significantly better using interactive computer graphics than with 2D images. Interactive computer graphics was also useful in helping to plan the surgical access corridor.

Automated circumferential construction of first-order aqueous humor outflow pathways using spectral-domain optical coherence tomography.

PubMed

Huang, Alex S; Belghith, Akram; Dastiridou, Anna; Chopra, Vikas; Zangwill, Linda M; Weinreb, Robert N

2017-06-01

The purpose was to create a three-dimensional (3-D) model of circumferential aqueous humor outflow (AHO) in a living human eye with an automated detection algorithm for Schlemm’s canal (SC) and first-order collector channels (CC) applied to spectral-domain optical coherence tomography (SD-OCT). Anterior segment SD-OCT scans from a subject were acquired circumferentially around the limbus. A Bayesian Ridge method was used to approximate the location of the SC on infrared confocal laser scanning ophthalmoscopic images with a cross multiplication tool developed to initiate SC/CC detection automated through a fuzzy hidden Markov Chain approach. Automatic segmentation of SC and initial CC’s was manually confirmed by two masked graders. Outflow pathways detected by the segmentation algorithm were reconstructed into a 3-D representation of AHO. Overall, only <1% of images (5114 total B-scans) were ungradable. Automatic segmentation algorithm performed well with SC detection 98.3% of the time and <0.1% false positive detection compared to expert grader consensus. CC was detected 84.2% of the time with 1.4% false positive detection. 3-D representation of AHO pathways demonstrated variably thicker and thinner SC with some clear CC roots. Circumferential (360 deg), automated, and validated AHO detection of angle structures in the living human eye with reconstruction was possible.

WE-A-17A-10: Fast, Automatic and Accurate Catheter Reconstruction in HDR Brachytherapy Using An Electromagnetic 3D Tracking System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poulin, E; Racine, E; Beaulieu, L

2014-06-15

Purpose: In high dose rate brachytherapy (HDR-B), actual catheter reconstruction protocols are slow and errors prompt. The purpose of this study was to evaluate the accuracy and robustness of an electromagnetic (EM) tracking system for improved catheter reconstruction in HDR-B protocols. Methods: For this proof-of-principle, a total of 10 catheters were inserted in gelatin phantoms with different trajectories. Catheters were reconstructed using a Philips-design 18G biopsy needle (used as an EM stylet) and the second generation Aurora Planar Field Generator from Northern Digital Inc. The Aurora EM system exploits alternating current technology and generates 3D points at 40 Hz. Phantomsmore » were also scanned using a μCT (GE Healthcare) and Philips Big Bore clinical CT system with a resolution of 0.089 mm and 2 mm, respectively. Reconstructions using the EM stylet were compared to μCT and CT. To assess the robustness of the EM reconstruction, 5 catheters were reconstructed twice and compared. Results: Reconstruction time for one catheter was 10 seconds or less. This would imply that for a typical clinical implant of 17 catheters, the total reconstruction time would be less than 3 minutes. When compared to the μCT, the mean EM tip identification error was 0.69 ± 0.29 mm while the CT error was 1.08 ± 0.67 mm. The mean 3D distance error was found to be 0.92 ± 0.37 mm and 1.74 ± 1.39 mm for the EM and CT, respectively. EM 3D catheter trajectories were found to be significantly more accurate (unpaired t-test, p < 0.05). A mean difference of less than 0.5 mm was found between successive EM reconstructions. Conclusion: The EM reconstruction was found to be faster, more accurate and more robust than the conventional methods used for catheter reconstruction in HDR-B. This approach can be applied to any type of catheters and applicators. We would like to disclose that the equipments, used in this study, is coming from a collaboration with Philips Medical.« less

Fast, automatic, and accurate catheter reconstruction in HDR brachytherapy using an electromagnetic 3D tracking system.

PubMed

Poulin, Eric; Racine, Emmanuel; Binnekamp, Dirk; Beaulieu, Luc

2015-03-01

In high dose rate brachytherapy (HDR-B), current catheter reconstruction protocols are relatively slow and error prone. The purpose of this technical note is to evaluate the accuracy and the robustness of an electromagnetic (EM) tracking system for automated and real-time catheter reconstruction. For this preclinical study, a total of ten catheters were inserted in gelatin phantoms with different trajectories. Catheters were reconstructed using a 18G biopsy needle, used as an EM stylet and equipped with a miniaturized sensor, and the second generation Aurora(®) Planar Field Generator from Northern Digital Inc. The Aurora EM system provides position and orientation value with precisions of 0.7 mm and 0.2°, respectively. Phantoms were also scanned using a μCT (GE Healthcare) and Philips Big Bore clinical computed tomography (CT) system with a spatial resolution of 89 μm and 2 mm, respectively. Reconstructions using the EM stylet were compared to μCT and CT. To assess the robustness of the EM reconstruction, five catheters were reconstructed twice and compared. Reconstruction time for one catheter was 10 s, leading to a total reconstruction time inferior to 3 min for a typical 17-catheter implant. When compared to the μCT, the mean EM tip identification error was 0.69 ± 0.29 mm while the CT error was 1.08 ± 0.67 mm. The mean 3D distance error was found to be 0.66 ± 0.33 mm and 1.08 ± 0.72 mm for the EM and CT, respectively. EM 3D catheter trajectories were found to be more accurate. A maximum difference of less than 0.6 mm was found between successive EM reconstructions. The EM reconstruction was found to be more accurate and precise than the conventional methods used for catheter reconstruction in HDR-B. This approach can be applied to any type of catheters and applicators.

Fast, automatic, and accurate catheter reconstruction in HDR brachytherapy using an electromagnetic 3D tracking system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poulin, Eric; Racine, Emmanuel; Beaulieu, Luc, E-mail: Luc.Beaulieu@phy.ulaval.ca

2015-03-15

Purpose: In high dose rate brachytherapy (HDR-B), current catheter reconstruction protocols are relatively slow and error prone. The purpose of this technical note is to evaluate the accuracy and the robustness of an electromagnetic (EM) tracking system for automated and real-time catheter reconstruction. Methods: For this preclinical study, a total of ten catheters were inserted in gelatin phantoms with different trajectories. Catheters were reconstructed using a 18G biopsy needle, used as an EM stylet and equipped with a miniaturized sensor, and the second generation Aurora{sup ®} Planar Field Generator from Northern Digital Inc. The Aurora EM system provides position andmore » orientation value with precisions of 0.7 mm and 0.2°, respectively. Phantoms were also scanned using a μCT (GE Healthcare) and Philips Big Bore clinical computed tomography (CT) system with a spatial resolution of 89 μm and 2 mm, respectively. Reconstructions using the EM stylet were compared to μCT and CT. To assess the robustness of the EM reconstruction, five catheters were reconstructed twice and compared. Results: Reconstruction time for one catheter was 10 s, leading to a total reconstruction time inferior to 3 min for a typical 17-catheter implant. When compared to the μCT, the mean EM tip identification error was 0.69 ± 0.29 mm while the CT error was 1.08 ± 0.67 mm. The mean 3D distance error was found to be 0.66 ± 0.33 mm and 1.08 ± 0.72 mm for the EM and CT, respectively. EM 3D catheter trajectories were found to be more accurate. A maximum difference of less than 0.6 mm was found between successive EM reconstructions. Conclusions: The EM reconstruction was found to be more accurate and precise than the conventional methods used for catheter reconstruction in HDR-B. This approach can be applied to any type of catheters and applicators.« less

Automatic Generation of Building Models with Levels of Detail 1-3

NASA Astrophysics Data System (ADS)

Nguatem, W.; Drauschke, M.; Mayer, H.

2016-06-01

We present a workflow for the automatic generation of building models with levels of detail (LOD) 1 to 3 according to the CityGML standard (Gröger et al., 2012). We start with orienting unsorted image sets employing (Mayer et al., 2012), we compute depth maps using semi-global matching (SGM) (Hirschmüller, 2008), and fuse these depth maps to reconstruct dense 3D point clouds (Kuhn et al., 2014). Based on planes segmented from these point clouds, we have developed a stochastic method for roof model selection (Nguatem et al., 2013) and window model selection (Nguatem et al., 2014). We demonstrate our workflow up to the export into CityGML.

a Low-Cost Panoramic Camera for the 3d Documentation of Contaminated Crime Scenes

NASA Astrophysics Data System (ADS)

Abate, D.; Toschi, I.; Sturdy-Colls, C.; Remondino, F.

2017-11-01

Crime scene documentation is a fundamental task which has to be undertaken in a fast, accurate and reliable way, highlighting evidence which can be further used for ensuring justice for victims and for guaranteeing the successful prosecution of perpetrators. The main focus of this paper is on the documentation of a typical crime scene and on the rapid recording of any possible contamination that could have influenced its original appearance. A 3D reconstruction of the environment is first generated by processing panoramas acquired with the low-cost Ricoh Theta 360 camera, and further analysed to highlight potentials and limits of this emerging and consumer-grade technology. Then, a methodology is proposed for the rapid recording of changes occurring between the original and the contaminated crime scene. The approach is based on an automatic 3D feature-based data registration, followed by a cloud-to-cloud distance computation, given as input the 3D point clouds generated before and after e.g. the misplacement of evidence. All the algorithms adopted for panoramas pre-processing, photogrammetric 3D reconstruction, 3D geometry registration and analysis, are presented and currently available in open-source or low-cost software solutions.

Study on the Feasibility of RGB Substitute CIR for Automatic Removal Vegetation Occlusion Based on Ground Close-Range Building Images

NASA Astrophysics Data System (ADS)

Li, C.; Li, F.; Liu, Y.; Li, X.; Liu, P.; Xiao, B.

2012-07-01

Building 3D reconstruction based on ground remote sensing data (image, video and lidar) inevitably faces the problem that buildings are always occluded by vegetation, so how to automatically remove and repair vegetation occlusion is a very important preprocessing work for image understanding, compute vision and digital photogrammetry. In the traditional multispectral remote sensing which is achieved by aeronautics and space platforms, the Red and Near-infrared (NIR) bands, such as NDVI (Normalized Difference Vegetation Index), are useful to distinguish vegetation and clouds, amongst other targets. However, especially in the ground platform, CIR (Color Infra Red) is little utilized by compute vision and digital photogrammetry which usually only take true color RBG into account. Therefore whether CIR is necessary for vegetation segmentation or not has significance in that most of close-range cameras don't contain such NIR band. Moreover, the CIE L*a*b color space, which transform from RGB, seems not of much interest by photogrammetrists despite its powerfulness in image classification and analysis. So, CIE (L, a, b) feature and support vector machine (SVM) is suggested for vegetation segmentation to substitute for CIR. Finally, experimental results of visual effect and automation are given. The conclusion is that it's feasible to remove and segment vegetation occlusion without NIR band. This work should pave the way for texture reconstruction and repair for future 3D reconstruction.

Shape: A 3D Modeling Tool for Astrophysics.

PubMed

Steffen, Wolfgang; Koning, Nicholas; Wenger, Stephan; Morisset, Christophe; Magnor, Marcus

2011-04-01

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type, and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.

3D Tracking of Mating Events in Wild Swarms of the Malaria Mosquito Anopheles gambiae

PubMed Central

Butail, Sachit; Manoukis, Nicholas; Diallo, Moussa; Yaro, Alpha S.; Dao, Adama; Traoré, Sekou F.; Ribeiro, José M.; Lehmann, Tovi; Paley, Derek A.

2013-01-01

We describe an automated tracking system that allows us to reconstruct the 3D kinematics of individual mosquitoes in swarms of Anopheles gambiae. The inputs to the tracking system are video streams recorded from a stereo camera system. The tracker uses a two-pass procedure to automatically localize and track mosquitoes within the swarm. A human-in-the-loop step verifies the estimates and connects broken tracks. The tracker performance is illustrated using footage of mating events filmed in Mali in August 2010. PMID:22254411

3D Medical Collaboration Technology to Enhance Emergency Healthcare

PubMed Central

Welch, Greg; Sonnenwald, Diane H; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Söderholm, Hanna M.; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Ampalam, Manoj; Krishnan, Srinivas; Noel, Vincent; Noland, Michael; Manning, James E.

2009-01-01

Two-dimensional (2D) videoconferencing has been explored widely in the past 15–20 years to support collaboration in healthcare. Two issues that arise in most evaluations of 2D videoconferencing in telemedicine are the difficulty obtaining optimal camera views and poor depth perception. To address these problems, we are exploring the use of a small array of cameras to reconstruct dynamic three-dimensional (3D) views of a remote environment and of events taking place within. The 3D views could be sent across wired or wireless networks to remote healthcare professionals equipped with fixed displays or with mobile devices such as personal digital assistants (PDAs). The remote professionals’ viewpoints could be specified manually or automatically (continuously) via user head or PDA tracking, giving the remote viewers head-slaved or hand-slaved virtual cameras for monoscopic or stereoscopic viewing of the dynamic reconstructions. We call this idea remote 3D medical collaboration. In this article we motivate and explain the vision for 3D medical collaboration technology; we describe the relevant computer vision, computer graphics, display, and networking research; we present a proof-of-concept prototype system; and we present evaluation results supporting the general hypothesis that 3D remote medical collaboration technology could offer benefits over conventional 2D videoconferencing in emergency healthcare. PMID:19521951

3D medical collaboration technology to enhance emergency healthcare.

PubMed

Welch, Gregory F; Sonnenwald, Diane H; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Söderholm, Hanna M; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Ampalam, Manoj K; Krishnan, Srinivas; Noel, Vincent; Noland, Michael; Manning, James E

2009-04-19

Two-dimensional (2D) videoconferencing has been explored widely in the past 15-20 years to support collaboration in healthcare. Two issues that arise in most evaluations of 2D videoconferencing in telemedicine are the difficulty obtaining optimal camera views and poor depth perception. To address these problems, we are exploring the use of a small array of cameras to reconstruct dynamic three-dimensional (3D) views of a remote environment and of events taking place within. The 3D views could be sent across wired or wireless networks to remote healthcare professionals equipped with fixed displays or with mobile devices such as personal digital assistants (PDAs). The remote professionals' viewpoints could be specified manually or automatically (continuously) via user head or PDA tracking, giving the remote viewers head-slaved or hand-slaved virtual cameras for monoscopic or stereoscopic viewing of the dynamic reconstructions. We call this idea remote 3D medical collaboration. In this article we motivate and explain the vision for 3D medical collaboration technology; we describe the relevant computer vision, computer graphics, display, and networking research; we present a proof-of-concept prototype system; and we present evaluation results supporting the general hypothesis that 3D remote medical collaboration technology could offer benefits over conventional 2D videoconferencing in emergency healthcare.

3D road marking reconstruction from street-level calibrated stereo pairs

NASA Astrophysics Data System (ADS)

Soheilian, Bahman; Paparoditis, Nicolas; Boldo, Didier

This paper presents an automatic approach to road marking reconstruction using stereo pairs acquired by a mobile mapping system in a dense urban area. Two types of road markings were studied: zebra crossings (crosswalks) and dashed lines. These two types of road markings consist of strips having known shape and size. These geometric specifications are used to constrain the recognition of strips. In both cases (i.e. zebra crossings and dashed lines), the reconstruction method consists of three main steps. The first step extracts edge points from the left and right images of a stereo pair and computes 3D linked edges using a matching process. The second step comprises a filtering process that uses the known geometric specifications of road marking objects. The goal is to preserve linked edges that can plausibly belong to road markings and to filter others out. The final step uses the remaining linked edges to fit a theoretical model to the data. The method developed has been used for processing a large number of images. Road markings are successfully and precisely reconstructed in dense urban areas under real traffic conditions.

Efficient workflows for 3D building full-color model reconstruction using LIDAR long-range laser and image-based modeling techniques

NASA Astrophysics Data System (ADS)

Shih, Chihhsiong

2005-01-01

Two efficient workflow are developed for the reconstruction of a 3D full color building model. One uses a point wise sensing device to sample an unknown object densely and attach color textures from a digital camera separately. The other uses an image based approach to reconstruct the model with color texture automatically attached. The point wise sensing device reconstructs the CAD model using a modified best view algorithm that collects the maximum number of construction faces in one view. The partial views of the point clouds data are then glued together using a common face between two consecutive views. Typical overlapping mesh removal and coarsening procedures are adapted to generate a unified 3D mesh shell structure. A post processing step is then taken to combine the digital image content from a separate camera with the 3D mesh shell surfaces. An indirect uv mapping procedure first divide the model faces into groups within which every face share the same normal direction. The corresponding images of these faces in a group is then adjusted using the uv map as a guidance. The final assembled image is then glued back to the 3D mesh to present a full colored building model. The result is a virtual building that can reflect the true dimension and surface material conditions of a real world campus building. The image based modeling procedure uses a commercial photogrammetry package to reconstruct the 3D model. A novel view planning algorithm is developed to guide the photos taking procedure. This algorithm successfully generate a minimum set of view angles. The set of pictures taken at these view angles can guarantee that each model face shows up at least in two of the pictures set and no more than three. The 3D model can then be reconstructed with minimum amount of labor spent in correlating picture pairs. The finished model is compared with the original object in both the topological and dimensional aspects. All the test cases show exact same topology and reasonably low dimension error ratio. Again proving the applicability of the algorithm.

Data-driven sampling method for building 3D anatomical models from serial histology

NASA Astrophysics Data System (ADS)

Salunke, Snehal Ulhas; Ablove, Tova; Danforth, Theresa; Tomaszewski, John; Doyle, Scott

2017-03-01

In this work, we investigate the effect of slice sampling on 3D models of tissue architecture using serial histopathology. We present a method for using a single fully-sectioned tissue block as pilot data, whereby we build a fully-realized 3D model and then determine the optimal set of slices needed to reconstruct the salient features of the model objects under biological investigation. In our work, we are interested in the 3D reconstruction of microvessel architecture in the trigone region between the vagina and the bladder. This region serves as a potential avenue for drug delivery to treat bladder infection. We collect and co-register 23 serial sections of CD31-stained tissue images (6 μm thick sections), from which four microvessels are selected for analysis. To build each model, we perform semi-automatic segmentation of the microvessels. Subsampled meshes are then created by removing slices from the stack, interpolating the missing data, and re-constructing the mesh. We calculate the Hausdorff distance between the full and subsampled meshes to determine the optimal sampling rate for the modeled structures. In our application, we found that a sampling rate of 50% (corresponding to just 12 slices) was sufficient to recreate the structure of the microvessels without significant deviation from the fullyrendered mesh. This pipeline effectively minimizes the number of histopathology slides required for 3D model reconstruction, and can be utilized to either (1) reduce the overall costs of a project, or (2) enable additional analysis on the intermediate slides.

Three-dimensional reconstruction of teeth and jaws based on segmentation of CT images using watershed transformation.

PubMed

Naumovich, S S; Naumovich, S A; Goncharenko, V G

2015-01-01

The objective of the present study was the development and clinical testing of a three-dimensional (3D) reconstruction method of teeth and a bone tissue of the jaw on the basis of CT images of the maxillofacial region. 3D reconstruction was performed using the specially designed original software based on watershed transformation. Computed tomograms in digital imaging and communications in medicine format obtained on multispiral CT and CBCT scanners were used for creation of 3D models of teeth and the jaws. The processing algorithm is realized in the stepwise threshold image segmentation with the placement of markers in the mode of a multiplanar projection in areas relating to the teeth and a bone tissue. The developed software initially creates coarse 3D models of the entire dentition and the jaw. Then, certain procedures specify the model of the jaw and cut the dentition into separate teeth. The proper selection of the segmentation threshold is very important for CBCT images having a low contrast and high noise level. The developed semi-automatic algorithm of multispiral and cone beam computed tomogram processing allows 3D models of teeth to be created separating them from a bone tissue of the jaws. The software is easy to install in a dentist's workplace, has an intuitive interface and takes little time in processing. The obtained 3D models can be used for solving a wide range of scientific and clinical tasks.

Optimized satellite image compression and reconstruction via evolution strategies

NASA Astrophysics Data System (ADS)

Babb, Brendan; Moore, Frank; Peterson, Michael

2009-05-01

This paper describes the automatic discovery, via an Evolution Strategy with Covariance Matrix Adaptation (CMA-ES), of vectors of real-valued coefficients representing matched forward and inverse transforms that outperform the 9/7 Cohen-Daubechies-Feauveau (CDF) discrete wavelet transform (DWT) for satellite image compression and reconstruction under conditions subject to quantization error. The best transform evolved during this study reduces the mean squared error (MSE) present in reconstructed satellite images by an average of 33.78% (1.79 dB), while maintaining the average information entropy (IE) of compressed images at 99.57% in comparison to the wavelet. In addition, this evolved transform achieves 49.88% (3.00 dB) average MSE reduction when tested on 80 images from the FBI fingerprint test set, and 42.35% (2.39 dB) average MSE reduction when tested on a set of 18 digital photographs, while achieving average IE of 104.36% and 100.08%, respectively. These results indicate that our evolved transform greatly improves the quality of reconstructed images without substantial loss of compression capability over a broad range of image classes.

Current status of 3D EPID-based in vivo dosimetry in The Netherlands Cancer Institute

NASA Astrophysics Data System (ADS)

Mijnheer, B.; Olaciregui-Ruiz, I.; Rozendaal, R.; Spreeuw, H.; van Herk, M.; Mans, A.

2015-01-01

3D in vivo dose verification using a-Si EPIDs is performed routinely in our institution for almost all RT treatments. The EPID-based 3D dose distribution is reconstructed using a back-projection algorithm and compared with the planned dose distribution using 3D gamma evaluation. Dose-reconstruction and gamma-evaluation software runs automatically, and deviations outside the alert criteria are immediately available and investigated, in combination with inspection of cone-beam CT scans. The implementation of our 3D EPID- based in vivo dosimetry approach was able to replace pre-treatment verification for more than 90% of the patient treatments. Clinically relevant deviations could be detected for approximately 1 out of 300 patient treatments (IMRT and VMAT). Most of these errors were patient related anatomical changes or deviations from the routine clinical procedure, and would not have been detected by pre-treatment verification. Moreover, 3D EPID-based in vivo dose verification is a fast and accurate tool to assure the safe delivery of RT treatments. It provides clinically more useful information and is less time consuming than pre-treatment verification measurements. Automated 3D in vivo dosimetry is therefore a prerequisite for large-scale implementation of patient-specific quality assurance of RT treatments.

Browsing Through Closed Books: Evaluation of Preprocessing Methods for Page Extraction of a 3-D CT Book Volume

NASA Astrophysics Data System (ADS)

Stromer, D.; Christlein, V.; Schön, T.; Holub, W.; Maier, A.

2017-09-01

It is often the case that a document can not be opened, page-turned or touched anymore due to damages caused by aging processes, moisture or fire. To counter this, special imaging systems can be used. One of our earlier work revealed that a common 3-D X-ray micro-CT scanner is well suited for imaging and reconstructing historical documents written with iron gall ink - an ink consisting of metallic particles. We acquired a volume of a self-made book without opening or page-turning with a single 3-D scan. However, when investigating the reconstructed volume, we faced the problem of a proper automatic extraction of single pages within the volume in an acceptable time without losing information of the writings. Within this work, we evaluate different appropriate pre-processing methods with respect to computation time and accuracy which are decisive for a proper extraction of book pages from the reconstructed X-ray volume and the subsequent ink identification. The different methods were tested for an extreme case with low resolution, noisy input data and wavy pages. Finally, we present results of the page extraction after applying the evaluated methods.

Geometry Processing of Conventionally Produced Mouse Brain Slice Images.

PubMed

Agarwal, Nitin; Xu, Xiangmin; Gopi, M

2018-04-21

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as one of the application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. To the best of our knowledge the presented work is the first that automatically registers both clean as well as highly damaged high-resolutions histological slices of mouse brain to a 3D annotated reference atlas space. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data. Copyright © 2018 Elsevier B.V. All rights reserved.

Image-Based Modeling Techniques for Architectural Heritage 3d Digitalization: Limits and Potentialities

NASA Astrophysics Data System (ADS)

Santagati, C.; Inzerillo, L.; Di Paola, F.

2013-07-01

3D reconstruction from images has undergone a revolution in the last few years. Computer vision techniques use photographs from data set collection to rapidly build detailed 3D models. The simultaneous applications of different algorithms (MVS), the different techniques of image matching, feature extracting and mesh optimization are inside an active field of research in computer vision. The results are promising: the obtained models are beginning to challenge the precision of laser-based reconstructions. Among all the possibilities we can mainly distinguish desktop and web-based packages. Those last ones offer the opportunity to exploit the power of cloud computing in order to carry out a semi-automatic data processing, thus allowing the user to fulfill other tasks on its computer; whereas desktop systems employ too much processing time and hard heavy approaches. Computer vision researchers have explored many applications to verify the visual accuracy of 3D model but the approaches to verify metric accuracy are few and no one is on Autodesk 123D Catch applied on Architectural Heritage Documentation. Our approach to this challenging problem is to compare the 3Dmodels by Autodesk 123D Catch and 3D models by terrestrial LIDAR considering different object size, from the detail (capitals, moldings, bases) to large scale buildings for practitioner purpose.

Co-Registration of DSMs Generated by Uav and Terrestrial Laser Scanning Systems

NASA Astrophysics Data System (ADS)

Ancil Persad, Ravi; Armenakis, Costas

2016-06-01

An approach for the co-registration of Digital Surface Models (DSMs) derived from Unmanned Aerial Vehicles (UAVs) and Terrestrial Laser Scanners (TLS) is proposed. Specifically, a wavelet-based feature descriptor for matching surface keypoints on the 2.5D DSMs is developed. DSMs are useful in wide-scope of various applications such as 3D building modelling and reconstruction, cultural heritage, urban and environmental planning, aircraft navigation/path routing, accident and crime scene reconstruction, mining as well as, topographic map revision and change detection. For these listed applications, it is not uncommon that there will be a need for automatically aligning multi-temporal DSMs which may have been acquired from multiple sensors, with different specifications over a period of time, and may have various overlaps. Terrestrial laser scanners usually capture urban facades in an accurate manner; however this is not the case for building roof structures. On the other hand, vertical photography from UAVs can capture the roofs. Therefore, the automatic fusion of UAV and laser-scanning based DSMs is addressed here as it serves various geospatial applications.

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages

PubMed Central

Nunez-Iglesias, Juan; Kennedy, Ryan; Plaza, Stephen M.; Chakraborty, Anirban; Katz, William T.

2014-01-01

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them. PMID:24772079

2D virtual texture on 3D real object with coded structured light

NASA Astrophysics Data System (ADS)

Molinier, Thierry; Fofi, David; Salvi, Joaquim; Gorria, Patrick

2008-02-01

Augmented reality is used to improve color segmentation on human body or on precious no touch artifacts. We propose a technique to project a synthesized texture on real object without contact. Our technique can be used in medical or archaeological application. By projecting a suitable set of light patterns onto the surface of a 3D real object and by capturing images with a camera, a large number of correspondences can be found and the 3D points can be reconstructed. We aim to determine these points of correspondence between cameras and projector from a scene without explicit points and normals. We then project an adjusted texture onto the real object surface. We propose a global and automatic method to virtually texture a 3D real object.

An Automatic Image-Based Modelling Method Applied to Forensic Infography

PubMed Central

Zancajo-Blazquez, Sandra; Gonzalez-Aguilera, Diego; Gonzalez-Jorge, Higinio; Hernandez-Lopez, David

2015-01-01

This paper presents a new method based on 3D reconstruction from images that demonstrates the utility and integration of close-range photogrammetry and computer vision as an efficient alternative to modelling complex objects and scenarios of forensic infography. The results obtained confirm the validity of the method compared to other existing alternatives as it guarantees the following: (i) flexibility, permitting work with any type of camera (calibrated and non-calibrated, smartphone or tablet) and image (visible, infrared, thermal, etc.); (ii) automation, allowing the reconstruction of three-dimensional scenarios in the absence of manual intervention, and (iii) high quality results, sometimes providing higher resolution than modern laser scanning systems. As a result, each ocular inspection of a crime scene with any camera performed by the scientific police can be transformed into a scaled 3d model. PMID:25793628

Model-based conifer crown surface reconstruction from multi-ocular high-resolution aerial imagery

NASA Astrophysics Data System (ADS)

Sheng, Yongwei

2000-12-01

Tree crown parameters such as width, height, shape and crown closure are desirable in forestry and ecological studies, but they are time-consuming and labor intensive to measure in the field. The stereoscopic capability of high-resolution aerial imagery provides a way to crown surface reconstruction. Existing photogrammetric algorithms designed to map terrain surfaces, however, cannot adequately extract crown surfaces, especially for steep conifer crowns. Considering crown surface reconstruction in a broader context of tree characterization from aerial images, we develop a rigorous perspective tree image formation model to bridge image-based tree extraction and crown surface reconstruction, and an integrated model-based approach to conifer crown surface reconstruction. Based on the fact that most conifer crowns are in a solid geometric form, conifer crowns are modeled as a generalized hemi-ellipsoid. Both the automatic and semi-automatic approaches are investigated to optimal tree model development from multi-ocular images. The semi-automatic 3D tree interpreter developed in this thesis is able to efficiently extract reliable tree parameters and tree models in complicated tree stands. This thesis starts with a sophisticated stereo matching algorithm, and incorporates tree models to guide stereo matching. The following critical problems are addressed in the model-based surface reconstruction process: (1) the problem of surface model composition from tree models, (2) the occlusion problem in disparity prediction from tree models, (3) the problem of integrating the predicted disparities into image matching, (4) the tree model edge effect reduction on the disparity map, (5) the occlusion problem in orthophoto production, and (6) the foreshortening problem in image matching, which is very serious for conifer crown surfaces. Solutions to the above problems are necessary for successful crown surface reconstruction. The model-based approach was applied to recover the canopy surface of a dense redwood stand using tri-ocular high-resolution images scanned from 1:2,400 aerial photographs. The results demonstrate the approach's ability to reconstruct complicated stands. The model-based approach proposed in this thesis is potentially applicable to other surfaces recovering problems with a priori knowledge about objects.

Three-dimensional reconstruction of coronary stents in vivo based on motion compensated X-ray angiography

NASA Astrophysics Data System (ADS)

Schäfer, Dirk; Movassaghi, Babak; Grass, Michael; Schoonenberg, Gert; Florent, Raoul; Wink, Onno; Klein, Andrew J. P.; Chen, James Y.; Garcia, Joel; Messenger, John C.; Carroll, John D.

2007-03-01

The complete expansion of the stent during a percutaneous transluminal coronary angioplasty (PTCA) procedure is essential for treatment of a stenotic segment of a coronary artery. Inadequate expansion of the stent is a major predisposing factor to in-stent restenosis and acute thrombosis. Stents are positioned and deployed by fluoroscopic guidance. Although the current generation of stents are made of materials with some degree of radio-opacity to detect their location after deployment, proper stent expansion is hard to asses. In this work, we introduce a new method for the three-dimensional (3D) reconstruction of the coronary stents in-vivo utilizing two-dimensional projection images acquired during rotational angiography (RA). The acquisition protocol consist of a propeller rotation of the X-ray C-arm system of 180°, which ensures sufficient angular coverage for volume reconstruction. The angiographic projections were acquired at 30 frames per second resulting in 180 projections during a 7 second rotational run. The motion of the stent is estimated from the automatically tracked 2D coordinates of the markers on the balloon catheter. This information is used within a motion-compensated reconstruction algorithm. Therefore, projections from different cardiac phases and motion states can be used, resulting in improved signal-to-noise ratio of the stent. Results of 3D reconstructed coronary stents in vivo, with high spatial resolution are presented. The proposed method allows for a comprehensive and unique quantitative 3D assessment of stent expansion that rivals current X-ray and intravascular ultrasound techniques.

Interactive High-Relief Reconstruction for Organic and Double-Sided Objects from a Photo.

PubMed

Yeh, Chih-Kuo; Huang, Shi-Yang; Jayaraman, Pradeep Kumar; Fu, Chi-Wing; Lee, Tong-Yee

2017-07-01

We introduce an interactive user-driven method to reconstruct high-relief 3D geometry from a single photo. Particularly, we consider two novel but challenging reconstruction issues: i) common non-rigid objects whose shapes are organic rather than polyhedral/symmetric, and ii) double-sided structures, where front and back sides of some curvy object parts are revealed simultaneously on image. To address these issues, we develop a three-stage computational pipeline. First, we construct a 2.5D model from the input image by user-driven segmentation, automatic layering, and region completion, handling three common types of occlusion. Second, users can interactively mark-up slope and curvature cues on the image to guide our constrained optimization model to inflate and lift up the image layers. We provide real-time preview of the inflated geometry to allow interactive editing. Third, we stitch and optimize the inflated layers to produce a high-relief 3D model. Compared to previous work, we can generate high-relief geometry with large viewing angles, handle complex organic objects with multiple occluded regions and varying shape profiles, and reconstruct objects with double-sided structures. Lastly, we demonstrate the applicability of our method on a wide variety of input images with human, animals, flowers, etc.

Reconstructing liver shape and position from MR image slices using an active shape model

NASA Astrophysics Data System (ADS)

Fenchel, Matthias; Thesen, Stefan; Schilling, Andreas

2008-03-01

We present an algorithm for fully automatic reconstruction of 3D position, orientation and shape of the human liver from a sparsely covering set of n 2D MR slice images. Reconstructing the shape of an organ from slice images can be used for scan planning, for surgical planning or other purposes where 3D anatomical knowledge has to be inferred from sparse slices. The algorithm is based on adapting an active shape model of the liver surface to a given set of slice images. The active shape model is created from a training set of liver segmentations from a group of volunteers. The training set is set up with semi-manual segmentations of T1-weighted volumetric MR images. Searching for the optimal shape model that best fits to the image data is done by maximizing a similarity measure based on local appearance at the surface. Two different algorithms for the active shape model search are proposed and compared: both algorithms seek to maximize the a-posteriori probability of the grey level appearance around the surface while constraining the surface to the space of valid shapes. The first algorithm works by using grey value profile statistics in normal direction. The second algorithm uses average and variance images to calculate the local surface appearance on the fly. Both algorithms are validated by fitting the active shape model to abdominal 2D slice images and comparing the shapes, which have been reconstructed, to the manual segmentations and to the results of active shape model searches from 3D image data. The results turn out to be promising and competitive to active shape model segmentations from 3D data.

Photogrammetry-Based Head Digitization for Rapid and Accurate Localization of EEG Electrodes and MEG Fiducial Markers Using a Single Digital SLR Camera.

PubMed

Clausner, Tommy; Dalal, Sarang S; Crespo-García, Maité

2017-01-01

The performance of EEG source reconstruction has benefited from the increasing use of advanced head modeling techniques that take advantage of MRI together with the precise positions of the recording electrodes. The prevailing technique for registering EEG electrode coordinates involves electromagnetic digitization. However, the procedure adds several minutes to experiment preparation and typical digitizers may not be accurate enough for optimal source reconstruction performance (Dalal et al., 2014). Here, we present a rapid, accurate, and cost-effective alternative method to register EEG electrode positions, using a single digital SLR camera, photogrammetry software, and computer vision techniques implemented in our open-source toolbox, janus3D . Our approach uses photogrammetry to construct 3D models from multiple photographs of the participant's head wearing the EEG electrode cap. Electrodes are detected automatically or semi-automatically using a template. The rigid facial features from these photo-based models are then surface-matched to MRI-based head reconstructions to facilitate coregistration to MRI space. This method yields a final electrode coregistration error of 0.8 mm, while a standard technique using an electromagnetic digitizer yielded an error of 6.1 mm. The technique furthermore reduces preparation time, and could be extended to a multi-camera array, which would make the procedure virtually instantaneous. In addition to EEG, the technique could likewise capture the position of the fiducial markers used in magnetoencephalography systems to register head position.

Photogrammetry-Based Head Digitization for Rapid and Accurate Localization of EEG Electrodes and MEG Fiducial Markers Using a Single Digital SLR Camera

PubMed Central

Clausner, Tommy; Dalal, Sarang S.; Crespo-García, Maité

2017-01-01

The performance of EEG source reconstruction has benefited from the increasing use of advanced head modeling techniques that take advantage of MRI together with the precise positions of the recording electrodes. The prevailing technique for registering EEG electrode coordinates involves electromagnetic digitization. However, the procedure adds several minutes to experiment preparation and typical digitizers may not be accurate enough for optimal source reconstruction performance (Dalal et al., 2014). Here, we present a rapid, accurate, and cost-effective alternative method to register EEG electrode positions, using a single digital SLR camera, photogrammetry software, and computer vision techniques implemented in our open-source toolbox, janus3D. Our approach uses photogrammetry to construct 3D models from multiple photographs of the participant's head wearing the EEG electrode cap. Electrodes are detected automatically or semi-automatically using a template. The rigid facial features from these photo-based models are then surface-matched to MRI-based head reconstructions to facilitate coregistration to MRI space. This method yields a final electrode coregistration error of 0.8 mm, while a standard technique using an electromagnetic digitizer yielded an error of 6.1 mm. The technique furthermore reduces preparation time, and could be extended to a multi-camera array, which would make the procedure virtually instantaneous. In addition to EEG, the technique could likewise capture the position of the fiducial markers used in magnetoencephalography systems to register head position. PMID:28559791

Accelerated Optical Projection Tomography Applied to In Vivo Imaging of Zebrafish

PubMed Central

Correia, Teresa; Yin, Jun; Ramel, Marie-Christine; Andrews, Natalie; Katan, Matilda; Bugeon, Laurence; Dallman, Margaret J.; McGinty, James; Frankel, Paul; French, Paul M. W.; Arridge, Simon

2015-01-01

Optical projection tomography (OPT) provides a non-invasive 3-D imaging modality that can be applied to longitudinal studies of live disease models, including in zebrafish. Current limitations include the requirement of a minimum number of angular projections for reconstruction of reasonable OPT images using filtered back projection (FBP), which is typically several hundred, leading to acquisition times of several minutes. It is highly desirable to decrease the number of required angular projections to decrease both the total acquisition time and the light dose to the sample. This is particularly important to enable longitudinal studies, which involve measurements of the same fish at different time points. In this work, we demonstrate that the use of an iterative algorithm to reconstruct sparsely sampled OPT data sets can provide useful 3-D images with 50 or fewer projections, thereby significantly decreasing the minimum acquisition time and light dose while maintaining image quality. A transgenic zebrafish embryo with fluorescent labelling of the vasculature was imaged to acquire densely sampled (800 projections) and under-sampled data sets of transmitted and fluorescence projection images. The under-sampled OPT data sets were reconstructed using an iterative total variation-based image reconstruction algorithm and compared against FBP reconstructions of the densely sampled data sets. To illustrate the potential for quantitative analysis following rapid OPT data acquisition, a Hessian-based method was applied to automatically segment the reconstructed images to select the vasculature network. Results showed that 3-D images of the zebrafish embryo and its vasculature of sufficient visual quality for quantitative analysis can be reconstructed using the iterative algorithm from only 32 projections—achieving up to 28 times improvement in imaging speed and leading to total acquisition times of a few seconds. PMID:26308086

A 3D reconstruction of pancreas development in the human embryos during embryonic period (Carnegie stages 15-23).

PubMed

Radi, M; Gaubert, J; Cristol-Gaubert, R; Baecker, V; Travo, P; Prudhomme, M; Godlewski, G; Prat-Pradal, D

2010-01-01

The goal in this paper was to rebuild a three dimensional (3D) reconstruction of the dorsal and ventral pancreatic buds, in the human embryos, at Carnegie stages 15-23. The early development of the pancreas is studied by tissue observation and reconstruction by a computer-assisted method, using a light micrograph images from consecutive serial sagittal sections (diameter 7 microm) of ten human embryos ranging from Carnegie stages 15-23, CRL 7-27 mm, fixed, dehydrated and embedded in paraffin, were stained alternately with haematoxylin-eosin or Heindenhain'Azan. The images were digitalized by Canon Camera 350 EOS D. The serial views were aligned automatically by software, manual alignment was performed, the data were analysed following segmentation and threshold. The two buds were clearly identified at stage 15. In stage 16, both pancreatic buds were in final position, and begin to merge in stage 17. From stage 18 to the stage 23, surrounding connective tissue differentiated. In the stage 23, the morphology of the pancreas was definitive. The superior portion of the anterior face of the pancreas's head was arising from the dorsal bud. The rest of the head including the uncinate process emanated from the ventral bud. The 3D computer-assisted reconstruction of the human pancreas visualized the relationships between the two pancreatic buds. This explains the disposition and the modality of the components fusion. This embryologic development permits a better understanding of congenital abnormalities.

SF3M 2.0: improvement of 3D photo-reconstruction interface based on freely available software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael R.; Pérez, Rafael; Gómez, Jose A.

2016-04-01

During recent years, a number of tools based on Structure-from-Motion algorithms have been released for full image-based 3D reconstruction either freely (e.g. Bundler, PMVS2, VisualSFM, MicMac) or commercially (e.g. Agisoft PhotoScan). The SF3M interface was developed in Matlab® to use link software developments (VisualSFM, CloudCompare) and new applications to create a semi-automated workflow including reconstruction, georeferencing and point-cloud filtering, and has been tested for gully erosion assessment with terrestrial images (Castillo et al., 2015). The main aim of this work to provide an improved freely-available and easy-to-use alternative for 3D reconstruction intended for public agencies, non-profit organisations, researchers and other stakeholders interested in 3D modelling. In this communication we present SF3M 2.0, a new version of the graphical user interface. In this case, the SfM module is based on MicMac, an open-software tool (Pierrot-Deseilligny and Cléry, 2011) which provides advanced features such as camera calibration and constrained bundle adjustment using ground control points. SF3M 2.0 will be tested in two scenarios: a) using the same ground-based image set tested in Castillo et al. (2015) to compare the performance of both versions and b) using aerial images taken from a helium balloon to assess a gully network in a 40-hectares catchment. In this study we explore the advantages of SF3M 2.0, explain its operation and evaluate its accuracy and performance. This tool will be also available for free download. References Castillo, C., James, M.R., Redel-Macías, M. D., Pérez, R., and Gómez, J.A.: SF3M software: 3-D photo-reconstruction for non-expert users and its application to a gully network, SOIL, 1, 583-594. Pierrot-Deseilligny, M and Cléry, I. APERO, an Open Source Bundle Adjusment Software for Automatic Calibration and Orientation of a Set of Images. Proceedings of the ISPRS Commission V Symposium, Image Engineering and Vision Metrology, Trento, Italy, 2-4 March 2011.

Large Scale Textured Mesh Reconstruction from Mobile Mapping Images and LIDAR Scans

NASA Astrophysics Data System (ADS)

Boussaha, M.; Vallet, B.; Rives, P.

2018-05-01

The representation of 3D geometric and photometric information of the real world is one of the most challenging and extensively studied research topics in the photogrammetry and robotics communities. In this paper, we present a fully automatic framework for 3D high quality large scale urban texture mapping using oriented images and LiDAR scans acquired by a terrestrial Mobile Mapping System (MMS). First, the acquired points and images are sliced into temporal chunks ensuring a reasonable size and time consistency between geometry (points) and photometry (images). Then, a simple, fast and scalable 3D surface reconstruction relying on the sensor space topology is performed on each chunk after an isotropic sampling of the point cloud obtained from the raw LiDAR scans. Finally, the algorithm proposed in (Waechter et al., 2014) is adapted to texture the reconstructed surface with the images acquired simultaneously, ensuring a high quality texture with no seams and global color adjustment. We evaluate our full pipeline on a dataset of 17 km of acquisition in Rouen, France resulting in nearly 2 billion points and 40000 full HD images. We are able to reconstruct and texture the whole acquisition in less than 30 computing hours, the entire process being highly parallel as each chunk can be processed independently in a separate thread or computer.

A graph edit dictionary for correcting errors in roof topology graphs reconstructed from point clouds

NASA Astrophysics Data System (ADS)

Xiong, B.; Oude Elberink, S.; Vosselman, G.

2014-07-01

In the task of 3D building model reconstruction from point clouds we face the problem of recovering a roof topology graph in the presence of noise, small roof faces and low point densities. Errors in roof topology graphs will seriously affect the final modelling results. The aim of this research is to automatically correct these errors. We define the graph correction as a graph-to-graph problem, similar to the spelling correction problem (also called the string-to-string problem). The graph correction is more complex than string correction, as the graphs are 2D while strings are only 1D. We design a strategy based on a dictionary of graph edit operations to automatically identify and correct the errors in the input graph. For each type of error the graph edit dictionary stores a representative erroneous subgraph as well as the corrected version. As an erroneous roof topology graph may contain several errors, a heuristic search is applied to find the optimum sequence of graph edits to correct the errors one by one. The graph edit dictionary can be expanded to include entries needed to cope with errors that were previously not encountered. Experiments show that the dictionary with only fifteen entries already properly corrects one quarter of erroneous graphs in about 4500 buildings, and even half of the erroneous graphs in one test area, achieving as high as a 95% acceptance rate of the reconstructed models.

Automated UAV-based video exploitation using service oriented architecture framework

NASA Astrophysics Data System (ADS)

Se, Stephen; Nadeau, Christian; Wood, Scott

2011-05-01

Airborne surveillance and reconnaissance are essential for successful military missions. Such capabilities are critical for troop protection, situational awareness, mission planning, damage assessment, and others. Unmanned Aerial Vehicles (UAVs) gather huge amounts of video data but it is extremely labour-intensive for operators to analyze hours and hours of received data. At MDA, we have developed a suite of tools that can process the UAV video data automatically, including mosaicking, change detection and 3D reconstruction, which have been integrated within a standard GIS framework. In addition, the mosaicking and 3D reconstruction tools have also been integrated in a Service Oriented Architecture (SOA) framework. The Visualization and Exploitation Workstation (VIEW) integrates 2D and 3D visualization, processing, and analysis capabilities developed for UAV video exploitation. Visualization capabilities are supported through a thick-client Graphical User Interface (GUI), which allows visualization of 2D imagery, video, and 3D models. The GUI interacts with the VIEW server, which provides video mosaicking and 3D reconstruction exploitation services through the SOA framework. The SOA framework allows multiple users to perform video exploitation by running a GUI client on the operator's computer and invoking the video exploitation functionalities residing on the server. This allows the exploitation services to be upgraded easily and allows the intensive video processing to run on powerful workstations. MDA provides UAV services to the Canadian and Australian forces in Afghanistan with the Heron, a Medium Altitude Long Endurance (MALE) UAV system. On-going flight operations service provides important intelligence, surveillance, and reconnaissance information to commanders and front-line soldiers.

a Critical Review of Automated Photogrammetric Processing of Large Datasets

NASA Astrophysics Data System (ADS)

Remondino, F.; Nocerino, E.; Toschi, I.; Menna, F.

2017-08-01

The paper reports some comparisons between commercial software able to automatically process image datasets for 3D reconstruction purposes. The main aspects investigated in the work are the capability to correctly orient large sets of image of complex environments, the metric quality of the results, replicability and redundancy. Different datasets are employed, each one featuring a diverse number of images, GSDs at cm and mm resolutions, and ground truth information to perform statistical analyses of the 3D results. A summary of (photogrammetric) terms is also provided, in order to provide rigorous terms of reference for comparisons and critical analyses.

The development of an automatically produced cholangiography procedure using the reconstruction of portal-phase multidetector-row computed tomography images: preliminary experience.

PubMed

Hirose, Tomoaki; Igami, Tsuyoshi; Koga, Kusuto; Hayashi, Yuichiro; Ebata, Tomoki; Yokoyama, Yukihiro; Sugawara, Gen; Mizuno, Takashi; Yamaguchi, Junpei; Mori, Kensaku; Nagino, Masato

2017-03-01

Fusion angiography using reconstructed multidetector-row computed tomography (MDCT) images, and cholangiography using reconstructed images from MDCT with a cholangiographic agent include an anatomical gap due to the different periods of MDCT scanning. To conquer such gaps, we attempted to develop a cholangiography procedure that automatically reconstructs a cholangiogram from portal-phase MDCT images. The automatically produced cholangiography procedure utilized an original software program that was developed by the Graduate School of Information Science, Nagoya University. This program structured 5 candidate biliary tracts, and automatically selected one as the candidate for cholangiography. The clinical value of the automatically produced cholangiography procedure was estimated based on a comparison with manually produced cholangiography. Automatically produced cholangiograms were reconstructed for 20 patients who underwent MDCT scanning before biliary drainage for distal biliary obstruction. The procedure showed the ability to extract the 5 main biliary branches and the 21 subsegmental biliary branches in 55 and 25 % of the cases, respectively. The extent of aberrant connections and aberrant extractions outside the biliary tract was acceptable. Among all of the cholangiograms, 5 were clinically applied with no correction, 8 were applied with modest improvements, and 3 produced a correct cholangiography before automatic selection. Although our procedure requires further improvement based on the analysis of additional patient data, it may represent an alternative to direct cholangiography in the future.

Brain tumor segmentation in MR slices using improved GrowCut algorithm

NASA Astrophysics Data System (ADS)

Ji, Chunhong; Yu, Jinhua; Wang, Yuanyuan; Chen, Liang; Shi, Zhifeng; Mao, Ying

2015-12-01

The detection of brain tumor from MR images is very significant for medical diagnosis and treatment. However, the existing methods are mostly based on manual or semiautomatic segmentation which are awkward when dealing with a large amount of MR slices. In this paper, a new fully automatic method for the segmentation of brain tumors in MR slices is presented. Based on the hypothesis of the symmetric brain structure, the method improves the interactive GrowCut algorithm by further using the bounding box algorithm in the pre-processing step. More importantly, local reflectional symmetry is used to make up the deficiency of the bounding box method. After segmentation, 3D tumor image is reconstructed. We evaluate the accuracy of the proposed method on MR slices with synthetic tumors and actual clinical MR images. Result of the proposed method is compared with the actual position of simulated 3D tumor qualitatively and quantitatively. In addition, our automatic method produces equivalent performance as manual segmentation and the interactive GrowCut with manual interference while providing fully automatic segmentation.

Multi-modal imaging, model-based tracking, and mixed reality visualisation for orthopaedic surgery

PubMed Central

Fuerst, Bernhard; Tateno, Keisuke; Johnson, Alex; Fotouhi, Javad; Osgood, Greg; Tombari, Federico; Navab, Nassir

2017-01-01

Orthopaedic surgeons are still following the decades old workflow of using dozens of two-dimensional fluoroscopic images to drill through complex 3D structures, e.g. pelvis. This Letter presents a mixed reality support system, which incorporates multi-modal data fusion and model-based surgical tool tracking for creating a mixed reality environment supporting screw placement in orthopaedic surgery. A red–green–blue–depth camera is rigidly attached to a mobile C-arm and is calibrated to the cone-beam computed tomography (CBCT) imaging space via iterative closest point algorithm. This allows real-time automatic fusion of reconstructed surface and/or 3D point clouds and synthetic fluoroscopic images obtained through CBCT imaging. An adapted 3D model-based tracking algorithm with automatic tool segmentation allows for tracking of the surgical tools occluded by hand. This proposed interactive 3D mixed reality environment provides an intuitive understanding of the surgical site and supports surgeons in quickly localising the entry point and orienting the surgical tool during screw placement. The authors validate the augmentation by measuring target registration error and also evaluate the tracking accuracy in the presence of partial occlusion. PMID:29184659

Patient-specific 3D models created by 3D imaging system or bi-planar imaging coupled with Moiré-Fringe projections: a comparative study of accuracy and reliability on spinal curvatures and vertebral rotation data.

PubMed

Hocquelet, Arnaud; Cornelis, François; Jirot, Anna; Castaings, Laurent; de Sèze, Mathieu; Hauger, Olivier

2016-10-01

The aim of this study is to compare the accuracy and reliability of spinal curvatures and vertebral rotation data based on patient-specific 3D models created by 3D imaging system or by bi-planar imaging coupled with Moiré-Fringe projections. Sixty-two consecutive patients from a single institution were prospectively included. For each patient, frontal and sagittal calibrated low-dose bi-planar X-rays were performed and coupled simultaneously with an optical Moiré back surface-based technology. The 3D reconstructions of spine and pelvis were performed independently by one radiologist and one technician in radiology using two different semi-automatic methods using 3D radio-imaging system (method 1) or bi-planar imaging coupled with Moiré projections (method 2). Both methods were compared using Bland-Altman analysis, and reliability using intraclass correlation coefficient (ICC). ICC showed good to very good agreement. Between the two techniques, the maximum 95 % prediction limits was -4.9° degrees for the measurements of spinal coronal curves and less than 5° for other parameters. Inter-rater reliability was excellent for all parameters across both methods, except for axial rotation with method 2 for which ICC was fair. Method 1 was faster for reconstruction time than method 2 for both readers (13.4 vs. 20.7 min and 10.6 vs. 13.9 min; p = 0.0001). While a lower accuracy was observed for the evaluation of the axial rotation, bi-planar imaging coupled with Moiré-Fringe projections may be an accurate and reliable tool to perform 3D reconstructions of the spine and pelvis.

Automatic correction of echo-planar imaging (EPI) ghosting artifacts in real-time interactive cardiac MRI using sensitivity encoding.

PubMed

Kim, Yoon-Chul; Nielsen, Jon-Fredrik; Nayak, Krishna S

2008-01-01

To develop a method that automatically corrects ghosting artifacts due to echo-misalignment in interleaved gradient-echo echo-planar imaging (EPI) in arbitrary oblique or double-oblique scan planes. An automatic ghosting correction technique was developed based on an alternating EPI acquisition and the phased-array ghost elimination (PAGE) reconstruction method. The direction of k-space traversal is alternated at every temporal frame, enabling lower temporal-resolution ghost-free coil sensitivity maps to be dynamically estimated. The proposed method was compared with conventional one-dimensional (1D) phase correction in axial, oblique, and double-oblique scan planes in phantom and cardiac in vivo studies. The proposed method was also used in conjunction with two-fold acceleration. The proposed method with nonaccelerated acquisition provided excellent suppression of ghosting artifacts in all scan planes, and was substantially more effective than conventional 1D phase correction in oblique and double-oblique scan planes. The feasibility of real-time reconstruction using the proposed technique was demonstrated in a scan protocol with 3.1-mm spatial and 60-msec temporal resolution. The proposed technique with nonaccelerated acquisition provides excellent ghost suppression in arbitrary scan orientations without a calibration scan, and can be useful for real-time interactive imaging, in which scan planes are frequently changed with arbitrary oblique orientations.

Towards automatic SAR-optical stereogrammetry over urban areas using very high resolution imagery

NASA Astrophysics Data System (ADS)

Qiu, Chunping; Schmitt, Michael; Zhu, Xiao Xiang

2018-04-01

In this paper we discuss the potential and challenges regarding SAR-optical stereogrammetry for urban areas, using very-high-resolution (VHR) remote sensing imagery. Since we do this mainly from a geometrical point of view, we first analyze the height reconstruction accuracy to be expected for different stereogrammetric configurations. Then, we propose a strategy for simultaneous tie point matching and 3D reconstruction, which exploits an epipolar-like search window constraint. To drive the matching and ensure some robustness, we combine different established hand-crafted similarity measures. For the experiments, we use real test data acquired by the Worldview-2, TerraSAR-X and MEMPHIS sensors. Our results show that SAR-optical stereogrammetry using VHR imagery is generally feasible with 3D positioning accuracies in the meter-domain, although the matching of these strongly hetereogeneous multi-sensor data remains very challenging.

Towards automatic SAR-optical stereogrammetry over urban areas using very high resolution imagery.

PubMed

Qiu, Chunping; Schmitt, Michael; Zhu, Xiao Xiang

2018-04-01

In this paper we discuss the potential and challenges regarding SAR-optical stereogrammetry for urban areas, using very-high-resolution (VHR) remote sensing imagery. Since we do this mainly from a geometrical point of view, we first analyze the height reconstruction accuracy to be expected for different stereogrammetric configurations. Then, we propose a strategy for simultaneous tie point matching and 3D reconstruction, which exploits an epipolar-like search window constraint. To drive the matching and ensure some robustness, we combine different established hand-crafted similarity measures. For the experiments, we use real test data acquired by the Worldview-2, TerraSAR-X and MEMPHIS sensors. Our results show that SAR-optical stereogrammetry using VHR imagery is generally feasible with 3D positioning accuracies in the meter-domain, although the matching of these strongly hetereogeneous multi-sensor data remains very challenging.

WASS: an open-source stereo processing pipeline for sea waves 3D reconstruction

NASA Astrophysics Data System (ADS)

Bergamasco, Filippo; Benetazzo, Alvise; Torsello, Andrea; Barbariol, Francesco; Carniel, Sandro; Sclavo, Mauro

2017-04-01

Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community. In fact, recent advances of both computer vision algorithms and CPU processing power can now allow the study of the spatio-temporal wave fields with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner so that the implementation of a 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well-tested software package that automates the steps from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS, a completely Open-Source stereo processing pipeline for sea waves 3D reconstruction, available at http://www.dais.unive.it/wass/. Our tool completely automates the recovery of dense point clouds from stereo images by providing three main functionalities. First, WASS can automatically recover the extrinsic parameters of the stereo rig (up to scale) so that no delicate calibration has to be performed on the field. Second, WASS implements a fast 3D dense stereo reconstruction procedure so that an accurate 3D point cloud can be computed from each stereo pair. We rely on the well-consolidated OpenCV library both for the image stereo rectification and disparity map recovery. Lastly, a set of 2D and 3D filtering techniques both on the disparity map and the produced point cloud are implemented to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface (examples are sun-glares, large white-capped areas, fog and water areosol, etc). Developed to be as fast as possible, WASS can process roughly four 5 MPixel stereo frames per minute (on a consumer i7 CPU) to produce a sequence of outlier-free point clouds with more than 3 million points each. Finally, it comes with an easy to use user interface and designed to be scalable on multiple parallel CPUs.

Integrated Fusion, Performance Prediction, and Sensor Management for Automatic Target Exploitation

DTIC Science & Technology

2007-05-30

with large region of attraction about the true minimum. The physical optics models provide features for high confidence identification of stationary...the detection test are used to estimate 3D object scattering; multiple images can be noncoherently combined to reconstruct a more complete object...Proc. SPIE Algorithms for Synthetic Aper- ture Radar Imagery XIII, The International Society for Optical Engineering, April 2006. [40] K. Varshney, M. C

MultiMap: A Tool to Automatically Extract and Analyse Spatial Microscopic Data From Large Stacks of Confocal Microscopy Images

PubMed Central

Varando, Gherardo; Benavides-Piccione, Ruth; Muñoz, Alberto; Kastanauskaite, Asta; Bielza, Concha; Larrañaga, Pedro; DeFelipe, Javier

2018-01-01

The development of 3D visualization and reconstruction methods to analyse microscopic structures at different levels of resolutions is of great importance to define brain microorganization and connectivity. MultiMap is a new tool that allows the visualization, 3D segmentation and quantification of fluorescent structures selectively in the neuropil from large stacks of confocal microscopy images. The major contribution of this tool is the posibility to easily navigate and create regions of interest of any shape and size within a large brain area that will be automatically 3D segmented and quantified to determine the density of puncta in the neuropil. As a proof of concept, we focused on the analysis of glutamatergic and GABAergic presynaptic axon terminals in the mouse hippocampal region to demonstrate its use as a tool to provide putative excitatory and inhibitory synaptic maps. The segmentation and quantification method has been validated over expert labeled images of the mouse hippocampus and over two benchmark datasets, obtaining comparable results to the expert detections. PMID:29875639

MultiMap: A Tool to Automatically Extract and Analyse Spatial Microscopic Data From Large Stacks of Confocal Microscopy Images.

PubMed

Varando, Gherardo; Benavides-Piccione, Ruth; Muñoz, Alberto; Kastanauskaite, Asta; Bielza, Concha; Larrañaga, Pedro; DeFelipe, Javier

2018-01-01

The development of 3D visualization and reconstruction methods to analyse microscopic structures at different levels of resolutions is of great importance to define brain microorganization and connectivity. MultiMap is a new tool that allows the visualization, 3D segmentation and quantification of fluorescent structures selectively in the neuropil from large stacks of confocal microscopy images. The major contribution of this tool is the posibility to easily navigate and create regions of interest of any shape and size within a large brain area that will be automatically 3D segmented and quantified to determine the density of puncta in the neuropil. As a proof of concept, we focused on the analysis of glutamatergic and GABAergic presynaptic axon terminals in the mouse hippocampal region to demonstrate its use as a tool to provide putative excitatory and inhibitory synaptic maps. The segmentation and quantification method has been validated over expert labeled images of the mouse hippocampus and over two benchmark datasets, obtaining comparable results to the expert detections.

Approach of automatic 3D geological mapping: the case of the Kovdor phoscorite-carbonatite complex, NW Russia.

PubMed

Kalashnikov, A O; Ivanyuk, G Yu; Mikhailova, J A; Sokharev, V A

2017-07-31

We have developed an approach for automatic 3D geological mapping based on conversion of chemical composition of rocks to mineral composition by logical computation. It allows to calculate mineral composition based on bulk rock chemistry, interpolate the mineral composition in the same way as chemical composition, and, finally, build a 3D geological model. The approach was developed for the Kovdor phoscorite-carbonatite complex containing the Kovdor baddeleyite-apatite-magnetite deposit. We used 4 bulk rock chemistry analyses - Fe magn , P 2 O 5 , CO 2 and SiO 2 . We used four techniques for prediction of rock types - calculation of normative mineral compositions (norms), multiple regression, artificial neural network and developed by logical evaluation. The two latter became the best. As a result, we distinguished 14 types of phoscorites (forsterite-apatite-magnetite-carbonate rock), carbonatite and host rocks. The results show good convergence with our petrographical studies of the deposit, and recent manually built maps. The proposed approach can be used as a tool of a deposit genesis reconstruction and preliminary geometallurgical modelling.

Segmenting the Femoral Head and Acetabulum in the Hip Joint Automatically Using a Multi-Step Scheme

NASA Astrophysics Data System (ADS)

Wang, Ji; Cheng, Yuanzhi; Fu, Yili; Zhou, Shengjun; Tamura, Shinichi

We describe a multi-step approach for automatic segmentation of the femoral head and the acetabulum in the hip joint from three dimensional (3D) CT images. Our segmentation method consists of the following steps: 1) construction of the valley-emphasized image by subtracting valleys from the original images; 2) initial segmentation of the bone regions by using conventional techniques including the initial threshold and binary morphological operations from the valley-emphasized image; 3) further segmentation of the bone regions by using the iterative adaptive classification with the initial segmentation result; 4) detection of the rough bone boundaries based on the segmented bone regions; 5) 3D reconstruction of the bone surface using the rough bone boundaries obtained in step 4) by a network of triangles; 6) correction of all vertices of the 3D bone surface based on the normal direction of vertices; 7) adjustment of the bone surface based on the corrected vertices. We evaluated our approach on 35 CT patient data sets. Our experimental results show that our segmentation algorithm is more accurate and robust against noise than other conventional approaches for automatic segmentation of the femoral head and the acetabulum. Average root-mean-square (RMS) distance from manual reference segmentations created by experienced users was approximately 0.68mm (in-plane resolution of the CT data).

Carotid stenosis assessment with multi-detector CT angiography: comparison between manual and automatic segmentation methods.

PubMed

Zhu, Chengcheng; Patterson, Andrew J; Thomas, Owen M; Sadat, Umar; Graves, Martin J; Gillard, Jonathan H

2013-04-01

Luminal stenosis is used for selecting the optimal management strategy for patients with carotid artery disease. The aim of this study is to evaluate the reproducibility of carotid stenosis quantification using manual and automated segmentation methods using submillimeter through-plane resolution Multi-Detector CT angiography (MDCTA). 35 patients having carotid artery disease with >30 % luminal stenosis as identified by carotid duplex imaging underwent contrast enhanced MDCTA. Two experienced CT readers quantified carotid stenosis from axial source images, reconstructed maximum intensity projection (MIP) and 3D-carotid geometry which was automatically segmented by an open-source toolkit (Vascular Modelling Toolkit, VMTK) using NASCET criteria. Good agreement among the measurement using axial images, MIP and automatic segmentation was observed. Automatic segmentation methods show better inter-observer agreement between the readers (intra-class correlation coefficient (ICC): 0.99 for diameter stenosis measurement) than manual measurement of axial (ICC = 0.82) and MIP (ICC = 0.86) images. Carotid stenosis quantification using an automatic segmentation method has higher reproducibility compared with manual methods.

DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.

PubMed

Symonova, Olga; Topp, Christopher N; Edelsbrunner, Herbert

2015-01-01

We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.

An automatic panoramic image reconstruction scheme from dental computed tomography images

PubMed Central

Papakosta, Thekla K; Savva, Antonis D; Economopoulos, Theodore L; Gröhndal, H G

2017-01-01

Objectives: Panoramic images of the jaws are extensively used for dental examinations and/or surgical planning because they provide a general overview of the patient's maxillary and mandibular regions. Panoramic images are two-dimensional projections of three-dimensional (3D) objects. Therefore, it should be possible to reconstruct them from 3D radiographic representations of the jaws, produced by CBCT scanning, obviating the need for additional exposure to X-rays, should there be a need of panoramic views. The aim of this article is to present an automated method for reconstructing panoramic dental images from CBCT data. Methods: The proposed methodology consists of a series of sequential processing stages for detecting a fitting dental arch which is used for projecting the 3D information of the CBCT data to the two-dimensional plane of the panoramic image. The detection is based on a template polynomial which is constructed from a training data set. Results: A total of 42 CBCT data sets of real clinical pre-operative and post-operative representations from 21 patients were used. Eight data sets were used for training the system and the rest for testing. Conclusions: The proposed methodology was successfully applied to CBCT data sets, producing corresponding panoramic images, suitable for examining pre-operatively and post-operatively the patients' maxillary and mandibular regions. PMID:28112548

3D modeling of building indoor spaces and closed doors from imagery and point clouds.

PubMed

Díaz-Vilariño, Lucía; Khoshelham, Kourosh; Martínez-Sánchez, Joaquín; Arias, Pedro

2015-02-03

3D models of indoor environments are increasingly gaining importance due to the wide range of applications to which they can be subjected: from redesign and visualization to monitoring and simulation. These models usually exist only for newly constructed buildings; therefore, the development of automatic approaches for reconstructing 3D indoors from imagery and/or point clouds can make the process easier, faster and cheaper. Among the constructive elements defining a building interior, doors are very common elements and their detection can be very useful either for knowing the environment structure, to perform an efficient navigation or to plan appropriate evacuation routes. The fact that doors are topologically connected to walls by being coplanar, together with the unavoidable presence of clutter and occlusions indoors, increases the inherent complexity of the automation of the recognition process. In this work, we present a pipeline of techniques used for the reconstruction and interpretation of building interiors based on point clouds and images. The methodology analyses the visibility problem of indoor environments and goes in depth with door candidate detection. The presented approach is tested in real data sets showing its potential with a high door detection rate and applicability for robust and efficient envelope reconstruction.

SF3M software: 3-D photo-reconstruction for non-expert users and its application to a gully network

NASA Astrophysics Data System (ADS)

Castillo, C.; James, M. R.; Redel-Macías, M. D.; Pérez, R.; Gómez, J. A.

2015-08-01

Three-dimensional photo-reconstruction (PR) techniques have been successfully used to produce high-resolution surface models for different applications and over different spatial scales. However, innovative approaches are required to overcome some limitations that this technique may present for field image acquisition in challenging scene geometries. Here, we evaluate SF3M, a new graphical user interface for implementing a complete PR workflow based on freely available software (including external calls to VisualSFM and CloudCompare), in combination with a low-cost survey design for the reconstruction of a several-hundred-metres-long gully network. SF3M provided a semi-automated workflow for 3-D reconstruction requiring ~ 49 h (of which only 17 % required operator assistance) for obtaining a final gully network model of > 17 million points over a gully plan area of 4230 m2. We show that a walking itinerary along the gully perimeter using two lightweight automatic cameras (1 s time-lapse mode) and a 6 m long pole is an efficient method for 3-D monitoring of gullies, at a low cost (~ EUR 1000 budget for the field equipment) and the time requirements (~ 90 min for image collection). A mean error of 6.9 cm at the ground control points was found, mainly due to model deformations derived from the linear geometry of the gully and residual errors in camera calibration. The straightforward image collection and processing approach can be of great benefit for non-expert users working on gully erosion assessment.

Normative biometrics for fetal ocular growth using volumetric MRI reconstruction.

PubMed

Velasco-Annis, Clemente; Gholipour, Ali; Afacan, Onur; Prabhu, Sanjay P; Estroff, Judy A; Warfield, Simon K

2015-04-01

To determine normative ranges for fetal ocular biometrics between 19 and 38 weeks gestational age (GA) using volumetric MRI reconstruction. The 3D images of 114 healthy fetuses between 19 and 38 weeks GA were created using super-resolution volume reconstructions from MRI slice acquisitions. These 3D images were semi-automatically segmented to measure fetal orbit volume, binocular distance (BOD), interocular distance (IOD), and ocular diameter (OD). All biometry correlated with GA (Volume, Pearson's correlation coefficient (CC) = 0.9680; BOD, CC = 0.9552; OD, CC = 0.9445; and IOD, CC = 0.8429), and growth curves were plotted against linear and quadratic growth models. Regression analysis showed quadratic models to best fit BOD, IOD, and OD and a linear model to best fit volume. Orbital volume had the greatest correlation with GA, although BOD and OD also showed strong correlation. The normative data found in this study may be helpful for the detection of congenital fetal anomalies with more consistent measurements than are currently available. © 2015 John Wiley & Sons, Ltd. © 2015 John Wiley & Sons, Ltd.

Radiofrequency ablation of hepatic tumors: simulation, planning, and contribution of virtual reality and haptics.

PubMed

Villard, Caroline; Soler, Luc; Gangi, Afshin

2005-08-01

For radiofrequency ablation (RFA) of liver tumors, evaluation of vascular architecture, post-RFA necrosis prediction, and the choice of a suitable needle placement strategy using conventional radiological techniques remain difficult. In an attempt to enhance the safety of RFA, a 3D simulator, treatment planning, and training tool, that simulates the insertion of the needle, the necrosis of the treated area, and proposes an optimal needle placement, has been developed. The 3D scenes are automatically reconstructed from enhanced spiral CT scans. The simulator takes into account the cooling effect of local vessels greater than 3 mm in diameter, making necrosis shapes more realistic. Optimal needle positioning can be automatically generated by the software to produce complete destruction of the tumor, with maximum respect of the healthy liver and of all major structures to avoid. We also studied how the use of virtual reality and haptic devices are valuable to make simulation and training realistic and effective.

Joint Simultaneous Reconstruction of Regularized Building Superstructures from Low-Density LIDAR Data Using Icp

NASA Astrophysics Data System (ADS)

Wichmann, Andreas; Kada, Martin

2016-06-01

There are many applications for 3D city models, e.g., in visualizations, analysis, and simulations; each one requiring a certain level of detail to be effective. The overall trend goes towards including various kinds of anthropogenic and natural objects therein with ever increasing geometric and semantic details. A few years back, the featured 3D building models had only coarse roof geometry. But nowadays, they are expected to include detailed roof superstructures like dormers and chimneys. Several methods have been proposed for the automatic reconstruction of 3D building models from airborne based point clouds. However, they are usually unable to reliably recognize and reconstruct small roof superstructures as these objects are often represented by only few point measurements, especially in low-density point clouds. In this paper, we propose a recognition and reconstruction approach that overcomes this problem by identifying and simultaneously reconstructing regularized superstructures of similar shape. For this purpose, candidate areas for superstructures are detected by taking into account virtual sub-surface points that are assumed to lie on the main roof faces below the measured points. The areas with similar superstructures are detected, extracted, grouped together, and registered to one another with the Iterative Closest Point (ICP) algorithm. As an outcome, the joint point density of each detected group is increased, which helps to recognize the shape of the superstructure more reliably and in more detail. Finally, all instances of each group of superstructures are modeled at once and transformed back to their original position. Because superstructures are reconstructed in groups, symmetries, alignments, and regularities can be enforced in a straight-forward way. The validity of the approach is presented on a number of example buildings from the Vaihingen test data set.

Using optically scanned 3D data in the restoration of Michelangelo's David

NASA Astrophysics Data System (ADS)

Scopigno, Roberto; Cignoni, Paolo; Callieri, Marco; Ganovelli, Fabio; Impoco, G.; Pingi, P.; Ponchio, F.

2003-10-01

Modern 3D scanning technologies allow to reconstruct 3D digital representations of Cultural Heritage artifacts in a semi-automatic way, characterized by very high accuracy and wealth of details. The availability of an accurate digital representation opens several possibilities of utilization to experts (restorers, archivists, museum curators), or to ordinary people (students, museum visitors). 3D scanned data are commonly used for the production of animations, interactive visualizations, or virtual reality applications. A much more exciting opportunity is to use these data in the restoration of Cultural Heritage artworks. The integration between 3D graphic and restoration represents an open research field where many new supporting tools are required; the David restoration project has given several starting points and guidelines to the definition and development of innovative solutions. Digital 3D models can be used in two different but not subsidiary modes: as an instrument for the execution of specific investigations and as a supporting media for the archival and integration of all the restoration-related information, gathered with the different studies and analysis performed on the artwork. In this paper we present some recent work done in the framework of the Michelangelo's David restoration project. A 3D model of the David was reconstructed by the Digital Michelangelo Project, using laser-based 3D scanning technology. We have developed some tools to make those data accessible and useful in the restoration. Preliminary results are reported here together with some directions for further research.

Automatic exposure control at single- and dual-heartbeat CTCA on a 320-MDCT volume scanner: effect of heart rate, exposure phase window setting, and reconstruction algorithm.

PubMed

Funama, Yoshinori; Utsunomiya, Daisuke; Taguchi, Katsuyuki; Oda, Seitaro; Shimonobo, Toshiaki; Yamashita, Yasuyuki

2014-05-01

To investigate whether electrocardiogram (ECG)-gated single- and dual-heartbeat computed tomography coronary angiography (CTCA) with automatic exposure control (AEC) yields images with uniform image noise at reduced radiation doses. Using an anthropomorphic chest CT phantom we performed prospectively ECG-gated single- and dual-heartbeat CTCA on a second-generation 320-multidetector CT volume scanner. The exposure phase window was set at 75%, 70-80%, 40-80%, and 0-100% and the heart rate at 60 or 80 or corr80 bpm; images were reconstructed with filtered back projection (FBP) or iterative reconstruction (IR, adaptive iterative dose reduction 3D). We applied AEC and set the image noise level to 20 or 25 HU. For each technique we determined the image noise and the radiation dose to the phantom center. With half-scan reconstruction at 60 bpm, a 70-80% phase window- and a 20-HU standard deviation (SD) setting, the imagenoise level and -variation along the z axis manifested similar curves with FBP and IR. With half-scan reconstruction, the radiation dose to the phantom center with 70-80% phase window was 18.89 and 12.34 mGy for FBP and 4.61 and 3.10 mGy for IR at an SD setting SD of 20 and 25 HU, respectively. At 80 bpm with two-segment reconstruction the dose was approximately twice that of 60 bpm at both SD settings. However, increasing radiation dose at corr80 bpm was suppressed to 1.39 times compared to 60 bpm. AEC at ECG-gated single- and dual-heartbeat CTCA controls the image noise at different radiation dose. Copyright © 2013 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Parameter Estimation of Fossil Oysters from High Resolution 3D Point Cloud and Image Data

NASA Astrophysics Data System (ADS)

Djuricic, Ana; Harzhauser, Mathias; Dorninger, Peter; Nothegger, Clemens; Mandic, Oleg; Székely, Balázs; Molnár, Gábor; Pfeifer, Norbert

2014-05-01

A unique fossil oyster reef was excavated at Stetten in Lower Austria, which is also the highlight of the geo-edutainment park 'Fossilienwelt Weinviertel'. It provides the rare opportunity to study the Early Miocene flora and fauna of the Central Paratethys Sea. The site presents the world's largest fossil oyster biostrome formed about 16.5 million years ago in a tropical estuary of the Korneuburg Basin. About 15,000 up to 80-cm-long shells of Crassostrea gryphoides cover a 400 m2 large area. Our project 'Smart-Geology for the World's largest fossil oyster reef' combines methods of photogrammetry, geology and paleontology to document, evaluate and quantify the shell bed. This interdisciplinary approach will be applied to test hypotheses on the genesis of the taphocenosis (e.g.: tsunami versus major storm) and to reconstruct pre- and post-event processes. Hence, we are focusing on using visualization technologies from photogrammetry in geology and paleontology in order to develop new methods for automatic and objective evaluation of 3D point clouds. These will be studied on the basis of a very dense surface reconstruction of the oyster reef. 'Smart Geology', as extension of the classic discipline, exploits massive data, automatic interpretation, and visualization. Photogrammetry provides the tools for surface acquisition and objective, automated interpretation. We also want to stress the economic aspect of using automatic shape detection in paleontology, which saves manpower and increases efficiency during the monitoring and evaluation process. Currently, there are many well known algorithms for 3D shape detection of certain objects. We are using dense 3D laser scanning data from an instrument utilizing the phase shift measuring principle, which provides accurate geometrical basis < 3 mm. However, the situation is difficult in this multiple object scenario where more than 15,000 complete or fragmentary parts of an object with random orientation are found. The goal is to investigate if the application of state-of-the-art 3D digitizing, data processing, and visualization technologies support the interpretation of this paleontological site. The obtained 3D data (approx. 1 billion points at the respective area) is analyzed with respect to their 3D structure in order to derive geometrical information. The aim of this contribution is to segment the 3D point cloud of laser scanning data into meaningful regions representing particular objects. Geometric parameters (curvature, tangent plane orientation, local minimum and maximum, etc.) are derived for every 3D point of the point cloud. A set of features is computed in each point using different kernel sizes to define neighborhoods of different size. This provides information on convexity (outer surface), concavity (inner surface) and locally flat areas, which shall be further utilized in fitting model of Crassostrea-shells. In addition, digitizing is performed manually in order to obtain a representative set of reference data for the evaluation of the obtained results. For evaluating these results the reference data (length and orientation of specimen) is then compared to the automatically derived segments of the point cloud. The study is supported by the Austrian Science Fund (FWF P 25883-N29).

Robust surface reconstruction by design-guided SEM photometric stereo

NASA Astrophysics Data System (ADS)

Miyamoto, Atsushi; Matsuse, Hiroki; Koutaki, Gou

2017-04-01

We present a novel approach that addresses the blind reconstruction problem in scanning electron microscope (SEM) photometric stereo for complicated semiconductor patterns to be measured. In our previous work, we developed a bootstrapping de-shadowing and self-calibration (BDS) method, which automatically calibrates the parameter of the gradient measurement formulas and resolves shadowing errors for estimating an accurate three-dimensional (3D) shape and underlying shadowless images. Experimental results on 3D surface reconstruction demonstrated the significance of the BDS method for simple shapes, such as an isolated line pattern. However, we found that complicated shapes, such as line-and-space (L&S) and multilayered patterns, produce deformed and inaccurate measurement results. This problem is due to brightness fluctuations in the SEM images, which are mainly caused by the energy fluctuations of the primary electron beam, variations in the electronic expanse inside a specimen, and electrical charging of specimens. Despite these being essential difficulties encountered in SEM photometric stereo, it is difficult to model accurately all the complicated physical phenomena of electronic behavior. We improved the robustness of the surface reconstruction in order to deal with these practical difficulties with complicated shapes. Here, design data are useful clues as to the pattern layout and layer information of integrated semiconductors. We used the design data as a guide of the measured shape and incorporated a geometrical constraint term to evaluate the difference between the measured and designed shapes into the objective function of the BDS method. Because the true shape does not necessarily correspond to the designed one, we use an iterative scheme to develop proper guide patterns and a 3D surface that provides both a less distorted and more accurate 3D shape after convergence. Extensive experiments on real image data demonstrate the robustness and effectiveness of our method.

Compensation of missing wedge effects with sequential statistical reconstruction in electron tomography.

PubMed

Paavolainen, Lassi; Acar, Erman; Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomäki, Varpu; Cheng, R Holland; Ruotsalainen, Ulla

2014-01-01

Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods.

Correction of patient motion in cone-beam CT using 3D-2D registration

NASA Astrophysics Data System (ADS)

Ouadah, S.; Jacobson, M.; Stayman, J. W.; Ehtiati, T.; Weiss, C.; Siewerdsen, J. H.

2017-12-01

Cone-beam CT (CBCT) is increasingly common in guidance of interventional procedures, but can be subject to artifacts arising from patient motion during fairly long (~5-60 s) scan times. We present a fiducial-free method to mitigate motion artifacts using 3D-2D image registration that simultaneously corrects residual errors in the intrinsic and extrinsic parameters of geometric calibration. The 3D-2D registration process registers each projection to a prior 3D image by maximizing gradient orientation using the covariance matrix adaptation-evolution strategy optimizer. The resulting rigid transforms are applied to the system projection matrices, and a 3D image is reconstructed via model-based iterative reconstruction. Phantom experiments were conducted using a Zeego robotic C-arm to image a head phantom undergoing 5-15 cm translations and 5-15° rotations. To further test the algorithm, clinical images were acquired with a CBCT head scanner in which long scan times were susceptible to significant patient motion. CBCT images were reconstructed using a penalized likelihood objective function. For phantom studies the structural similarity (SSIM) between motion-free and motion-corrected images was  >0.995, with significant improvement (p  <  0.001) compared to the SSIM values of uncorrected images. Additionally, motion-corrected images exhibited a point-spread function with full-width at half maximum comparable to that of the motion-free reference image. Qualitative comparison of the motion-corrupted and motion-corrected clinical images demonstrated a significant improvement in image quality after motion correction. This indicates that the 3D-2D registration method could provide a useful approach to motion artifact correction under assumptions of local rigidity, as in the head, pelvis, and extremities. The method is highly parallelizable, and the automatic correction of residual geometric calibration errors provides added benefit that could be valuable in routine use.

Robust Spacecraft Component Detection in Point Clouds.

PubMed

Wei, Quanmao; Jiang, Zhiguo; Zhang, Haopeng

2018-03-21

Automatic component detection of spacecraft can assist in on-orbit operation and space situational awareness. Spacecraft are generally composed of solar panels and cuboidal or cylindrical modules. These components can be simply represented by geometric primitives like plane, cuboid and cylinder. Based on this prior, we propose a robust automatic detection scheme to automatically detect such basic components of spacecraft in three-dimensional (3D) point clouds. In the proposed scheme, cylinders are first detected in the iteration of the energy-based geometric model fitting and cylinder parameter estimation. Then, planes are detected by Hough transform and further described as bounded patches with their minimum bounding rectangles. Finally, the cuboids are detected with pair-wise geometry relations from the detected patches. After successive detection of cylinders, planar patches and cuboids, a mid-level geometry representation of the spacecraft can be delivered. We tested the proposed component detection scheme on spacecraft 3D point clouds synthesized by computer-aided design (CAD) models and those recovered by image-based reconstruction, respectively. Experimental results illustrate that the proposed scheme can detect the basic geometric components effectively and has fine robustness against noise and point distribution density.

Robust Spacecraft Component Detection in Point Clouds

PubMed Central

Wei, Quanmao; Jiang, Zhiguo

2018-01-01

Automatic component detection of spacecraft can assist in on-orbit operation and space situational awareness. Spacecraft are generally composed of solar panels and cuboidal or cylindrical modules. These components can be simply represented by geometric primitives like plane, cuboid and cylinder. Based on this prior, we propose a robust automatic detection scheme to automatically detect such basic components of spacecraft in three-dimensional (3D) point clouds. In the proposed scheme, cylinders are first detected in the iteration of the energy-based geometric model fitting and cylinder parameter estimation. Then, planes are detected by Hough transform and further described as bounded patches with their minimum bounding rectangles. Finally, the cuboids are detected with pair-wise geometry relations from the detected patches. After successive detection of cylinders, planar patches and cuboids, a mid-level geometry representation of the spacecraft can be delivered. We tested the proposed component detection scheme on spacecraft 3D point clouds synthesized by computer-aided design (CAD) models and those recovered by image-based reconstruction, respectively. Experimental results illustrate that the proposed scheme can detect the basic geometric components effectively and has fine robustness against noise and point distribution density. PMID:29561828

High-Speed Surface Reconstruction of Flying Birds Using Structured Light

NASA Astrophysics Data System (ADS)

Deetjen, Marc; Lentink, David

2017-11-01

Birds fly effectively through complex environments, and in order to understand the strategies that enable them to do so, we need to determine the shape and movement of their wings. Previous studies show that even small perturbations in wing shape have dramatic aerodynamic effects, but these shape changes have not been quantified automatically at high temporal and spatial resolutions. Hence, we developed a custom 3D surface mapping method which uses a high-speed camera to view a grid of stripes projected onto a flying bird. Because the light is binary rather than grayscale, and each frame is separately analyzed, this method can function at any frame rate with sufficient light. The method is automated, non-invasive, and able to measure a volume by simultaneously reconstructing from multiple views. We use this technique to reconstruct the 3D shape of the surface of a parrotlet during flapping flight at 3200 fps. We then analyze key dynamic parameters such as wing twist and angle of attack, and compute aerodynamic parameters such as lift and drag. While this novel system is designed to quantify bird wing shape and motion, it is adaptable for tracking other objects such as quickly deforming fish, especially those which are difficult to reconstruct using other 3D tracking methods. The presenter needs to leave by 3 pm on the final day of the conference (11/21) in order to make his flight. Please account for this in the scheduling if possible by scheduling the presentation earlier in the day or a different day.

Comparison of the effects of model-based iterative reconstruction and filtered back projection algorithms on software measurements in pulmonary subsolid nodules.

PubMed

Cohen, Julien G; Kim, Hyungjin; Park, Su Bin; van Ginneken, Bram; Ferretti, Gilbert R; Lee, Chang Hyun; Goo, Jin Mo; Park, Chang Min

2017-08-01

To evaluate the differences between filtered back projection (FBP) and model-based iterative reconstruction (MBIR) algorithms on semi-automatic measurements in subsolid nodules (SSNs). Unenhanced CT scans of 73 SSNs obtained using the same protocol and reconstructed with both FBP and MBIR algorithms were evaluated by two radiologists. Diameter, mean attenuation, mass and volume of whole nodules and their solid components were measured. Intra- and interobserver variability and differences between FBP and MBIR were then evaluated using Bland-Altman method and Wilcoxon tests. Longest diameter, volume and mass of nodules and those of their solid components were significantly higher using MBIR (p < 0.05) with mean differences of 1.1% (limits of agreement, -6.4 to 8.5%), 3.2% (-20.9 to 27.3%) and 2.9% (-16.9 to 22.7%) and 3.2% (-20.5 to 27%), 6.3% (-51.9 to 64.6%), 6.6% (-50.1 to 63.3%), respectively. The limits of agreement between FBP and MBIR were within the range of intra- and interobserver variability for both algorithms with respect to the diameter, volume and mass of nodules and their solid components. There were no significant differences in intra- or interobserver variability between FBP and MBIR (p > 0.05). Semi-automatic measurements of SSNs significantly differed between FBP and MBIR; however, the differences were within the range of measurement variability. • Intra- and interobserver reproducibility of measurements did not differ between FBP and MBIR. • Differences in SSNs' semi-automatic measurement induced by reconstruction algorithms were not clinically significant. • Semi-automatic measurement may be conducted regardless of reconstruction algorithm. • SSNs' semi-automated classification agreement (pure vs. part-solid) did not significantly differ between algorithms.

Automatic Large-Scalae 3d Building Shape Refinement Using Conditional Generative Adversarial Networks

NASA Astrophysics Data System (ADS)

Bittner, K.; d'Angelo, P.; Körner, M.; Reinartz, P.

2018-05-01

Three-dimensional building reconstruction from remote sensing imagery is one of the most difficult and important 3D modeling problems for complex urban environments. The main data sources provided the digital representation of the Earths surface and related natural, cultural, and man-made objects of the urban areas in remote sensing are the digital surface models (DSMs). The DSMs can be obtained either by light detection and ranging (LIDAR), SAR interferometry or from stereo images. Our approach relies on automatic global 3D building shape refinement from stereo DSMs using deep learning techniques. This refinement is necessary as the DSMs, which are extracted from image matching point clouds, suffer from occlusions, outliers, and noise. Though most previous works have shown promising results for building modeling, this topic remains an open research area. We present a new methodology which not only generates images with continuous values representing the elevation models but, at the same time, enhances the 3D object shapes, buildings in our case. Mainly, we train a conditional generative adversarial network (cGAN) to generate accurate LIDAR-like DSM height images from the noisy stereo DSM input. The obtained results demonstrate the strong potential of creating large areas remote sensing depth images where the buildings exhibit better-quality shapes and roof forms.

Validation of 2 noninvasive, markerless reconstruction techniques in biplane high-speed fluoroscopy for 3-dimensional research of bovine distal limb kinematics.

PubMed

Weiss, M; Reich, E; Grund, S; Mülling, C K W; Geiger, S M

2017-10-01

Lameness severely impairs cattle's locomotion, and it is among the most important threats to animal welfare, performance, and productivity in the modern dairy industry. However, insight into the pathological alterations of claw biomechanics leading to lameness and an understanding of the biomechanics behind development of claw lesions causing lameness are limited. Biplane high-speed fluoroscopic kinematography is a new approach for the analysis of skeletal motion. Biplane high-speed videos in combination with bone scans can be used for 3-dimensional (3D) animations of bones moving in 3D space. The gold standard, marker-based animation, requires implantation of radio-opaque markers into bones, which impairs the practicability for lameness research in live animals. Therefore, the purpose of this study was to evaluate the comparative accuracy of 2 noninvasive, markerless animation techniques (semi-automatic and manual) in 3D animation of the bovine distal limb. Tantalum markers were implanted into each of the distal, middle, and proximal phalanges of 5 isolated bovine distal forelimbs, and biplane high-speed x-ray videos of each limb were recorded to capture the simulation of one step. The limbs were scanned by computed tomography to create bone models of the 6 digital bones, and 3D animation of the bones' movements were subsequently reconstructed using the marker-based, the semi-automatic, and the manual animation techniques. Manual animation translational bias and precision varied from 0.63 ± 0.26 mm to 0.80 ± 0.49 mm, and rotational bias and precision ranged from 2.41 ± 1.43° to 6.75 ± 4.67°. Semi-automatic translational values for bias and precision ranged from 1.26 ± 1.28 mm to 2.75 ± 2.17 mm, and rotational values varied from 3.81 ± 2.78° to 11.7 ± 8.11°. In our study, we demonstrated the successful application of biplane high-speed fluoroscopic kinematography to gait analysis of bovine distal limb. Using the manual animation technique, kinematics can be measured with sub-millimeter accuracy without the need for invasive marker implantation. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Application of 2D and 3D image technologies to characterise morphological attributes of grapevine clusters.

PubMed

Tello, Javier; Cubero, Sergio; Blasco, José; Tardaguila, Javier; Aleixos, Nuria; Ibáñez, Javier

2016-10-01

Grapevine cluster morphology influences the quality and commercial value of wine and table grapes. It is routinely evaluated by subjective and inaccurate methods that do not meet the requirements set by the food industry. Novel two-dimensional (2D) and three-dimensional (3D) machine vision technologies emerge as promising tools for its automatic and fast evaluation. The automatic evaluation of cluster length, width and elongation was successfully achieved by the analysis of 2D images, significant and strong correlations with the manual methods being found (r = 0.959, 0.861 and 0.852, respectively). The classification of clusters according to their shape can be achieved by evaluating their conicity in different sections of the cluster. The geometric reconstruction of the morphological volume of the cluster from 2D features worked better than the direct 3D laser scanning system, showing a high correlation (r = 0.956) with the manual approach (water displacement method). In addition, we constructed and validated a simple linear regression model for cluster compactness estimation. It showed a high predictive capacity for both the training and validation subsets of clusters (R(2)  = 84.5 and 71.1%, respectively). The methodologies proposed in this work provide continuous and accurate data for the fast and objective characterisation of cluster morphology. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

PubMed

Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

2010-01-01

A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

Representation and Reconconstruction of Triangular Irregular Networks with Vertical Walls

NASA Astrophysics Data System (ADS)

Gorte, B.; Lesparre, J.

2012-06-01

Point clouds obtained by aerial laser scanning are a convenient input source for high resolution 2.5d elevation models, such as the Dutch AHN-2. More challenging is the fully automatic reconstruction of 3d city models. An actual demand for a combined 2.5d terrain and 3d city model for an urban hydrology application led to the design of an extension to the well-known Delaunay triangulated irregular networks (TINs) as to accommodate vertical walls. In addition we introduce methods to generate and refine models adhering to our data structure. These are based on combining two approaches: a representation of the TIN using stars of vertices and triangles, together with segmenting the TIN on the basis of coplanarity of adjacent triangles. The approach is supposed to deliver the complete model including walls at the correct locations, without relying on additional map data, as these often lack completeness, actuality and accuracy, and moreover most of the time do not account for parts facades not going down to street level. However, automatic detection of height discontinuities to obtain the exact location of the walls is currently still under implementation.

Automated discrete electron tomography - Towards routine high-fidelity reconstruction of nanomaterials.

PubMed

Zhuge, Xiaodong; Jinnai, Hiroshi; Dunin-Borkowski, Rafal E; Migunov, Vadim; Bals, Sara; Cool, Pegie; Bons, Anton-Jan; Batenburg, Kees Joost

2017-04-01

Electron tomography is an essential imaging technique for the investigation of morphology and 3D structure of nanomaterials. This method, however, suffers from well-known missing wedge artifacts due to a restricted tilt range, which limits the objectiveness, repeatability and efficiency of quantitative structural analysis. Discrete tomography represents one of the promising reconstruction techniques for materials science, potentially capable of delivering higher fidelity reconstructions by exploiting the prior knowledge of the limited number of material compositions in a specimen. However, the application of discrete tomography to practical datasets remains a difficult task due to the underlying challenging mathematical problem. In practice, it is often hard to obtain consistent reconstructions from experimental datasets. In addition, numerous parameters need to be tuned manually, which can lead to bias and non-repeatability. In this paper, we present the application of a new iterative reconstruction technique, named TVR-DART, for discrete electron tomography. The technique is capable of consistently delivering reconstructions with significantly reduced missing wedge artifacts for a variety of challenging data and imaging conditions, and can automatically estimate its key parameters. We describe the principles of the technique and apply it to datasets from three different types of samples acquired under diverse imaging modes. By further reducing the available tilt range and number of projections, we show that the proposed technique can still produce consistent reconstructions with minimized missing wedge artifacts. This new development promises to provide the electron microscopy community with an easy-to-use and robust tool for high-fidelity 3D characterization of nanomaterials. Copyright © 2017 Elsevier B.V. All rights reserved.

Real Time Computation of Kinetic Constraints to Support Equilibrium Reconstruction

NASA Astrophysics Data System (ADS)

Eggert, W. J.; Kolemen, E.; Eldon, D.

2016-10-01

A new method for quickly and automatically applying kinetic constraints to EFIT equilibrium reconstructions using readily available data is presented. The ultimate goal is to produce kinetic equilibrium reconstructions in real time and use them to constrain the DCON stability code as part of a disruption avoidance scheme. A first effort presented here replaces CPU-time expensive modules, such as the fast ion pressure profile calculation, with a simplified model. We show with a DIII-D database analysis that we can achieve reasonable predictions for selected applications by modeling the fast ion pressure profile and determining the fit parameters as functions of easily measured quantities including neutron rate and electron temperature on axis. Secondly, we present a strategy for treating Thomson scattering and Charge Exchange Recombination data to automatically form constraints for a kinetic equilibrium reconstruction, a process that historically was performed by hand. Work supported by US DOE DE-AC02-09CH11466 and DE-FC02-04ER54698.

Estimation of aortic valve leaflets from 3D CT images using local shape dictionaries and linear coding

NASA Astrophysics Data System (ADS)

Liang, Liang; Martin, Caitlin; Wang, Qian; Sun, Wei; Duncan, James

2016-03-01

Aortic valve (AV) disease is a significant cause of morbidity and mortality. The preferred treatment modality for severe AV disease is surgical resection and replacement of the native valve with either a mechanical or tissue prosthetic. In order to develop effective and long-lasting treatment methods, computational analyses, e.g., structural finite element (FE) and computational fluid dynamic simulations, are very effective for studying valve biomechanics. These computational analyses are based on mesh models of the aortic valve, which are usually constructed from 3D CT images though many hours of manual annotation, and therefore an automatic valve shape reconstruction method is desired. In this paper, we present a method for estimating the aortic valve shape from 3D cardiac CT images, which is represented by triangle meshes. We propose a pipeline for aortic valve shape estimation which includes novel algorithms for building local shape dictionaries and for building landmark detectors and curve detectors using local shape dictionaries. The method is evaluated on real patient image dataset using a leave-one-out approach and achieves an average accuracy of 0.69 mm. The work will facilitate automatic patient-specific computational modeling of the aortic valve.

New solutions and applications of 3D computer tomography image processing

NASA Astrophysics Data System (ADS)

Effenberger, Ira; Kroll, Julia; Verl, Alexander

2008-02-01

As nowadays the industry aims at fast and high quality product development and manufacturing processes a modern and efficient quality inspection is essential. Compared to conventional measurement technologies, industrial computer tomography (CT) is a non-destructive technology for 3D-image data acquisition which helps to overcome their disadvantages by offering the possibility to scan complex parts with all outer and inner geometric features. In this paper new and optimized methods for 3D image processing, including innovative ways of surface reconstruction and automatic geometric feature detection of complex components, are presented, especially our work of developing smart online data processing and data handling methods, with an integrated intelligent online mesh reduction. Hereby the processing of huge and high resolution data sets is guaranteed. Besides, new approaches for surface reconstruction and segmentation based on statistical methods are demonstrated. On the extracted 3D point cloud or surface triangulation automated and precise algorithms for geometric inspection are deployed. All algorithms are applied to different real data sets generated by computer tomography in order to demonstrate the capabilities of the new tools. Since CT is an emerging technology for non-destructive testing and inspection more and more industrial application fields will use and profit from this new technology.

ARCHAEO-SCAN: Portable 3D shape measurement system for archaeological field work

NASA Astrophysics Data System (ADS)

Knopf, George K.; Nelson, Andrew J.

2004-10-01

Accurate measurement and thorough documentation of excavated artifacts are the essential tasks of archaeological fieldwork. The on-site recording and long-term preservation of fragile evidence can be improved using 3D spatial data acquisition and computer-aided modeling technologies. Once the artifact is digitized and geometry created in a virtual environment, the scientist can manipulate the pieces in a virtual reality environment to develop a "realistic" reconstruction of the object without physically handling or gluing the fragments. The ARCHAEO-SCAN system is a flexible, affordable 3D coordinate data acquisition and geometric modeling system for acquiring surface and shape information of small to medium sized artifacts and bone fragments. The shape measurement system is being developed to enable the field archaeologist to manually sweep the non-contact sensor head across the relic or artifact surface. A series of unique data acquisition, processing, registration and surface reconstruction algorithms are then used to integrate 3D coordinate information from multiple views into a single reference frame. A novel technique for automatically creating a hexahedral mesh of the recovered fragments is presented. The 3D model acquisition system is designed to operate from a standard laptop with minimal additional hardware and proprietary software support. The captured shape data can be pre-processed and displayed on site, stored digitally on a CD, or transmitted via the Internet to the researcher's home institution.

A set of parallel, implicit methods for a reconstructed discontinuous Galerkin method for compressible flows on 3D hybrid grids

DOE PAGES

Xia, Yidong; Luo, Hong; Frisbey, Megan; ...

2014-07-01

A set of implicit methods are proposed for a third-order hierarchical WENO reconstructed discontinuous Galerkin method for compressible flows on 3D hybrid grids. An attractive feature in these methods are the application of the Jacobian matrix based on the P1 element approximation, resulting in a huge reduction of memory requirement compared with DG (P2). Also, three approaches -- analytical derivation, divided differencing, and automatic differentiation (AD) are presented to construct the Jacobian matrix respectively, where the AD approach shows the best robustness. A variety of compressible flow problems are computed to demonstrate the fast convergence property of the implemented flowmore » solver. Furthermore, an SPMD (single program, multiple data) programming paradigm based on MPI is proposed to achieve parallelism. The numerical results on complex geometries indicate that this low-storage implicit method can provide a viable and attractive DG solution for complicated flows of practical importance.« less

Automatic cable artifact removal for cardiac C-arm CT imaging

NASA Astrophysics Data System (ADS)

Haase, C.; Schäfer, D.; Kim, M.; Chen, S. J.; Carroll, J.; Eshuis, P.; Dössel, O.; Grass, M.

2014-03-01

Cardiac C-arm computed tomography (CT) imaging using interventional C-arm systems can be applied in various areas of interventional cardiology ranging from structural heart disease and electrophysiology interventions to valve procedures in hybrid operating rooms. In contrast to conventional CT systems, the reconstruction field of view (FOV) of C-arm systems is limited to a region of interest in cone-beam (along the patient axis) and fan-beam (in the transaxial plane) direction. Hence, highly X-ray opaque objects (e.g. cables from the interventional setup) outside the reconstruction field of view, yield streak artifacts in the reconstruction volume. To decrease the impact of these streaks a cable tracking approach on the 2D projection sequences with subsequent interpolation is applied. The proposed approach uses the fact that the projected position of objects outside the reconstruction volume depends strongly on the projection perspective. By tracking candidate points over multiple projections only objects outside the reconstruction volume are segmented in the projections. The method is quantitatively evaluated based on 30 simulated CT data sets. The 3D root mean square deviation to a reference image could be reduced for all cases by an average of 50 % (min 16 %, max 76 %). Image quality improvement is shown for clinical whole heart data sets acquired on an interventional C-arm system.

Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed MR images: proof-of-concept for subsecond position tracking.

PubMed

Thörmer, Gregor; Garnov, Nikita; Moche, Michael; Haase, Jürgen; Kahn, Thomas; Busse, Harald

2012-04-01

To determine whether a greatly reduced spatial resolution of fully reconstructed projection MR images can be used for the simultaneous 3D localization of multiple MR-visible markers and to assess the feasibility of a subsecond position tracking for clinical purposes. Miniature, inductively coupled RF coils were imaged in three orthogonal planes with a balanced steady-state free precession (SSFP) sequence and automatically localized using a two-dimensional template fitting and a subsequent three-dimensional (3D) matching of the coordinates. Precision, accuracy, speed and robustness of 3D localization were assessed for decreasing in-plane resolutions (0.6-4.7 mm). The feasibility of marker tracking was evaluated at the lowest resolution by following a robotically driven needle on a complex 3D trajectory. Average 3D precision and accuracy, sensitivity and specificity of localization ranged between 0.1 and 0.4 mm, 0.5 and 1.0 mm, 100% and 95%, and 100% and 96%, respectively. At the lowest resolution, imaging and localization took ≈350 ms and provided an accuracy of ≈1.0 mm. In the tracking experiment, the needle was clearly depicted on the oblique scan planes defined by the markers. Image-based marker localization at a greatly reduced spatial resolution is considered a feasible approach to monitor reference points or rigid instruments at subsecond update rates. Copyright © 2012 Elsevier Inc. All rights reserved.

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.

PubMed

Li, Haiou; Lyu, Qiang; Cheng, Jianlin

2016-12-01

Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search. 3DRobot (a program that automatically generates diverse and well-packed protein structure decoys) was used to generate initial decoy models for the target from the templates. A stacked denoising autoencoder was trained on the decoys to obtain a deep learning model for the target protein. The trained deep model was then used to reconstruct the final structural model for the target sequence. With target proteins that have highly similar template proteins as benchmarks, the GDT-TS score of the predicted structures is greater than 0.7, suggesting that the deep autoencoder is a promising method for protein structure reconstruction.

On the feasibility of automatically selecting similar patients in highly individualized radiotherapy dose reconstruction for historic data of pediatric cancer survivors.

PubMed

Virgolin, Marco; van Dijk, Irma W E M; Wiersma, Jan; Ronckers, Cécile M; Witteveen, Cees; Bel, Arjan; Alderliesten, Tanja; Bosman, Peter A N

2018-04-01

The aim of this study is to establish the first step toward a novel and highly individualized three-dimensional (3D) dose distribution reconstruction method, based on CT scans and organ delineations of recently treated patients. Specifically, the feasibility of automatically selecting the CT scan of a recently treated childhood cancer patient who is similar to a given historically treated child who suffered from Wilms' tumor is assessed. A cohort of 37 recently treated children between 2- and 6-yr old are considered. Five potential notions of ground-truth similarity are proposed, each focusing on different anatomical aspects. These notions are automatically computed from CT scans of the abdomen and 3D organ delineations (liver, spleen, spinal cord, external body contour). The first is based on deformable image registration, the second on the Dice similarity coefficient, the third on the Hausdorff distance, the fourth on pairwise organ distances, and the last is computed by means of the overlap volume histogram. The relationship between typically available features of historically treated patients and the proposed ground-truth notions of similarity is studied by adopting state-of-the-art machine learning techniques, including random forest. Also, the feasibility of automatically selecting the most similar patient is assessed by comparing ground-truth rankings of similarity with predicted rankings. Similarities (mainly) based on the external abdomen shape and on the pairwise organ distances are highly correlated (Pearson r p ≥ 0.70) and are successfully modeled with random forests based on historically recorded features (pseudo-R 2 ≥ 0.69). In contrast, similarities based on the shape of internal organs cannot be modeled. For the similarities that random forest can reliably model, an estimation of feature relevance indicates that abdominal diameters and weight are the most important. Experiments on automatically selecting similar patients lead to coarse, yet quite robust results: the most similar patient is retrieved only 22% of the times, however, the error in worst-case scenarios is limited, with the fourth most similar patient being retrieved. Results demonstrate that automatically selecting similar patients is feasible when focusing on the shape of the external abdomen and on the position of internal organs. Moreover, whereas the common practice in phantom-based dose reconstruction is to select a representative phantom using age, height, and weight as discriminant factors for any treatment scenario, our analysis on abdominal tumor treatment for children shows that the most relevant features are weight and the anterior-posterior and left-right abdominal diameters. © 2018 American Association of Physicists in Medicine.

Automatic reconstruction of the muscle architecture from the superficial layer fibres data.

PubMed

Kohout, Josef; Cholt, David

2017-10-01

Physiological cross-sectional area (PCSA) of a muscle plays a significant role in determining the force contribution of muscle fascicles to skeletal movement. This parameter is typically calculated from the lengths of muscle fibres selectively sampled from the superficial layer of the muscle. However, recent studies have found that the length of fibres in the superficial layer often differs significantly (p < 0.5) from the length of fibres in the deep layer. As a result, PCSA estimation is inaccurate. In this paper, we propose a method to automatically reconstruct fibres in the whole volume of a muscle from those selectively sampled on the superficial layer. The method performs a centripetal Catmull-Rom interpolation of the input fibres within the volume of a muscle represented by its 3D surface model, automatically distributing the fibres among multiple heads of the muscle and shortening the deep fibres to support large attachment areas with extremely acute angles. Our C++ implementation runs in a couple of seconds on commodity hardware providing realistic results for both artificial and real data sets we tested. The fibres produced by the method can be used directly to determine the personalised mechanical muscle functioning. Our implementation is publicly available for the researchers at https://mi.kiv.zcu.cz/. Copyright © 2017 Elsevier B.V. All rights reserved.

Automatic techniques for 3D reconstruction of critical workplace body postures from range imaging data

NASA Astrophysics Data System (ADS)

Westfeld, Patrick; Maas, Hans-Gerd; Bringmann, Oliver; Gröllich, Daniel; Schmauder, Martin

2013-11-01

The paper shows techniques for the determination of structured motion parameters from range camera image sequences. The core contribution of the work presented here is the development of an integrated least squares 3D tracking approach based on amplitude and range image sequences to calculate dense 3D motion vector fields. Geometric primitives of a human body model are fitted to time series of range camera point clouds using these vector fields as additional information. Body poses and motion information for individual body parts are derived from the model fit. On the basis of these pose and motion parameters, critical body postures are detected. The primary aim of the study is to automate ergonomic studies for risk assessments regulated by law, identifying harmful movements and awkward body postures in a workplace.

3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells

PubMed Central

Luo, Tong; Chen, Huan; Kassab, Ghassan S.

2016-01-01

Aims The 3D geometry of individual vascular smooth muscle cells (VSMCs), which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. Methods and Results A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI) selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell’s initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations) was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9μm, 4.6±0.6μm and 6.2±1.8μm (mean±SD). In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle) was found to be 8±7.6° with median as 5.7°. Conclusions A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function. PMID:26882342

Registration of in vivo MR to histology of rodent brains using blockface imaging

NASA Astrophysics Data System (ADS)

Uberti, Mariano; Liu, Yutong; Dou, Huanyu; Mosley, R. Lee; Gendelman, Howard E.; Boska, Michael

2009-02-01

Registration of MRI to histopathological sections can enhance bioimaging validation for use in pathobiologic, diagnostic, and therapeutic evaluations. However, commonly used registration methods fall short of this goal due to tissue shrinkage and tearing after brain extraction and preparation. In attempts to overcome these limitations we developed a software toolbox using 3D blockface imaging as the common space of reference. This toolbox includes a semi-automatic brain extraction technique using constraint level sets (CLS), 3D reconstruction methods for the blockface and MR volume, and a 2D warping technique using thin-plate splines with landmark optimization. Using this toolbox, the rodent brain volume is first extracted from the whole head MRI using CLS. The blockface volume is reconstructed followed by 3D brain MRI registration to the blockface volume to correct the global deformations due to brain extraction and fixation. Finally, registered MRI and histological slices are warped to corresponding blockface images to correct slice specific deformations. The CLS brain extraction technique was validated by comparing manual results showing 94% overlap. The image warping technique was validated by calculating target registration error (TRE). Results showed a registration accuracy of a TRE < 1 pixel. Lastly, the registration method and the software tools developed were used to validate cell migration in murine human immunodeficiency virus type one encephalitis.

Anthropometric Body Measurements Based on Multi-View Stereo Image Reconstruction*

PubMed Central

Li, Zhaoxin; Jia, Wenyan; Mao, Zhi-Hong; Li, Jie; Chen, Hsin-Chen; Zuo, Wangmeng; Wang, Kuanquan; Sun, Mingui

2013-01-01

Anthropometric measurements, such as the circumferences of the hip, arm, leg and waist, waist-to-hip ratio, and body mass index, are of high significance in obesity and fitness evaluation. In this paper, we present a home based imaging system capable of conducting automatic anthropometric measurements. Body images are acquired at different angles using a home camera and a simple rotating disk. Advanced image processing algorithms are utilized for 3D body surface reconstruction. A coarse body shape model is first established from segmented body silhouettes. Then, this model is refined through an inter-image consistency maximization process based on an energy function. Our experimental results using both a mannequin surrogate and a real human body validate the feasibility of proposed system. PMID:24109700

Interactive 3d Landscapes on Line

NASA Astrophysics Data System (ADS)

Fanini, B.; Calori, L.; Ferdani, D.; Pescarin, S.

2011-09-01

The paper describes challenges identified while developing browser embedded 3D landscape rendering applications, our current approach and work-flow and how recent development in browser technologies could affect. All the data, even if processed by optimization and decimation tools, result in very huge databases that require paging, streaming and Level-of-Detail techniques to be implemented to allow remote web based real time fruition. Our approach has been to select an open source scene-graph based visual simulation library with sufficient performance and flexibility and adapt it to the web by providing a browser plug-in. Within the current Montegrotto VR Project, content produced with new pipelines has been integrated. The whole Montegrotto Town has been generated procedurally by CityEngine. We used this procedural approach, based on algorithms and procedures because it is particularly functional to create extensive and credible urban reconstructions. To create the archaeological sites we used optimized mesh acquired with laser scanning and photogrammetry techniques whereas to realize the 3D reconstructions of the main historical buildings we adopted computer-graphic software like blender and 3ds Max. At the final stage, semi-automatic tools have been developed and used up to prepare and clusterise 3D models and scene graph routes for web publishing. Vegetation generators have also been used with the goal of populating the virtual scene to enhance the user perceived realism during the navigation experience. After the description of 3D modelling and optimization techniques, the paper will focus and discuss its results and expectations.

The influence of image reconstruction algorithms on linear thorax EIT image analysis of ventilation.

PubMed

Zhao, Zhanqi; Frerichs, Inéz; Pulletz, Sven; Müller-Lisse, Ullrich; Möller, Knut

2014-06-01

Analysis methods of electrical impedance tomography (EIT) images based on different reconstruction algorithms were examined. EIT measurements were performed on eight mechanically ventilated patients with acute respiratory distress syndrome. A maneuver with step increase of airway pressure was performed. EIT raw data were reconstructed offline with (1) filtered back-projection (BP); (2) the Dräger algorithm based on linearized Newton-Raphson (DR); (3) the GREIT (Graz consensus reconstruction algorithm for EIT) reconstruction algorithm with a circular forward model (GR(C)) and (4) GREIT with individual thorax geometry (GR(T)). Individual thorax contours were automatically determined from the routine computed tomography images. Five indices were calculated on the resulting EIT images respectively: (a) the ratio between tidal and deep inflation impedance changes; (b) tidal impedance changes in the right and left lungs; (c) center of gravity; (d) the global inhomogeneity index and (e) ventilation delay at mid-dorsal regions. No significant differences were found in all examined indices among the four reconstruction algorithms (p > 0.2, Kruskal-Wallis test). The examined algorithms used for EIT image reconstruction do not influence the selected indices derived from the EIT image analysis. Indices that validated for images with one reconstruction algorithm are also valid for other reconstruction algorithms.

3D Surface Reconstruction and Volume Calculation of Rills

NASA Astrophysics Data System (ADS)

Brings, Christine; Gronz, Oliver; Becker, Kerstin; Wirtz, Stefan; Seeger, Manuel; Ries, Johannes B.

2015-04-01

We use the low-cost, user-friendly photogrammetric Structure from Motion (SfM) technique, which is implemented in the Software VisualSfM, for 3D surface reconstruction and volume calculation of an 18 meter long rill in Luxembourg. The images were taken with a Canon HD video camera 1) before a natural rainfall event, 2) after a natural rainfall event and before a rill experiment and 3) after a rill experiment. Recording with a video camera results compared to a photo camera not only a huge time advantage, the method also guarantees more than adequately overlapping sharp images. For each model, approximately 8 minutes of video were taken. As SfM needs single images, we automatically selected the sharpest image from 15 frame intervals. The sharpness was estimated using a derivative-based metric. Then, VisualSfM detects feature points in each image, searches matching feature points in all image pairs, recovers the camera positions and finally by triangulation of camera positions and feature points the software reconstructs a point cloud of the rill surface. From the point cloud, 3D surface models (meshes) are created and via difference calculations of the pre and post models a visualization of the changes (erosion and accumulation areas) and quantification of erosion volumes are possible. The calculated volumes are presented in spatial units of the models and so real values must be converted via references. The outputs are three models at three different points in time. The results show that especially using images taken from suboptimal videos (bad lighting conditions, low contrast of the surface, too much in-motion unsharpness), the sharpness algorithm leads to much more matching features. Hence the point densities of the 3D models are increased and thereby clarify the calculations.

An Open Source Low-Cost Automatic System for Image-Based 3d Digitization

NASA Astrophysics Data System (ADS)

Menna, F.; Nocerino, E.; Morabito, D.; Farella, E. M.; Perini, M.; Remondino, F.

2017-11-01

3D digitization of heritage artefacts, reverse engineering of industrial components or rapid prototyping-driven design are key topics today. Indeed, millions of archaeological finds all over the world need to be surveyed in 3D either to allow convenient investigations by researchers or because they are inaccessible to visitors and scientists or, unfortunately, because they are seriously endangered by wars and terrorist attacks. On the other hand, in case of industrial and design components there is often the need of deformation analyses or physical replicas starting from reality-based 3D digitisations. The paper is aligned with these needs and presents the realization of the ORION (arduinO Raspberry pI rOtating table for image based 3D recostructioN) prototype system, with its hardware and software components, providing critical insights about its modular design. ORION is an image-based 3D reconstruction system based on automated photogrammetric acquisitions and processing. The system is being developed under a collaborative educational project between FBK Trento, the University of Trento and internship programs with high school in the Trentino province (Italy).

A Visual Servoing-Based Method for ProCam Systems Calibration

PubMed Central

Berry, Francois; Aider, Omar Ait; Mosnier, Jeremie

2013-01-01

Projector-camera systems are currently used in a wide field of applications, such as 3D reconstruction and augmented reality, and can provide accurate measurements, depending on the configuration and calibration. Frequently, the calibration task is divided into two steps: camera calibration followed by projector calibration. The latter still poses certain problems that are not easy to solve, such as the difficulty in obtaining a set of 2D–3D points to compute the projection matrix between the projector and the world. Existing methods are either not sufficiently accurate or not flexible. We propose an easy and automatic method to calibrate such systems that consists in projecting a calibration pattern and superimposing it automatically on a known printed pattern. The projected pattern is provided by a virtual camera observing a virtual pattern in an OpenGL model. The projector displays what the virtual camera visualizes. Thus, the projected pattern can be controlled and superimposed on the printed one with the aid of visual servoing. Our experimental results compare favorably with those of other methods considering both usability and accuracy. PMID:24084121

Reliability of a semi-automated 3D-CT measuring method for tunnel diameters after anterior cruciate ligament reconstruction: A comparison between soft-tissue single-bundle allograft vs. autograft.

PubMed

Robbrecht, Cedric; Claes, Steven; Cromheecke, Michiel; Mahieu, Peter; Kakavelakis, Kyriakos; Victor, Jan; Bellemans, Johan; Verdonk, Peter

2014-10-01

Post-operative widening of tibial and/or femoral bone tunnels is a common observation after ACL reconstruction, especially with soft-tissue grafts. There are no studies comparing tunnel widening in hamstring autografts versus tibialis anterior allografts. The goal of this study was to observe the difference in tunnel widening after the use of allograft vs. autograft for ACL reconstruction, by measuring it with a novel 3-D computed tomography based method. Thirty-five ACL-deficient subjects were included, underwent anatomic single-bundle ACL reconstruction and were evaluated at one year after surgery with the use of 3-D CT imaging. Three independent observers semi-automatically delineated femoral and tibial tunnel outlines, after which a best-fit cylinder was derived and the tunnel diameter was determined. Finally, intra- and inter-observer reliability of this novel measurement protocol was defined. In femoral tunnels, the intra-observer ICC was 0.973 (95% CI: 0.922-0.991) and the inter-observer ICC was 0.992 (95% CI: 0.982-0.996). In tibial tunnels, the intra-observer ICC was 0.955 (95% CI: 0.875-0.985). The combined inter-observer ICC was 0.970 (95% CI: 0.987-0.917). Tunnel widening was significantly higher in allografts compared to autografts, in the tibial tunnels (p=0.013) as well as in the femoral tunnels (p=0.007). To our knowledge, this novel, semi-automated 3D-computed tomography image processing method has shown to yield highly reproducible results for the measurement of bone tunnel diameter and area. This series showed a significantly higher amount of tunnel widening observed in the allograft group at one-year follow-up. Level II, Prospective comparative study. Copyright © 2014 Elsevier B.V. All rights reserved.

Beat to beat 3-dimensional intracardiac echocardiography: theoretical approach and practical experiences.

PubMed

Stapf, Daniel; Franke, Andreas; Schreckenberg, Marcus; Schummers, Georg; Mischke, Karl; Marx, Nikolaus; Schauerte, Patrick; Knackstedt, Christian

2013-04-01

Three-dimensional (3D)-imaging provides important information on cardiac anatomy during electrophysiological procedures. Real-time updates of modalities with high soft-tissue contrast are particularly advantageous during cardiac procedures. Therefore, a beat to beat 3D visualization of cardiac anatomy by intracardiac echocardiography (ICE) was developed and tested in phantoms and animals. An electronic phased-array 5-10 MHz ICE-catheter (Acuson, AcuNav/Siemens Medical Solutions USA/64 elements) providing a 90° sector image was used for ICE-imaging. A custom-made mechanical prototype controlled by a servo motor allowed automatic rotation of the ICE-catheter around its longitudinal axis. During a single heartbeat, the ICE-catheter was rotated and 2D-images were acquired. Reconstruction into a 3D volume and rendering by a prototype software was performed beat to beat. After experimental validation using a rigid phantom, the system was tested in an animal study and afterwards, for quantitative validation, in a dynamic phantom. Acquisition of beat to beat 3D-reconstruction was technically feasible. However, twisting of the ICE-catheter shaft due to friction and torsion was found and rotation was hampered. Also, depiction of catheters was not always ensured in case of parallel alignment. Using a curved sheath for depiction of cardiac anatomy there was no congruent depiction of shape and dimension of static and moving objects. Beat to beat 3D-ICE-imaging is feasible. However, shape and dimension of static and moving objects cannot always be displayed with necessary steadiness as needed in the clinical setting. As catheter depiction is also limited, clinical use seems impossible.

Context-Based Urban Terrain Reconstruction from Uav-Videos for Geoinformation Applications

NASA Astrophysics Data System (ADS)

Bulatov, D.; Solbrig, P.; Gross, H.; Wernerus, P.; Repasi, E.; Heipke, C.

2011-09-01

Urban terrain reconstruction has many applications in areas of civil engineering, urban planning, surveillance and defense research. Therefore the needs of covering ad-hoc demand and performing a close-range urban terrain reconstruction with miniaturized and relatively inexpensive sensor platforms are constantly growing. Using (miniaturized) unmanned aerial vehicles, (M)UAVs, represents one of the most attractive alternatives to conventional large-scale aerial imagery. We cover in this paper a four-step procedure of obtaining georeferenced 3D urban models from video sequences. The four steps of the procedure - orientation, dense reconstruction, urban terrain modeling and geo-referencing - are robust, straight-forward, and nearly fully-automatic. The two last steps - namely, urban terrain modeling from almost-nadir videos and co-registration of models 6ndash; represent the main contribution of this work and will therefore be covered with more detail. The essential substeps of the third step include digital terrain model (DTM) extraction, segregation of buildings from vegetation, as well as instantiation of building and tree models. The last step is subdivided into quasi- intrasensorial registration of Euclidean reconstructions and intersensorial registration with a geo-referenced orthophoto. Finally, we present reconstruction results from a real data-set and outline ideas for future work.

Markov Random Field Based Automatic Image Alignment for ElectronTomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moussavi, Farshid; Amat, Fernando; Comolli, Luis R.

2007-11-30

Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors.more » To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.« less

Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis.

PubMed

Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J; Grau, Raúl; Barat, José M

2016-10-19

A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0-6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead's pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R² of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness.

Predicting Gilthead Sea Bream (Sparus aurata) Freshness by a Novel Combined Technique of 3D Imaging and SW-NIR Spectral Analysis

PubMed Central

Ivorra, Eugenio; Verdu, Samuel; Sánchez, Antonio J.; Grau, Raúl; Barat, José M.

2016-01-01

A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0–6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead’s pupils and irises. Once these regions are positioned, the hyperspectral camera acquires spectral information and a multivariate statistical study is done. The best region is the pupil with an R2 of 0.92 and an RMSE of 0.651 for predictions. We conclude that the combination of 3D technology with the hyperspectral analysis offers plenty of potential and is a very promising technique to non destructively predict gilthead freshness. PMID:27775556

Modeling mechanical cardiopulmonary interactions for virtual environments.

PubMed

Kaye, J M

1997-01-01

We have developed a computer system for modeling mechanical cardiopulmonary behavior in an interactive, 3D virtual environment. The system consists of a compact, scalar description of cardiopulmonary mechanics, with an emphasis on respiratory mechanics, that drives deformable 3D anatomy to simulate mechanical behaviors of and interactions between physiological systems. Such an environment can be used to facilitate exploration of cardiopulmonary physiology, particularly in situations that are difficult to reproduce clinically. We integrate 3D deformable body dynamics with new, formal models of (scalar) cardiorespiratory physiology, associating the scalar physiological variables and parameters with corresponding 3D anatomy. Our approach is amenable to modeling patient-specific circumstances in two ways. First, using CT scan data, we apply semi-automatic methods for extracting and reconstructing the anatomy to use in our simulations. Second, our scalar models are defined in terms of clinically-measurable, patient-specific parameters. This paper describes our approach and presents a sample of results showing normal breathing and acute effects of pneumothoraces.

3D reconstruction of the optic nerve head using stereo fundus images for computer-aided diagnosis of glaucoma

NASA Astrophysics Data System (ADS)

Tang, Li; Kwon, Young H.; Alward, Wallace L. M.; Greenlee, Emily C.; Lee, Kyungmoo; Garvin, Mona K.; Abràmoff, Michael D.

2010-03-01

The shape of the optic nerve head (ONH) is reconstructed automatically using stereo fundus color images by a robust stereo matching algorithm, which is needed for a quantitative estimate of the amount of nerve fiber loss for patients with glaucoma. Compared to natural scene stereo, fundus images are noisy because of the limits on illumination conditions and imperfections of the optics of the eye, posing challenges to conventional stereo matching approaches. In this paper, multi scale pixel feature vectors which are robust to noise are formulated using a combination of both pixel intensity and gradient features in scale space. Feature vectors associated with potential correspondences are compared with a disparity based matching score. The deep structures of the optic disc are reconstructed with a stack of disparity estimates in scale space. Optical coherence tomography (OCT) data was collected at the same time, and depth information from 3D segmentation was registered with the stereo fundus images to provide the ground truth for performance evaluation. In experiments, the proposed algorithm produces estimates for the shape of the ONH that are close to the OCT based shape, and it shows great potential to help computer-aided diagnosis of glaucoma and other related retinal diseases.

3D multimodal cardiac data reconstruction using angiography and computerized tomographic angiography registration.

PubMed

Moosavi Tayebi, Rohollah; Wirza, Rahmita; Sulaiman, Puteri S B; Dimon, Mohd Zamrin; Khalid, Fatimah; Al-Surmi, Aqeel; Mazaheri, Samaneh

2015-04-22

Computerized tomographic angiography (3D data representing the coronary arteries) and X-ray angiography (2D X-ray image sequences providing information about coronary arteries and their stenosis) are standard and popular assessment tools utilized for medical diagnosis of coronary artery diseases. At present, the results of both modalities are individually analyzed by specialists and it is difficult for them to mentally connect the details of these two techniques. The aim of this work is to assist medical diagnosis by providing specialists with the relationship between computerized tomographic angiography and X-ray angiography. In this study, coronary arteries from two modalities are registered in order to create a 3D reconstruction of the stenosis position. The proposed method starts with coronary artery segmentation and labeling for both modalities. Then, stenosis and relevant labeled artery in X-ray angiography image are marked by a specialist. Proper control points for the marked artery in both modalities are automatically detected and normalized. Then, a geometrical transformation function is computed using these control points. Finally, this function is utilized to register the marked artery from the X-ray angiography image on the computerized tomographic angiography and get the 3D position of the stenosis lesion. The result is a 3D informative model consisting of stenosis and coronary arteries' information from the X-ray angiography and computerized tomographic angiography modalities. The results of the proposed method for coronary artery segmentation, labeling and 3D reconstruction are evaluated and validated on the dataset containing both modalities. The advantage of this method is to aid specialists to determine a visual relationship between the correspondent coronary arteries from two modalities and also set up a connection between stenosis points from an X-ray angiography along with their 3D positions on the coronary arteries from computerized tomographic angiography. Moreover, another benefit of this work is that the medical acquisition standards remain unchanged, which means that no calibration in the acquisition devices is required. It can be applied on most computerized tomographic angiography and angiography devices.

Adjustments of the TaD electron density reconstruction model with GNSS-TEC parameters for operational application purposes

NASA Astrophysics Data System (ADS)

Kutiev, Ivan; Marinov, Pencho; Fidanova, Stefka; Belehaki, Anna; Tsagouri, Ioanna

2012-12-01

Validation results on the latest version of TaD model (TaDv2) show realistic reconstruction of the electron density profiles (EDPs) with an average error of 3 TECU, similar to the error obtained from GNSS-TEC calculated paremeters. The work presented here has the aim to further improve the accuracy of the TaD topside reconstruction, adjusting the TEC parameter calculated from TaD model with the TEC parameter calculated by GNSS transmitting RINEX files provided by receivers co-located with the Digisondes. The performance of the new version is tested during a storm period demonstrating further improvements in respect to the previous version. Statistical comparison of modeled and observed TEC confirms the validity of the proposed adjustment. A significant benefit of the proposed upgrade is that it facilitates the real-time implementation of TaD. The model needs a reliable measure of the scale height at the peak height, which is supposed to be provided by Digisondes. Oftenly, the automatic scaling software fails to correctly calculate the scale height at the peak, Hm, due to interferences in the receiving signal. Consequently the model estimated topside scale height is wrongly calculated leading to unrealistic results for the modeled EDP. The proposed TEC adjustment forces the model to correctly reproduce the topside scale height, despite the inaccurate values of Hm. This adjustment is very important for the application of TaD in an operational environment.

Unsupervised building detection from irregularly spaced LiDAR and aerial imagery

NASA Astrophysics Data System (ADS)

Shorter, Nicholas Sven

As more data sources containing 3-D information are becoming available, an increased interest in 3-D imaging has emerged. Among these is the 3-D reconstruction of buildings and other man-made structures. A necessary preprocessing step is the detection and isolation of individual buildings that subsequently can be reconstructed in 3-D using various methodologies. Applications for both building detection and reconstruction have commercial use for urban planning, network planning for mobile communication (cell phone tower placement), spatial analysis of air pollution and noise nuisances, microclimate investigations, geographical information systems, security services and change detection from areas affected by natural disasters. Building detection and reconstruction are also used in the military for automatic target recognition and in entertainment for virtual tourism. Previously proposed building detection and reconstruction algorithms solely utilized aerial imagery. With the advent of Light Detection and Ranging (LiDAR) systems providing elevation data, current algorithms explore using captured LiDAR data as an additional feasible source of information. Additional sources of information can lead to automating techniques (alleviating their need for manual user intervention) as well as increasing their capabilities and accuracy. Several building detection approaches surveyed in the open literature have fundamental weaknesses that hinder their use; such as requiring multiple data sets from different sensors, mandating certain operations to be carried out manually, and limited functionality to only being able to detect certain types of buildings. In this work, a building detection system is proposed and implemented which strives to overcome the limitations seen in existing techniques. The developed framework is flexible in that it can perform building detection from just LiDAR data (first or last return), or just nadir, color aerial imagery. If data from both LiDAR and aerial imagery are available, then the algorithm will use them both for improved accuracy. Additionally, the proposed approach does not employ severely limiting assumptions thus enabling the end user to apply the approach to a wider variety of different building types. The proposed approach is extensively tested using real data sets and it is also compared with other existing techniques. Experimental results are presented.

ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs.

PubMed

Fernández-de-Manúel, Laura; Díaz-Díaz, Covadonga; Jiménez-Carretero, Daniel; Torres, Miguel; Montoya, María C

2017-05-01

Embryonic stem cells (ESCs) can be established as permanent cell lines, and their potential to differentiate into adult tissues has led to widespread use for studying the mechanisms and dynamics of stem cell differentiation and exploring strategies for tissue repair. Imaging live ESCs during development is now feasible due to advances in optical imaging and engineering of genetically encoded fluorescent reporters; however, a major limitation is the low spatio-temporal resolution of long-term 3-D imaging required for generational and neighboring reconstructions. Here, we present the ESC-Track (ESC-T) workflow, which includes an automated cell and nuclear segmentation and tracking tool for 4-D (3-D + time) confocal image data sets as well as a manual editing tool for visual inspection and error correction. ESC-T automatically identifies cell divisions and membrane contacts for lineage tree and neighborhood reconstruction and computes quantitative features from individual cell entities, enabling analysis of fluorescence signal dynamics and tracking of cell morphology and motion. We use ESC-T to examine Myc intensity fluctuations in the context of mouse ESC (mESC) lineage and neighborhood relationships. ESC-T is a powerful tool for evaluation of the genealogical and microenvironmental cues that maintain ESC fitness.

Automatic 3d Building Model Generations with Airborne LiDAR Data

NASA Astrophysics Data System (ADS)

Yastikli, N.; Cetin, Z.

2017-11-01

LiDAR systems become more and more popular because of the potential use for obtaining the point clouds of vegetation and man-made objects on the earth surface in an accurate and quick way. Nowadays, these airborne systems have been frequently used in wide range of applications such as DEM/DSM generation, topographic mapping, object extraction, vegetation mapping, 3 dimensional (3D) modelling and simulation, change detection, engineering works, revision of maps, coastal management and bathymetry. The 3D building model generation is the one of the most prominent applications of LiDAR system, which has the major importance for urban planning, illegal construction monitoring, 3D city modelling, environmental simulation, tourism, security, telecommunication and mobile navigation etc. The manual or semi-automatic 3D building model generation is costly and very time-consuming process for these applications. Thus, an approach for automatic 3D building model generation is needed in a simple and quick way for many studies which includes building modelling. In this study, automatic 3D building models generation is aimed with airborne LiDAR data. An approach is proposed for automatic 3D building models generation including the automatic point based classification of raw LiDAR point cloud. The proposed point based classification includes the hierarchical rules, for the automatic production of 3D building models. The detailed analyses for the parameters which used in hierarchical rules have been performed to improve classification results using different test areas identified in the study area. The proposed approach have been tested in the study area which has partly open areas, forest areas and many types of the buildings, in Zekeriyakoy, Istanbul using the TerraScan module of TerraSolid. The 3D building model was generated automatically using the results of the automatic point based classification. The obtained results of this research on study area verified that automatic 3D building models can be generated successfully using raw LiDAR point cloud data.

High-Resolution Surface Reconstruction from Imagery for Close Range Cultural Heritage Applications

NASA Astrophysics Data System (ADS)

Wenzel, K.; Abdel-Wahab, M.; Cefalu, A.; Fritsch, D.

2012-07-01

The recording of high resolution point clouds with sub-mm resolution is a demanding and cost intensive task, especially with current equipment like handheld laser scanners. We present an image based approached, where techniques of image matching and dense surface reconstruction are combined with a compact and affordable rig of off-the-shelf industry cameras. Such cameras provide high spatial resolution with low radiometric noise, which enables a one-shot solution and thus an efficient data acquisition while satisfying high accuracy requirements. However, the largest drawback of image based solutions is often the acquisition of surfaces with low texture where the image matching process might fail. Thus, an additional structured light projector is employed, represented here by the pseudo-random pattern projector of the Microsoft Kinect. Its strong infrared-laser projects speckles of different sizes. By using dense image matching techniques on the acquired images, a 3D point can be derived for almost each pixel. The use of multiple cameras enables the acquisition of a high resolution point cloud with high accuracy for each shot. For the proposed system up to 3.5 Mio. 3D points with sub-mm accuracy can be derived per shot. The registration of multiple shots is performed by Structure and Motion reconstruction techniques, where feature points are used to derive the camera positions and rotations automatically without initial information.

SU-E-J-29: Automatic Image Registration Performance of Three IGRT Systems for Prostate Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barber, J; University of Sydney, Sydney, NSW; Sykes, J

Purpose: To compare the performance of an automatic image registration algorithm on image sets collected on three commercial image guidance systems, and explore its relationship with imaging parameters such as dose and sharpness. Methods: Images of a CIRS Virtually Human Male Pelvis phantom (VHMP) were collected on the CBCT systems of Varian TrueBeam/OBI and Elekta Synergy/XVI linear accelerators, across a range of mAs settings; and MVCT on a Tomotherapy Hi-ART accelerator with a range of pitch. Using the 6D correlation ratio algorithm of XVI, each image was registered to a mask of the prostate volume with a 5 mm expansion.more » Registrations were repeated 100 times, with random initial offsets introduced to simulate daily matching. Residual registration errors were calculated by correcting for the initial phantom set-up error. Automatic registration was also repeated after reconstructing images with different sharpness filters. Results: All three systems showed good registration performance, with residual translations <0.5mm (1σ) for typical clinical dose and reconstruction settings. Residual rotational error had larger range, with 0.8°, 1.2° and 1.9° for 1σ in XVI, OBI and Tomotherapy respectively. The registration accuracy of XVI images showed a strong dependence on imaging dose, particularly below 4mGy. No evidence of reduced performance was observed at the lowest dose settings for OBI and Tomotherapy, but these were above 4mGy. Registration failures (maximum target registration error > 3.6 mm on the surface of a 30mm sphere) occurred in 5% to 10% of registrations. Changing the sharpness of image reconstruction had no significant effect on registration performance. Conclusions: Using the present automatic image registration algorithm, all IGRT systems tested provided satisfactory registrations for clinical use, within a normal range of acquisition settings.« less

Reconstruction of improvised explosive device blast loading to personnel in the open

NASA Astrophysics Data System (ADS)

Wiri, Suthee; Needham, Charles

2016-05-01

Significant advances in reconstructing attacks by improvised explosive devices (IEDs) and other blast events are reported. A high-fidelity three-dimensional computational fluid dynamics tool, called Second-order Hydrodynamic Automatic Mesh Refinement Code, was used for the analysis. Computer-aided design models for subjects or vehicles in the scene accurately represent geometries of objects in the blast field. A wide range of scenario types and blast exposure levels were reconstructed including free field blast, enclosed space of vehicle cabin, IED attack on a vehicle, buried charges, recoilless rifle operation, rocket-propelled grenade attack and missile attack with single subject or multiple subject exposure to pressure levels from ˜ 27.6 kPa (˜ 4 psi) to greater than 690 kPa (>100 psi). To create a full 3D pressure time-resolved reconstruction of a blast event for injury and blast exposure analysis, a combination of intelligence data and Blast Gauge data can be used to reconstruct an actual in-theatre blast event. The methodology to reconstruct an event and the "lessons learned" from multiple reconstructions in open space are presented. The analysis uses records of blast pressure at discrete points, and the output is a spatial and temporal blast load distribution for all personnel involved.

Network design and quality checks in automatic orientation of close-range photogrammetric blocks.

PubMed

Dall'Asta, Elisa; Thoeni, Klaus; Santise, Marina; Forlani, Gianfranco; Giacomini, Anna; Roncella, Riccardo

2015-04-03

Due to the recent improvements of automatic measurement procedures in photogrammetry, multi-view 3D reconstruction technologies are becoming a favourite survey tool. Rapidly widening structure-from-motion (SfM) software packages offer significantly easier image processing workflows than traditional photogrammetry packages. However, while most orientation and surface reconstruction strategies will almost always succeed in any given task, estimating the quality of the result is, to some extent, still an open issue. An assessment of the precision and reliability of block orientation is necessary and should be included in every processing pipeline. Such a need was clearly felt from the results of close-range photogrammetric surveys of in situ full-scale and laboratory-scale experiments. In order to study the impact of the block control and the camera network design on the block orientation accuracy, a series of Monte Carlo simulations was performed. Two image block configurations were investigated: a single pseudo-normal strip and a circular highly-convergent block. The influence of surveying and data processing choices, such as the number and accuracy of the ground control points, autofocus and camera calibration was investigated. The research highlights the most significant aspects and processes to be taken into account for adequate in situ and laboratory surveys, when modern SfM software packages are used, and evaluates their effect on the quality of the results of the surface reconstruction.

Real-time 3D image reconstruction guidance in liver resection surgery.

PubMed

Soler, Luc; Nicolau, Stephane; Pessaux, Patrick; Mutter, Didier; Marescaux, Jacques

2014-04-01

Minimally invasive surgery represents one of the main evolutions of surgical techniques. However, minimally invasive surgery adds difficulty that can be reduced through computer technology. From a patient's medical image [US, computed tomography (CT) or MRI], we have developed an Augmented Reality (AR) system that increases the surgeon's intraoperative vision by providing a virtual transparency of the patient. AR is based on two major processes: 3D modeling and visualization of anatomical or pathological structures appearing in the medical image, and the registration of this visualization onto the real patient. We have thus developed a new online service, named Visible Patient, providing efficient 3D modeling of patients. We have then developed several 3D visualization and surgical planning software tools to combine direct volume rendering and surface rendering. Finally, we have developed two registration techniques, one interactive and one automatic providing intraoperative augmented reality view. From January 2009 to June 2013, 769 clinical cases have been modeled by the Visible Patient service. Moreover, three clinical validations have been realized demonstrating the accuracy of 3D models and their great benefit, potentially increasing surgical eligibility in liver surgery (20% of cases). From these 3D models, more than 50 interactive AR-assisted surgical procedures have been realized illustrating the potential clinical benefit of such assistance to gain safety, but also current limits that automatic augmented reality will overcome. Virtual patient modeling should be mandatory for certain interventions that have now to be defined, such as liver surgery. Augmented reality is clearly the next step of the new surgical instrumentation but remains currently limited due to the complexity of organ deformations during surgery. Intraoperative medical imaging used in new generation of automated augmented reality should solve this issue thanks to the development of Hybrid OR.

An Automatic Procedure for Combining Digital Images and Laser Scanner Data

NASA Astrophysics Data System (ADS)

Moussa, W.; Abdel-Wahab, M.; Fritsch, D.

2012-07-01

Besides improving both the geometry and the visual quality of the model, the integration of close-range photogrammetry and terrestrial laser scanning techniques directs at filling gaps in laser scanner point clouds to avoid modeling errors, reconstructing more details in higher resolution and recovering simple structures with less geometric details. Thus, within this paper a flexible approach for the automatic combination of digital images and laser scanner data is presented. Our approach comprises two methods for data fusion. The first method starts by a marker-free registration of digital images based on a point-based environment model (PEM) of a scene which stores the 3D laser scanner point clouds associated with intensity and RGB values. The PEM allows the extraction of accurate control information for the direct computation of absolute camera orientations with redundant information by means of accurate space resection methods. In order to use the computed relations between the digital images and the laser scanner data, an extended Helmert (seven-parameter) transformation is introduced and its parameters are estimated. Precedent to that, in the second method, the local relative orientation parameters of the camera images are calculated by means of an optimized Structure and Motion (SaM) reconstruction method. Then, using the determined transformation parameters results in having absolute oriented images in relation to the laser scanner data. With the resulting absolute orientations we have employed robust dense image reconstruction algorithms to create oriented dense image point clouds, which are automatically combined with the laser scanner data to form a complete detailed representation of a scene. Examples of different data sets are shown and experimental results demonstrate the effectiveness of the presented procedures.

Incremental Refinement of FAÇADE Models with Attribute Grammar from 3d Point Clouds

NASA Astrophysics Data System (ADS)

Dehbi, Y.; Staat, C.; Mandtler, L.; Pl¨umer, L.

2016-06-01

Data acquisition using unmanned aerial vehicles (UAVs) has gotten more and more attention over the last years. Especially in the field of building reconstruction the incremental interpretation of such data is a demanding task. In this context formal grammars play an important role for the top-down identification and reconstruction of building objects. Up to now, the available approaches expect offline data in order to parse an a-priori known grammar. For mapping on demand an on the fly reconstruction based on UAV data is required. An incremental interpretation of the data stream is inevitable. This paper presents an incremental parser of grammar rules for an automatic 3D building reconstruction. The parser enables a model refinement based on new observations with respect to a weighted attribute context-free grammar (WACFG). The falsification or rejection of hypotheses is supported as well. The parser can deal with and adapt available parse trees acquired from previous interpretations or predictions. Parse trees derived so far are updated in an iterative way using transformation rules. A diagnostic step searches for mismatches between current and new nodes. Prior knowledge on façades is incorporated. It is given by probability densities as well as architectural patterns. Since we cannot always assume normal distributions, the derivation of location and shape parameters of building objects is based on a kernel density estimation (KDE). While the level of detail is continuously improved, the geometrical, semantic and topological consistency is ensured.

Stereoscopic 3D reconstruction using motorized zoom lenses within an embedded system

NASA Astrophysics Data System (ADS)

Liu, Pengcheng; Willis, Andrew; Sui, Yunfeng

2009-02-01

This paper describes a novel embedded system capable of estimating 3D positions of surfaces viewed by a stereoscopic rig consisting of a pair of calibrated cameras. Novel theoretical and technical aspects of the system are tied to two aspects of the design that deviate from typical stereoscopic reconstruction systems: (1) incorporation of an 10x zoom lens (Rainbow- H10x8.5) and (2) implementation of the system on an embedded system. The system components include a DSP running μClinux, an embedded version of the Linux operating system, and an FPGA. The DSP orchestrates data flow within the system and performs complex computational tasks and the FPGA provides an interface to the system devices which consist of a CMOS camera pair and a pair of servo motors which rotate (pan) each camera. Calibration of the camera pair is accomplished using a collection of stereo images that view a common chess board calibration pattern for a set of pre-defined zoom positions. Calibration settings for an arbitrary zoom setting are estimated by interpolation of the camera parameters. A low-computational cost method for dense stereo matching is used to compute depth disparities for the stereo image pairs. Surface reconstruction is accomplished by classical triangulation of the matched points from the depth disparities. This article includes our methods and results for the following problems: (1) automatic computation of the focus and exposure settings for the lens and camera sensor, (2) calibration of the system for various zoom settings and (3) stereo reconstruction results for several free form objects.

A Method for Automatic Surface Inspection Using a Model-Based 3D Descriptor.

PubMed

Madrigal, Carlos A; Branch, John W; Restrepo, Alejandro; Mery, Domingo

2017-10-02

Automatic visual inspection allows for the identification of surface defects in manufactured parts. Nevertheless, when defects are on a sub-millimeter scale, detection and recognition are a challenge. This is particularly true when the defect generates topological deformations that are not shown with strong contrast in the 2D image. In this paper, we present a method for recognizing surface defects in 3D point clouds. Firstly, we propose a novel 3D local descriptor called the Model Point Feature Histogram (MPFH) for defect detection. Our descriptor is inspired from earlier descriptors such as the Point Feature Histogram (PFH). To construct the MPFH descriptor, the models that best fit the local surface and their normal vectors are estimated. For each surface model, its contribution weight to the formation of the surface region is calculated and from the relative difference between models of the same region a histogram is generated representing the underlying surface changes. Secondly, through a classification stage, the points on the surface are labeled according to five types of primitives and the defect is detected. Thirdly, the connected components of primitives are projected to a plane, forming a 2D image. Finally, 2D geometrical features are extracted and by a support vector machine, the defects are recognized. The database used is composed of 3D simulated surfaces and 3D reconstructions of defects in welding, artificial teeth, indentations in materials, ceramics and 3D models of defects. The quantitative and qualitative results showed that the proposed method of description is robust to noise and the scale factor, and it is sufficiently discriminative for detecting some surface defects. The performance evaluation of the proposed method was performed for a classification task of the 3D point cloud in primitives, reporting an accuracy of 95%, which is higher than for other state-of-art descriptors. The rate of recognition of defects was close to 94%.

A Method for Automatic Surface Inspection Using a Model-Based 3D Descriptor

PubMed Central

Branch, John W.

2017-01-01

Automatic visual inspection allows for the identification of surface defects in manufactured parts. Nevertheless, when defects are on a sub-millimeter scale, detection and recognition are a challenge. This is particularly true when the defect generates topological deformations that are not shown with strong contrast in the 2D image. In this paper, we present a method for recognizing surface defects in 3D point clouds. Firstly, we propose a novel 3D local descriptor called the Model Point Feature Histogram (MPFH) for defect detection. Our descriptor is inspired from earlier descriptors such as the Point Feature Histogram (PFH). To construct the MPFH descriptor, the models that best fit the local surface and their normal vectors are estimated. For each surface model, its contribution weight to the formation of the surface region is calculated and from the relative difference between models of the same region a histogram is generated representing the underlying surface changes. Secondly, through a classification stage, the points on the surface are labeled according to five types of primitives and the defect is detected. Thirdly, the connected components of primitives are projected to a plane, forming a 2D image. Finally, 2D geometrical features are extracted and by a support vector machine, the defects are recognized. The database used is composed of 3D simulated surfaces and 3D reconstructions of defects in welding, artificial teeth, indentations in materials, ceramics and 3D models of defects. The quantitative and qualitative results showed that the proposed method of description is robust to noise and the scale factor, and it is sufficiently discriminative for detecting some surface defects. The performance evaluation of the proposed method was performed for a classification task of the 3D point cloud in primitives, reporting an accuracy of 95%, which is higher than for other state-of-art descriptors. The rate of recognition of defects was close to 94%. PMID:28974037

Automatic falx cerebri and tentorium cerebelli segmentation from magnetic resonance images

NASA Astrophysics Data System (ADS)

Glaister, Jeffrey; Carass, Aaron; Pham, Dzung L.; Butman, John A.; Prince, Jerry L.

2017-03-01

The falx cerebri and tentorium cerebelli are dural structures found in the brain. Due to the roles both structures play in constraining brain motion, the falx and tentorium must be identified and included in finite element models of the head to accurately predict brain dynamics during injury events. To date there has been very little research work on automatically segmenting these two structures, which is understandable given that their 1) thin structure challenges the resolution limits of in vivo 3D imaging, and 2) contrast with respect to surrounding tissue is low in standard magnetic resonance imaging. An automatic segmentation algorithm to find the falx and tentorium which uses the results of a multi-atlas segmentation and cortical reconstruction algorithm is proposed. Gray matter labels are used to find the location of the falx and tentorium. The proposed algorithm is applied to five datasets with manual delineations. 3D visualizations of the final results are provided, and Hausdorff distance (HD) and mean surface distance (MSD) is calculated to quantify the accuracy of the proposed method. For the falx, the mean HD is 43.84 voxels and the mean MSD is 2.78 voxels, with the largest errors occurring at the frontal inferior falx boundary. For the tentorium, the mean HD is 14.50 voxels and mean MSD is 1.38 voxels.

Automatic falx cerebri and tentorium cerebelli segmentation from Magnetic Resonance Images.

PubMed

Glaister, Jeffrey; Carass, Aaron; Pham, Dzung L; Butman, John A; Prince, Jerry L

2017-02-01

The falx cerebri and tentorium cerebelli are dural structures found in the brain. Due to the roles both structures play in constraining brain motion, the falx and tentorium must be identified and included in finite element models of the head to accurately predict brain dynamics during injury events. To date there has been very little research work on automatically segmenting these two structures, which is understandable given that their 1) thin structure challenges the resolution limits of in vivo 3D imaging, and 2) contrast with respect to surrounding tissue is low in standard magnetic resonance imaging. An automatic segmentation algorithm to find the falx and tentorium which uses the results of a multi-atlas segmentation and cortical reconstruction algorithm is proposed. Gray matter labels are used to find the location of the falx and tentorium. The proposed algorithm is applied to five datasets with manual delineations. 3D visualizations of the final results are provided, and Hausdorff distance (HD) and mean surface distance (MSD) is calculated to quantify the accuracy of the proposed method. For the falx, the mean HD is 43.84 voxels and the mean MSD is 2.78 voxels, with the largest errors occurring at the frontal inferior falx boundary. For the tentorium, the mean HD is 14.50 voxels and mean MSD is 1.38 voxels.

75 FR 68200 - Medical Devices; Radiology Devices; Reclassification of Full-Field Digital Mammography System

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-05

... exposure control, image processing and reconstruction programs, patient and equipment supports, component..., acquisition workstation, automatic exposure control, image processing and reconstruction programs, patient and... may include was revised by adding automatic exposure control, image processing and reconstruction...

TU-CD-207-11: Patient-Driven Automatic Exposure Control for Dedicated Breast CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez, A; Gazi, P; Department of Radiology, UC Davis Medical Center, Sacramento, CA

Purpose: To implement automatic exposure control (AEC) in dedicated breast CT (bCT) on a patient-specific basis using only the pre-scan scout views. Methods: Using a large cohort (N=153) of bCT data sets, the breast effective diameter (D) and width in orthogonal planes (Wa,Wb) were calculated from the reconstructed bCT image and pre-scan scout views, respectively. D, Wa, and Wb were measured at the breast center-of-mass (COM), making use of the known geometry of our bCT system. These data were then fit to a second-order polynomial “D=F(Wa,Wb)” in a least squares sense in order to provide a functional form for determiningmore » the breast diameter. The coefficient of determination (R{sup 2}) and mean percent error between the measured breast diameter and fit breast diameter were used to evaluate the overall robustness of the polynomial fit. Lastly, previously-reported bCT technique factors derived from Monte Carlo simulations were used to determine the tube current required for each breast diameter in order to match two-view mammographic dose levels. Results: F(Wa,Wb) provided fitted breast diameters in agreement with the measured breast diameters resulting in R{sup 2} values ranging from 0.908 to 0.929 and mean percent errors ranging from 3.2% to 3.7%. For all 153 bCT data sets used in this study, the fitted breast diameters ranged from 7.9 cm to 15.7 cm corresponding to tube current values ranging from 0.6 mA to 4.9 mA in order to deliver the same dose as two-view mammography in a 50% glandular breast with a 80 kV x-ray beam and 16.6 second scan time. Conclusion: The present work provides a robust framework for AEC in dedicated bCT using only the width measurements derived from the two orthogonal pre-scan scout views. Future work will investigate how these automatically chosen exposure levels affect the quality of the reconstructed image.« less

A CNN Regression Approach for Real-Time 2D/3D Registration.

PubMed

Shun Miao; Wang, Z Jane; Rui Liao

2016-05-01

In this paper, we present a Convolutional Neural Network (CNN) regression approach to address the two major limitations of existing intensity-based 2-D/3-D registration technology: 1) slow computation and 2) small capture range. Different from optimization-based methods, which iteratively optimize the transformation parameters over a scalar-valued metric function representing the quality of the registration, the proposed method exploits the information embedded in the appearances of the digitally reconstructed radiograph and X-ray images, and employs CNN regressors to directly estimate the transformation parameters. An automatic feature extraction step is introduced to calculate 3-D pose-indexed features that are sensitive to the variables to be regressed while robust to other factors. The CNN regressors are then trained for local zones and applied in a hierarchical manner to break down the complex regression task into multiple simpler sub-tasks that can be learned separately. Weight sharing is furthermore employed in the CNN regression model to reduce the memory footprint. The proposed approach has been quantitatively evaluated on 3 potential clinical applications, demonstrating its significant advantage in providing highly accurate real-time 2-D/3-D registration with a significantly enlarged capture range when compared to intensity-based methods.

3D Surface Reconstruction of Rills in a Spanish Olive Grove

NASA Astrophysics Data System (ADS)

Brings, Christine; Gronz, Oliver; Seeger, Manuel; Wirtz, Stefan; Taguas, Encarnación; Ries, Johannes B.

2016-04-01

The low-cost, user-friendly photogrammetric Structure from Motion (SfM) technique is used for 3D surface reconstruction and difference calculation of an 18 meter long rill in South Spain (Andalusia, Puente Genil). The images were taken with a Canon HD video camera before and after a rill experiment in an olive grove. Recording with a video camera has compared to a photo camera a huge time advantage and the method also guarantees more than adequately overlapping sharp images. For each model, approximately 20 minutes of video were taken. As SfM needs single images, the sharpest image was automatically selected from 8 frame intervals. The sharpness was estimated using a derivative-based metric. Then, VisualSfM detects feature points in each image, searches matching feature points in all image pairs and recovers the camera and feature positions. Finally, by triangulation of camera positions and feature points the software reconstructs a point cloud of the rill surface. From the point cloud, 3D surface models (meshes) are created and via difference calculations of the pre and post model a visualization of the changes (erosion and accumulation areas) and quantification of erosion volumes are possible. The calculated volumes are presented in spatial units of the models and so real values must be converted via references. The results show that rills in olive groves have a high dynamic due to the lack of vegetation cover under the trees, so that the rill can incise until the bedrock. Another reason for the high activity is the intensive employment of machinery.

Localization of liver tumors in freehand 3D laparoscopic ultrasound

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Dictionary learning-based spatiotemporal regularization for 3D dense speckle tracking

NASA Astrophysics Data System (ADS)

Lu, Allen; Zontak, Maria; Parajuli, Nripesh; Stendahl, John C.; Boutagy, Nabil; Eberle, Melissa; O'Donnell, Matthew; Sinusas, Albert J.; Duncan, James S.

2017-03-01

Speckle tracking is a common method for non-rigid tissue motion analysis in 3D echocardiography, where unique texture patterns are tracked through the cardiac cycle. However, poor tracking often occurs due to inherent ultrasound issues, such as image artifacts and speckle decorrelation; thus regularization is required. Various methods, such as optical flow, elastic registration, and block matching techniques have been proposed to track speckle motion. Such methods typically apply spatial and temporal regularization in a separate manner. In this paper, we propose a joint spatiotemporal regularization method based on an adaptive dictionary representation of the dense 3D+time Lagrangian motion field. Sparse dictionaries have good signal adaptive and noise-reduction properties; however, they are prone to quantization errors. Our method takes advantage of the desirable noise suppression, while avoiding the undesirable quantization error. The idea is to enforce regularization only on the poorly tracked trajectories. Specifically, our method 1.) builds data-driven 4-dimensional dictionary of Lagrangian displacements using sparse learning, 2.) automatically identifies poorly tracked trajectories (outliers) based on sparse reconstruction errors, and 3.) performs sparse reconstruction of the outliers only. Our approach can be applied on dense Lagrangian motion fields calculated by any method. We demonstrate the effectiveness of our approach on a baseline block matching speckle tracking and evaluate performance of the proposed algorithm using tracking and strain accuracy analysis.

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.

Comparison between manual and semi-automatic segmentation of nasal cavity and paranasal sinuses from CT images.

PubMed

Tingelhoff, K; Moral, A I; Kunkel, M E; Rilk, M; Wagner, I; Eichhorn, K G; Wahl, F M; Bootz, F

2007-01-01

Segmentation of medical image data is getting more and more important over the last years. The results are used for diagnosis, surgical planning or workspace definition of robot-assisted systems. The purpose of this paper is to find out whether manual or semi-automatic segmentation is adequate for ENT surgical workflow or whether fully automatic segmentation of paranasal sinuses and nasal cavity is needed. We present a comparison of manual and semi-automatic segmentation of paranasal sinuses and the nasal cavity. Manual segmentation is performed by custom software whereas semi-automatic segmentation is realized by a commercial product (Amira). For this study we used a CT dataset of the paranasal sinuses which consists of 98 transversal slices, each 1.0 mm thick, with a resolution of 512 x 512 pixels. For the analysis of both segmentation procedures we used volume, extension (width, length and height), segmentation time and 3D-reconstruction. The segmentation time was reduced from 960 minutes with manual to 215 minutes with semi-automatic segmentation. We found highest variances segmenting nasal cavity. For the paranasal sinuses manual and semi-automatic volume differences are not significant. Dependent on the segmentation accuracy both approaches deliver useful results and could be used for e.g. robot-assisted systems. Nevertheless both procedures are not useful for everyday surgical workflow, because they take too much time. Fully automatic and reproducible segmentation algorithms are needed for segmentation of paranasal sinuses and nasal cavity.

Online 3D EPID-based dose verification: Proof of concept.

PubMed

Spreeuw, Hanno; Rozendaal, Roel; Olaciregui-Ruiz, Igor; González, Patrick; Mans, Anton; Mijnheer, Ben; van Herk, Marcel

2016-07-01

Delivery errors during radiotherapy may lead to medical harm and reduced life expectancy for patients. Such serious incidents can be avoided by performing dose verification online, i.e., while the patient is being irradiated, creating the possibility of halting the linac in case of a large overdosage or underdosage. The offline EPID-based 3D in vivo dosimetry system clinically employed at our institute is in principle suited for online treatment verification, provided the system is able to complete 3D dose reconstruction and verification within 420 ms, the present acquisition time of a single EPID frame. It is the aim of this study to show that our EPID-based dosimetry system can be made fast enough to achieve online 3D in vivo dose verification. The current dose verification system was sped up in two ways. First, a new software package was developed to perform all computations that are not dependent on portal image acquisition separately, thus removing the need for doing these calculations in real time. Second, the 3D dose reconstruction algorithm was sped up via a new, multithreaded implementation. Dose verification was implemented by comparing planned with reconstructed 3D dose distributions delivered to two regions in a patient: the target volume and the nontarget volume receiving at least 10 cGy. In both volumes, the mean dose is compared, while in the nontarget volume, the near-maximum dose (D2) is compared as well. The real-time dosimetry system was tested by irradiating an anthropomorphic phantom with three VMAT plans: a 6 MV head-and-neck treatment plan, a 10 MV rectum treatment plan, and a 10 MV prostate treatment plan. In all plans, two types of serious delivery errors were introduced. The functionality of automatically halting the linac was also implemented and tested. The precomputation time per treatment was ∼180 s/treatment arc, depending on gantry angle resolution. The complete processing of a single portal frame, including dose verification, took 266 ± 11 ms on a dual octocore Intel Xeon E5-2630 CPU running at 2.40 GHz. The introduced delivery errors were detected after 5-10 s irradiation time. A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for two different kinds of gross delivery errors. Thus, online 3D dose verification has been technologically achieved.

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 potential to improve analyses of cam-type lesions of the FHN junction for large-scale morphometric and clinical MR investigations of the human hip region.

Quantification of tumor morphology via 3D histology: application to oral cavity cancers

NASA Astrophysics Data System (ADS)

Doyle, Scott; Brandwein-Gensler, Margaret; Tomaszewski, John

2016-03-01

Traditional histopathology quantifies disease through the study of glass slides, i.e. two-dimensional samples that are representative of the overall process. We hypothesize that 3D reconstruction can enhance our understanding of histopathologic interpretations. To test this hypothesis, we perform a pilot study of the risk model for oral cavity cancer (OCC), which stratifies patients into low-, intermediate-, and high-risk for locoregional disease-free survival. Classification is based on study of hematoxylin and eosin (H and E) stained tissues sampled from the resection specimens. In this model, the Worst Pattern of Invasion (WPOI) is assessed, representing specific architectural features at the interface between cancer and non-cancer tissue. Currently, assessment of WPOI is based on 2D sections of tissue, representing complex 3D structures of tumor growth. We believe that by reconstructing a 3D model of tumor growth and quantifying the tumor-host interface, we can obtain important diagnostic information that is difficult to assess in 2D. Therefore, we introduce a pilot study framework for visualizing tissue architecture and morphology in 3D from serial sections of histopathology. This framework can be used to enhance predictive models for diseases where severity is determined by 3D biological structure. In this work we utilize serial H and E-stained OCC resections obtained from 7 patients exhibiting WPOI-3 (low risk of recurrence) through WPOI-5 (high risk of recurrence). A supervised classifier automatically generates a map of tumor regions on each slide, which are then co-registered using an elastic deformation algorithm. A smooth 3D model of the tumor region is generated from the registered maps, which is suitable for quantitative tumor interface morphology feature extraction. We report our preliminary models created with this system and suggest further enhancements to traditional histology scoring mechanisms that take spatial architecture into consideration.

Computed reconstruction of spatial ammonoid-shell orientation captured from digitized grinding and landmark data

NASA Astrophysics Data System (ADS)

Lukeneder, Susanne; Lukeneder, Alexander; Weber, Gerhard W.

2014-03-01

The internal orientation of fossil mass occurrences can be exploited as useful source of information about their primary depositional conditions. A series of studies, using different kinds of fossils, especially those with elongated shape (e.g., elongated gastropods), deal with their orientation and the subsequent reconstruction of the depositional conditions (e.g., paleocurrents and transport mechanisms). However, disk-shaped fossils like planispiral cephalopods or gastropods were used, up to now, with caution for interpreting paleocurrents. Moreover, most studies just deal with the topmost surface of such mass occurrences, due to the easier accessibility. Within this study, a new method for three-dimensional reconstruction of the internal structure of a fossil mass occurrence and the subsequent calculation of its spatial shell orientation is established. A 234 million-years-old (Carnian, Triassic) monospecific mass occurrence of the ammonoid Kasimlarceltites krystyni from the Taurus Mountains in Turkey, embedded in limestone, is used for this pilot study. Therefore, a 150×45×140 mm3 block of the ammonoid bearing limestone bed has been grinded to 70 slices, with a distance of 2 mm between each slice. By using a semi-automatic region growing algorithm of the 3D-visualization software Amira, ammonoids of a part of this mass occurrence were segmented and a 3D-model reconstructed. Landmarks, trigonometric and vector-based calculations were used to compute the diameters and the spatial orientation of each ammonoid. The spatial shell orientation was characterized by dip and dip-direction and aperture direction of the longitudinal axis, as well as by dip and azimuth of an imaginary sagittal-plane through each ammonoid. The exact spatial shell orientation was determined for a sample of 675 ammonoids, and their statistical orientation analyzed (i.e., NW/SE). The study combines classical orientation analysis with modern 3D-visualization techniques, and establishes a novel spatial orientation analyzing method, which can be adapted to any kind of abundant solid matter.

A point cloud modeling method based on geometric constraints mixing the robust least squares method

NASA Astrophysics Data System (ADS)

Yue, JIanping; Pan, Yi; Yue, Shun; Liu, Dapeng; Liu, Bin; Huang, Nan

2016-10-01

The appearance of 3D laser scanning technology has provided a new method for the acquisition of spatial 3D information. It has been widely used in the field of Surveying and Mapping Engineering with the characteristics of automatic and high precision. 3D laser scanning data processing process mainly includes the external laser data acquisition, the internal industry laser data splicing, the late 3D modeling and data integration system. For the point cloud modeling, domestic and foreign researchers have done a lot of research. Surface reconstruction technology mainly include the point shape, the triangle model, the triangle Bezier surface model, the rectangular surface model and so on, and the neural network and the Alfa shape are also used in the curved surface reconstruction. But in these methods, it is often focused on single surface fitting, automatic or manual block fitting, which ignores the model's integrity. It leads to a serious problems in the model after stitching, that is, the surfaces fitting separately is often not satisfied with the well-known geometric constraints, such as parallel, vertical, a fixed angle, or a fixed distance. However, the research on the special modeling theory such as the dimension constraint and the position constraint is not used widely. One of the traditional modeling methods adding geometric constraints is a method combing the penalty function method and the Levenberg-Marquardt algorithm (L-M algorithm), whose stability is pretty good. But in the research process, it is found that the method is greatly influenced by the initial value. In this paper, we propose an improved method of point cloud model taking into account the geometric constraint. We first apply robust least-squares to enhance the initial value's accuracy, and then use penalty function method to transform constrained optimization problems into unconstrained optimization problems, and finally solve the problems using the L-M algorithm. The experimental results show that the internal accuracy is improved, and it is shown that the improved method for point clouds modeling proposed by this paper outperforms the traditional point clouds modeling methods.

Combined Use of Automatic Tube Voltage Selection and Current Modulation with Iterative Reconstruction for CT Evaluation of Small Hypervascular Hepatocellular Carcinomas: Effect on Lesion Conspicuity and Image Quality

PubMed Central

Lv, Peijie; Liu, Jie; Zhang, Rui; Jia, Yan

2015-01-01

Objective To assess the lesion conspicuity and image quality in CT evaluation of small (≤ 3 cm) hepatocellular carcinomas (HCCs) using automatic tube voltage selection (ATVS) and automatic tube current modulation (ATCM) with or without iterative reconstruction. Materials and Methods One hundred and five patients with 123 HCC lesions were included. Fifty-seven patients were scanned using both ATVS and ATCM and images were reconstructed using either filtered back-projection (FBP) (group A1) or sinogram-affirmed iterative reconstruction (SAFIRE) (group A2). Forty-eight patients were imaged using only ATCM, with a fixed tube potential of 120 kVp and FBP reconstruction (group B). Quantitative parameters (image noise in Hounsfield unit and contrast-to-noise ratio of the aorta, the liver, and the hepatic tumors) and qualitative visual parameters (image noise, overall image quality, and lesion conspicuity as graded on a 5-point scale) were compared among the groups. Results Group A2 scanned with the automatically chosen 80 kVp and 100 kVp tube voltages ranked the best in lesion conspicuity and subjective and objective image quality (p values ranging from < 0.001 to 0.004) among the three groups, except for overall image quality between group A2 and group B (p = 0.022). Group A1 showed higher image noise (p = 0.005) but similar lesion conspicuity and overall image quality as compared with group B. The radiation dose in group A was 19% lower than that in group B (p = 0.022). Conclusion CT scanning with combined use of ATVS and ATCM and image reconstruction with SAFIRE algorithm provides higher lesion conspicuity and better image quality for evaluating small hepatic HCCs with radiation dose reduction. PMID:25995682

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

PubMed

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

2013-04-01

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. Copyright © 2012 Elsevier B.V. All rights reserved.

Local motion-compensated method for high-quality 3D coronary artery reconstruction

PubMed Central

Liu, Bo; Bai, Xiangzhi; Zhou, Fugen

2016-01-01

The 3D reconstruction of coronary artery from X-ray angiograms rotationally acquired on C-arm has great clinical value. While cardiac-gated reconstruction has shown promising results, it suffers from the problem of residual motion. This work proposed a new local motion-compensated reconstruction method to handle this issue. An initial image was firstly reconstructed using a regularized iterative reconstruction method. Then a 3D/2D registration method was proposed to estimate the residual vessel motion. Finally, the residual motion was compensated in the final reconstruction using the extended iterative reconstruction method. Through quantitative evaluation, it was found that high-quality 3D reconstruction could be obtained and the result was comparable to state-of-the-art method. PMID:28018741

Toward realistic radiofrequency ablation of hepatic tumors 3D simulation and planning

NASA Astrophysics Data System (ADS)

Villard, Caroline; Soler, Luc; Gangi, Afshin; Mutter, Didier; Marescaux, Jacques

2004-05-01

Radiofrequency ablation (RFA) has become an increasingly used technique in the treatment of patients with unresectable hepatic tumors. Evaluation of vascular architecture, post-RFA tissue necrosis prediction, and the choice of a suitable needle placement strategy using conventional radiological techniques remain difficult. In an attempt to enhance the safety of RFA, a 3D simulator and treatment planning tool, that simulates the necrosis of the treated area, and proposes an optimal placement for the needle, has been developed. From enhanced spiral CT scans with 2 mm cuts, 3D reconstructions of patients with liver metastases are automatically generated. Virtual needles can be added to the 3D scene, together with their corresponding zones of necrosis that are displayed as a meshed spheroids representing the 60° C isosurface. The simulator takes into account the cooling effect of local vessels greater than 3mm in diameter, making necrosis shapes more realistic. Using a voxel-based algorithm, RFA spheroids are deformed following the shape of the vessels, extended by an additional cooled area. This operation is performed in real-time, allowing updates while needle is adjusted. This allows to observe whether the considered needle placement strategy would burn the whole cancerous zone or not. Planned needle positioning can also be automatically generated by the software to produce complete destruction of the tumor with a 1 cm margin, with maximum respect of the healthy liver and of all major extrahepatic and intrahepatic structures to avoid. If he wishes, the radiologist can select on the skin an insertion window for the needle, focusing the research of the trajectory.

Towards Automatic Semantic Labelling of 3D City Models

NASA Astrophysics Data System (ADS)

Rook, M.; Biljecki, F.; Diakité, A. A.

2016-10-01

The lack of semantic information in many 3D city models is a considerable limiting factor in their use, as a lot of applications rely on semantics. Such information is not always available, since it is not collected at all times, it might be lost due to data transformation, or its lack may be caused by non-interoperability in data integration from other sources. This research is a first step in creating an automatic workflow that semantically labels plain 3D city model represented by a soup of polygons, with semantic and thematic information, as defined in the CityGML standard. The first step involves the reconstruction of the topology, which is used in a region growing algorithm that clusters upward facing adjacent triangles. Heuristic rules, embedded in a decision tree, are used to compute a likeliness score for these regions that either represent the ground (terrain) or a RoofSurface. Regions with a high likeliness score, to one of the two classes, are used to create a decision space, which is used in a support vector machine (SVM). Next, topological relations are utilised to select seeds that function as a start in a region growing algorithm, to create regions of triangles of other semantic classes. The topological relationships of the regions are used in the aggregation of the thematic building features. Finally, the level of detail is detected to generate the correct output in CityGML. The results show an accuracy between 85 % and 99 % in the automatic semantic labelling on four different test datasets. The paper is concluded by indicating problems and difficulties implying the next steps in the research.

Reduction of effective dose and organ dose to the eye lens in head MDCT using iterative image reconstruction and automatic tube current modulation.

PubMed

Ryska, Pavel; Kvasnicka, Tomas; Jandura, Jiri; Klzo, Ludovit; Grepl, Jakub; Zizka, Jan

2014-06-01

To compare the effective and eye lens radiation dose in helical MDCT brain examinations using automatic tube current modulation in conjunction with either standard filtered back projection (FBP) technique or iterative reconstruction in image space (IRIS). Of 400 adult brain MDCT examinations, 200 were performed using FBP and 200 using IRIS with the following parameters: tube voltage 120 kV, rotation period 1 second, pitch factor 0.55, automatic tube current modulation in both transverse and longitudinal planes with reference mAs 300 (FBP) and 200 (IRIS). Doses were calculated from CT dose index and dose length product values utilising ImPACT software; the organ dose to the lens was derived from the actual tube current-time product value applied to the lens. Image quality was assessed by two independent readers blinded to the type of image reconstruction technique. The average effective scan dose was 1.47±0.26 mSv (FBP) and 0.98±0.15 mSv (IRIS), respectively (33.3% decrease). The average organ dose to the eye lens decreased from 40.0±3.3 mGy (FBP) to 26.6±2.0 mGy (IRIS, 33.5% decrease). No significant change in diagnostic image quality was noted between IRIS and FBP scans (P=0.17). Iterative reconstruction of cerebral MDCT examinations enables reduction of both effective and organ eye lens dose by one third without signficant loss of image quality.

Automatic Non-Destructive Growth Measurement of Leafy Vegetables Based on Kinect

PubMed Central

Hu, Yang; Wang, Le; Xiang, Lirong; Wu, Qian; Jiang, Huanyu

2018-01-01

Non-destructive plant growth measurement is essential for plant growth and health research. As a 3D sensor, Kinect v2 has huge potentials in agriculture applications, benefited from its low price and strong robustness. The paper proposes a Kinect-based automatic system for non-destructive growth measurement of leafy vegetables. The system used a turntable to acquire multi-view point clouds of the measured plant. Then a series of suitable algorithms were applied to obtain a fine 3D reconstruction for the plant, while measuring the key growth parameters including relative/absolute height, total/projected leaf area and volume. In experiment, 63 pots of lettuce in different growth stages were measured. The result shows that the Kinect-measured height and projected area have fine linear relationship with reference measurements. While the measured total area and volume both follow power law distributions with reference data. All these data have shown good fitting goodness (R2 = 0.9457–0.9914). In the study of biomass correlations, the Kinect-measured volume was found to have a good power law relationship (R2 = 0.9281) with fresh weight. In addition, the system practicality was validated by performance and robustness analysis. PMID:29518958

Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model

PubMed Central

Verhey, Janko F; Nathan, Nadia S

2004-01-01

Background Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS©. Methods In this prospective study TomTec LV Analysis TEE© Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen©, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV. Results This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room. Conclusion For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein. PMID:15473901

Three Dimensional Imaging of Paraffin Embedded Human Lung Tissue Samples by Micro-Computed Tomography

PubMed Central

Scott, Anna E.; Vasilescu, Dragos M.; Seal, Katherine A. D.; Keyes, Samuel D.; Mavrogordato, Mark N.; Hogg, James C.; Sinclair, Ian; Warner, Jane A.; Hackett, Tillie-Louise; Lackie, Peter M.

2015-01-01

Background Understanding the three-dimensional (3-D) micro-architecture of lung tissue can provide insights into the pathology of lung disease. Micro computed tomography (µCT) has previously been used to elucidate lung 3D histology and morphometry in fixed samples that have been stained with contrast agents or air inflated and dried. However, non-destructive microstructural 3D imaging of formalin-fixed paraffin embedded (FFPE) tissues would facilitate retrospective analysis of extensive tissue archives of lung FFPE lung samples with linked clinical data. Methods FFPE human lung tissue samples (n = 4) were scanned using a Nikon metrology µCT scanner. Semi-automatic techniques were used to segment the 3D structure of airways and blood vessels. Airspace size (mean linear intercept, Lm) was measured on µCT images and on matched histological sections from the same FFPE samples imaged by light microscopy to validate µCT imaging. Results The µCT imaging protocol provided contrast between tissue and paraffin in FFPE samples (15mm x 7mm). Resolution (voxel size 6.7 µm) in the reconstructed images was sufficient for semi-automatic image segmentation of airways and blood vessels as well as quantitative airspace analysis. The scans were also used to scout for regions of interest, enabling time-efficient preparation of conventional histological sections. The Lm measurements from µCT images were not significantly different to those from matched histological sections. Conclusion We demonstrated how non-destructive imaging of routinely prepared FFPE samples by laboratory µCT can be used to visualize and assess the 3D morphology of the lung including by morphometric analysis. PMID:26030902

"3D_Fault_Offsets," a Matlab Code to Automatically Measure Lateral and Vertical Fault Offsets in Topographic Data: Application to San Andreas, Owens Valley, and Hope Faults

NASA Astrophysics Data System (ADS)

Stewart, N.; Gaudemer, Y.; Manighetti, I.; Serreau, L.; Vincendeau, A.; Dominguez, S.; Mattéo, L.; Malavieille, J.

2018-01-01

Measuring fault offsets preserved at the ground surface is of primary importance to recover earthquake and long-term slip distributions and understand fault mechanics. The recent explosion of high-resolution topographic data, such as Lidar and photogrammetric digital elevation models, offers an unprecedented opportunity to measure dense collections of fault offsets. We have developed a new Matlab code, 3D_Fault_Offsets, to automate these measurements. In topographic data, 3D_Fault_Offsets mathematically identifies and represents nine of the most prominent geometric characteristics of common sublinear markers along faults (especially strike slip) in 3-D, such as the streambed (minimum elevation), top, free face and base of channel banks or scarps (minimum Laplacian, maximum gradient, and maximum Laplacian), and ridges (maximum elevation). By calculating best fit lines through the nine point clouds on either side of the fault, the code computes the lateral and vertical offsets between the piercing points of these lines onto the fault plane, providing nine lateral and nine vertical offset measures per marker. Through a Monte Carlo approach, the code calculates the total uncertainty on each offset. It then provides tools to statistically analyze the dense collection of measures and to reconstruct the prefaulted marker geometry in the horizontal and vertical planes. We applied 3D_Fault_Offsets to remeasure previously published offsets across 88 markers on the San Andreas, Owens Valley, and Hope faults. We obtained 5,454 lateral and vertical offset measures. These automatic measures compare well to prior ones, field and remote, while their rich record provides new insights on the preservation of fault displacements in the morphology.

Feature detection on 3D images of dental imprints

NASA Astrophysics Data System (ADS)

Mokhtari, Marielle; Laurendeau, Denis

1994-09-01

A computer vision approach for the extraction of feature points on 3D images of dental imprints is presented. The position of feature points are needed for the measurement of a set of parameters for automatic diagnosis of malocclusion problems in orthodontics. The system for the acquisition of the 3D profile of the imprint, the procedure for the detection of the interstices between teeth, and the approach for the identification of the type of tooth are described, as well as the algorithm for the reconstruction of the surface of each type of tooth. A new approach for the detection of feature points, called the watershed algorithm, is described in detail. The algorithm is a two-stage procedure which tracks the position of local minima at four different scales and produces a final map of the position of the minima. Experimental results of the application of the watershed algorithm on actual 3D images of dental imprints are presented for molars, premolars and canines. The segmentation approach for the analysis of the shape of incisors is also described in detail.

A three-dimensional virtual environment for modeling mechanical cardiopulmonary interactions.

PubMed

Kaye, J M; Primiano, F P; Metaxas, D N

1998-06-01

We have developed a real-time computer system for modeling mechanical physiological behavior in an interactive, 3-D virtual environment. Such an environment can be used to facilitate exploration of cardiopulmonary physiology, particularly in situations that are difficult to reproduce clinically. We integrate 3-D deformable body dynamics with new, formal models of (scalar) cardiorespiratory physiology, associating the scalar physiological variables and parameters with the corresponding 3-D anatomy. Our framework enables us to drive a high-dimensional system (the 3-D anatomical models) from one with fewer parameters (the scalar physiological models) because of the nature of the domain and our intended application. Our approach is amenable to modeling patient-specific circumstances in two ways. First, using CT scan data, we apply semi-automatic methods for extracting and reconstructing the anatomy to use in our simulations. Second, our scalar physiological models are defined in terms of clinically measurable, patient-specific parameters. This paper describes our approach, problems we have encountered and a sample of results showing normal breathing and acute effects of pneumothoraces.

Line segment extraction for large scale unorganized point clouds

NASA Astrophysics Data System (ADS)

Lin, Yangbin; Wang, Cheng; Cheng, Jun; Chen, Bili; Jia, Fukai; Chen, Zhonggui; Li, Jonathan

2015-04-01

Line segment detection in images is already a well-investigated topic, although it has received considerably less attention in 3D point clouds. Benefiting from current LiDAR devices, large-scale point clouds are becoming increasingly common. Most human-made objects have flat surfaces. Line segments that occur where pairs of planes intersect give important information regarding the geometric content of point clouds, which is especially useful for automatic building reconstruction and segmentation. This paper proposes a novel method that is capable of accurately extracting plane intersection line segments from large-scale raw scan points. The 3D line-support region, namely, a point set near a straight linear structure, is extracted simultaneously. The 3D line-support region is fitted by our Line-Segment-Half-Planes (LSHP) structure, which provides a geometric constraint for a line segment, making the line segment more reliable and accurate. We demonstrate our method on the point clouds of large-scale, complex, real-world scenes acquired by LiDAR devices. We also demonstrate the application of 3D line-support regions and their LSHP structures on urban scene abstraction.

3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display.

PubMed

Fan, Zhencheng; Weng, Yitong; Chen, Guowen; Liao, Hongen

2017-07-01

Three-dimensional (3D) visualization of preoperative and intraoperative medical information becomes more and more important in minimally invasive surgery. We develop a 3D interactive surgical visualization system using mobile spatial information acquisition and autostereoscopic display for surgeons to observe surgical target intuitively. The spatial information of regions of interest (ROIs) is captured by the mobile device and transferred to a server for further image processing. Triangular patches of intraoperative data with texture are calculated with a dimension-reduced triangulation algorithm and a projection-weighted mapping algorithm. A point cloud selection-based warm-start iterative closest point (ICP) algorithm is also developed for fusion of the reconstructed 3D intraoperative image and the preoperative image. The fusion images are rendered for 3D autostereoscopic display using integral videography (IV) technology. Moreover, 3D visualization of medical image corresponding to observer's viewing direction is updated automatically using mutual information registration method. Experimental results show that the spatial position error between the IV-based 3D autostereoscopic fusion image and the actual object was 0.38±0.92mm (n=5). The system can be utilized in telemedicine, operating education, surgical planning, navigation, etc. to acquire spatial information conveniently and display surgical information intuitively. Copyright © 2017 Elsevier Inc. All rights reserved.

Parallel image reconstruction for 3D positron emission tomography from incomplete 2D projection data

NASA Astrophysics Data System (ADS)

Guerrero, Thomas M.; Ricci, Anthony R.; Dahlbom, Magnus; Cherry, Simon R.; Hoffman, Edward T.

1993-07-01

The problem of excessive computational time in 3D Positron Emission Tomography (3D PET) reconstruction is defined, and we present an approach for solving this problem through the construction of an inexpensive parallel processing system and the adoption of the FAVOR algorithm. Currently, the 3D reconstruction of the 610 images of a total body procedure would require 80 hours and the 3D reconstruction of the 620 images of a dynamic study would require 110 hours. An inexpensive parallel processing system for 3D PET reconstruction is constructed from the integration of board level products from multiple vendors. The system achieves its computational performance through the use of 6U VME four i860 processor boards, the processor boards from five manufacturers are discussed from our perspective. The new 3D PET reconstruction algorithm FAVOR, FAst VOlume Reconstructor, that promises a substantial speed improvement is adopted. Preliminary results from parallelizing FAVOR are utilized in formulating architectural improvements for this problem. In summary, we are addressing the problem of excessive computational time in 3D PET image reconstruction, through the construction of an inexpensive parallel processing system and the parallelization of a 3D reconstruction algorithm that uses the incomplete data set that is produced by current PET systems.

Intra-operative 3D guidance and edema detection in prostate brachytherapy using a non-isocentric C-arm

PubMed Central

Jain, A.; Deguet, A.; Iordachita, I.; Chintalapani, G.; Vikal, S.; Blevins, J.; Le, Y.; Armour, E.; Burdette, C.; Song, D.; Fichtinger, G.

2015-01-01

Purpose Brachytherapy (radioactive seed insertion) has emerged as one of the most effective treatment options for patients with prostate cancer, with the added benefit of a convenient outpatient procedure. The main limitation in contemporary brachytherapy is faulty seed placement, predominantly due to the presence of intra-operative edema (tissue expansion). Though currently not available, the capability to intra-operatively monitor the seed distribution, can make a significant improvement in cancer control. We present such a system here. Methods Intra-operative measurement of edema in prostate brachytherapy requires localization of inserted radioactive seeds relative to the prostate. Seeds were reconstructed using a typical non-isocentric C-arm, and exported to a commercial brachytherapy treatment planning system. Technical obstacles for 3D reconstruction on a non-isocentric C-arm include pose-dependent C-arm calibration; distortion correction; pose estimation of C-arm images; seed reconstruction; and C-arm to TRUS registration. Results In precision-machined hard phantoms with 40–100 seeds and soft tissue phantoms with 45–87 seeds, we correctly reconstructed the seed implant shape with an average 3D precision of 0.35 mm and 0.24 mm, respectively. In a DoD Phase-1 clinical trial on six patients with 48–82 planned seeds, we achieved intra-operative monitoring of seed distribution and dosimetry, correcting for dose inhomogeneities by inserting an average of over four additional seeds in the six enrolled patients (minimum 1; maximum 9). Additionally, in each patient, the system automatically detected intra-operative seed migration induced due to edema (mean 3.84 mm, STD 2.13 mm, Max 16.19 mm). Conclusions The proposed system is the first of a kind that makes intra-operative detection of edema (and subsequent re-optimization) possible on any typical non-isocentric C-arm, at negligible additional cost to the existing clinical installation. It achieves a significantly more homogeneous seed distribution, and has the potential to affect a paradigm shift in clinical practice. Large scale studies and commercialization are currently underway. PMID:21168357

Roof Type Selection Based on Patch-Based Classification Using Deep Learning for High Resolution Satellite Imagery

NASA Astrophysics Data System (ADS)

Partovi, T.; Fraundorfer, F.; Azimi, S.; Marmanis, D.; Reinartz, P.

2017-05-01

3D building reconstruction from remote sensing image data from satellites is still an active research topic and very valuable for 3D city modelling. The roof model is the most important component to reconstruct the Level of Details 2 (LoD2) for a building in 3D modelling. While the general solution for roof modelling relies on the detailed cues (such as lines, corners and planes) extracted from a Digital Surface Model (DSM), the correct detection of the roof type and its modelling can fail due to low quality of the DSM generated by dense stereo matching. To reduce dependencies of roof modelling on DSMs, the pansharpened satellite images as a rich resource of information are used in addition. In this paper, two strategies are employed for roof type classification. In the first one, building roof types are classified in a state-of-the-art supervised pre-trained convolutional neural network (CNN) framework. In the second strategy, deep features from deep layers of different pre-trained CNN model are extracted and then an RBF kernel using SVM is employed to classify the building roof type. Based on roof complexity of the scene, a roof library including seven types of roofs is defined. A new semi-automatic method is proposed to generate training and test patches of each roof type in the library. Using the pre-trained CNN model does not only decrease the computation time for training significantly but also increases the classification accuracy.

An Efficient Method for Automatic Road Extraction Based on Multiple Features from LiDAR Data

NASA Astrophysics Data System (ADS)

Li, Y.; Hu, X.; Guan, H.; Liu, P.

2016-06-01

The road extraction in urban areas is difficult task due to the complicated patterns and many contextual objects. LiDAR data directly provides three dimensional (3D) points with less occlusions and smaller shadows. The elevation information and surface roughness are distinguishing features to separate roads. However, LiDAR data has some disadvantages are not beneficial to object extraction, such as the irregular distribution of point clouds and lack of clear edges of roads. For these problems, this paper proposes an automatic road centerlines extraction method which has three major steps: (1) road center point detection based on multiple feature spatial clustering for separating road points from ground points, (2) local principal component analysis with least squares fitting for extracting the primitives of road centerlines, and (3) hierarchical grouping for connecting primitives into complete roads network. Compared with MTH (consist of Mean shift algorithm, Tensor voting, and Hough transform) proposed in our previous article, this method greatly reduced the computational cost. To evaluate the proposed method, the Vaihingen data set, a benchmark testing data provided by ISPRS for "Urban Classification and 3D Building Reconstruction" project, was selected. The experimental results show that our method achieve the same performance by less time in road extraction using LiDAR data.

Automatic identification of cochlear implant electrode arrays for post-operative assessment

NASA Astrophysics Data System (ADS)

Noble, Jack H.; Schuman, Theodore A.; Wright, Charles G.; Labadie, Robert F.; Dawant, Benoit M.

2011-03-01

Cochlear implantation is a procedure performed to treat profound hearing loss. Accurately determining the postoperative position of the implant in vivo would permit studying the correlations between implant position and hearing restoration. To solve this problem, we present an approach based on parametric Gradient Vector Flow snakes to segment the electrode array in post-operative CT. By combining this with existing methods for localizing intra-cochlear anatomy, we have developed a system that permits accurate assessment of the implant position in vivo. The system is validated using a set of seven temporal bone specimens. The algorithms were run on pre- and post-operative CTs of the specimens, and the results were compared to histological images. It was found that the position of the arrays observed in the histological images is in excellent agreement with the position of their automatically generated 3D reconstructions in the CT scans.

Improved Feature Matching for Mobile Devices with IMU.

PubMed

Masiero, Andrea; Vettore, Antonio

2016-08-05

Thanks to the recent diffusion of low-cost high-resolution digital cameras and to the development of mostly automated procedures for image-based 3D reconstruction, the popularity of photogrammetry for environment surveys is constantly increasing in the last years. Automatic feature matching is an important step in order to successfully complete the photogrammetric 3D reconstruction: this step is the fundamental basis for the subsequent estimation of the geometry of the scene. This paper reconsiders the feature matching problem when dealing with smart mobile devices (e.g., when using the standard camera embedded in a smartphone as imaging sensor). More specifically, this paper aims at exploiting the information on camera movements provided by the inertial navigation system (INS) in order to make the feature matching step more robust and, possibly, computationally more efficient. First, a revised version of the affine scale-invariant feature transform (ASIFT) is considered: this version reduces the computational complexity of the original ASIFT, while still ensuring an increase of correct feature matches with respect to the SIFT. Furthermore, a new two-step procedure for the estimation of the essential matrix E (and the camera pose) is proposed in order to increase its estimation robustness and computational efficiency.

Comparison Between Laser Scanning and Automated 3d Modelling Techniques to Reconstruct Complex and Extensive Cultural Heritage Areas

NASA Astrophysics Data System (ADS)

Fassi, F.; Fregonese, L.; Ackermann, S.; De Troia, V.

2013-02-01

In Cultural Heritage field, the necessity to survey objects in a fast manner, with the ability to repeat the measurements several times for deformation or degradation monitoring purposes, is increasing. In this paper, two significant cases, an architectonical one and an archaeological one, are presented. Due to different reasons and emergency situations, the finding of the optimal solution to enable quick and well-timed survey for a complete digital reconstruction of the object is required. In both cases, two survey methods have been tested and used: a laser scanning approach that allows to obtain high-resolution and complete scans within a short time and a photogrammetric one that allows the three-dimensional reconstruction of the object from images. In the last months, several methodologies, including free or low cost techniques, have arisen. These kinds of software allow the fully automatically three-dimensional reconstruction of objects from images, giving back a dense point cloud and, in some case, a surfaced mesh model. In this paper some comparisons between the two methodologies above mentioned are presented, using the example of some real cases of study. The surveys have been performed by employing both photogrammetry and laser scanner techniques. The methodological operational choices, depending on the required goal, the difficulties encountered during the survey with these methods, the execution time (that is the key parameter), and finally the obtained results, are fully described and examinated. On the final 3D model, an analytical comparison has been made, to analyse the differences, the tolerances, the possibility of accuracy improvement and the future developments.

a Low-Cost and Portable System for 3d Reconstruction of Texture-Less Objects

NASA Astrophysics Data System (ADS)

Hosseininaveh, A.; Yazdan, R.; Karami, A.; Moradi, M.; Ghorbani, F.

2015-12-01

The optical methods for 3D modelling of objects can be classified into two categories including image-based and range-based methods. Structure from Motion is one of the image-based methods implemented in commercial software. In this paper, a low-cost and portable system for 3D modelling of texture-less objects is proposed. This system includes a rotating table designed and developed by using a stepper motor and a very light rotation plate. The system also has eight laser light sources with very dense and strong beams which provide a relatively appropriate pattern on texture-less objects. In this system, regarding to the step of stepper motor, images are semi automatically taken by a camera. The images can be used in structure from motion procedures implemented in Agisoft software.To evaluate the performance of the system, two dark objects were used. The point clouds of these objects were obtained by spraying a light powders on the objects and exploiting a GOM laser scanner. Then these objects were placed on the proposed turntable. Several convergent images were taken from each object while the laser light sources were projecting the pattern on the objects. Afterward, the images were imported in VisualSFM as a fully automatic software package for generating an accurate and complete point cloud. Finally, the obtained point clouds were compared to the point clouds generated by the GOM laser scanner. The results showed the ability of the proposed system to produce a complete 3D model from texture-less objects.

Registration uncertainties between 3D cone beam computed tomography and different reference CT datasets in lung stereotactic body radiation therapy.

PubMed

Oechsner, Markus; Chizzali, Barbara; Devecka, Michal; Combs, Stephanie Elisabeth; Wilkens, Jan Jakob; Duma, Marciana Nona

2016-10-26

The aim of this study was to analyze differences in couch shifts (setup errors) resulting from image registration of different CT datasets with free breathing cone beam CTs (FB-CBCT). As well automatic as manual image registrations were performed and registration results were correlated to tumor characteristics. FB-CBCT image registration was performed for 49 patients with lung lesions using slow planning CT (PCT), average intensity projection (AIP), maximum intensity projection (MIP) and mid-ventilation CTs (MidV) as reference images. Both, automatic and manual image registrations were applied. Shift differences were evaluated between the registered CT datasets for automatic and manual registration, respectively. Furthermore, differences between automatic and manual registration were analyzed for the same CT datasets. The registration results were statistically analyzed and correlated to tumor characteristics (3D tumor motion, tumor volume, superior-inferior (SI) distance, tumor environment). Median 3D shift differences over all patients were between 0.5 mm (AIPvsMIP) and 1.9 mm (MIPvsPCT and MidVvsPCT) for the automatic registration and between 1.8 mm (AIPvsPCT) and 2.8 mm (MIPvsPCT and MidVvsPCT) for the manual registration. For some patients, large shift differences (>5.0 mm) were found (maximum 10.5 mm, automatic registration). Comparing automatic vs manual registrations for the same reference CTs, ∆AIP achieved the smallest (1.1 mm) and ∆MIP the largest (1.9 mm) median 3D shift differences. The standard deviation (variability) for the 3D shift differences was also the smallest for ∆AIP (1.1 mm). Significant correlations (p < 0.01) between 3D shift difference and 3D tumor motion (AIPvsMIP, MIPvsMidV) and SI distance (AIPvsMIP) (automatic) and also for 3D tumor motion (∆PCT, ∆MidV; automatic vs manual) were found. Using different CT datasets for image registration with FB-CBCTs can result in different 3D couch shifts. Manual registrations achieved partly different 3D shifts than automatic registrations. AIP CTs yielded the smallest shift differences and might be the most appropriate CT dataset for registration with 3D FB-CBCTs.

Virtual reality and 3D animation in forensic visualization.

PubMed

Ma, Minhua; Zheng, Huiru; Lallie, Harjinder

2010-09-01

Computer-generated three-dimensional (3D) animation is an ideal media to accurately visualize crime or accident scenes to the viewers and in the courtrooms. Based upon factual data, forensic animations can reproduce the scene and demonstrate the activity at various points in time. The use of computer animation techniques to reconstruct crime scenes is beginning to replace the traditional illustrations, photographs, and verbal descriptions, and is becoming popular in today's forensics. This article integrates work in the areas of 3D graphics, computer vision, motion tracking, natural language processing, and forensic computing, to investigate the state-of-the-art in forensic visualization. It identifies and reviews areas where new applications of 3D digital technologies and artificial intelligence could be used to enhance particular phases of forensic visualization to create 3D models and animations automatically and quickly. Having discussed the relationships between major crime types and level-of-detail in corresponding forensic animations, we recognized that high level-of-detail animation involving human characters, which is appropriate for many major crime types but has had limited use in courtrooms, could be useful for crime investigation. © 2010 American Academy of Forensic Sciences.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beaudry, J.; Bergman, A.; British Columbia Cancer Agency - Vancouver Centre, Vancouver, BC

Lung tumours move due to respiratory motion. This is managed during planning by acquiring a 4DCT and capturing the excursion of the GTV (gross tumour volume) throughout the breathing cycle within an IGTV (Internal Gross Tumour Volume) contour. Patients undergo a verification cone-beam CT (CBCT) scan immediately prior to treatment. 3D reconstructed images do not consider tumour motion, resulting in image artefacts, such as blurring. This may lead to difficulty in identifying the tumour on reconstructed images. It would be valuable to create a 4DCBCT reconstruction of the tumour motion to confirm that does indeed remain within the planned IGTV.more » CBCT projections of a Quasar Respiratory Motion Phantom are acquired in Treatment mode (half-fan scan) on a Varian TrueBeam accelerator. This phantom contains a mobile, low-density lung insert with an embedded 3cm diameter tumour object. It is programmed to create a 15s periodic, 2cm (sup/inf) displacement. A Varian Real-time Position Management (RPM) tracking-box is placed on the phantom breathing platform. Breathing phase information is automatically integrated into the projection image files. Using in-house Matlab programs and RTK (Reconstruction Tool Kit) open-source toolboxes, the projections are re-binned into 10 phases and a 4DCBCT scan reconstructed. The planning IGTV is registered to the 4DCBCT and the tumour excursion is verified to remain within the planned contour. This technique successfully reconstructs 4DCBCT images using clinical modes for a breathing phantom. UBC-BCCA ethics approval has been obtained to perform 4DCBCT reconstructions on lung patients (REB#H12-00192). Clinical images will be accrued starting April 2014.« less

Accuracy and reliability of coronal and sagittal spinal curvature data based on patient-specific three-dimensional models created by the EOS 2D/3D imaging system.

PubMed

Somoskeöy, Szabolcs; Tunyogi-Csapó, Miklós; Bogyó, Csaba; Illés, Tamás

2012-11-01

Three-dimensional (3D) deformations of the spine are predominantly characterized by two-dimensional (2D) angulation measurements in coronal and sagittal planes, using anteroposterior and lateral X-ray images. For coronal curves, a method originally described by Cobb and for sagittal curves a modified Cobb method are most widely used in practice, and these methods have been shown to exhibit good-to-excellent reliability and reproducibility, carried out either manually or by computer-based tools. Recently, an ultralow radiation dose-integrated radioimaging solution was introduced with special software for realistic 3D visualization and parametric characterization of the spinal column. Comparison of accuracy, correlation of measurement values, intraobserver and interrater reliability of methods by conventional manual 2D and sterEOS 3D measurements in a routine clinical setting. Retrospective nonrandomized study of diagnostic X-ray images created as part of a routine clinical protocol of eligible patients examined at our clinic during a 30-month period between July 2007 and December 2009. In total, 201 individuals (170 females, 31 males; mean age, 19.88 years) including 10 healthy athletes with normal spine and patients with adolescent idiopathic scoliosis (175 cases), adult degenerative scoliosis (11 cases), and Scheuermann hyperkyphosis (5 cases). Overall range of coronal curves was between 2.4° and 117.5°. Analysis of accuracy and reliability of measurements were carried out on a group of all patients and in subgroups based on coronal plane deviation: 0° to 10° (Group 1, n=36), 10° to 25° (Group 2, n=25), 25° to 50° (Group 3, n=69), 50° to 75° (Group 4, n=49), and more than 75° (Group 5, n=22). Coronal and sagittal curvature measurements were determined by three experienced examiners, using either traditional 2D methods or automatic measurements based on sterEOS 3D reconstructions. Manual measurements were performed three times, and sterEOS 3D reconstructions and automatic measurements were performed two times by each examiner. Means comparison t test, Pearson bivariate correlation analysis, reliability analysis by intraclass correlation coefficients for intraobserver reproducibility and interrater reliability were performed using SPSS v16.0 software (IBM Corp., Armonk, NY, USA). No funds were received in support of this work. No benefits in any form have been or will be received from a commercial party related directly or indirectly to the subject of this article. In comparison with manual 2D methods, only small and nonsignificant differences were detectable in sterEOS 3D-based curvature data. Intraobserver reliability was excellent for both methods, and interrater reproducibility was consistently higher for sterEOS 3D methods that was found to be unaffected by the magnitude of coronal curves or sagittal plane deviations. This is the first clinical report on EOS 2D/3D system (EOS Imaging, Paris, France) and its sterEOS 3D software, documenting an excellent capability for accurate, reliable, and reproducible spinal curvature measurements. Copyright © 2012 Elsevier Inc. All rights reserved.

Combinatorial clustering and Its Application to 3D Polygonal Traffic Sign Reconstruction From Multiple Images

NASA Astrophysics Data System (ADS)

Vallet, B.; Soheilian, B.; Brédif, M.

2014-08-01

The 3D reconstruction of similar 3D objects detected in 2D faces a major issue when it comes to grouping the 2D detections into clusters to be used to reconstruct the individual 3D objects. Simple clustering heuristics fail as soon as similar objects are close. This paper formulates a framework to use the geometric quality of the reconstruction as a hint to do a proper clustering. We present a methodology to solve the resulting combinatorial optimization problem with some simplifications and approximations in order to make it tractable. The proposed method is applied to the reconstruction of 3D traffic signs from their 2D detections to demonstrate its capacity to solve ambiguities.

System Design, Calibration and Performance Analysis of a Novel 360° Stereo Panoramic Mobile Mapping System

NASA Astrophysics Data System (ADS)

Blaser, S.; Nebiker, S.; Cavegn, S.

2017-05-01

Image-based mobile mapping systems enable the efficient acquisition of georeferenced image sequences, which can later be exploited in cloud-based 3D geoinformation services. In order to provide a 360° coverage with accurate 3D measuring capabilities, we present a novel 360° stereo panoramic camera configuration. By using two 360° panorama cameras tilted forward and backward in combination with conventional forward and backward looking stereo camera systems, we achieve a full 360° multi-stereo coverage. We furthermore developed a fully operational new mobile mapping system based on our proposed approach, which fulfils our high accuracy requirements. We successfully implemented a rigorous sensor and system calibration procedure, which allows calibrating all stereo systems with a superior accuracy compared to that of previous work. Our study delivered absolute 3D point accuracies in the range of 4 to 6 cm and relative accuracies of 3D distances in the range of 1 to 3 cm. These results were achieved in a challenging urban area. Furthermore, we automatically reconstructed a 3D city model of our study area by employing all captured and georeferenced mobile mapping imagery. The result is a very high detailed and almost complete 3D city model of the street environment.

Multi-Level Building Reconstruction for Automatic Enhancement of High Resolution Dsms

NASA Astrophysics Data System (ADS)

Arefi, H.; Reinartz, P.

2012-07-01

In this article a multi-level approach is proposed for reconstruction-based improvement of high resolution Digital Surface Models (DSMs). The concept of Levels of Detail (LOD) defined by CityGML standard has been considered as basis for abstraction levels of building roof structures. Here, the LOD1 and LOD2 which are related to prismatic and parametric roof shapes are reconstructed. Besides proposing a new approach for automatic LOD1 and LOD2 generation from high resolution DSMs, the algorithm contains two generalization levels namely horizontal and vertical. Both generalization levels are applied to prismatic model of buildings. The horizontal generalization allows controlling the approximation level of building footprints which is similar to cartographic generalization concept of the urban maps. In vertical generalization, the prismatic model is formed using an individual building height and continuous to included all flat structures locating in different height levels. The concept of LOD1 generation is based on approximation of the building footprints into rectangular or non-rectangular polygons. For a rectangular building containing one main orientation a method based on Minimum Bounding Rectangle (MBR) in employed. In contrast, a Combined Minimum Bounding Rectangle (CMBR) approach is proposed for regularization of non-rectilinear polygons, i.e. buildings without perpendicular edge directions. Both MBRand CMBR-based approaches are iteratively employed on building segments to reduce the original building footprints to a minimum number of nodes with maximum similarity to original shapes. A model driven approach based on the analysis of the 3D points of DSMs in a 2D projection plane is proposed for LOD2 generation. Accordingly, a building block is divided into smaller parts according to the direction and number of existing ridge lines. The 3D model is derived for each building part and finally, a complete parametric model is formed by merging all the 3D models of the individual parts and adjusting the nodes after the merging step. In order to provide an enhanced DSM, a surface model is provided for each building by interpolation of the internal points of the generated models. All interpolated models are situated on a Digital Terrain Model (DTM) of corresponding area to shape the enhanced DSM. Proposed DSM enhancement approach has been tested on a dataset from Munich central area. The original DSM is created using robust stereo matching of Worldview-2 stereo images. A quantitative assessment of the new DSM by comparing the heights of the ridges and eaves shows a standard deviation of better than 50cm.

Hierarchical automated clustering of cloud point set by ellipsoidal skeleton: application to organ geometric modeling from CT-scan images

NASA Astrophysics Data System (ADS)

Banegas, Frederic; Michelucci, Dominique; Roelens, Marc; Jaeger, Marc

1999-05-01

We present a robust method for automatically constructing an ellipsoidal skeleton (e-skeleton) from a set of 3D points taken from NMR or TDM images. To ensure steadiness and accuracy, all points of the objects are taken into account, including the inner ones, which is different from the existing techniques. This skeleton will be essentially useful for object characterization, for comparisons between various measurements and as a basis for deformable models. It also provides good initial guess for surface reconstruction algorithms. On output of the entire process, we obtain an analytical description of the chosen entity, semantically zoomable (local features only or reconstructed surfaces), with any level of detail (LOD) by discretization step control in voxel or polygon format. This capability allows us to handle objects at interactive frame rates once the e-skeleton is computed. Each e-skeleton is stored as a multiscale CSG implicit tree.

DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution

PubMed Central

Cerutti, Guillaume; Ali, Olivier; Godin, Christophe

2017-01-01

Context: The shoot apical meristem (SAM), origin of all aerial organs of the plant, is a restricted niche of stem cells whose growth is regulated by a complex network of genetic, hormonal and mechanical interactions. Studying the development of this area at cell level using 3D microscopy time-lapse imaging is a newly emerging key to understand the processes controlling plant morphogenesis. Computational models have been proposed to simulate those mechanisms, however their validation on real-life data is an essential step that requires an adequate representation of the growing tissue to be carried out. Achievements: The tool we introduce is a two-stage computational pipeline that generates a complete 3D triangular mesh of the tissue volume based on a segmented tissue image stack. DRACO (Dual Reconstruction by Adjacency Complex Optimization) is designed to retrieve the underlying 3D topological structure of the tissue and compute its dual geometry, while STEM (SAM Tissue Enhanced Mesh) returns a faithful triangular mesh optimized along several quality criteria (intrinsic quality, tissue reconstruction, visual adequacy). Quantitative evaluation tools measuring the performance of the method along those different dimensions are also provided. The resulting meshes can be used as input and validation for biomechanical simulations. Availability: DRACO-STEM is supplied as a package of the open-source multi-platform plant modeling library OpenAlea (http://openalea.github.io/) implemented in Python, and is freely distributed on GitHub (https://github.com/VirtualPlants/draco-stem) along with guidelines for installation and use. PMID:28424704

Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography.

PubMed

Töpperwien, Mareike; van der Meer, Franziska; Stadelmann, Christine; Salditt, Tim

2018-06-18

To quantitatively evaluate brain tissue and its corresponding function, knowledge of the 3D cellular distribution is essential. The gold standard to obtain this information is histology, a destructive and labor-intensive technique where the specimen is sliced and examined under a light microscope, providing 3D information at nonisotropic resolution. To overcome the limitations of conventional histology, we use phase-contrast X-ray tomography with optimized optics, reconstruction, and image analysis, both at a dedicated synchrotron radiation endstation, which we have equipped with X-ray waveguide optics for coherence and wavefront filtering, and at a compact laboratory source. As a proof-of-concept demonstration we probe the 3D cytoarchitecture in millimeter-sized punches of unstained human cerebellum embedded in paraffin and show that isotropic subcellular resolution can be reached at both setups throughout the specimen. To enable a quantitative analysis of the reconstructed data, we demonstrate automatic cell segmentation and localization of over 1 million neurons within the cerebellar cortex. This allows for the analysis of the spatial organization and correlation of cells in all dimensions by borrowing concepts from condensed-matter physics, indicating a strong short-range order and local clustering of the cells in the granular layer. By quantification of 3D neuronal "packing," we can hence shed light on how the human cerebellum accommodates 80% of the total neurons in the brain in only 10% of its volume. In addition, we show that the distribution of neighboring neurons in the granular layer is anisotropic with respect to the Purkinje cell dendrites. Copyright © 2018 the Author(s). Published by PNAS.

3D reconstructions with pixel-based images are made possible by digitally clearing plant and animal tissue

USDA-ARS?s Scientific Manuscript database

Reconstruction of 3D images from a series of 2D images has been restricted by the limited capacity to decrease the opacity of surrounding tissue. Commercial software that allows color-keying and manipulation of 2D images in true 3D space allowed us to produce 3D reconstructions from pixel based imag...

3D reconstruction of SEM images by use of optical photogrammetry software.

PubMed

Eulitz, Mona; Reiss, Gebhard

2015-08-01

Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching. Copyright © 2015 Elsevier Inc. All rights reserved.

Integration of real-time 3D capture, reconstruction, and light-field display

NASA Astrophysics Data System (ADS)

Zhang, Zhaoxing; Geng, Zheng; Li, Tuotuo; Pei, Renjing; Liu, Yongchun; Zhang, Xiao

2015-03-01

Effective integration of 3D acquisition, reconstruction (modeling) and display technologies into a seamless systems provides augmented experience of visualizing and analyzing real objects and scenes with realistic 3D sensation. Applications can be found in medical imaging, gaming, virtual or augmented reality and hybrid simulations. Although 3D acquisition, reconstruction, and display technologies have gained significant momentum in recent years, there seems a lack of attention on synergistically combining these components into a "end-to-end" 3D visualization system. We designed, built and tested an integrated 3D visualization system that is able to capture in real-time 3D light-field images, perform 3D reconstruction to build 3D model of the objects, and display the 3D model on a large autostereoscopic screen. In this article, we will present our system architecture and component designs, hardware/software implementations, and experimental results. We will elaborate on our recent progress on sparse camera array light-field 3D acquisition, real-time dense 3D reconstruction, and autostereoscopic multi-view 3D display. A prototype is finally presented with test results to illustrate the effectiveness of our proposed integrated 3D visualization system.

Experimental study of sector and linear array ultrasound accuracy and the influence of navigated 3D-reconstruction as compared to MRI in a brain tumor model.

PubMed

Siekmann, Max; Lothes, Thomas; König, Ralph; Wirtz, Christian Rainer; Coburger, Jan

2018-03-01

Currently, intraoperative ultrasound in brain tumor surgery is a rapidly propagating option in imaging technology. We examined the accuracy and resolution limits of different ultrasound probes and the influence of 3D-reconstruction in a phantom and compared these results to MRI in an intraoperative setting (iMRI). An agarose gel phantom with predefined gel targets was examined with iMRI, a sector (SUS) and a linear (LUS) array probe with two-dimensional images. Additionally, 3D-reconstructed sweeps in perpendicular directions were made of every target with both probes, resulting in 392 measurements. Statistical calculations were performed, and comparative boxplots were generated. Every measurement of iMRI and LUS was more precise than SUS, while there was no apparent difference in height of iMRI and 3D-reconstructed LUS. Measurements with 3D-reconstructed LUS were always more accurate than in 2D-LUS, while 3D-reconstruction of SUS showed nearly no differences to 2D-SUS in some measurements. We found correlations of 3D-reconstructed SUS and LUS length and width measurements with 2D results in the same image orientation. LUS provides an accuracy and resolution comparable to iMRI, while SUS is less exact than LUS and iMRI. 3D-reconstruction showed the potential to distinctly improve accuracy and resolution of ultrasound images, although there is a strong correlation with the sweep direction during data acquisition.

3D skin surface reconstruction from a single image by merging global curvature and local texture using the guided filtering for 3D haptic palpation.

PubMed

Lee, K; Kim, M; Kim, K

2018-05-11

Skin surface evaluation has been studied using various imaging techniques. However, all these studies had limited impact because they were performed using visual exam only. To improve on this scenario with haptic feedback, we propose 3D reconstruction of the skin surface using a single image. Unlike extant 3D skin surface reconstruction algorithms, we utilize the local texture and global curvature regions, combining the results for reconstruction. The first entails the reconstruction of global curvature, achieved by bilateral filtering that removes noise on the surface while maintaining the edge (ie, furrow) to obtain the overall curvature. The second entails the reconstruction of local texture, representing the fine wrinkles of the skin, using an advanced form of bilateral filtering. The final image is then composed by merging the two reconstructed images. We tested the curvature reconstruction part by comparing the resulting curvatures with measured values from real phantom objects while local texture reconstruction was verified by measuring skin surface roughness. Then, we showed the reconstructed result of our proposed algorithm via the reconstruction of various real skin surfaces. The experimental results demonstrate that our approach is a promising technology to reconstruct an accurate skin surface with a single skin image. We proposed 3D skin surface reconstruction using only a single camera. We highlighted the utility of global curvature, which has not been considered important in the past. Thus, we proposed a new method for 3D reconstruction that can be used for 3D haptic palpation, dividing the concepts of local and global regions. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

3D and 4D magnetic susceptibility tomography based on complex MR images

DOEpatents

Chen, Zikuan; Calhoun, Vince D

2014-11-11

Magnetic susceptibility is the physical property for T2*-weighted magnetic resonance imaging (T2*MRI). The invention relates to methods for reconstructing an internal distribution (3D map) of magnetic susceptibility values, .chi. (x,y,z), of an object, from 3D T2*MRI phase images, by using Computed Inverse Magnetic Resonance Imaging (CIMRI) tomography. The CIMRI technique solves the inverse problem of the 3D convolution by executing a 3D Total Variation (TV) regularized iterative convolution scheme, using a split Bregman iteration algorithm. The reconstruction of .chi. (x,y,z) can be designed for low-pass, band-pass, and high-pass features by using a convolution kernel that is modified from the standard dipole kernel. Multiple reconstructions can be implemented in parallel, and averaging the reconstructions can suppress noise. 4D dynamic magnetic susceptibility tomography can be implemented by reconstructing a 3D susceptibility volume from a 3D phase volume by performing 3D CIMRI magnetic susceptibility tomography at each snapshot time.

Statistical shape model-based reconstruction of a scaled, patient-specific surface model of the pelvis from a single standard AP x-ray radiograph

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng Guoyan

2010-04-15

Purpose: The aim of this article is to investigate the feasibility of using a statistical shape model (SSM)-based reconstruction technique to derive a scaled, patient-specific surface model of the pelvis from a single standard anteroposterior (AP) x-ray radiograph and the feasibility of estimating the scale of the reconstructed surface model by performing a surface-based 3D/3D matching. Methods: Data sets of 14 pelvises (one plastic bone, 12 cadavers, and one patient) were used to validate the single-image based reconstruction technique. This reconstruction technique is based on a hybrid 2D/3D deformable registration process combining a landmark-to-ray registration with a SSM-based 2D/3D reconstruction.more » The landmark-to-ray registration was used to find an initial scale and an initial rigid transformation between the x-ray image and the SSM. The estimated scale and rigid transformation were used to initialize the SSM-based 2D/3D reconstruction. The optimal reconstruction was then achieved in three stages by iteratively matching the projections of the apparent contours extracted from a 3D model derived from the SSM to the image contours extracted from the x-ray radiograph: Iterative affine registration, statistical instantiation, and iterative regularized shape deformation. The image contours are first detected by using a semiautomatic segmentation tool based on the Livewire algorithm and then approximated by a set of sparse dominant points that are adaptively sampled from the detected contours. The unknown scales of the reconstructed models were estimated by performing a surface-based 3D/3D matching between the reconstructed models and the associated ground truth models that were derived from a CT-based reconstruction method. Such a matching also allowed for computing the errors between the reconstructed models and the associated ground truth models. Results: The technique could reconstruct the surface models of all 14 pelvises directly from the landmark-based initialization. Depending on the surface-based matching techniques, the reconstruction errors were slightly different. When a surface-based iterative affine registration was used, an average reconstruction error of 1.6 mm was observed. This error was increased to 1.9 mm, when a surface-based iterative scaled rigid registration was used. Conclusions: It is feasible to reconstruct a scaled, patient-specific surface model of the pelvis from single standard AP x-ray radiograph using the present approach. The unknown scale of the reconstructed model can be estimated by performing a surface-based 3D/3D matching.« less

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 and no rays passed through the area). Voids in the voxel space are manifested as unsampled voxels. A similar line-of-sight analysis can then be used to pinpoint locations at aircraft altitude at which the voids in the point clouds could theoretically be imaged. This work is based on the assumption that inclusion of more images of the void areas in the 3D reconstruction process will reduce the number of voids in the point cloud that were a result of lack of coverage. Voids resulting from texturally difficult areas will not benefit from more imagery in the reconstruction process, and thus are identified and removed prior to the determination of future potential imaging locations.

Three-dimensional/two-dimensional multiplanar stereotactic planning system: hardware and software configuration

NASA Astrophysics Data System (ADS)

Zamorano, Lucia J.; Dujovny, Manuel; Ausman, James I.

1990-01-01

"Real time" surgical treatment planning utilizing multimodality imaging (CT, MRI, DA) has been developed to provide the neurosurgeon with 2D multiplanar and 3D views of a patient's lesion for stereotactic planning. Both diagnostic and therapeutic stereotactic procedures have been implemented utilizing workstation (SUN 1/10) and specially developed software and hardware (developed in collaboration with TOMO Medical Imaging Technology, Southfield, MI). This provides complete 3D and 2D free-tilt views as part of the system instrumentation. The 2D Multiplanar includes reformatted sagittal, coronal, paraaxial and free tilt oblique vectors at any arbitrary plane of the patient's lesion. The 3D includes features for extracting a view of the target volume localized by a process including steps of automatic segmentation, thresholding, and/or boundary detection with 3D display of the volumes of interest. The system also includes the capability of interactive playback of reconstructed 3D movies, which can be viewed at any hospital network having compatible software on strategical locations or at remote sites through data transmission and record documentation by image printers. Both 2D and 3D menus include real time stereotactic coordinate measurements and trajectory definition capabilities as well as statistical functions for computing distances, angles, areas, and volumes. A combined interactive 3D-2D multiplanar menu allows simultaneous display of selected trajectory, final optimization, and multiformat 2D display of free-tilt reformatted images perpendicular to selected trajectory of the entire target volume.

Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints

PubMed Central

Diament, Alon; Tuller, Tamir

2015-01-01

The study of the 3D architecture of chromosomes has been advancing rapidly in recent years. While a number of methods for 3D reconstruction of genomic models based on Hi-C data were proposed, most of the analyses in the field have been performed on different 3D representation forms (such as graphs). Here, we reproduce most of the previous results on the 3D genomic organization of the eukaryote Saccharomyces cerevisiae using analysis of 3D reconstructions. We show that many of these results can be reproduced in sparse reconstructions, generated from a small fraction of the experimental data (5% of the data), and study the properties of such models. Finally, we propose for the first time a novel approach for improving the accuracy of 3D reconstructions by introducing additional predicted physical interactions to the model, based on orthologous interactions in an evolutionary-related organism and based on predicted functional interactions between genes. We demonstrate that this approach indeed leads to the reconstruction of improved models. PMID:26000633

Photogrammetry for rapid prototyping: development of noncontact 3D reconstruction technologies

NASA Astrophysics Data System (ADS)

Knyaz, Vladimir A.

2002-04-01

An important stage of rapid prototyping technology is generating computer 3D model of an object to be reproduced. Wide variety of techniques for 3D model generation exists beginning with manual 3D models generation and finishing with full-automated reverse engineering system. The progress in CCD sensors and computers provides the background for integration of photogrammetry as an accurate 3D data source with CAD/CAM. The paper presents the results of developing photogrammetric methods for non-contact spatial coordinates measurements and generation of computer 3D model of real objects. The technology is based on object convergent images processing for calculating its 3D coordinates and surface reconstruction. The hardware used for spatial coordinates measurements is based on PC as central processing unit and video camera as image acquisition device. The original software for Windows 9X realizes the complete technology of 3D reconstruction for rapid input of geometry data in CAD/CAM systems. Technical characteristics of developed systems are given along with the results of applying for various tasks of 3D reconstruction. The paper describes the techniques used for non-contact measurements and the methods providing metric characteristics of reconstructed 3D model. Also the results of system application for 3D reconstruction of complex industrial objects are presented.

[Three-dimensional tooth model reconstruction based on fusion of dental computed tomography images and laser-scanned images].

PubMed

Zhang, Dongxia; Gan, Yangzhou; Xiong, Jing; Xia, Zeyang

2017-02-01

Complete three-dimensional(3D) tooth model provides essential information to assist orthodontists for diagnosis and treatment planning. Currently, 3D tooth model is mainly obtained by segmentation and reconstruction from dental computed tomography(CT) images. However, the accuracy of 3D tooth model reconstructed from dental CT images is low and not applicable for invisalign design. And another serious problem also occurs, i.e. frequentative dental CT scan during different intervals of orthodontic treatment often leads to radiation to the patients. Hence, this paper proposed a method to reconstruct tooth model based on fusion of dental CT images and laser-scanned images. A complete3 D tooth model was reconstructed with the registration and fusion between the root reconstructed from dental CT images and the crown reconstructed from laser-scanned images. The crown of the complete 3D tooth model reconstructed with the proposed method has higher accuracy. Moreover, in order to reconstruct complete 3D tooth model of each orthodontic treatment interval, only one pre-treatment CT scan is needed and in the orthodontic treatment process only the laser-scan is required. Therefore, radiation to the patients can be reduced significantly.

Real-time 3D image reconstruction guidance in liver resection surgery

PubMed Central

Nicolau, Stephane; Pessaux, Patrick; Mutter, Didier; Marescaux, Jacques

2014-01-01

Background Minimally invasive surgery represents one of the main evolutions of surgical techniques. However, minimally invasive surgery adds difficulty that can be reduced through computer technology. Methods From a patient’s medical image [US, computed tomography (CT) or MRI], we have developed an Augmented Reality (AR) system that increases the surgeon’s intraoperative vision by providing a virtual transparency of the patient. AR is based on two major processes: 3D modeling and visualization of anatomical or pathological structures appearing in the medical image, and the registration of this visualization onto the real patient. We have thus developed a new online service, named Visible Patient, providing efficient 3D modeling of patients. We have then developed several 3D visualization and surgical planning software tools to combine direct volume rendering and surface rendering. Finally, we have developed two registration techniques, one interactive and one automatic providing intraoperative augmented reality view. Results From January 2009 to June 2013, 769 clinical cases have been modeled by the Visible Patient service. Moreover, three clinical validations have been realized demonstrating the accuracy of 3D models and their great benefit, potentially increasing surgical eligibility in liver surgery (20% of cases). From these 3D models, more than 50 interactive AR-assisted surgical procedures have been realized illustrating the potential clinical benefit of such assistance to gain safety, but also current limits that automatic augmented reality will overcome. Conclusions Virtual patient modeling should be mandatory for certain interventions that have now to be defined, such as liver surgery. Augmented reality is clearly the next step of the new surgical instrumentation but remains currently limited due to the complexity of organ deformations during surgery. Intraoperative medical imaging used in new generation of automated augmented reality should solve this issue thanks to the development of Hybrid OR. PMID:24812598

Automatic Texture Mapping of Architectural and Archaeological 3d Models

NASA Astrophysics Data System (ADS)

Kersten, T. P.; Stallmann, D.

2012-07-01

Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

Motion and positional error correction for cone beam 3D-reconstruction with mobile C-arms.

PubMed

Bodensteiner, C; Darolti, C; Schumacher, H; Matthäus, L; Schweikard, A

2007-01-01

CT-images acquired by mobile C-arm devices can contain artefacts caused by positioning errors. We propose a data driven method based on iterative 3D-reconstruction and 2D/3D-registration to correct projection data inconsistencies. With a 2D/3D-registration algorithm, transformations are computed to align the acquired projection images to a previously reconstructed volume. In an iterative procedure, the reconstruction algorithm uses the results of the registration step. This algorithm also reduces small motion artefacts within 3D-reconstructions. Experiments with simulated projections from real patient data show the feasibility of the proposed method. In addition, experiments with real projection data acquired with an experimental robotised C-arm device have been performed with promising results.

Online 3D EPID-based dose verification: Proof of concept

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spreeuw, Hanno; Rozendaal, Roel, E-mail: r.rozenda

Purpose: Delivery errors during radiotherapy may lead to medical harm and reduced life expectancy for patients. Such serious incidents can be avoided by performing dose verification online, i.e., while the patient is being irradiated, creating the possibility of halting the linac in case of a large overdosage or underdosage. The offline EPID-based 3D in vivo dosimetry system clinically employed at our institute is in principle suited for online treatment verification, provided the system is able to complete 3D dose reconstruction and verification within 420 ms, the present acquisition time of a single EPID frame. It is the aim of thismore » study to show that our EPID-based dosimetry system can be made fast enough to achieve online 3D in vivo dose verification. Methods: The current dose verification system was sped up in two ways. First, a new software package was developed to perform all computations that are not dependent on portal image acquisition separately, thus removing the need for doing these calculations in real time. Second, the 3D dose reconstruction algorithm was sped up via a new, multithreaded implementation. Dose verification was implemented by comparing planned with reconstructed 3D dose distributions delivered to two regions in a patient: the target volume and the nontarget volume receiving at least 10 cGy. In both volumes, the mean dose is compared, while in the nontarget volume, the near-maximum dose (D2) is compared as well. The real-time dosimetry system was tested by irradiating an anthropomorphic phantom with three VMAT plans: a 6 MV head-and-neck treatment plan, a 10 MV rectum treatment plan, and a 10 MV prostate treatment plan. In all plans, two types of serious delivery errors were introduced. The functionality of automatically halting the linac was also implemented and tested. Results: The precomputation time per treatment was ∼180 s/treatment arc, depending on gantry angle resolution. The complete processing of a single portal frame, including dose verification, took 266 ± 11 ms on a dual octocore Intel Xeon E5-2630 CPU running at 2.40 GHz. The introduced delivery errors were detected after 5–10 s irradiation time. Conclusions: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for two different kinds of gross delivery errors. Thus, online 3D dose verification has been technologically achieved.« less

A modified sparse reconstruction method for three-dimensional synthetic aperture radar image

NASA Astrophysics Data System (ADS)

Zhang, Ziqiang; Ji, Kefeng; Song, Haibo; Zou, Huanxin

2018-03-01

There is an increasing interest in three-dimensional Synthetic Aperture Radar (3-D SAR) imaging from observed sparse scattering data. However, the existing 3-D sparse imaging method requires large computing times and storage capacity. In this paper, we propose a modified method for the sparse 3-D SAR imaging. The method processes the collection of noisy SAR measurements, usually collected over nonlinear flight paths, and outputs 3-D SAR imagery. Firstly, the 3-D sparse reconstruction problem is transformed into a series of 2-D slices reconstruction problem by range compression. Then the slices are reconstructed by the modified SL0 (smoothed l0 norm) reconstruction algorithm. The improved algorithm uses hyperbolic tangent function instead of the Gaussian function to approximate the l0 norm and uses the Newton direction instead of the steepest descent direction, which can speed up the convergence rate of the SL0 algorithm. Finally, numerical simulation results are given to demonstrate the effectiveness of the proposed algorithm. It is shown that our method, compared with existing 3-D sparse imaging method, performs better in reconstruction quality and the reconstruction time.

Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.

PubMed

Wacker, Irene; Chockley, Peter; Bartels, Carolin; Spomer, Waldemar; Hofmann, Andreas; Gengenbach, Ulrich; Singh, Sachin; Thaler, Marlene; Grabher, Clemens; Schröder, Rasmus R

2015-08-01

For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Automatic segmentation of the puborectalis muscle in 3D transperineal ultrasound.

PubMed

van den Noort, Frieda; Grob, Anique T M; Slump, Cornelis H; van der Vaart, Carl H; van Stralen, Marijn

2017-10-11

The introduction of 3D analysis of the puborectalis muscle, for diagnostic purposes, into daily practice is hindered by the need for appropriate training of the observers. Automatic 3D segmentation of the puborectalis muscle in 3D transperineal ultrasound may aid to its adaption in clinical practice. A manual 3D segmentation protocol was developed to segment the puborectalis muscle. The data of 20 women, in their first trimester of pregnancy, was used to validate the reproducibility of this protocol. For automatic segmentation, active appearance models of the puborectalis muscle were developed. Those models were trained using manual segmentation data of 50 women. The performance of both manual and automatic segmentation was analyzed by measuring the overlap and distance between the segmentations. Also, the interclass correlation coefficients and their 95% confidence intervals were determined for mean echogenicity and volume of the puborectalis muscle. The ICC values of mean echogenicity (0.968-0.991) and volume (0.626-0.910) are good to very good for both automatic and manual segmentation. The results of overlap and distance for manual segmentation are as expected, showing only few pixels (2-3) mismatch on average and a reasonable overlap. Based on overlap and distance 5 mismatches in automatic segmentation were detected, resulting in an automatic segmentation a success rate of 90%. In conclusion, this study presents a reliable manual and automatic 3D segmentation of the puborectalis muscle. This will facilitate future investigation of the puborectalis muscle. It also allows for reliable measurements of clinically potentially valuable parameters like mean echogenicity. This article is protected by copyright. All rights reserved.

Extracting Topological Relations Between Indoor Spaces from Point Clouds

NASA Astrophysics Data System (ADS)

Tran, H.; Khoshelham, K.; Kealy, A.; Díaz-Vilariño, L.

2017-09-01

3D models of indoor environments are essential for many application domains such as navigation guidance, emergency management and a range of indoor location-based services. The principal components defined in different BIM standards contain not only building elements, such as floors, walls and doors, but also navigable spaces and their topological relations, which are essential for path planning and navigation. We present an approach to automatically reconstruct topological relations between navigable spaces from point clouds. Three types of topological relations, namely containment, adjacency and connectivity of the spaces are modelled. The results of initial experiments demonstrate the potential of the method in supporting indoor navigation.

cisTEM, user-friendly software for single-particle image processing.

PubMed

Grant, Timothy; Rohou, Alexis; Grigorieff, Nikolaus

2018-03-07

We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k - 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cis TEM is available for download from cistem.org. © 2018, Grant et al.

cisTEM, user-friendly software for single-particle image processing

PubMed Central

2018-01-01

We have developed new open-source software called cisTEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cisTEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction. Some of these steps implement newly-developed algorithms; others were adapted from previously published algorithms. The software is optimized to enable processing of typical datasets (2000 micrographs, 200 k – 300 k particles) on a high-end, CPU-based workstation in half a day or less, comparable to GPU-accelerated processing. Jobs can also be scheduled on large computer clusters using flexible run profiles that can be adapted for most computing environments. cisTEM is available for download from cistem.org. PMID:29513216

Four-dimensional volume-of-interest reconstruction for cone-beam computed tomography-guided radiation therapy.

PubMed

Ahmad, Moiz; Balter, Peter; Pan, Tinsu

2011-10-01

Data sufficiency are a major problem in four-dimensional cone-beam computed tomography (4D-CBCT) on linear accelerator-integrated scanners for image-guided radiotherapy. Scan times must be in the range of 4-6 min to avoid undersampling artifacts. Various image reconstruction algorithms have been proposed to accommodate undersampled data acquisitions, but these algorithms are computationally expensive, may require long reconstruction times, and may require algorithm parameters to be optimized. The authors present a novel reconstruction method, 4D volume-of-interest (4D-VOI) reconstruction which suppresses undersampling artifacts and resolves lung tumor motion for undersampled 1-min scans. The 4D-VOI reconstruction is much less computationally expensive than other 4D-CBCT algorithms. The 4D-VOI method uses respiration-correlated projection data to reconstruct a four-dimensional (4D) image inside a VOI containing the moving tumor, and uncorrelated projection data to reconstruct a three-dimensional (3D) image outside the VOI. Anatomical motion is resolved inside the VOI and blurred outside the VOI. The authors acquired a 1-min. scan of an anthropomorphic chest phantom containing a moving water-filled sphere. The authors also used previously acquired 1-min scans for two lung cancer patients who had received CBCT-guided radiation therapy. The same raw data were used to test and compare the 4D-VOI reconstruction with the standard 4D reconstruction and the McKinnon-Bates (MB) reconstruction algorithms. Both the 4D-VOI and the MB reconstructions suppress nearly all the streak artifacts compared with the standard 4D reconstruction, but the 4D-VOI has 3-8 times greater contrast-to-noise ratio than the MB reconstruction. In the dynamic chest phantom study, the 4D-VOI and the standard 4D reconstructions both resolved a moving sphere with an 18 mm displacement. The 4D-VOI reconstruction shows a motion blur of only 3 mm, whereas the MB reconstruction shows a motion blur of 13 mm. With graphics processing unit hardware used to accelerate computations, the 4D-VOI reconstruction required a 40-s reconstruction time. 4D-VOI reconstruction effectively reduces undersampling artifacts and resolves lung tumor motion in 4D-CBCT. The 4D-VOI reconstruction is computationally inexpensive compared with more sophisticated iterative algorithms. Compared with these algorithms, our 4D-VOI reconstruction is an attractive alternative in 4D-CBCT for reconstructing target motion without generating numerous streak artifacts.

Four-dimensional volume-of-interest reconstruction for cone-beam computed tomography-guided radiation therapy

PubMed Central

Ahmad, Moiz; Balter, Peter; Pan, Tinsu

2011-01-01

Purpose: Data sufficiency are a major problem in four-dimensional cone-beam computed tomography (4D-CBCT) on linear accelerator-integrated scanners for image-guided radiotherapy. Scan times must be in the range of 4–6 min to avoid undersampling artifacts. Various image reconstruction algorithms have been proposed to accommodate undersampled data acquisitions, but these algorithms are computationally expensive, may require long reconstruction times, and may require algorithm parameters to be optimized. The authors present a novel reconstruction method, 4D volume-of-interest (4D-VOI) reconstruction which suppresses undersampling artifacts and resolves lung tumor motion for undersampled 1-min scans. The 4D-VOI reconstruction is much less computationally expensive than other 4D-CBCT algorithms. Methods: The 4D-VOI method uses respiration-correlated projection data to reconstruct a four-dimensional (4D) image inside a VOI containing the moving tumor, and uncorrelated projection data to reconstruct a three-dimensional (3D) image outside the VOI. Anatomical motion is resolved inside the VOI and blurred outside the VOI. The authors acquired a 1-min. scan of an anthropomorphic chest phantom containing a moving water-filled sphere. The authors also used previously acquired 1-min scans for two lung cancer patients who had received CBCT-guided radiation therapy. The same raw data were used to test and compare the 4D-VOI reconstruction with the standard 4D reconstruction and the McKinnon-Bates (MB) reconstruction algorithms. Results: Both the 4D-VOI and the MB reconstructions suppress nearly all the streak artifacts compared with the standard 4D reconstruction, but the 4D-VOI has 3–8 times greater contrast-to-noise ratio than the MB reconstruction. In the dynamic chest phantom study, the 4D-VOI and the standard 4D reconstructions both resolved a moving sphere with an 18 mm displacement. The 4D-VOI reconstruction shows a motion blur of only 3 mm, whereas the MB reconstruction shows a motion blur of 13 mm. With graphics processing unit hardware used to accelerate computations, the 4D-VOI reconstruction required a 40-s reconstruction time. Conclusions: 4D-VOI reconstruction effectively reduces undersampling artifacts and resolves lung tumor motion in 4D-CBCT. The 4D-VOI reconstruction is computationally inexpensive compared with more sophisticated iterative algorithms. Compared with these algorithms, our 4D-VOI reconstruction is an attractive alternative in 4D-CBCT for reconstructing target motion without generating numerous streak artifacts. PMID:21992381

Effects of the approximations of light propagation on quantitative photoacoustic tomography using two-dimensional photon diffusion equation and linearization

NASA Astrophysics Data System (ADS)

Okawa, Shinpei; Hirasawa, Takeshi; Kushibiki, Toshihiro; Ishihara, Miya

2017-12-01

Quantitative photoacoustic tomography (QPAT) employing a light propagation model will play an important role in medical diagnoses by quantifying the concentration of hemoglobin or a contrast agent. However, QPAT by the light propagation model with the three-dimensional (3D) radiative transfer equation (RTE) requires a huge computational load in the iterative forward calculations involved in the updating process to reconstruct the absorption coefficient. The approximations of the light propagation improve the efficiency of the image reconstruction for the QPAT. In this study, we compared the 3D/two-dimensional (2D) photon diffusion equation (PDE) approximating 3D RTE with the Monte Carlo simulation based on 3D RTE. Then, the errors in a 2D PDE-based linearized image reconstruction caused by the approximations were quantitatively demonstrated and discussed in the numerical simulations. It was clearly observed that the approximations affected the reconstructed absorption coefficient. The 2D PDE-based linearized algorithm succeeded in the image reconstruction of the region with a large absorption coefficient in the 3D phantom. The value reconstructed in the phantom experiment agreed with that in the numerical simulation, so that it was validated that the numerical simulation of the image reconstruction predicted the relationship between the true absorption coefficient of the target in the 3D medium and the reconstructed value with the 2D PDE-based linearized algorithm. Moreover, the the true absorption coefficient in 3D medium was estimated from the 2D reconstructed image on the basis of the prediction by the numerical simulation. The estimation was successful in the phantom experiment, although some limitations were revealed.

Cardiac C-arm computed tomography using a 3D + time ROI reconstruction method with spatial and temporal regularization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mory, Cyril, E-mail: cyril.mory@philips.com; Philips Research Medisys, 33 rue de Verdun, 92156 Suresnes; Auvray, Vincent

2014-02-15

Purpose: Reconstruction of the beating heart in 3D + time in the catheter laboratory using only the available C-arm system would improve diagnosis, guidance, device sizing, and outcome control for intracardiac interventions, e.g., electrophysiology, valvular disease treatment, structural or congenital heart disease. To obtain such a reconstruction, the patient's electrocardiogram (ECG) must be recorded during the acquisition and used in the reconstruction. In this paper, the authors present a 4D reconstruction method aiming to reconstruct the heart from a single sweep 10 s acquisition. Methods: The authors introduce the 4D RecOnstructiOn using Spatial and TEmporal Regularization (short 4D ROOSTER) method,more » which reconstructs all cardiac phases at once, as a 3D + time volume. The algorithm alternates between a reconstruction step based on conjugate gradient and four regularization steps: enforcing positivity, averaging along time outside a motion mask that contains the heart and vessels, 3D spatial total variation minimization, and 1D temporal total variation minimization. Results: 4D ROOSTER recovers the different temporal representations of a moving Shepp and Logan phantom, and outperforms both ECG-gated simultaneous algebraic reconstruction technique and prior image constrained compressed sensing on a clinical case. It generates 3D + time reconstructions with sharp edges which can be used, for example, to estimate the patient's left ventricular ejection fraction. Conclusions: 4D ROOSTER can be applied for human cardiac C-arm CT, and potentially in other dynamic tomography areas. It can easily be adapted to other problems as regularization is decoupled from projection and back projection.« less

Automatic non-proliferative diabetic retinopathy screening system based on color fundus image.

PubMed

Xiao, Zhitao; Zhang, Xinpeng; Geng, Lei; Zhang, Fang; Wu, Jun; Tong, Jun; Ogunbona, Philip O; Shan, Chunyan

2017-10-26

Non-proliferative diabetic retinopathy is the early stage of diabetic retinopathy. Automatic detection of non-proliferative diabetic retinopathy is significant for clinical diagnosis, early screening and course progression of patients. This paper introduces the design and implementation of an automatic system for screening non-proliferative diabetic retinopathy based on color fundus images. Firstly, the fundus structures, including blood vessels, optic disc and macula, are extracted and located, respectively. In particular, a new optic disc localization method using parabolic fitting is proposed based on the physiological structure characteristics of optic disc and blood vessels. Then, early lesions, such as microaneurysms, hemorrhages and hard exudates, are detected based on their respective characteristics. An equivalent optical model simulating human eyes is designed based on the anatomical structure of retina. Main structures and early lesions are reconstructed in the 3D space for better visualization. Finally, the severity of each image is evaluated based on the international criteria of diabetic retinopathy. The system has been tested on public databases and images from hospitals. Experimental results demonstrate that the proposed system achieves high accuracy for main structures and early lesions detection. The results of severity classification for non-proliferative diabetic retinopathy are also accurate and suitable. Our system can assist ophthalmologists for clinical diagnosis, automatic screening and course progression of patients.

Deep Learning for Lowtextured Image Matching

NASA Astrophysics Data System (ADS)

Kniaz, V. V.; Fedorenko, V. V.; Fomin, N. A.

2018-05-01

Low-textured objects pose challenges for an automatic 3D model reconstruction. Such objects are common in archeological applications of photogrammetry. Most of the common feature point descriptors fail to match local patches in featureless regions of an object. Hence, automatic documentation of the archeological process using Structure from Motion (SfM) methods is challenging. Nevertheless, such documentation is possible with the aid of a human operator. Deep learning-based descriptors have outperformed most of common feature point descriptors recently. This paper is focused on the development of a new Wide Image Zone Adaptive Robust feature Descriptor (WIZARD) based on the deep learning. We use a convolutional auto-encoder to compress discriminative features of a local path into a descriptor code. We build a codebook to perform point matching on multiple images. The matching is performed using the nearest neighbor search and a modified voting algorithm. We present a new "Multi-view Amphora" (Amphora) dataset for evaluation of point matching algorithms. The dataset includes images of an Ancient Greek vase found at Taman Peninsula in Southern Russia. The dataset provides color images, a ground truth 3D model, and a ground truth optical flow. We evaluated the WIZARD descriptor on the "Amphora" dataset to show that it outperforms the SIFT and SURF descriptors on the complex patch pairs.

Reconstruction of 3d grain boundaries from rock thin sections, using polarised light

NASA Astrophysics Data System (ADS)

Markus Hammes, Daniel; Peternell, Mark

2016-04-01

Grain boundaries affect the physical and chemical properties of polycrystalline materials significantly by initiating reactions and collecting impurities (Birchenall, 1959), and play an essential role in recrystallization (Doherty et al. 1997). In particular, the shape and crystallographic orientation of grain boundaries reveal the deformation and annealing history of rocks (Kruhl and Peternell 2002, Kuntcheva et al. 2006). However, there is a lack of non-destructive and easy-to-use computer supported methods to determine grain boundary geometries in 3D. The only available instrument using optical light to measure grain boundary angles is still the polarising microscope with attached universal stage; operated manually and time-consuming in use. Here we present a new approach to determine 3d grain boundary orientations from 2D rock thin sections. The data is recorded by using an automatic fabric analyser microscope (Peternell et al., 2010). Due to its unique arrangement of 9 light directions the highest birefringence colour due to each light direction and crystal orientation (retardation) can be determined at each pixel in the field of view. Retardation profiles across grain boundaries enable the calculation of grain boundary angle and direction. The data for all positions separating the grains are combined and further processed. In combination with the lateral position of the grain boundary, acquired using the FAME software (Hammes and Peternell, in review), the data is used to reconstruct a 3d grain boundary model. The processing of data is almost fully automatic by using MATLAB®. Only minor manual input is required. The applicability was demonstrated on quartzite samples, but the method is not solely restricted on quartz grains and other birefringent polycrystalline materials could be used instead. References: Birchenall, C.E., 1959: Physical Metallurgy. McGraw-Hill, New York. Doherty, R.D., Hughes, D.A., Humphreys, F.J., Jonas, J.J., Juul Jensen, D., Kassner, M.E., King, W.E., McNelley, T.R., McQueen, H.J., Rollett, A.D., 1997: Current issues in recrystallization: a review. Materials Science and Engineering A 238, 219-274. Hammes, D.M., Peternell, M., in review. FAME: Software for analysing rock microstructures. Computers & Geoscience. Kruhl, J.H., Peternell, M., 2002. The equilibration of high-angle grain boundaries in dynamically recrystallized quartz: the effect of crystallography and temperature. Journal of Structural Geology 24, 1125-1137. Kuntcheva, B., Kruhl, J.H. & Kunze, K., 2006. Crystallographic orientation of high-angle grain boundaries in dynamically recrystallized quartz: First results. Tectonophysics 421, 331-346. Peternell, M., Hasalová, P., Wilson, J.L., Piaziolo, S., Schulmann, K., 2010. Evaluating quartz crystallographic preferred orientations and the role of deformation partitioning using EBSD and fabric analyser techniques. Journal of Structural Geology 32, 803-817.

Real time 3D scanner: investigations and results

NASA Astrophysics Data System (ADS)

Nouri, Taoufik; Pflug, Leopold

1993-12-01

This article presents a concept of reconstruction of 3-D objects using non-invasive and touch loss techniques. The principle of this method is to display parallel interference optical fringes on an object and then to record the object under two angles of view. According to an appropriated treatment one reconstructs the 3-D object even when the object has no symmetrical plan. The 3-D surface data is available immediately in digital form for computer- visualization and for analysis software tools. The optical set-up for recording the 3-D object, the 3-D data extraction and treatment, as well as the reconstruction of the 3-D object are reported and commented on. This application is dedicated for reconstructive/cosmetic surgery, CAD, animation and research purposes.

Three-dimensional monochromatic x-ray computed tomography using synchrotron radiation

NASA Astrophysics Data System (ADS)

Saito, Tsuneo; Kudo, Hiroyuki; Takeda, Tohoru; Itai, Yuji; Tokumori, Kenji; Toyofuku, Fukai; Hyodo, Kazuyuki; Ando, Masami; Nishimura, Katsuyuki; Uyama, Chikao

1998-08-01

We describe a technique of 3D computed tomography (3D CT) using monochromatic x rays generated by synchrotron radiation, which performs a direct reconstruction of a 3D volume image of an object from its cone-beam projections. For the development, we propose a practical scanning orbit of the x-ray source to obtain complete 3D information on an object, and its corresponding 3D image reconstruction algorithm. The validity and usefulness of the proposed scanning orbit and reconstruction algorithm were confirmed by computer simulation studies. Based on these investigations, we have developed a prototype 3D monochromatic x-ray CT using synchrotron radiation, which provides exact 3D reconstruction and material-selective imaging by using the K-edge energy subtraction technique.

Efficient content-based low-altitude images correlated network and strips reconstruction

NASA Astrophysics Data System (ADS)

He, Haiqing; You, Qi; Chen, Xiaoyong

2017-01-01

The manual intervention method is widely used to reconstruct strips for further aerial triangulation in low-altitude photogrammetry. Clearly the method for fully automatic photogrammetric data processing is not an expected way. In this paper, we explore a content-based approach without manual intervention or external information for strips reconstruction. Feature descriptors in the local spatial patterns are extracted by SIFT to construct vocabulary tree, in which these features are encoded in terms of TF-IDF numerical statistical algorithm to generate new representation for each low-altitude image. Then images correlated network is reconstructed by similarity measure, image matching and geometric graph theory. Finally, strips are reconstructed automatically by tracing straight lines and growing adjacent images gradually. Experimental results show that the proposed approach is highly effective in automatically rearranging strips of lowaltitude images and can provide rough relative orientation for further aerial triangulation.

Sci-Sat AM(2): Brachy-07: Tomosynthesis-based seed reconstruction in LDR prostate brachytherapy: A clinical study.

PubMed

Brunet-Benkhoucha, M; Verhaegen, F; Lassalle, S; Béliveau-Nadeau, D; Reniers, B; Donath, D; Taussky, D; Carrier, J-F

2008-07-01

To develop a tomosynthesis-based dose assessment procedure that can be performed after an I-125 prostate seed implantation, while the patient is still under anaesthesia on the treatment table. Our seed detection procedure involves the reconstruction of a volume of interest based on the backprojection of 7 seed-only binary images acquired over an angle of 60° with an isocentric imaging system. A binary seed-only volume is generated by a simple thresholding of the volume of interest. Seeds positions are extracted from this volume with a 3D connected component analysis and a statistical classifier that determines the number of seeds in each cluster of connected voxels. A graphical user interface (GUI) allows to visualize the result and to introduce corrections, if needed. A phantom and a clinical study (24 patients) were carried out to validate the technique. A phantom study demonstrated a very good localization accuracy of (0.4+/-0.4) mm when compared to CT-based reconstruction. This leads to dosimetric error on D90 and V100 of respectively 0.5% and 0.1%. In a patient study with an average of 56 seeds per implant, the automatic tomosynthesis-based reconstruction yields a detection rate of 96% of the seeds and less than 1.5% of false-positives. With the help of the GUI, the user can achieve a 100% detection rate in an average of 3 minutes. This technique would allow to identify possible underdosage and to correct it by potentially reimplanting additional seeds. A more uniform dose coverage could then be achieved in LDR prostate brachytherapy. © 2008 American Association of Physicists in Medicine.

Design and implementation of coded aperture coherent scatter spectral imaging of cancerous and healthy breast tissue samples

PubMed Central

Lakshmanan, Manu N.; Greenberg, Joel A.; Samei, Ehsan; Kapadia, Anuj J.

2016-01-01

Abstract. A scatter imaging technique for the differentiation of cancerous and healthy breast tissue in a heterogeneous sample is introduced in this work. Such a technique has potential utility in intraoperative margin assessment during lumpectomy procedures. In this work, we investigate the feasibility of the imaging method for tumor classification using Monte Carlo simulations and physical experiments. The coded aperture coherent scatter spectral imaging technique was used to reconstruct three-dimensional (3-D) images of breast tissue samples acquired through a single-position snapshot acquisition, without rotation as is required in coherent scatter computed tomography. We perform a quantitative assessment of the accuracy of the cancerous voxel classification using Monte Carlo simulations of the imaging system; describe our experimental implementation of coded aperture scatter imaging; show the reconstructed images of the breast tissue samples; and present segmentations of the 3-D images in order to identify the cancerous and healthy tissue in the samples. From the Monte Carlo simulations, we find that coded aperture scatter imaging is able to reconstruct images of the samples and identify the distribution of cancerous and healthy tissues (i.e., fibroglandular, adipose, or a mix of the two) inside them with a cancerous voxel identification sensitivity, specificity, and accuracy of 92.4%, 91.9%, and 92.0%, respectively. From the experimental results, we find that the technique is able to identify cancerous and healthy tissue samples and reconstruct differential coherent scatter cross sections that are highly correlated with those measured by other groups using x-ray diffraction. Coded aperture scatter imaging has the potential to provide scatter images that automatically differentiate cancerous and healthy tissue inside samples within a time on the order of a minute per slice. PMID:26962543

Design and implementation of coded aperture coherent scatter spectral imaging of cancerous and healthy breast tissue samples.

PubMed

Lakshmanan, Manu N; Greenberg, Joel A; Samei, Ehsan; Kapadia, Anuj J

2016-01-01

A scatter imaging technique for the differentiation of cancerous and healthy breast tissue in a heterogeneous sample is introduced in this work. Such a technique has potential utility in intraoperative margin assessment during lumpectomy procedures. In this work, we investigate the feasibility of the imaging method for tumor classification using Monte Carlo simulations and physical experiments. The coded aperture coherent scatter spectral imaging technique was used to reconstruct three-dimensional (3-D) images of breast tissue samples acquired through a single-position snapshot acquisition, without rotation as is required in coherent scatter computed tomography. We perform a quantitative assessment of the accuracy of the cancerous voxel classification using Monte Carlo simulations of the imaging system; describe our experimental implementation of coded aperture scatter imaging; show the reconstructed images of the breast tissue samples; and present segmentations of the 3-D images in order to identify the cancerous and healthy tissue in the samples. From the Monte Carlo simulations, we find that coded aperture scatter imaging is able to reconstruct images of the samples and identify the distribution of cancerous and healthy tissues (i.e., fibroglandular, adipose, or a mix of the two) inside them with a cancerous voxel identification sensitivity, specificity, and accuracy of 92.4%, 91.9%, and 92.0%, respectively. From the experimental results, we find that the technique is able to identify cancerous and healthy tissue samples and reconstruct differential coherent scatter cross sections that are highly correlated with those measured by other groups using x-ray diffraction. Coded aperture scatter imaging has the potential to provide scatter images that automatically differentiate cancerous and healthy tissue inside samples within a time on the order of a minute per slice.

GPU accelerated generation of digitally reconstructed radiographs for 2-D/3-D image registration.

PubMed

Dorgham, Osama M; Laycock, Stephen D; Fisher, Mark H

2012-09-01

Recent advances in programming languages for graphics processing units (GPUs) provide developers with a convenient way of implementing applications which can be executed on the CPU and GPU interchangeably. GPUs are becoming relatively cheap, powerful, and widely available hardware components, which can be used to perform intensive calculations. The last decade of hardware performance developments shows that GPU-based computation is progressing significantly faster than CPU-based computation, particularly if one considers the execution of highly parallelisable algorithms. Future predictions illustrate that this trend is likely to continue. In this paper, we introduce a way of accelerating 2-D/3-D image registration by developing a hybrid system which executes on the CPU and utilizes the GPU for parallelizing the generation of digitally reconstructed radiographs (DRRs). Based on the advancements of the GPU over the CPU, it is timely to exploit the benefits of many-core GPU technology by developing algorithms for DRR generation. Although some previous work has investigated the rendering of DRRs using the GPU, this paper investigates approximations which reduce the computational overhead while still maintaining a quality consistent with that needed for 2-D/3-D registration with sufficient accuracy to be clinically acceptable in certain applications of radiation oncology. Furthermore, by comparing implementations of 2-D/3-D registration on the CPU and GPU, we investigate current performance and propose an optimal framework for PC implementations addressing the rigid registration problem. Using this framework, we are able to render DRR images from a 256×256×133 CT volume in ~24 ms using an NVidia GeForce 8800 GTX and in ~2 ms using NVidia GeForce GTX 580. In addition to applications requiring fast automatic patient setup, these levels of performance suggest image-guided radiation therapy at video frame rates is technically feasible using relatively low cost PC architecture.

3D reconstruction based on light field images

NASA Astrophysics Data System (ADS)

Zhu, Dong; Wu, Chunhong; Liu, Yunluo; Fu, Dongmei

2018-04-01

This paper proposed a method of reconstructing three-dimensional (3D) scene from two light field images capture by Lytro illium. The work was carried out by first extracting the sub-aperture images from light field images and using the scale-invariant feature transform (SIFT) for feature registration on the selected sub-aperture images. Structure from motion (SFM) algorithm is further used on the registration completed sub-aperture images to reconstruct the three-dimensional scene. 3D sparse point cloud was obtained in the end. The method shows that the 3D reconstruction can be implemented by only two light field camera captures, rather than at least a dozen times captures by traditional cameras. This can effectively solve the time-consuming, laborious issues for 3D reconstruction based on traditional digital cameras, to achieve a more rapid, convenient and accurate reconstruction.

A new method for automatic tracking of facial landmarks in 3D motion captured images (4D).

PubMed

Al-Anezi, T; Khambay, B; Peng, M J; O'Leary, E; Ju, X; Ayoub, A

2013-01-01

The aim of this study was to validate the automatic tracking of facial landmarks in 3D image sequences. 32 subjects (16 males and 16 females) aged 18-35 years were recruited. 23 anthropometric landmarks were marked on the face of each subject with non-permanent ink using a 0.5mm pen. The subjects were asked to perform three facial animations (maximal smile, lip purse and cheek puff) from rest position. Each animation was captured by the 3D imaging system. A single operator manually digitised the landmarks on the 3D facial models and their locations were compared with those of the automatically tracked ones. To investigate the accuracy of manual digitisation, the operator re-digitised the same set of 3D images of 10 subjects (5 male and 5 female) at 1 month interval. The discrepancies in x, y and z coordinates between the 3D position of the manual digitised landmarks and that of the automatic tracked facial landmarks were within 0.17mm. The mean distance between the manually digitised and the automatically tracked landmarks using the tracking software was within 0.55 mm. The automatic tracking of facial landmarks demonstrated satisfactory accuracy which would facilitate the analysis of the dynamic motion during facial animations. Copyright © 2012 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

A quantitative evaluation of the three dimensional reconstruction of patients' coronary arteries.

PubMed

Klein, J L; Hoff, J G; Peifer, J W; Folks, R; Cooke, C D; King, S B; Garcia, E V

1998-04-01

Through extensive training and experience angiographers learn to mentally reconstruct the three dimensional (3D) relationships of the coronary arterial branches. Graphic computer technology can assist angiographers to more quickly visualize the coronary 3D structure from limited initial views and then help to determine additional helpful views by predicting subsequent angiograms before they are obtained. A new computer method for facilitating 3D reconstruction and visualization of human coronary arteries was evaluated by reconstructing biplane left coronary angiograms from 30 patients. The accuracy of the reconstruction was assessed in two ways: 1) by comparing the vessel's centerlines of the actual angiograms with the centerlines of a 2D projection of the 3D model projected into the exact angle of the actual angiogram; and 2) by comparing two 3D models generated by different simultaneous pairs on angiograms. The inter- and intraobserver variability of reconstruction were evaluated by mathematically comparing the 3D model centerlines of repeated reconstructions. The average absolute corrected displacement of 14,662 vessel centerline points in 2D from 30 patients was 1.64 +/- 2.26 mm. The average corrected absolute displacement of 3D models generated from different biplane pairs was 7.08 +/- 3.21 mm. The intraobserver variability of absolute 3D corrected displacement was 5.22 +/- 3.39 mm. The interobserver variability was 6.6 +/- 3.1 mm. The centerline analyses show that the reconstruction algorithm is mathematically accurate and reproducible. The figures presented in this report put these measurement errors into clinical perspective showing that they yield an accurate representation of the clinically relevant information seen on the actual angiograms. These data show that this technique can be clinically useful by accurately displaying in three dimensions the complex relationships of the branches of the coronary arterial tree.

Appearance of bony lesions on 3-D CT reconstructions: a case study in variable renderings

NASA Astrophysics Data System (ADS)

Mankovich, Nicholas J.; White, Stuart C.

1992-05-01

This paper discusses conventional 3-D reconstruction for bone visualization and presents a case study to demonstrate the dangers of performing 3-D reconstructions without careful selection of the bone threshold. The visualization of midface bone lesions directly from axial CT images is difficult because of the complex anatomic relationships. Three-dimensional reconstructions made from the CT to provide graphic images showing lesions in relation to adjacent facial bones. Most commercially available 3-D image reconstruction requires that the radiologist or technologist identify a threshold image intensity value that can be used to distinguish bone from other tissues. Much has been made of the many disadvantages of this technique, but it continues as the predominant method in producing 3-D pictures for clinical use. This paper is intended to provide a clear demonstration for the physician of the caveats that should accompany 3-D reconstructions. We present a case of recurrent odontogenic keratocyst in the anterior maxilla where the 3-D reconstructions, made with different bone thresholds (windows), are compared to the resected specimen. A DMI 3200 computer was used to convert the scan data from a GE 9800 CT into a 3-D shaded surface image. Threshold values were assigned to (1) generate the most clinically pleasing image, (2) produce maximum theoretical fidelity (using the midpoint image intensity between average cortical bone and average soft tissue), and (3) cover stepped threshold intensities between these two methods. We compared the computer lesions with the resected specimen and noted measurement errors of up to 44 percent introduced by inappropriate bone threshold levels. We suggest clinically applicable standardization techniques in the 3-D reconstruction as well as cautionary language that should accompany the 3-D images.

Task-Driven Tube Current Modulation and Regularization Design in Computed Tomography with Penalized-Likelihood Reconstruction.

PubMed

Gang, G J; Siewerdsen, J H; Stayman, J W

2016-02-01

This work applies task-driven optimization to design CT tube current modulation and directional regularization in penalized-likelihood (PL) reconstruction. The relative performance of modulation schemes commonly adopted for filtered-backprojection (FBP) reconstruction were also evaluated for PL in comparison. We adopt a task-driven imaging framework that utilizes a patient-specific anatomical model and information of the imaging task to optimize imaging performance in terms of detectability index ( d' ). This framework leverages a theoretical model based on implicit function theorem and Fourier approximations to predict local spatial resolution and noise characteristics of PL reconstruction as a function of the imaging parameters to be optimized. Tube current modulation was parameterized as a linear combination of Gaussian basis functions, and regularization was based on the design of (directional) pairwise penalty weights for the 8 in-plane neighboring voxels. Detectability was optimized using a covariance matrix adaptation evolutionary strategy algorithm. Task-driven designs were compared to conventional tube current modulation strategies for a Gaussian detection task in an abdomen phantom. The task-driven design yielded the best performance, improving d' by ~20% over an unmodulated acquisition. Contrary to FBP, PL reconstruction using automatic exposure control and modulation based on minimum variance (in FBP) performed worse than the unmodulated case, decreasing d' by 16% and 9%, respectively. This work shows that conventional tube current modulation schemes suitable for FBP can be suboptimal for PL reconstruction. Thus, the proposed task-driven optimization provides additional opportunities for improved imaging performance and dose reduction beyond that achievable with conventional acquisition and reconstruction.

Reconstruction of brachytherapy seed positions and orientations from cone-beam CT x-ray projections via a novel iterative forward projection matching method.

PubMed

Pokhrel, Damodar; Murphy, Martin J; Todor, Dorin A; Weiss, Elisabeth; Williamson, Jeffrey F

2011-01-01

To generalize and experimentally validate a novel algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a set of a few measured 2D cone-beam CT (CBCT) x-ray projections. The iterative forward projection matching (IFPM) algorithm was generalized to reconstruct the 3D pose, as well as the centroid, of brachytherapy seeds from three to ten measured 2D projections. The gIFPM algorithm finds the set of seed poses that minimizes the sum-of-squared-difference of the pixel-by-pixel intensities between computed and measured autosegmented radiographic projections of the implant. Numerical simulations of clinically realistic brachytherapy seed configurations were performed to demonstrate the proof of principle. An in-house machined brachytherapy phantom, which supports precise specification of seed position and orientation at known values for simulated implant geometries, was used to experimentally validate this algorithm. The phantom was scanned on an ACUITY CBCT digital simulator over a full 660 sinogram projections. Three to ten x-ray images were selected from the full set of CBCT sinogram projections and postprocessed to create binary seed-only images. In the numerical simulations, seed reconstruction position and orientation errors were approximately 0.6 mm and 5 degrees, respectively. The physical phantom measurements demonstrated an absolute positional accuracy of (0.78 +/- 0.57) mm or less. The theta and phi angle errors were found to be (5.7 +/- 4.9) degrees and (6.0 +/- 4.1) degrees, respectively, or less when using three projections; with six projections, results were slightly better. The mean registration error was better than 1 mm/6 degrees compared to the measured seed projections. Each test trial converged in 10-20 iterations with computation time of 12-18 min/iteration on a 1 GHz processor. This work describes a novel, accurate, and completely automatic method for reconstructing seed orientations, as well as centroids, from a small number of radiographic projections, in support of intraoperative planning and adaptive replanning. Unlike standard back-projection methods, gIFPM avoids the need to match corresponding seed images on the projections. This algorithm also successfully reconstructs overlapping clustered and highly migrated seeds in the implant. The accuracy of better than 1 mm and 6 degrees demonstrates that gIFPM has the potential to support 2D Task Group 43 calculations in clinical practice.

Reconstruction of brachytherapy seed positions and orientations from cone-beam CT x-ray projections via a novel iterative forward projection matching method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pokhrel, Damodar; Murphy, Martin J.; Todor, Dorin A.

2011-01-15

Purpose: To generalize and experimentally validate a novel algorithm for reconstructing the 3D pose (position and orientation) of implanted brachytherapy seeds from a set of a few measured 2D cone-beam CT (CBCT) x-ray projections. Methods: The iterative forward projection matching (IFPM) algorithm was generalized to reconstruct the 3D pose, as well as the centroid, of brachytherapy seeds from three to ten measured 2D projections. The gIFPM algorithm finds the set of seed poses that minimizes the sum-of-squared-difference of the pixel-by-pixel intensities between computed and measured autosegmented radiographic projections of the implant. Numerical simulations of clinically realistic brachytherapy seed configurations weremore » performed to demonstrate the proof of principle. An in-house machined brachytherapy phantom, which supports precise specification of seed position and orientation at known values for simulated implant geometries, was used to experimentally validate this algorithm. The phantom was scanned on an ACUITY CBCT digital simulator over a full 660 sinogram projections. Three to ten x-ray images were selected from the full set of CBCT sinogram projections and postprocessed to create binary seed-only images. Results: In the numerical simulations, seed reconstruction position and orientation errors were approximately 0.6 mm and 5 deg., respectively. The physical phantom measurements demonstrated an absolute positional accuracy of (0.78{+-}0.57) mm or less. The {theta} and {phi} angle errors were found to be (5.7{+-}4.9) deg. and (6.0{+-}4.1) deg., respectively, or less when using three projections; with six projections, results were slightly better. The mean registration error was better than 1 mm/6 deg. compared to the measured seed projections. Each test trial converged in 10-20 iterations with computation time of 12-18 min/iteration on a 1 GHz processor. Conclusions: This work describes a novel, accurate, and completely automatic method for reconstructing seed orientations, as well as centroids, from a small number of radiographic projections, in support of intraoperative planning and adaptive replanning. Unlike standard back-projection methods, gIFPM avoids the need to match corresponding seed images on the projections. This algorithm also successfully reconstructs overlapping clustered and highly migrated seeds in the implant. The accuracy of better than 1 mm and 6 deg. demonstrates that gIFPM has the potential to support 2D Task Group 43 calculations in clinical practice.« less

Residual motion compensation in ECG-gated interventional cardiac vasculature reconstruction

NASA Astrophysics Data System (ADS)

Schwemmer, C.; Rohkohl, C.; Lauritsch, G.; Müller, K.; Hornegger, J.

2013-06-01

Three-dimensional reconstruction of cardiac vasculature from angiographic C-arm CT (rotational angiography) data is a major challenge. Motion artefacts corrupt image quality, reducing usability for diagnosis and guidance. Many state-of-the-art approaches depend on retrospective ECG-gating of projection data for image reconstruction. A trade-off has to be made regarding the size of the ECG-gating window. A large temporal window is desirable to avoid undersampling. However, residual motion will occur in a large window, causing motion artefacts. We present an algorithm to correct for residual motion. Our approach is based on a deformable 2D-2D registration between the forward projection of an initial, ECG-gated reconstruction, and the original projection data. The approach is fully automatic and does not require any complex segmentation of vasculature, or landmarks. The estimated motion is compensated for during the backprojection step of a subsequent reconstruction. We evaluated the method using the publicly available CAVAREV platform and on six human clinical datasets. We found a better visibility of structure, reduced motion artefacts, and increased sharpness of the vessels in the compensated reconstructions compared to the initial reconstructions. At the time of writing, our algorithm outperforms the leading result of the CAVAREV ranking list. For the clinical datasets, we found an average reduction of motion artefacts by 13 ± 6%. Vessel sharpness was improved by 25 ± 12% on average.

Automatic Reconstruction of 3D Building Models from Terrestrial Laser Scanner Data

NASA Astrophysics Data System (ADS)

El Meouche, R.; Rezoug, M.; Hijazi, I.; Maes, D.

2013-11-01

With modern 3D laser scanners we can acquire a large amount of 3D data in only a few minutes. This technology results in a growing number of applications ranging from the digitalization of historical artifacts to facial authentication. The modeling process demands a lot of time and work (Tim Volodine, 2007). In comparison with the other two stages, the acquisition and the registration, the degree of automation of the modeling stage is almost zero. In this paper, we propose a new surface reconstruction technique for buildings to process the data obtained by a 3D laser scanner. These data are called a point cloud which is a collection of points sampled from the surface of a 3D object. Such a point cloud can consist of millions of points. In order to work more efficiently, we worked with simplified models which contain less points and so less details than a point cloud obtained in situ. The goal of this study was to facilitate the modeling process of a building starting from 3D laser scanner data. In order to do this, we wrote two scripts for Rhinoceros 5.0 based on intelligent algorithms. The first script finds the exterior outline of a building. With a minimum of human interaction, there is a thin box drawn around the surface of a wall. This box is able to rotate 360° around an axis in a corner of the wall in search for the points of other walls. In this way we can eliminate noise points. These are unwanted or irrelevant points. If there is an angled roof, the box can also turn around the edge of the wall and the roof. With the different positions of the box we can calculate the exterior outline. The second script draws the interior outline in a surface of a building. By interior outline we mean the outline of the openings like windows or doors. This script is based on the distances between the points and vector characteristics. Two consecutive points with a relative big distance will form the outline of an opening. Once those points are found, the interior outline can be drawn. The designed scripts are able to ensure for simple point clouds: the elimination of almost all noise points and the reconstruction of a CAD model.

Challenges in Flying Quadrotor Unmanned Aerial Vehicle for 3d Indoor Reconstruction

NASA Astrophysics Data System (ADS)

Yan, J.; Grasso, N.; Zlatanova, S.; Braggaar, R. C.; Marx, D. B.

2017-09-01

Three-dimensional modelling plays a vital role in indoor 3D tracking, navigation, guidance and emergency evacuation. Reconstruction of indoor 3D models is still problematic, in part, because indoor spaces provide challenges less-documented than their outdoor counterparts. Challenges include obstacles curtailing image and point cloud capture, restricted accessibility and a wide array of indoor objects, each with unique semantics. Reconstruction of indoor environments can be achieved through a photogrammetric approach, e.g. by using image frames, aligned using recurring corresponding image points (CIP) to build coloured point clouds. Our experiments were conducted by flying a QUAV in three indoor environments and later reconstructing 3D models which were analysed under different conditions. Point clouds and meshes were created using Agisoft PhotoScan Professional. We concentrated on flight paths from two vantage points: 1) safety and security while flying indoors and 2) data collection needed for reconstruction of 3D models. We surmised that the main challenges in providing safe flight paths are related to the physical configuration of indoor environments, privacy issues, the presence of people and light conditions. We observed that the quality of recorded video used for 3D reconstruction has a high dependency on surface materials, wall textures and object types being reconstructed. Our results show that 3D indoor reconstruction predicated on video capture using a QUAV is indeed feasible, but close attention should be paid to flight paths and conditions ultimately influencing the quality of 3D models. Moreover, it should be decided in advance which objects need to be reconstructed, e.g. bare rooms or detailed furniture.

3D noise power spectrum applied on clinical MDCT scanners: effects of reconstruction algorithms and reconstruction filters

NASA Astrophysics Data System (ADS)

Miéville, Frédéric A.; Bolard, Gregory; Benkreira, Mohamed; Ayestaran, Paul; Gudinchet, François; Bochud, François; Verdun, Francis R.

2011-03-01

The noise power spectrum (NPS) is the reference metric for understanding the noise content in computed tomography (CT) images. To evaluate the noise properties of clinical multidetector (MDCT) scanners, local 2D and 3D NPSs were computed for different acquisition reconstruction parameters. A 64- and a 128-MDCT scanners were employed. Measurements were performed on a water phantom in axial and helical acquisition modes. CT dose index was identical for both installations. Influence of parameters such as the pitch, the reconstruction filter (soft, standard and bone) and the reconstruction algorithm (filtered-back projection (FBP), adaptive statistical iterative reconstruction (ASIR)) were investigated. Images were also reconstructed in the coronal plane using a reformat process. Then 2D and 3D NPS methods were computed. In axial acquisition mode, the 2D axial NPS showed an important magnitude variation as a function of the z-direction when measured at the phantom center. In helical mode, a directional dependency with lobular shape was observed while the magnitude of the NPS was kept constant. Important effects of the reconstruction filter, pitch and reconstruction algorithm were observed on 3D NPS results for both MDCTs. With ASIR, a reduction of the NPS magnitude and a shift of the NPS peak to the low frequency range were visible. 2D coronal NPS obtained from the reformat images was impacted by the interpolation when compared to 2D coronal NPS obtained from 3D measurements. The noise properties of volume measured in last generation MDCTs was studied using local 3D NPS metric. However, impact of the non-stationarity noise effect may need further investigations.

The Potential of Low-Cost Rpas for Multi-View Reconstruction of Sub-Vertical Rock Faces

NASA Astrophysics Data System (ADS)

Thoeni, K.; Guccione, D. E.; Santise, M.; Giacomini, A.; Roncella, R.; Forlani, G.

2016-06-01

The current work investigates the potential of two low-cost off-the-shelf quadcopters for multi-view reconstruction of sub-vertical rock faces. The two platforms used are a DJI Phantom 1 equipped with a Gopro Hero 3+ Black and a DJI Phantom 3 Professional with integrated camera. The study area is a small sub-vertical rock face. Several flights were performed with both cameras set in time-lapse mode. Hence, images were taken automatically but the flights were performed manually as the investigated rock face is very irregular which required manual adjustment of the yaw and roll for optimal coverage. The digital images were processed with commercial SfM software packages. Several processing settings were investigated in order to find out the one providing the most accurate 3D reconstruction of the rock face. To this aim, all 3D models produced with both platforms are compared to a point cloud obtained with a terrestrial laser scanner. Firstly, the difference between the use of coded ground control targets and the use of natural features was studied. Coded targets generally provide the best accuracy, but they need to be placed on the surface, which is not always possible, as sub-vertical rock faces are not easily accessible. Nevertheless, natural features can provide a good alternative if wisely chosen as shown in this work. Secondly, the influence of using fixed interior orientation parameters or self-calibration was investigated. The results show that, in the case of the used sensors and camera networks, self-calibration provides better results. To support such empirical finding, a numerical investigation using a Monte Carlo simulation was performed.

Managing multiple image stacks from confocal laser scanning microscopy

NASA Astrophysics Data System (ADS)

Zerbe, Joerg; Goetze, Christian H.; Zuschratter, Werner

1999-05-01

A major goal in neuroanatomy is to obtain precise information about the functional organization of neuronal assemblies and their interconnections. Therefore, the analysis of histological sections frequently requires high resolution images in combination with an overview about the structure. To overcome this conflict we have previously introduced a software for the automatic acquisition of multiple image stacks (3D-MISA) in confocal laser scanning microscopy. Here, we describe a Windows NT based software for fast and easy navigation through the multiple images stacks (MIS-browser), the visualization of individual channels and layers and the selection of user defined subregions. In addition, the MIS browser provides useful tools for the visualization and evaluation of the datavolume, as for instance brightness and contrast corrections of individual layers and channels. Moreover, it includes a maximum intensity projection, panning and zoom in/out functions within selected channels or focal planes (x/y) and tracking along the z-axis. The import module accepts any tiff-format and reconstructs the original image arrangement after the user has defined the sequence of images in x/y and z and the number of channels. The implemented export module allows storage of user defined subregions (new single image stacks) for further 3D-reconstruction and evaluation.

Automatic generation of endocardial surface meshes with 1-to-1 correspondence from cine-MR images

NASA Astrophysics Data System (ADS)

Su, Yi; Teo, S.-K.; Lim, C. W.; Zhong, L.; Tan, R. S.

2015-03-01

In this work, we develop an automatic method to generate a set of 4D 1-to-1 corresponding surface meshes of the left ventricle (LV) endocardial surface which are motion registered over the whole cardiac cycle. These 4D meshes have 1- to-1 point correspondence over the entire set, and is suitable for advanced computational processing, such as shape analysis, motion analysis and finite element modelling. The inputs to the method are the set of 3D LV endocardial surface meshes of the different frames/phases of the cardiac cycle. Each of these meshes is reconstructed independently from border-delineated MR images and they have no correspondence in terms of number of vertices/points and mesh connectivity. To generate point correspondence, the first frame of the LV mesh model is used as a template to be matched to the shape of the meshes in the subsequent phases. There are two stages in the mesh correspondence process: (1) a coarse matching phase, and (2) a fine matching phase. In the coarse matching phase, an initial rough matching between the template and the target is achieved using a radial basis function (RBF) morphing process. The feature points on the template and target meshes are automatically identified using a 16-segment nomenclature of the LV. In the fine matching phase, a progressive mesh projection process is used to conform the rough estimate to fit the exact shape of the target. In addition, an optimization-based smoothing process is used to achieve superior mesh quality and continuous point motion.

3D frequency-domain ultrasound waveform tomography breast imaging

NASA Astrophysics Data System (ADS)

Sandhu, Gursharan Yash; West, Erik; Li, Cuiping; Roy, Olivier; Duric, Neb

2017-03-01

Frequency-domain ultrasound waveform tomography is a promising method for the visualization and characterization of breast disease. It has previously been shown to accurately reconstruct the sound speed distributions of breasts of varying densities. The reconstructed images show detailed morphological and quantitative information that can help differentiate different types of breast disease including benign and malignant lesions. The attenuation properties of an ex vivo phantom have also been assessed. However, the reconstruction algorithms assumed a 2D geometry while the actual data acquisition process was not. Although clinically useful sound speed images can be reconstructed assuming this mismatched geometry, artifacts from the reconstruction process exist within the reconstructed images. This is especially true for registration across different modalities and when the 2D assumption is violated. For example, this happens when a patient's breast is rapidly sloping. It is also true for attenuation imaging where energy lost or gained out of the plane gets transformed into artifacts within the image space. In this paper, we will briefly review ultrasound waveform tomography techniques, give motivation for pursuing the 3D method, discuss the 3D reconstruction algorithm, present the results of 3D forward modeling, show the mismatch that is induced by the violation of 3D modeling via numerical simulations, and present a 3D inversion of a numerical phantom.

Multisensor Fusion for Change Detection

NASA Astrophysics Data System (ADS)

Schenk, T.; Csatho, B.

2005-12-01

Combining sensors that record different properties of a 3-D scene leads to complementary and redundant information. If fused properly, a more robust and complete scene description becomes available. Moreover, fusion facilitates automatic procedures for object reconstruction and modeling. For example, aerial imaging sensors, hyperspectral scanning systems, and airborne laser scanning systems generate complementary data. We describe how data from these sensors can be fused for such diverse applications as mapping surface erosion and landslides, reconstructing urban scenes, monitoring urban land use and urban sprawl, and deriving velocities and surface changes of glaciers and ice sheets. An absolute prerequisite for successful fusion is a rigorous co-registration of the sensors involved. We establish a common 3-D reference frame by using sensor invariant features. Such features are caused by the same object space phenomena and are extracted in multiple steps from the individual sensors. After extracting, segmenting and grouping the features into more abstract entities, we discuss ways on how to automatically establish correspondences. This is followed by a brief description of rigorous mathematical models suitable to deal with linear and area features. In contrast to traditional, point-based registration methods, lineal and areal features lend themselves to a more robust and more accurate registration. More important, the chances to automate the registration process increases significantly. The result of the co-registration of the sensors is a unique transformation between the individual sensors and the object space. This makes spatial reasoning of extracted information more versatile; reasoning can be performed in sensor space or in 3-D space where domain knowledge about features and objects constrains reasoning processes, reduces the search space, and helps to make the problem well-posed. We demonstrate the feasibility of the proposed multisensor fusion approach with detecting surface elevation changes on the Byrd Glacier, Antarctica, with aerial imagery from 1980s and ICESat laser altimetry data from 2003-05. Change detection from such disparate data sets is an intricate fusion problem, beginning with sensor alignment, and on to reasoning with spatial information as to where changes occurred and to what extent.

SU-G-JeP2-14: MRI-Based HDR Prostate Brachytherapy: A Phantom Study for Interstitial Catheter Reconstruction with 0.35T MRI Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, S; Kamrava, M; Yang, Y

Purpose: To evaluate the accuracy of interstitial catheter reconstruction with 0.35T MRI images for MRI-based HDR prostate brachytherapy. Methods: Recently, a real-time MRI-guided radiotherapy system combining a 0.35T MRI system and three cobalt 60 heads (MRIdian System, ViewRay, Cleveland, OH, USA) was installed in our department. A TrueFISP sequence for MRI acquisition at lower field on Viewray was chosen due to its fast speed and high signal-to-noise efficiency. Interstitial FlexiGuide needles were implanted into a tissue equivalent ultrasound prostate phantom (CIRS, Norfolk, Virginia, USA). After an initial 15s pilot MRI to confirm the location of the phantom, planning MRI wasmore » acquired with a 172s TrueFISP sequence. The pulse sequence parameters included: flip angle = 60 degree, echo time (TE) =1.45 ms, repetition time (TR) = 3.37 ms, slice thickness = 1.5 mm, field of view (FOV) =500 × 450mm. For a reference image, a CT scan was followed. The CT and MR scans were then fused with the MIM Maestro (MIM software Inc., Cleveland, OH, USA) and sent to the Oncentra Brachy planning system (Elekta, Veenendaal, Netherlands). Automatic catheter reconstruction using CT and MR image intensities followed by manual reconstruction was used to digitize catheters. The accuracy of catheter reconstruction was evaluated from the catheter tip location. Results: The average difference between the catheter tip locations reconstructed from the CT and MR in the transverse, anteroposterior, and craniocaudal directions was −0.1 ± 0.1 mm (left), 0.2 ± 0.2 mm (anterior), and −2.3 ± 0.5 mm (cranio). The average distance in 3D was 2.3 mm ± 0.5 mm. Conclusion: This feasibility study proved that interstitial catheters can be reconstructed with 0.35T MRI images. For more accurate catheter reconstruction which can affect final dose distribution, a systematic shift should be applied to the MR based catheter reconstruction in HDR prostate brachytherapy.« less

D Reconstruction from Multi-View Medical X-Ray Images - Review and Evaluation of Existing Methods

NASA Astrophysics Data System (ADS)

Hosseinian, S.; Arefi, H.

2015-12-01

The 3D concept is extremely important in clinical studies of human body. Accurate 3D models of bony structures are currently required in clinical routine for diagnosis, patient follow-up, surgical planning, computer assisted surgery and biomechanical applications. However, 3D conventional medical imaging techniques such as computed tomography (CT) scan and magnetic resonance imaging (MRI) have serious limitations such as using in non-weight-bearing positions, costs and high radiation dose(for CT). Therefore, 3D reconstruction methods from biplanar X-ray images have been taken into consideration as reliable alternative methods in order to achieve accurate 3D models with low dose radiation in weight-bearing positions. Different methods have been offered for 3D reconstruction from X-ray images using photogrammetry which should be assessed. In this paper, after demonstrating the principles of 3D reconstruction from X-ray images, different existing methods of 3D reconstruction of bony structures from radiographs are classified and evaluated with various metrics and their advantages and disadvantages are mentioned. Finally, a comparison has been done on the presented methods with respect to several metrics such as accuracy, reconstruction time and their applications. With regards to the research, each method has several advantages and disadvantages which should be considered for a specific application.

A defocus-information-free autostereoscopic three-dimensional (3D) digital reconstruction method using direct extraction of disparity information (DEDI)

NASA Astrophysics Data System (ADS)

Li, Da; Cheung, Chifai; Zhao, Xing; Ren, Mingjun; Zhang, Juan; Zhou, Liqiu

2016-10-01

Autostereoscopy based three-dimensional (3D) digital reconstruction has been widely applied in the field of medical science, entertainment, design, industrial manufacture, precision measurement and many other areas. The 3D digital model of the target can be reconstructed based on the series of two-dimensional (2D) information acquired by the autostereoscopic system, which consists multiple lens and can provide information of the target from multiple angles. This paper presents a generalized and precise autostereoscopic three-dimensional (3D) digital reconstruction method based on Direct Extraction of Disparity Information (DEDI) which can be used to any transform autostereoscopic systems and provides accurate 3D reconstruction results through error elimination process based on statistical analysis. The feasibility of DEDI method has been successfully verified through a series of optical 3D digital reconstruction experiments on different autostereoscopic systems which is highly efficient to perform the direct full 3D digital model construction based on tomography-like operation upon every depth plane with the exclusion of the defocused information. With the absolute focused information processed by DEDI method, the 3D digital model of the target can be directly and precisely formed along the axial direction with the depth information.

Opti-acoustic stereo imaging: on system calibration and 3-D target reconstruction.

PubMed

Negahdaripour, Shahriar; Sekkati, Hicham; Pirsiavash, Hamed

2009-06-01

Utilization of an acoustic camera for range measurements is a key advantage for 3-D shape recovery of underwater targets by opti-acoustic stereo imaging, where the associated epipolar geometry of optical and acoustic image correspondences can be described in terms of conic sections. In this paper, we propose methods for system calibration and 3-D scene reconstruction by maximum likelihood estimation from noisy image measurements. The recursive 3-D reconstruction method utilized as initial condition a closed-form solution that integrates the advantages of two other closed-form solutions, referred to as the range and azimuth solutions. Synthetic data tests are given to provide insight into the merits of the new target imaging and 3-D reconstruction paradigm, while experiments with real data confirm the findings based on computer simulations, and demonstrate the merits of this novel 3-D reconstruction paradigm.

Evaluation of feature-based 3-d registration of probabilistic volumetric scenes

NASA Astrophysics Data System (ADS)

Restrepo, Maria I.; Ulusoy, Ali O.; Mundy, Joseph L.

2014-12-01

Automatic estimation of the world surfaces from aerial images has seen much attention and progress in recent years. Among current modeling technologies, probabilistic volumetric models (PVMs) have evolved as an alternative representation that can learn geometry and appearance in a dense and probabilistic manner. Recent progress, in terms of storage and speed, achieved in the area of volumetric modeling, opens the opportunity to develop new frameworks that make use of the PVM to pursue the ultimate goal of creating an entire map of the earth, where one can reason about the semantics and dynamics of the 3-d world. Aligning 3-d models collected at different time-instances constitutes an important step for successful fusion of large spatio-temporal information. This paper evaluates how effectively probabilistic volumetric models can be aligned using robust feature-matching techniques, while considering different scenarios that reflect the kind of variability observed across aerial video collections from different time instances. More precisely, this work investigates variability in terms of discretization, resolution and sampling density, errors in the camera orientation, and changes in illumination and geographic characteristics. All results are given for large-scale, outdoor sites. In order to facilitate the comparison of the registration performance of PVMs to that of other 3-d reconstruction techniques, the registration pipeline is also carried out using Patch-based Multi-View Stereo (PMVS) algorithm. Registration performance is similar for scenes that have favorable geometry and the appearance characteristics necessary for high quality reconstruction. In scenes containing trees, such as a park, or many buildings, such as a city center, registration performance is significantly more accurate when using the PVM.

Significance of coupling device for vessel anastomosis in esophageal reconstruction.

PubMed

Watanabe, Y; Horiuchi, A; Yamamoto, Y; Kikkawa, H; Kusunose, H; Sugishita, H; Sato, K; Yoshida, M; Yukumi, S; Kawachi, K

2005-01-01

To prevent an anastomotic failure due to impaired blood supply, several trials have been performed such as preoperative ischemic conditioning by transarterial embolization of the left gastric, right gastric and splenic arteries or microvascular anastomosis. We assess the significance of an automatic anastomotic coupling device for vessel anastomosis, which we have continuously utilized, to simplify the task and shorten the anastomotic time since March 1999. 8 patients who underwent venous anastomosis by an automatic anastomotic coupling device were evaluated for the time of anastomosis, total ischemic time and outcomes. Venous anastomosis was completed within 5 minutes on average. Microscopic arterial anastomosis by hand took 35 minutes on average. For gastric tube reconstruction, venous anastomosis by an automatic coupling device took only 5 minutes. The top of the gastric tube showed congestion before venous anastomosis, but rapidly recovered from it after anastomosis. Postoperative endoscopic observation of the mucosal color of the replaced intestine or gastric tube was started 3 days after surgery and revealed no ischemia or congestion. The postoperative course was uneventful except one case suffering from pneumonia but leakage was not observed in any case. An automatic anastomotic coupling device can perform an easy and reliable vascular anastomosis for patients who undergo esophageal reconstruction. The device may shorten the operating time and consequently the ischemic time of the gastric tube or jejunal or colonic graft, which in turn may lead to a decrease of complications.

Comparison of reconstruction methods and quantitative accuracy in Siemens Inveon PET scanner

NASA Astrophysics Data System (ADS)

Ram Yu, A.; Kim, Jin Su; Kang, Joo Hyun; Moo Lim, Sang

2015-04-01

PET reconstruction is key to the quantification of PET data. To our knowledge, no comparative study of reconstruction methods has been performed to date. In this study, we compared reconstruction methods with various filters in terms of their spatial resolution, non-uniformities (NU), recovery coefficients (RCs), and spillover ratios (SORs). In addition, the linearity of reconstructed radioactivity between linearity of measured and true concentrations were also assessed. A Siemens Inveon PET scanner was used in this study. Spatial resolution was measured with NEMA standard by using a 1 mm3 sized 18F point source. Image quality was assessed in terms of NU, RC and SOR. To measure the effect of reconstruction algorithms and filters, data was reconstructed using FBP, 3D reprojection algorithm (3DRP), ordered subset expectation maximization 2D (OSEM 2D), and maximum a posteriori (MAP) with various filters or smoothing factors (β). To assess the linearity of reconstructed radioactivity, image quality phantom filled with 18F was used using FBP, OSEM and MAP (β =1.5 & 5 × 10-5). The highest achievable volumetric resolution was 2.31 mm3 and the highest RCs were obtained when OSEM 2D was used. SOR was 4.87% for air and 3.97% for water, obtained OSEM 2D reconstruction was used. The measured radioactivity of reconstruction image was proportional to the injected one for radioactivity below 16 MBq/ml when FBP or OSEM 2D reconstruction methods were used. By contrast, when the MAP reconstruction method was used, activity of reconstruction image increased proportionally, regardless of the amount of injected radioactivity. When OSEM 2D or FBP were used, the measured radioactivity concentration was reduced by 53% compared with true injected radioactivity for radioactivity <16 MBq/ml. The OSEM 2D reconstruction method provides the highest achievable volumetric resolution and highest RC among all the tested methods and yields a linear relation between the measured and true concentrations for radioactivity Our data collectively showed that OSEM 2D reconstruction method provides quantitatively accurate reconstructed PET data results.

A Regularized Volumetric Fusion Framework for Large-Scale 3D Reconstruction

NASA Astrophysics Data System (ADS)

Rajput, Asif; Funk, Eugen; Börner, Anko; Hellwich, Olaf

2018-07-01

Modern computational resources combined with low-cost depth sensing systems have enabled mobile robots to reconstruct 3D models of surrounding environments in real-time. Unfortunately, low-cost depth sensors are prone to produce undesirable estimation noise in depth measurements which result in either depth outliers or introduce surface deformations in the reconstructed model. Conventional 3D fusion frameworks integrate multiple error-prone depth measurements over time to reduce noise effects, therefore additional constraints such as steady sensor movement and high frame-rates are required for high quality 3D models. In this paper we propose a generic 3D fusion framework with controlled regularization parameter which inherently reduces noise at the time of data fusion. This allows the proposed framework to generate high quality 3D models without enforcing additional constraints. Evaluation of the reconstructed 3D models shows that the proposed framework outperforms state of art techniques in terms of both absolute reconstruction error and processing time.

[The dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modeling language (VRML)].

PubMed

Yu, Zhengyang; Zheng, Shusen; Chen, Huaiqing; Wang, Jianjun; Xiong, Qingwen; Jing, Wanjun; Zeng, Yu

2006-10-01

This research studies the process of dynamic concision and 3D reconstruction from medical body data using VRML and JavaScript language, focuses on how to realize the dynamic concision of 3D medical model built with VRML. The 2D medical digital images firstly are modified and manipulated by 2D image software. Then, based on these images, 3D mould is built with VRML and JavaScript language. After programming in JavaScript to control 3D model, the function of dynamic concision realized by Script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be formed in high quality near to those got in traditional methods. By this way, with the function of dynamic concision, VRML browser can offer better windows of man-computer interaction in real time environment than before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and has a promising prospect in the fields of medical image.

Very fast road database verification using textured 3D city models obtained from airborne imagery

NASA Astrophysics Data System (ADS)

Bulatov, Dimitri; Ziems, Marcel; Rottensteiner, Franz; Pohl, Melanie

2014-10-01

Road databases are known to be an important part of any geodata infrastructure, e.g. as the basis for urban planning or emergency services. Updating road databases for crisis events must be performed quickly and with the highest possible degree of automation. We present a semi-automatic algorithm for road verification using textured 3D city models, starting from aerial or even UAV-images. This algorithm contains two processes, which exchange input and output, but basically run independently from each other. These processes are textured urban terrain reconstruction and road verification. The first process contains a dense photogrammetric reconstruction of 3D geometry of the scene using depth maps. The second process is our core procedure, since it contains various methods for road verification. Each method represents a unique road model and a specific strategy, and thus is able to deal with a specific type of roads. Each method is designed to provide two probability distributions, where the first describes the state of a road object (correct, incorrect), and the second describes the state of its underlying road model (applicable, not applicable). Based on the Dempster-Shafer Theory, both distributions are mapped to a single distribution that refers to three states: correct, incorrect, and unknown. With respect to the interaction of both processes, the normalized elevation map and the digital orthophoto generated during 3D reconstruction are the necessary input - together with initial road database entries - for the road verification process. If the entries of the database are too obsolete or not available at all, sensor data evaluation enables classification of the road pixels of the elevation map followed by road map extraction by means of vectorization and filtering of the geometrically and topologically inconsistent objects. Depending on the time issue and availability of a geo-database for buildings, the urban terrain reconstruction procedure has semantic models of buildings, trees, and ground as output. Building s and ground are textured by means of available images. This facilitates the orientation in the model and the interactive verification of the road objects that where initially classified as unknown. The three main modules of the texturing algorithm are: Pose estimation (if the videos are not geo-referenced), occlusion analysis, and texture synthesis.

2D and 3D MALDI-imaging: conceptual strategies for visualization and data mining.

PubMed

Thiele, Herbert; Heldmann, Stefan; Trede, Dennis; Strehlow, Jan; Wirtz, Stefan; Dreher, Wolfgang; Berger, Judith; Oetjen, Janina; Kobarg, Jan Hendrik; Fischer, Bernd; Maass, Peter

2014-01-01

3D imaging has a significant impact on many challenges in life sciences, because biology is a 3-dimensional phenomenon. Current 3D imaging-technologies (various types MRI, PET, SPECT) are labeled, i.e. they trace the localization of a specific compound in the body. In contrast, 3D MALDI mass spectrometry-imaging (MALDI-MSI) is a label-free method imaging the spatial distribution of molecular compounds. It complements 3D imaging labeled methods, immunohistochemistry, and genetics-based methods. However, 3D MALDI-MSI cannot tap its full potential due to the lack of statistical methods for analysis and interpretation of large and complex 3D datasets. To overcome this, we established a complete and robust 3D MALDI-MSI pipeline combined with efficient computational data analysis methods for 3D edge preserving image denoising, 3D spatial segmentation as well as finding colocalized m/z values, which will be reviewed here in detail. Furthermore, we explain, why the integration and correlation of the MALDI imaging data with other imaging modalities allows to enhance the interpretation of the molecular data and provides visualization of molecular patterns that may otherwise not be apparent. Therefore, a 3D data acquisition workflow is described generating a set of 3 different dimensional images representing the same anatomies. First, an in-vitro MRI measurement is performed which results in a three-dimensional image modality representing the 3D structure of the measured object. After sectioning the 3D object into N consecutive slices, all N slices are scanned using an optical digital scanner, enabling for performing the MS measurements. Scanning the individual sections results into low-resolution images, which define the base coordinate system for the whole pipeline. The scanned images conclude the information from the spatial (MRI) and the mass spectrometric (MALDI-MSI) dimension and are used for the spatial three-dimensional reconstruction of the object performed by image registration techniques. Different strategies for automatic serial image registration applied to MS datasets are outlined in detail. The third image modality is histology driven, i.e. a digital scan of the histological stained slices in high-resolution. After fusion of reconstructed scan images and MRI the slice-related coordinates of the mass spectra can be propagated into 3D-space. After image registration of scan images and histological stained images, the anatomical information from histology is fused with the mass spectra from MALDI-MSI. As a result of the described pipeline we have a set of 3 dimensional images representing the same anatomies, i.e. the reconstructed slice scans, the spectral images as well as corresponding clustering results, and the acquired MRI. Great emphasis is put on the fact that the co-registered MRI providing anatomical details improves the interpretation of 3D MALDI images. The ability to relate mass spectrometry derived molecular information with in vivo and in vitro imaging has potentially important implications. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013. Published by Elsevier B.V.

An interactive display system for large-scale 3D models

NASA Astrophysics Data System (ADS)

Liu, Zijian; Sun, Kun; Tao, Wenbing; Liu, Liman

2018-04-01

With the improvement of 3D reconstruction theory and the rapid development of computer hardware technology, the reconstructed 3D models are enlarging in scale and increasing in complexity. Models with tens of thousands of 3D points or triangular meshes are common in practical applications. Due to storage and computing power limitation, it is difficult to achieve real-time display and interaction with large scale 3D models for some common 3D display software, such as MeshLab. In this paper, we propose a display system for large-scale 3D scene models. We construct the LOD (Levels of Detail) model of the reconstructed 3D scene in advance, and then use an out-of-core view-dependent multi-resolution rendering scheme to realize the real-time display of the large-scale 3D model. With the proposed method, our display system is able to render in real time while roaming in the reconstructed scene and 3D camera poses can also be displayed. Furthermore, the memory consumption can be significantly decreased via internal and external memory exchange mechanism, so that it is possible to display a large scale reconstructed scene with over millions of 3D points or triangular meshes in a regular PC with only 4GB RAM.

An object-oriented simulator for 3D digital breast tomosynthesis imaging system.

PubMed

Seyyedi, Saeed; Cengiz, Kubra; Kamasak, Mustafa; Yildirim, Isa

2013-01-01

Digital breast tomosynthesis (DBT) is an innovative imaging modality that provides 3D reconstructed images of breast to detect the breast cancer. Projections obtained with an X-ray source moving in a limited angle interval are used to reconstruct 3D image of breast. Several reconstruction algorithms are available for DBT imaging. Filtered back projection algorithm has traditionally been used to reconstruct images from projections. Iterative reconstruction algorithms such as algebraic reconstruction technique (ART) were later developed. Recently, compressed sensing based methods have been proposed in tomosynthesis imaging problem. We have developed an object-oriented simulator for 3D digital breast tomosynthesis (DBT) imaging system using C++ programming language. The simulator is capable of implementing different iterative and compressed sensing based reconstruction methods on 3D digital tomosynthesis data sets and phantom models. A user friendly graphical user interface (GUI) helps users to select and run the desired methods on the designed phantom models or real data sets. The simulator has been tested on a phantom study that simulates breast tomosynthesis imaging problem. Results obtained with various methods including algebraic reconstruction technique (ART) and total variation regularized reconstruction techniques (ART+TV) are presented. Reconstruction results of the methods are compared both visually and quantitatively by evaluating performances of the methods using mean structural similarity (MSSIM) values.

An Object-Oriented Simulator for 3D Digital Breast Tomosynthesis Imaging System

PubMed Central

Cengiz, Kubra

2013-01-01

Digital breast tomosynthesis (DBT) is an innovative imaging modality that provides 3D reconstructed images of breast to detect the breast cancer. Projections obtained with an X-ray source moving in a limited angle interval are used to reconstruct 3D image of breast. Several reconstruction algorithms are available for DBT imaging. Filtered back projection algorithm has traditionally been used to reconstruct images from projections. Iterative reconstruction algorithms such as algebraic reconstruction technique (ART) were later developed. Recently, compressed sensing based methods have been proposed in tomosynthesis imaging problem. We have developed an object-oriented simulator for 3D digital breast tomosynthesis (DBT) imaging system using C++ programming language. The simulator is capable of implementing different iterative and compressed sensing based reconstruction methods on 3D digital tomosynthesis data sets and phantom models. A user friendly graphical user interface (GUI) helps users to select and run the desired methods on the designed phantom models or real data sets. The simulator has been tested on a phantom study that simulates breast tomosynthesis imaging problem. Results obtained with various methods including algebraic reconstruction technique (ART) and total variation regularized reconstruction techniques (ART+TV) are presented. Reconstruction results of the methods are compared both visually and quantitatively by evaluating performances of the methods using mean structural similarity (MSSIM) values. PMID:24371468

Concept and development of a computerized positioning of prosthetic teeth for complete dentures.

PubMed

Busch, M; Kordass, B

2006-04-01

To date, CAD/CAM technology has made no noteworthy inroads into removable dentures. We want to present a new area of application for this in our study. Models of the maxilla and edentulous mandible were 3D scanned. The software detects and automatically reconstructs the reference structures that are anatomically important for the set-up of artificial teeth, such as the alveolar ridge centerlines and the interalveolar relations between the alveolar ridges. In a further step, the occlusal plane is semiautomatically defined and the front dental arch is designed. After these design features have been determined, artificial teeth are selected from a database and set up automatically. The dental technician can assess the esthetics and function of the suggested dental set-up on the computer screen and make slight corrections if necessary. Summarizing: The interplay of hardware and software components within on integrated solution including conversion of the "virtual" into a real positioning of prosthetic teeth is presented.

Multisensory System for the Detection and Localization of Peripheral Subcutaneous Veins

PubMed Central

Fernández, Roemi; Armada, Manuel

2017-01-01

This paper proposes a multisensory system for the detection and localization of peripheral subcutaneous veins, as a first step for achieving automatic robotic insertion of catheters in the near future. The multisensory system is based on the combination of a SWIR (Short-Wave Infrared) camera, a TOF (Time-Of-Flight) camera and a NIR (Near Infrared) lighting source. The associated algorithm consists of two main parts: one devoted to the features extraction from the SWIR image, and another envisaged for the registration of the range data provided by the TOF camera, with the SWIR image and the results of the peripheral veins detection. In this way, the detected subcutaneous veins are mapped onto the 3D reconstructed surface, providing a full representation of the region of interest for the automatic catheter insertion. Several experimental tests were carried out in order to evaluate the capabilities of the presented approach. Preliminary results demonstrate the feasibility of the proposed design and highlight the potential benefits of the solution. PMID:28422075

GIS Data Based Automatic High-Fidelity 3D Road Network Modeling

NASA Technical Reports Server (NTRS)

Wang, Jie; Shen, Yuzhong

2011-01-01

3D road models are widely used in many computer applications such as racing games and driving simulations_ However, almost all high-fidelity 3D road models were generated manually by professional artists at the expense of intensive labor. There are very few existing methods for automatically generating 3D high-fidelity road networks, especially those existing in the real world. This paper presents a novel approach thai can automatically produce 3D high-fidelity road network models from real 2D road GIS data that mainly contain road. centerline in formation. The proposed method first builds parametric representations of the road centerlines through segmentation and fitting . A basic set of civil engineering rules (e.g., cross slope, superelevation, grade) for road design are then selected in order to generate realistic road surfaces in compliance with these rules. While the proposed method applies to any types of roads, this paper mainly addresses automatic generation of complex traffic interchanges and intersections which are the most sophisticated elements in the road networks

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

PubMed Central

Ukwatta, Eranga; Arevalo, Hermenegild; Rajchl, Martin; White, James; Pashakhanloo, Farhad; Prakosa, Adityo; Herzka, Daniel A.; McVeigh, Elliot; Lardo, Albert C.; Trayanova, Natalia A.; Vadakkumpadan, Fijoy

2015-01-01

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations. PMID:26233186

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ukwatta, Eranga, E-mail: eukwatt1@jhu.edu; Arevalo, Hermenegild; Pashakhanloo, Farhad

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitlymore » represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.« less

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML).

PubMed

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-07-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging.

Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML)*

PubMed Central

Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

2005-01-01

This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging. PMID:15973760

Automatic three-dimensional rib centerline extraction from CT scans for enhanced visualization and anatomical context

NASA Astrophysics Data System (ADS)

Ramakrishnan, Sowmya; Alvino, Christopher; Grady, Leo; Kiraly, Atilla

2011-03-01

We present a complete automatic system to extract 3D centerlines of ribs from thoracic CT scans. Our rib centerline system determines the positional information for the rib cage consisting of extracted rib centerlines, spinal canal centerline, pairing and labeling of ribs. We show an application of this output to produce an enhanced visualization of the rib cage by the method of Kiraly et al., in which the ribs are digitally unfolded along their centerlines. The centerline extraction consists of three stages: (a) pre-trace processing for rib localization, (b) rib centerline tracing, and (c) post-trace processing to merge the rib traces. Then we classify ribs from non-ribs and determine anatomical rib labeling. Our novel centerline tracing technique uses the Random Walker algorithm to segment the structural boundary of the rib in successive 2D cross sections orthogonal to the longitudinal direction of the ribs. Then the rib centerline is progressively traced along the rib using a 3D Kalman filter. The rib centerline extraction framework was evaluated on 149 CT datasets with varying slice spacing, dose, and under a variety of reconstruction kernels. The results of the evaluation are presented. The extraction takes approximately 20 seconds on a modern radiology workstation and performs robustly even in the presence of partial volume effects or rib pathologies such as bone metastases or fractures, making the system suitable for assisting clinicians in expediting routine rib reading for oncology and trauma applications.

Cervical vertebrae maturation index estimates on cone beam CT: 3D reconstructions vs sagittal sections.

PubMed

Bonfim, Marco A E; Costa, André L F; Fuziy, Acácio; Ximenez, Michel E L; Cotrim-Ferreira, Flávio A; Ferreira-Santos, Rívea I

2016-01-01

The aim of this study was to evaluate the performance of CBCT three-dimensional (3D) reconstructions and sagittal sections for estimates of cervical vertebrae maturation index (CVMI). The sample consisted of 72 CBCT examinations from patients aged 8-16 years (45 females and 27 males) selected from the archives of two private clinics. Two calibrated observers (kappa scores: ≥0.901) interpreted the CBCT settings twice. Intra- and interobserver agreement for both imaging exhibition modes was analyzed by kappa statistics, which was also used to analyze the agreement between 3D reconstructions and sagittal sections. Correlations between cervical vertebrae maturation estimates and chronological age, as well as between the assessments by 3D reconstructions and sagittal sections, were analyzed using gamma Goodman-Kruskal coefficients (α = 0.05). The kappa scores evidenced almost perfect agreement between the first and second assessments of the cervical vertebrae by 3D reconstructions (0.933-0.983) and sagittal sections (0.983-1.000). Similarly, the agreement between 3D reconstructions and sagittal sections was almost perfect (kappa index: 0.983). In most divergent cases, the difference between 3D reconstructions and sagittal sections was one stage of CVMI. Strongly positive correlations (>0.8, p < 0.001) were found not only between chronological age and CVMI but also between the estimates by 3D reconstructions and sagittal sections (p < 0.001). Although CBCT imaging must not be used exclusively for this purpose, it may be suitable for skeletal maturity assessments.

Cervical vertebrae maturation index estimates on cone beam CT: 3D reconstructions vs sagittal sections

PubMed Central

Bonfim, Marco A E; Costa, André L F; Ximenez, Michel E L; Cotrim-Ferreira, Flávio A; Ferreira-Santos, Rívea I

2016-01-01

Objectives: The aim of this study was to evaluate the performance of CBCT three-dimensional (3D) reconstructions and sagittal sections for estimates of cervical vertebrae maturation index (CVMI). Methods: The sample consisted of 72 CBCT examinations from patients aged 8–16 years (45 females and 27 males) selected from the archives of two private clinics. Two calibrated observers (kappa scores: ≥0.901) interpreted the CBCT settings twice. Intra- and interobserver agreement for both imaging exhibition modes was analyzed by kappa statistics, which was also used to analyze the agreement between 3D reconstructions and sagittal sections. Correlations between cervical vertebrae maturation estimates and chronological age, as well as between the assessments by 3D reconstructions and sagittal sections, were analyzed using gamma Goodman–Kruskal coefficients (α = 0.05). Results: The kappa scores evidenced almost perfect agreement between the first and second assessments of the cervical vertebrae by 3D reconstructions (0.933–0.983) and sagittal sections (0.983–1.000). Similarly, the agreement between 3D reconstructions and sagittal sections was almost perfect (kappa index: 0.983). In most divergent cases, the difference between 3D reconstructions and sagittal sections was one stage of CVMI. Strongly positive correlations (>0.8, p < 0.001) were found not only between chronological age and CVMI but also between the estimates by 3D reconstructions and sagittal sections (p < 0.001). Conclusions: Although CBCT imaging must not be used exclusively for this purpose, it may be suitable for skeletal maturity assessments. PMID:26509559

3D equilibrium reconstruction with islands

NASA Astrophysics Data System (ADS)

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.; Shafer, M. W.

2018-04-01

This paper presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wall limited L-mode case with an n = 1 error field applied. Flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase. ).

Low-Cost 3D Printing Orbital Implant Templates in Secondary Orbital Reconstructions.

PubMed

Callahan, Alison B; Campbell, Ashley A; Petris, Carisa; Kazim, Michael

Despite its increasing use in craniofacial reconstructions, three-dimensional (3D) printing of customized orbital implants has not been widely adopted. Limitations include the cost of 3D printers able to print in a biocompatible material suitable for implantation in the orbit and the breadth of available implant materials. The authors report the technique of low-cost 3D printing of orbital implant templates used in complex, often secondary, orbital reconstructions. A retrospective case series of 5 orbital reconstructions utilizing a technique of 3D printed orbital implant templates is presented. Each patient's Digital Imaging and Communications in Medicine data were uploaded and processed to create 3D renderings upon which a customized implant was designed and sent electronically to printers open for student use at our affiliated institutions. The mock implants were sterilized and used intraoperatively as a stencil and mold. The final implant material was chosen by the surgeons based on the requirements of the case. Five orbital reconstructions were performed with this technique: 3 tumor reconstructions and 2 orbital fractures. Four of the 5 cases were secondary reconstructions. Molded Medpor Titan (Stryker, Kalamazoo, MI) implants were used in 4 cases and titanium mesh in 1 case. The stenciled and molded implants were adjusted no more than 2 times before anchored in place (mean 1). No case underwent further revision. The technique and cases presented demonstrate 1) the feasibility and accessibility of low-cost, independent use of 3D printing technology to fashion patient-specific implants in orbital reconstructions, 2) the ability to apply this technology to the surgeon's preference of any routinely implantable material, and 3) the utility of this technique in complex, secondary reconstructions.

Three-dimensional monochromatic x-ray CT

NASA Astrophysics Data System (ADS)

Saito, Tsuneo; Kudo, Hiroyuki; Takeda, Tohoru; Itai, Yuji; Tokumori, Kenji; Toyofuku, Fukai; Hyodo, Kazuyuki; Ando, Masami; Nishimura, Ktsuyuki; Uyama, Chikao

1995-08-01

In this paper, we describe a 3D computed tomography (3D CT) using monochromatic x-rays generated by synchrotron radiation, which performs a direct reconstruction of 3D volume image of an object from its cone-beam projections. For the develpment of 3D CT, scanning orbit of x-ray source to obtain complete 3D information about an object and corresponding 3D image reconstruction algorithm are considered. Computer simulation studies demonstrate the validities of proposed scanning method and reconstruction algorithm. A prototype experimental system of 3D CT was constructed. Basic phantom examinations and specific material CT image by energy subtraction obtained in this experimental system are shown.

Sensor data fusion for textured reconstruction and virtual representation of alpine scenes

NASA Astrophysics Data System (ADS)

Häufel, Gisela; Bulatov, Dimitri; Solbrig, Peter

2017-10-01

The concept of remote sensing is to provide information about a wide-range area without making physical contact with this area. If, additionally to satellite imagery, images and videos taken by drones provide a more up-to-date data at a higher resolution, or accurate vector data is downloadable from the Internet, one speaks of sensor data fusion. The concept of sensor data fusion is relevant for many applications, such as virtual tourism, automatic navigation, hazard assessment, etc. In this work, we describe sensor data fusion aiming to create a semantic 3D model of an extremely interesting yet challenging dataset: An alpine region in Southern Germany. A particular challenge of this work is that rock faces including overhangs are present in the input airborne laser point cloud. The proposed procedure for identification and reconstruction of overhangs from point clouds comprises four steps: Point cloud preparation, filtering out vegetation, mesh generation and texturing. Further object types are extracted in several interesting subsections of the dataset: Building models with textures from UAV (Unmanned Aerial Vehicle) videos, hills reconstructed as generic surfaces and textured by the orthophoto, individual trees detected by the watershed algorithm, as well as the vector data for roads retrieved from openly available shapefiles and GPS-device tracks. We pursue geo-specific reconstruction by assigning texture and width to roads of several pre-determined types and modeling isolated trees and rocks using commercial software. For visualization and simulation of the area, we have chosen the simulation system Virtual Battlespace 3 (VBS3). It becomes clear that the proposed concept of sensor data fusion allows a coarse reconstruction of a large scene and, at the same time, an accurate and up-to-date representation of its relevant subsections, in which simulation can take place.

3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology

PubMed Central

Egger, Robert; Narayanan, Rajeevan T.; Helmstaedter, Moritz; de Kock, Christiaan P. J.; Oberlaender, Marcel

2012-01-01

The three-dimensional (3D) structure of neural circuits is commonly studied by reconstructing individual or small groups of neurons in separate preparations. Investigation of structural organization principles or quantification of dendritic and axonal innervation thus requires integration of many reconstructed morphologies into a common reference frame. Here we present a standardized 3D model of the rat vibrissal cortex and introduce an automated registration tool that allows for precise placement of single neuron reconstructions. We (1) developed an automated image processing pipeline to reconstruct 3D anatomical landmarks, i.e., the barrels in Layer 4, the pia and white matter surfaces and the blood vessel pattern from high-resolution images, (2) quantified these landmarks in 12 different rats, (3) generated an average 3D model of the vibrissal cortex and (4) used rigid transformations and stepwise linear scaling to register 94 neuron morphologies, reconstructed from in vivo stainings, to the standardized cortex model. We find that anatomical landmarks vary substantially across the vibrissal cortex within an individual rat. In contrast, the 3D layout of the entire vibrissal cortex remains remarkably preserved across animals. This allows for precise registration of individual neuron reconstructions with approximately 30 µm accuracy. Our approach could be used to reconstruct and standardize other anatomically defined brain areas and may ultimately lead to a precise digital reference atlas of the rat brain. PMID:23284282

Large-scale subject-specific cerebral arterial tree modeling using automated parametric mesh generation for blood flow simulation.

PubMed

Ghaffari, Mahsa; Tangen, Kevin; Alaraj, Ali; Du, Xinjian; Charbel, Fady T; Linninger, Andreas A

2017-12-01

In this paper, we present a novel technique for automatic parametric mesh generation of subject-specific cerebral arterial trees. This technique generates high-quality and anatomically accurate computational meshes for fast blood flow simulations extending the scope of 3D vascular modeling to a large portion of cerebral arterial trees. For this purpose, a parametric meshing procedure was developed to automatically decompose the vascular skeleton, extract geometric features and generate hexahedral meshes using a body-fitted coordinate system that optimally follows the vascular network topology. To validate the anatomical accuracy of the reconstructed vasculature, we performed statistical analysis to quantify the alignment between parametric meshes and raw vascular images using receiver operating characteristic curve. Geometric accuracy evaluation showed an agreement with area under the curves value of 0.87 between the constructed mesh and raw MRA data sets. Parametric meshing yielded on-average, 36.6% and 21.7% orthogonal and equiangular skew quality improvement over the unstructured tetrahedral meshes. The parametric meshing and processing pipeline constitutes an automated technique to reconstruct and simulate blood flow throughout a large portion of the cerebral arterial tree down to the level of pial vessels. This study is the first step towards fast large-scale subject-specific hemodynamic analysis for clinical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Corneal Vibrations during Intraocular Pressure Measurement with an Air-Puff Method

PubMed Central

Wilczyński, Sławomir

2018-01-01

Introduction The paper presents a commentary on the method of analysis of corneal vibrations occurring during eye pressure measurements with air-puff tonometers, for example, Corvis. The presented definition and measurement method allow for the analysis of image sequences of eye responses—cornea deformation. In particular, the outer corneal contour and sclera fragments are analysed, and 3D reconstruction is performed. Methods On this basis, well-known parameters such as eyeball reaction or corneal response are determined. The next steps of analysis allow for automatic and reproducible separation of four different corneal vibrations. These vibrations are associated with (1) the location of the maximum of cornea deformation; (2) the cutoff area measured in relation to the cornea in a steady state; (3) the maximum of peaks occurring between applanations; and (4) the other characteristic points of the corneal contour. Results The results obtained enable (1) automatic determination of the amplitude of vibrations; (2) determination of the frequency of vibrations; and (3) determination of the correlation between the selected types of vibrations. Conclusions These are diagnostic features that can be directly applied clinically for new and archived data. PMID:29610655

Simultaneous reconstruction of the activity image and registration of the CT image in TOF-PET

NASA Astrophysics Data System (ADS)

Rezaei, Ahmadreza; Michel, Christian; Casey, Michael E.; Nuyts, Johan

2016-02-01

Previously, maximum-likelihood methods have been proposed to jointly estimate the activity image and the attenuation image or the attenuation sinogram from time-of-flight (TOF) positron emission tomography (PET) data. In this contribution, we propose a method that addresses the possible alignment problem of the TOF-PET emission data and the computed tomography (CT) attenuation data, by combining reconstruction and registration. The method, called MLRR, iteratively reconstructs the activity image while registering the available CT-based attenuation image, so that the pair of activity and attenuation images maximise the likelihood of the TOF emission sinogram. The algorithm is slow to converge, but some acceleration could be achieved by using Nesterov’s momentum method and by applying a multi-resolution scheme for the non-rigid displacement estimation. The latter also helps to avoid local optima, although convergence to the global optimum cannot be guaranteed. The results are evaluated on 2D and 3D simulations as well as a respiratory gated clinical scan. Our experiments indicate that the proposed method is able to correct for possible misalignment of the CT-based attenuation image, and is therefore a very promising approach to suppressing attenuation artefacts in clinical PET/CT. When applied to respiratory gated data of a patient scan, it produced deformations that are compatible with breathing motion and which reduced the well known attenuation artefact near the dome of the liver. Since the method makes use of the energy-converted CT attenuation image, the scale problem of joint reconstruction is automatically solved.

Lensfree diffractive tomography for the imaging of 3D cell cultures

NASA Astrophysics Data System (ADS)

Berdeu, Anthony; Momey, Fabien; Dinten, Jean-Marc; Gidrol, Xavier; Picollet-D'hahan, Nathalie; Allier, Cédric

2017-02-01

New microscopes are needed to help reaching the full potential of 3D organoid culture studies by gathering large quantitative and systematic data over extended periods of time while preserving the integrity of the living sample. In order to reconstruct large volumes while preserving the ability to catch every single cell, we propose new imaging platforms based on lens-free microscopy, a technic which is addressing these needs in the context of 2D cell culture, providing label-free and non-phototoxic acquisition of large datasets. We built lens-free diffractive tomography setups performing multi-angle acquisitions of 3D organoid cultures embedded in Matrigel and developed dedicated 3D holographic reconstruction algorithms based on the Fourier diffraction theorem. Nonetheless, holographic setups do not record the phase of the incident wave front and the biological samples in Petri dish strongly limit the angular coverage. These limitations introduce numerous artefacts in the sample reconstruction. We developed several methods to overcome them, such as multi-wavelength imaging or iterative phase retrieval. The most promising technic currently developed is based on a regularised inverse problem approach directly applied on the 3D volume to reconstruct. 3D reconstructions were performed on several complex samples such as 3D networks or spheroids embedded in capsules with large reconstructed volumes up to 25 mm3 while still being able to identify single cells. To our knowledge, this is the first time that such an inverse problem approach is implemented in the context of lens-free diffractive tomography enabling to reconstruct large fully 3D volumes of unstained biological samples.

A new approach to the form and position error measurement of the auto frame surface based on laser

NASA Astrophysics Data System (ADS)

Wang, Hua; Li, Wei

2013-03-01

Auto frame is a very large workpiece, with length up to 12 meters and width up to 2 meters, and it's very easy to know that it's inconvenient and not automatic to measure such a large workpiece by independent manual operation. In this paper we propose a new approach to reconstruct the 3D model of the large workpiece, especially the auto truck frame, based on multiple pulsed lasers, for the purpose of measuring the form and position errors. In a concerned area, it just needs one high-speed camera and two lasers. It is a fast, high-precision and economical approach.

Investigation of undersampling and reconstruction algorithm dependence on respiratory correlated 4D-MRI for online MR-guided radiation therapy

NASA Astrophysics Data System (ADS)

Mickevicius, Nikolai J.; Paulson, Eric S.

2017-04-01

The purpose of this work is to investigate the effects of undersampling and reconstruction algorithm on the total processing time and image quality of respiratory phase-resolved 4D MRI data. Specifically, the goal is to obtain quality 4D-MRI data with a combined acquisition and reconstruction time of five minutes or less, which we reasoned would be satisfactory for pre-treatment 4D-MRI in online MRI-gRT. A 3D stack-of-stars, self-navigated, 4D-MRI acquisition was used to scan three healthy volunteers at three image resolutions and two scan durations. The NUFFT, CG-SENSE, SPIRiT, and XD-GRASP reconstruction algorithms were used to reconstruct each dataset on a high performance reconstruction computer. The overall image quality, reconstruction time, artifact prevalence, and motion estimates were compared. The CG-SENSE and XD-GRASP reconstructions provided superior image quality over the other algorithms. The combination of a 3D SoS sequence and parallelized reconstruction algorithms using computing hardware more advanced than those typically seen on product MRI scanners, can result in acquisition and reconstruction of high quality respiratory correlated 4D-MRI images in less than five minutes.

Three-dimensional dictionary-learning reconstruction of (23)Na MRI data.

PubMed

Behl, Nicolas G R; Gnahm, Christine; Bachert, Peter; Ladd, Mark E; Nagel, Armin M

2016-04-01

To reduce noise and artifacts in (23)Na MRI with a Compressed Sensing reconstruction and a learned dictionary as sparsifying transform. A three-dimensional dictionary-learning compressed sensing reconstruction algorithm (3D-DLCS) for the reconstruction of undersampled 3D radial (23)Na data is presented. The dictionary used as the sparsifying transform is learned with a K-singular-value-decomposition (K-SVD) algorithm. The reconstruction parameters are optimized on simulated data, and the quality of the reconstructions is assessed with peak signal-to-noise ratio (PSNR) and structural similarity (SSIM). The performance of the algorithm is evaluated in phantom and in vivo (23)Na MRI data of seven volunteers and compared with nonuniform fast Fourier transform (NUFFT) and other Compressed Sensing reconstructions. The reconstructions of simulated data have maximal PSNR and SSIM for an undersampling factor (USF) of 10 with numbers of averages equal to the USF. For 10-fold undersampling, the PSNR is increased by 5.1 dB compared with the NUFFT reconstruction, and the SSIM by 24%. These results are confirmed by phantom and in vivo (23)Na measurements in the volunteers that show markedly reduced noise and undersampling artifacts in the case of 3D-DLCS reconstructions. The 3D-DLCS algorithm enables precise reconstruction of undersampled (23)Na MRI data with markedly reduced noise and artifact levels compared with NUFFT reconstruction. Small structures are well preserved. © 2015 Wiley Periodicals, Inc.

A medical application integrating remote 3D visualization tools to access picture archiving and communication system on mobile devices.

PubMed

He, Longjun; Ming, Xing; Liu, Qian

2014-04-01

With computing capability and display size growing, the mobile device has been used as a tool to help clinicians view patient information and medical images anywhere and anytime. However, for direct interactive 3D visualization, which plays an important role in radiological diagnosis, the mobile device cannot provide a satisfactory quality of experience for radiologists. This paper developed a medical system that can get medical images from the picture archiving and communication system on the mobile device over the wireless network. In the proposed application, the mobile device got patient information and medical images through a proxy server connecting to the PACS server. Meanwhile, the proxy server integrated a range of 3D visualization techniques, including maximum intensity projection, multi-planar reconstruction and direct volume rendering, to providing shape, brightness, depth and location information generated from the original sectional images for radiologists. Furthermore, an algorithm that changes remote render parameters automatically to adapt to the network status was employed to improve the quality of experience. Finally, performance issues regarding the remote 3D visualization of the medical images over the wireless network of the proposed application were also discussed. The results demonstrated that this proposed medical application could provide a smooth interactive experience in the WLAN and 3G networks.

Tools to Perform Local Dense 3D Reconstruction of Shallow Water Seabed ‡

PubMed Central

Avanthey, Loïca; Beaudoin, Laurent; Gademer, Antoine; Roux, Michel

2016-01-01

Tasks such as distinguishing or identifying individual objects of interest require the production of dense local clouds at the scale of these individual objects of interest. Due to the physical and dynamic properties of an underwater environment, the usual dense matching algorithms must be rethought in order to be adaptive. These properties also imply that the scene must be observed at close range. Classic robotized acquisition systems are oversized for local studies in shallow water while the systematic acquisition of data is not guaranteed with divers. We address these two major issues through a multidisciplinary approach. To efficiently acquire on-demand stereoscopic pairs using simple logistics in small areas of shallow water, we devised an agile light-weight dedicated system which is easy to reproduce. To densely match two views in a reliable way, we devised a reconstruction algorithm that automatically accounts for the dynamics, variability and light absorption of the underwater environment. Field experiments in the Mediterranean Sea were used to assess the results. PMID:27196913

3D equilibrium reconstruction with islands

DOE PAGES

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.; ...

2018-02-15

This study presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wallmore » limited L-mode case with an n = 1 error field applied. Finally, flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase.« less

3D equilibrium reconstruction with islands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cianciosa, M.; Hirshman, S. P.; Seal, S. K.

This study presents the development of a 3D equilibrium reconstruction tool and the results of the first-ever reconstruction of an island equilibrium. The SIESTA non-nested equilibrium solver has been coupled to the V3FIT 3D equilibrium reconstruction code. Computed from a coupled VMEC and SIESTA model, synthetic signals are matched to measured signals by finding an optimal set of equilibrium parameters. By using the normalized pressure in place of normalized flux, non-equilibrium quantities needed by diagnostic signals can be efficiently mapped to the equilibrium. The effectiveness of this tool is demonstrated by reconstructing an island equilibrium of a DIII-D inner wallmore » limited L-mode case with an n = 1 error field applied. Finally, flat spots in Thomson and ECE temperature diagnostics show the reconstructed islands have the correct size and phase.« less

Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.

PubMed

Oi, Takao; Enomoto, Sakiko; Nakao, Tomoyo; Arai, Shigeo; Yamane, Koji; Taniguchi, Mitsutaka

2017-07-01

Ultrathin sections of rice leaf blades observed two-dimensionally using a transmission electron microscope (TEM) show that the chlorenchyma is composed of lobed mesophyll cells, with intricate cell boundaries, and lined with chloroplasts. The lobed cell shape and chloroplast positioning are believed to enhance the area available for the gas exchange surface for photosynthesis in rice leaves. However, a cell image revealing the three-dimensional (3-D) ultrastructure of rice mesophyll cells has not been visualized. In this study, a whole rice mesophyll cell was observed using a focused ion beam scanning electron microscope (FIB-SEM), which provides many serial sections automatically, rapidly and correctly, thereby enabling 3-D cell structure reconstruction. Rice leaf blades were fixed chemically using the method for conventional TEM observation, embedded in resin and subsequently set in the FIB-SEM chamber. Specimen blocks were sectioned transversely using the FIB, and block-face images were captured using the SEM. The sectioning and imaging were repeated overnight for 200-500 slices (each 50 nm thick). The resultant large-volume image stacks ( x = 25 μm, y = 25 μm, z = 10-25 μm) contained one or two whole mesophyll cells. The 3-D models of whole mesophyll cells were reconstructed using image processing software. The reconstructed cell models were discoid shaped with several lobes around the cell periphery. The cell shape increased the surface area, and the ratio of surface area to volume was twice that of a cylinder having the same volume. The chloroplasts occupied half the cell volume and spread as sheets along the cell lobes, covering most of the inner cell surface, with adjacent chloroplasts in close contact with each other. Cellular and sub-cellular ultrastructures of a whole mesophyll cell in a rice leaf blade are demonstrated three-dimensionally using a FIB-SEM. The 3-D models and numerical information support the hypothesis that rice mesophyll cells enhance their CO 2 absorption with increased cell surface and sheet-shaped chloroplasts. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A Dynamic Multi-Projection-Contour Approximating Framework for the 3D Reconstruction of Buildings by Super-Generalized Optical Stereo-Pairs.

PubMed

Yan, Yiming; Su, Nan; Zhao, Chunhui; Wang, Liguo

2017-09-19

In this paper, a novel framework of the 3D reconstruction of buildings is proposed, focusing on remote sensing super-generalized stereo-pairs (SGSPs). As we all know, 3D reconstruction cannot be well performed using nonstandard stereo pairs, since reliable stereo matching could not be achieved when the image-pairs are collected at a great difference of views, and we always failed to obtain dense 3D points for regions of buildings, and cannot do further 3D shape reconstruction. We defined SGSPs as two or more optical images collected in less constrained views but covering the same buildings. It is even more difficult to reconstruct the 3D shape of a building by SGSPs using traditional frameworks. As a result, a dynamic multi-projection-contour approximating (DMPCA) framework was introduced for SGSP-based 3D reconstruction. The key idea is that we do an optimization to find a group of parameters of a simulated 3D model and use a binary feature-image that minimizes the total differences between projection-contours of the building in the SGSPs and that in the simulated 3D model. Then, the simulated 3D model, defined by the group of parameters, could approximate the actual 3D shape of the building. Certain parameterized 3D basic-unit-models of typical buildings were designed, and a simulated projection system was established to obtain a simulated projection-contour in different views. Moreover, the artificial bee colony algorithm was employed to solve the optimization. With SGSPs collected by the satellite and our unmanned aerial vehicle, the DMPCA framework was verified by a group of experiments, which demonstrated the reliability and advantages of this work.

Design and experimental validation of novel 3D optical scanner with zoom lens unit

NASA Astrophysics Data System (ADS)

Huang, Jyun-Cheng; Liu, Chien-Sheng; Chiang, Pei-Ju; Hsu, Wei-Yan; Liu, Jian-Liang; Huang, Bai-Hao; Lin, Shao-Ru

2017-10-01

Optical scanners play a key role in many three-dimensional (3D) printing and CAD/CAM applications. However, existing optical scanners are generally designed to provide either a wide scanning area or a high 3D reconstruction accuracy from a lens with a fixed focal length. In the former case, the scanning area is increased at the expense of the reconstruction accuracy, while in the latter case, the reconstruction performance is improved at the expense of a more limited scanning range. In other words, existing optical scanners compromise between the scanning area and the reconstruction accuracy. Accordingly, the present study proposes a new scanning system including a zoom-lens unit, which combines both a wide scanning area and a high 3D reconstruction accuracy. In the proposed approach, the object is scanned initially under a suitable low-magnification setting for the object size (setting 1), resulting in a wide scanning area but a poor reconstruction resolution in complicated regions of the object. The complicated regions of the object are then rescanned under a high-magnification setting (setting 2) in order to improve the accuracy of the original reconstruction results. Finally, the models reconstructed after each scanning pass are combined to obtain the final reconstructed 3D shape of the object. The feasibility of the proposed method is demonstrated experimentally using a laboratory-built prototype. It is shown that the scanner has a high reconstruction accuracy over a large scanning area. In other words, the proposed optical scanner has significant potential for 3D engineering applications.

3D Printing: current use in facial plastic and reconstructive surgery.

PubMed

Hsieh, Tsung-Yen; Dedhia, Raj; Cervenka, Brian; Tollefson, Travis T

2017-08-01

To review the use of three-dimensional (3D) printing in facial plastic and reconstructive surgery, with a focus on current uses in surgical training, surgical planning, clinical outcomes, and biomedical research. To evaluate the limitations and future implications of 3D printing in facial plastic and reconstructive surgery. Studies reviewed demonstrated 3D printing applications in surgical planning including accurate anatomic biomodels, surgical cutting guides in reconstruction, and patient-specific implants fabrication. 3D printing technology also offers access to well tolerated, reproducible, and high-fidelity/patient-specific models for surgical training. Emerging research in 3D biomaterial printing have led to the development of biocompatible scaffolds with potential for tissue regeneration in reconstruction cases involving significant tissue absence or loss. Major limitations of utilizing 3D printing technology include time and cost, which may be offset by decreased operating times and collaboration between departments to diffuse in-house printing costs SUMMARY: The current state of the literature shows promising results, but has not yet been validated by large studies or randomized controlled trials. Ultimately, further research and advancements in 3D printing technology should be supported as there is potential to improve resident training, patient care, and surgical outcomes.

Reconstruction of Consistent 3d CAD Models from Point Cloud Data Using a Priori CAD Models

NASA Astrophysics Data System (ADS)

Bey, A.; Chaine, R.; Marc, R.; Thibault, G.; Akkouche, S.

2011-09-01

We address the reconstruction of 3D CAD models from point cloud data acquired in industrial environments, using a pre-existing 3D model as an initial estimate of the scene to be processed. Indeed, this prior knowledge can be used to drive the reconstruction so as to generate an accurate 3D model matching the point cloud. We more particularly focus our work on the cylindrical parts of the 3D models. We propose to state the problem in a probabilistic framework: we have to search for the 3D model which maximizes some probability taking several constraints into account, such as the relevancy with respect to the point cloud and the a priori 3D model, and the consistency of the reconstructed model. The resulting optimization problem can then be handled using a stochastic exploration of the solution space, based on the random insertion of elements in the configuration under construction, coupled with a greedy management of the conflicts which efficiently improves the configuration at each step. We show that this approach provides reliable reconstructed 3D models by presenting some results on industrial data sets.

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

DOE PAGES

Pryor, Alan; Yang, Yongsoo; Rana, Arjun; ...

2017-09-05

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pryor, Alan; Yang, Yongsoo; Rana, Arjun

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), for high-resolution 3D reconstruction from a limited number of 2D projections. GENFIRE first assembles a 3D Fourier grid with oversampling and then iteratesmore » between real and reciprocal space to search for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques through numerical simulations and by experimentally reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. As a result, equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.« less

Comparing performance of many-core CPUs and GPUs for static and motion compensated reconstruction of C-arm CT data.

PubMed

Hofmann, Hannes G; Keck, Benjamin; Rohkohl, Christopher; Hornegger, Joachim

2011-01-01

Interventional reconstruction of 3-D volumetric data from C-arm CT projections is a computationally demanding task. Hardware optimization is not an option but mandatory for interventional image processing and, in particular, for image reconstruction due to the high demands on performance. Several groups have published fast analytical 3-D reconstruction on highly parallel hardware such as GPUs to mitigate this issue. The authors show that the performance of modern CPU-based systems is in the same order as current GPUs for static 3-D reconstruction and outperforms them for a recent motion compensated (3-D+time) image reconstruction algorithm. This work investigates two algorithms: Static 3-D reconstruction as well as a recent motion compensated algorithm. The evaluation was performed using a standardized reconstruction benchmark, RABBITCT, to get comparable results and two additional clinical data sets. The authors demonstrate for a parametric B-spline motion estimation scheme that the derivative computation, which requires many write operations to memory, performs poorly on the GPU and can highly benefit from modern CPU architectures with large caches. Moreover, on a 32-core Intel Xeon server system, the authors achieve linear scaling with the number of cores used and reconstruction times almost in the same range as current GPUs. Algorithmic innovations in the field of motion compensated image reconstruction may lead to a shift back to CPUs in the future. For analytical 3-D reconstruction, the authors show that the gap between GPUs and CPUs became smaller. It can be performed in less than 20 s (on-the-fly) using a 32-core server.

A semi-automatic 2D-to-3D video conversion with adaptive key-frame selection

NASA Astrophysics Data System (ADS)

Ju, Kuanyu; Xiong, Hongkai

2014-11-01

To compensate the deficit of 3D content, 2D to 3D video conversion (2D-to-3D) has recently attracted more attention from both industrial and academic communities. The semi-automatic 2D-to-3D conversion which estimates corresponding depth of non-key-frames through key-frames is more desirable owing to its advantage of balancing labor cost and 3D effects. The location of key-frames plays a role on quality of depth propagation. This paper proposes a semi-automatic 2D-to-3D scheme with adaptive key-frame selection to keep temporal continuity more reliable and reduce the depth propagation errors caused by occlusion. The potential key-frames would be localized in terms of clustered color variation and motion intensity. The distance of key-frame interval is also taken into account to keep the accumulated propagation errors under control and guarantee minimal user interaction. Once their depth maps are aligned with user interaction, the non-key-frames depth maps would be automatically propagated by shifted bilateral filtering. Considering that depth of objects may change due to the objects motion or camera zoom in/out effect, a bi-directional depth propagation scheme is adopted where a non-key frame is interpolated from two adjacent key frames. The experimental results show that the proposed scheme has better performance than existing 2D-to-3D scheme with fixed key-frame interval.

3-D reconstruction of neurons from multichannel confocal laser scanning image series.

PubMed

Wouterlood, Floris G

2014-04-10

A confocal laser scanning microscope (CLSM) collects information from a thin, focal plane and ignores out-of-focus information. Scanning of a specimen, with stepwise axial (Z-) movement of the stage in between each scan, produces Z-series of confocal images of a tissue volume, which then can be used to 3-D reconstruct structures of interest. The operator first configures separate channels (e.g., laser, filters, and detector settings) for each applied fluorochrome and then acquires Z-series of confocal images: one series per channel. Channel signal separation is extremely important. Measures to avoid bleaching are vital. Post-acquisition deconvolution of the image series is often performed to increase resolution before 3-D reconstruction takes place. In the 3-D reconstruction programs described in this unit, reconstructions can be inspected in real time from any viewing angle. By altering viewing angles and by switching channels off and on, the spatial relationships of 3-D-reconstructed structures with respect to structures visualized in other channels can be studied. Since each brand of CLSM, computer program, and 3-D reconstruction package has its own proprietary set of procedures, a general approach is provided in this protocol wherever possible. Copyright © 2014 John Wiley & Sons, Inc.

Surface models of the male urogenital organs built from the Visible Korean using popular software

PubMed Central

Shin, Dong Sun; Park, Jin Seo; Shin, Byeong-Seok

2011-01-01

Unlike volume models, surface models, which are empty three-dimensional images, have a small file size, so they can be displayed, rotated, and modified in real time. Thus, surface models of male urogenital organs can be effectively applied to an interactive computer simulation and contribute to the clinical practice of urologists. To create high-quality surface models, the urogenital organs and other neighboring structures were outlined in 464 sectioned images of the Visible Korean male using Adobe Photoshop; the outlines were interpolated on Discreet Combustion; then an almost automatic volume reconstruction followed by surface reconstruction was performed on 3D-DOCTOR. The surface models were refined and assembled in their proper positions on Maya, and a surface model was coated with actual surface texture acquired from the volume model of the structure on specially programmed software. In total, 95 surface models were prepared, particularly complete models of the urinary and genital tracts. These surface models will be distributed to encourage other investigators to develop various kinds of medical training simulations. Increasingly automated surface reconstruction technology using commercial software will enable other researchers to produce their own surface models more effectively. PMID:21829759

Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

PubMed Central

Jeong, Won-Ki; Beyer, Johanna; Hadwiger, Markus; Vazquez, Amelio; Pfister, Hanspeter; Whitaker, Ross T.

2011-01-01

Recent advances in scanning technology provide high resolution EM (Electron Microscopy) datasets that allow neuroscientists to reconstruct complex neural connections in a nervous system. However, due to the enormous size and complexity of the resulting data, segmentation and visualization of neural processes in EM data is usually a difficult and very time-consuming task. In this paper, we present NeuroTrace, a novel EM volume segmentation and visualization system that consists of two parts: a semi-automatic multiphase level set segmentation with 3D tracking for reconstruction of neural processes, and a specialized volume rendering approach for visualization of EM volumes. It employs view-dependent on-demand filtering and evaluation of a local histogram edge metric, as well as on-the-fly interpolation and ray-casting of implicit surfaces for segmented neural structures. Both methods are implemented on the GPU for interactive performance. NeuroTrace is designed to be scalable to large datasets and data-parallel hardware architectures. A comparison of NeuroTrace with a commonly used manual EM segmentation tool shows that our interactive workflow is faster and easier to use for the reconstruction of complex neural processes. PMID:19834227

Silhouette-based approach of 3D image reconstruction for automated image acquisition using robotic arm

NASA Astrophysics Data System (ADS)

Azhar, N.; Saad, W. H. M.; Manap, N. A.; Saad, N. M.; Syafeeza, A. R.

2017-06-01

This study presents the approach of 3D image reconstruction using an autonomous robotic arm for the image acquisition process. A low cost of the automated imaging platform is created using a pair of G15 servo motor connected in series to an Arduino UNO as a main microcontroller. Two sets of sequential images were obtained using different projection angle of the camera. The silhouette-based approach is used in this study for 3D reconstruction from the sequential images captured from several different angles of the object. Other than that, an analysis based on the effect of different number of sequential images on the accuracy of 3D model reconstruction was also carried out with a fixed projection angle of the camera. The effecting elements in the 3D reconstruction are discussed and the overall result of the analysis is concluded according to the prototype of imaging platform.

Optimization of Stereo Matching in 3D Reconstruction Based on Binocular Vision

NASA Astrophysics Data System (ADS)

Gai, Qiyang

2018-01-01

Stereo matching is one of the key steps of 3D reconstruction based on binocular vision. In order to improve the convergence speed and accuracy in 3D reconstruction based on binocular vision, this paper adopts the combination method of polar constraint and ant colony algorithm. By using the line constraint to reduce the search range, an ant colony algorithm is used to optimize the stereo matching feature search function in the proposed search range. Through the establishment of the stereo matching optimization process analysis model of ant colony algorithm, the global optimization solution of stereo matching in 3D reconstruction based on binocular vision system is realized. The simulation results show that by the combining the advantage of polar constraint and ant colony algorithm, the stereo matching range of 3D reconstruction based on binocular vision is simplified, and the convergence speed and accuracy of this stereo matching process are improved.

A fast 4D cone beam CT reconstruction method based on the OSC-TV algorithm.

PubMed

Mascolo-Fortin, Julia; Matenine, Dmitri; Archambault, Louis; Després, Philippe

2018-01-01

Four-dimensional cone beam computed tomography allows for temporally resolved imaging with useful applications in radiotherapy, but raises particular challenges in terms of image quality and computation time. The purpose of this work is to develop a fast and accurate 4D algorithm by adapting a GPU-accelerated ordered subsets convex algorithm (OSC), combined with the total variation minimization regularization technique (TV). Different initialization schemes were studied to adapt the OSC-TV algorithm to 4D reconstruction: each respiratory phase was initialized either with a 3D reconstruction or a blank image. Reconstruction algorithms were tested on a dynamic numerical phantom and on a clinical dataset. 4D iterations were implemented for a cluster of 8 GPUs. All developed methods allowed for an adequate visualization of the respiratory movement and compared favorably to the McKinnon-Bates and adaptive steepest descent projection onto convex sets algorithms, while the 4D reconstructions initialized from a prior 3D reconstruction led to better overall image quality. The most suitable adaptation of OSC-TV to 4D CBCT was found to be a combination of a prior FDK reconstruction and a 4D OSC-TV reconstruction with a reconstruction time of 4.5 minutes. This relatively short reconstruction time could facilitate a clinical use.

Incremental Multi-view 3D Reconstruction Starting from Two Images Taken by a Stereo Pair of Cameras

NASA Astrophysics Data System (ADS)

El hazzat, Soulaiman; Saaidi, Abderrahim; Karam, Antoine; Satori, Khalid

2015-03-01

In this paper, we present a new method for multi-view 3D reconstruction based on the use of a binocular stereo vision system constituted of two unattached cameras to initialize the reconstruction process. Afterwards , the second camera of stereo vision system (characterized by varying parameters) moves to capture more images at different times which are used to obtain an almost complete 3D reconstruction. The first two projection matrices are estimated by using a 3D pattern with known properties. After that, 3D scene points are recovered by triangulation of the matched interest points between these two images. The proposed approach is incremental. At each insertion of a new image, the camera projection matrix is estimated using the 3D information already calculated and new 3D points are recovered by triangulation from the result of the matching of interest points between the inserted image and the previous image. For the refinement of the new projection matrix and the new 3D points, a local bundle adjustment is performed. At first, all projection matrices are estimated, the matches between consecutive images are detected and Euclidean sparse 3D reconstruction is obtained. So, to increase the number of matches and have a more dense reconstruction, the Match propagation algorithm, more suitable for interesting movement of the camera, was applied on the pairs of consecutive images. The experimental results show the power and robustness of the proposed approach.

Implications of Artefacts Reduction in the Planning CT Originating from Implanted Fiducial Markers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kassim, Iskandar, E-mail: i.binkassim@erasmusmc.n; Joosten, Hans; Barnhoorn, Jaco C.

The efficacy of metal artefact reduction (MAR) software to suppress artefacts in reconstructed computed tomography (CT) images originating from small metal objects, like tumor markers and surgical clips, was evaluated. In addition, possible implications of using digital reconstructed radiographs (DRRs), based on the MAR CT images, for setup verification were analyzed. A phantom and 15 patients with different tumor sites and implanted markers were imaged with a multislice CT scanner. The raw image data was reconstructed both with the clinically used filtered-backprojection (FBP) and with the MAR software. Using the MAR software, improvements in image quality were often observed inmore » CT slices with markers or clips. Especially when several markers were located near to each other, fewer streak artefacts were observed than with the FBP algorithm. In addition, the shape and size of markers could be identified more accurately, reducing the contoured marker volumes by a factor of 2. For the phantom study, the CT numbers measured near to the markers corresponded more closely to the expected values. However, the MAR images were slightly more smoothed compared with the images reconstructed with FBP. For 8 prostate cancer patients in this study, the interobserver variation in 3D marker definition was similar (<0.4 mm) when using DRRs based on either FBP or MAR CT scans. Automatic marker matches also showed a similar success rate. However, differences in automatic match results up to 1 mm, caused by differences in the marker definition, were observed, which turned out to be (borderline) statistically significant (p = 0.06) for 2 patients. In conclusion, the MAR software might improve image quality by suppressing metal artefacts, probably allowing for a more reliable delineation of structures. When implanted markers or clips are used for setup verification, the accuracy may slightly be improved as well, which is relevant when using very tight clinical target volume (CTV) to planning target volume (PTV) margins for planning.« less

D Reconstruction of Ancient Egyptian Rock-Cut Tombs: the Case of M.I.D.A.N.05.

NASA Astrophysics Data System (ADS)

Nabil, M.; Betrò, M.; Metwally, M. N.

2013-07-01

In this paper we present an on-going work to reconstruct a 3D model of M.I.D.A.N.05., an ancient Egyptian tomb located in Luxor. The reconstruction aims at producing a high quality 3D model of the tomb to help in archaeological investigation and other scientific uses. We present details about the different stages of the used reconstruction pipeline, the results so far, and the evaluation of the results in view of the project objectives.

Three-dimensional simulation, surgical navigation and thoracoscopic lung resection

PubMed Central

Kanzaki, Masato; Kikkawa, Takuma; Sakamoto, Kei; Maeda, Hideyuki; Wachi, Naoko; Komine, Hiroshi; Oyama, Kunihiro; Murasugi, Masahide; Onuki, Takamasa

2013-01-01

This report describes a 3-dimensional (3-D) video-assisted thoracoscopic lung resection guided by a 3-D video navigation system having a patient-specific 3-D reconstructed pulmonary model obtained by preoperative simulation. A 78-year-old man was found to have a small solitary pulmonary nodule in the left upper lobe in chest computed tomography. By a virtual 3-D pulmonary model the tumor was found to be involved in two subsegments (S1 + 2c and S3a). Complete video-assisted thoracoscopic surgery bi-subsegmentectomy was selected in simulation and was performed with lymph node dissection. A 3-D digital vision system was used for 3-D thoracoscopic performance. Wearing 3-D glasses, the patient's actual reconstructed 3-D model on 3-D liquid-crystal displays was observed, and the 3-D intraoperative field and the picture of 3-D reconstructed pulmonary model were compared. PMID:24964426

A principal component analysis of the relationship between the external body shape and internal skeleton for the upper body.

PubMed

Nerot, A; Skalli, W; Wang, X

2016-10-03

Recent progress in 3D scanning technologies allows easy access to 3D human body envelope. To create personalized human models with an articulated linkage for realistic re-posturing and motion analyses, an accurate estimation of internal skeleton points, including joint centers, from the external envelope is required. For this research project, 3D reconstructions of both internal skeleton and external envelope from low dose biplanar X-rays of 40 male adults were obtained. Using principal component analysis technique (PCA), a low-dimensional dataset was used to predict internal points of the upper body from the trunk envelope. A least squares method was used to find PC scores that fit the PCA-based model to the envelope of a new subject. To validate the proposed approach, estimated internal points were evaluated using a leave-one-out (LOO) procedure, i.e. successively considering each individual from our dataset as an extra-subject. In addition, different methods were proposed to reduce the variability in data and improve the performance of the PCA-based prediction. The best method was considered as the one providing the smallest errors between estimated and reference internal points with an average error of 8.3mm anterior-posteriorly, 6.7mm laterally and 6.5mm vertically. As the proposed approach relies on few or no bony landmarks, it could be easily applicable and generalizable to surface scans from any devices. Combined with automatic body scanning techniques, this study could potentially constitute a new step towards automatic generation of external/internal subject-specific manikins. Copyright © 2016 Elsevier Ltd. All rights reserved.

Validation of lower limb segmental volumetry with hand-held, self-positioning three-dimensional laser scanner against water displacement.

PubMed

Mestre, Sandrine; Veye, Florent; Perez-Martin, Antonia; Behar, Thomas; Triboulet, Jean; Berron, Nicolas; Demattei, Christophe; Quéré, Isabelle

2014-01-01

Measurement of limb volume is helpful for the evaluation and follow-up of edema, especially in patients with chronic venous insufficiency (CVI) or lymphedema. Water displacement (WD) is the reference method for limb volumetry but is not really suitable for clinical routine. Indirect volumetry based on circumference measurements as well as the more expansive but automatic optoelectronic techniques do not allow detailed measurement at the extremity of the limb. We used a self-positioning laser scanner with dynamic referencing for acquisition and real-time three-dimensional (3D) reconstruction of the lower limb volume in 30 patients with CVI, 30 patients with lymphedema, and 30 healthy controls. Two independent observers performed either one or two laser scans, whose results were tested for intra- and interobserver reproducibility and compared with WD volumetry by Lin's concordance correlation coefficient and Bland and Altman graphic analysis. Automatic volume calculation from 3D laser scanning data failed in one patient with major lymphedema. Lin's concordance correlation coefficient was 0.99 and 0.98, respectively, for intraobserver no. 1 and no. 2, 0.98 for interobserver reproducibility, and 0.98 and 0.96, respectively, for observer no. 1 and observer no. 2 vs WD comparison. The 3D laser scanning yielded 1.99% precision. Accuracy was 3.12% for observer no. 1 and 2.71% for observer no. 2, laser scanning values being 90 mL higher than WD, which could be attributed to the different posture during measurement. Three-dimensional laser scanning is accurate and reproducible, and appears suitable for the evaluation of limb volume in patients with CVI or lymphedema. Copyright © 2014 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Evaluating the morphological completeness of a training image.

PubMed

Gao, Mingliang; Teng, Qizhi; He, Xiaohai; Feng, Junxi; Han, Xue

2017-05-01

Understanding the three-dimensional (3D) stochastic structure of a porous medium is helpful for studying its physical properties. A 3D stochastic structure can be reconstructed from a two-dimensional (2D) training image (TI) using mathematical modeling. In order to predict what specific morphology belonging to a TI can be reconstructed at the 3D orthogonal slices by the method of 3D reconstruction, this paper begins by introducing the concept of orthogonal chords. After analyzing the relationship among TI morphology, orthogonal chords, and the 3D morphology of orthogonal slices, a theory for evaluating the morphological completeness of a TI is proposed for the cases of three orthogonal slices and of two orthogonal slices. The proposed theory is evaluated using four TIs of porous media that represent typical but distinct morphological types. The significance of this theoretical evaluation lies in two aspects: It allows special morphologies, for which the attributes of a TI can be reconstructed at a special orthogonal slice of a 3D structure, to be located and quantified, and it can guide the selection of an appropriate reconstruction method for a special TI.

WE-G-18A-04: 3D Dictionary Learning Based Statistical Iterative Reconstruction for Low-Dose Cone Beam CT Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, T; UT Southwestern Medical Center, Dallas, TX; Yan, H

2014-06-15

Purpose: To develop a 3D dictionary learning based statistical reconstruction algorithm on graphic processing units (GPU), to improve the quality of low-dose cone beam CT (CBCT) imaging with high efficiency. Methods: A 3D dictionary containing 256 small volumes (atoms) of 3x3x3 voxels was trained from a high quality volume image. During reconstruction, we utilized a Cholesky decomposition based orthogonal matching pursuit algorithm to find a sparse representation on this dictionary basis of each patch in the reconstructed image, in order to regularize the image quality. To accelerate the time-consuming sparse coding in the 3D case, we implemented our algorithm inmore » a parallel fashion by taking advantage of the tremendous computational power of GPU. Evaluations are performed based on a head-neck patient case. FDK reconstruction with full dataset of 364 projections is used as the reference. We compared the proposed 3D dictionary learning based method with a tight frame (TF) based one using a subset data of 121 projections. The image qualities under different resolutions in z-direction, with or without statistical weighting are also studied. Results: Compared to the TF-based CBCT reconstruction, our experiments indicated that 3D dictionary learning based CBCT reconstruction is able to recover finer structures, to remove more streaking artifacts, and is less susceptible to blocky artifacts. It is also observed that statistical reconstruction approach is sensitive to inconsistency between the forward and backward projection operations in parallel computing. Using high a spatial resolution along z direction helps improving the algorithm robustness. Conclusion: 3D dictionary learning based CBCT reconstruction algorithm is able to sense the structural information while suppressing noise, and hence to achieve high quality reconstruction. The GPU realization of the whole algorithm offers a significant efficiency enhancement, making this algorithm more feasible for potential clinical application. A high zresolution is preferred to stabilize statistical iterative reconstruction. This work was supported in part by NIH(1R01CA154747-01), NSFC((No. 61172163), Research Fund for the Doctoral Program of Higher Education of China (No. 20110201110011), China Scholarship Council.« less

Ionospheric tomography using ADS-B signals

NASA Astrophysics Data System (ADS)

Cushley, A. C.; Noël, J.-M.

2014-07-01

Numerical modeling has demonstrated that Automatic Dependent Surveillance Broadcast (ADS-B) signals can be used to reconstruct two-dimensional (2-D) electron density maps of the ionosphere using techniques for computerized tomography. Ray tracing techniques were used to determine the characteristics of individual waves, including the wave path and the state of polarization at the satellite receiver. The modeled Faraday rotation was computed and converted to total electron content (TEC) along the raypaths. The resulting TEC was used as input for computerized ionospheric tomography (CIT) using algebraic reconstruction technique. This study concentrated on reconstructing mesoscale structures 25-100 km in horizontal extent. The primary scientific interest of this study was to show that ADS-B signals can be used as a new source of data for CIT to image the ionosphere and to obtain a better understanding of magneto-ionic wave propagation.

Three-Dimensional Analysis and Surgical Planning in Craniomaxillofacial Surgery.

PubMed

Steinbacher, Derek M

2015-12-01

Three-dimensional (3D) analysis and planning are powerful tools in craniofacial and reconstructive surgery. The elements include 1) analysis, 2) planning, 3) virtual surgery, 4) 3D printouts of guides or implants, and 5) verification of actual to planned results. The purpose of this article is to review different applications of 3D planning in craniomaxillofacial surgery. Case examples involving 3D analysis and planning were reviewed. Common threads pertaining to all types of reconstruction are highlighted and contrasted with unique aspects specific to new applications in craniomaxillofacial surgery. Six examples of 3D planning are described: 1) cranial reconstruction, 2) craniosynostosis, 3) midface advancement, 4) mandibular distraction, 5) mandibular reconstruction, and 6) orthognathic surgery. Planning in craniomaxillofacial surgery is useful and has applicability across different procedures and reconstructions. Three-dimensional planning and virtual surgery enhance efficiency, accuracy, creativity, and reproducibility in craniomaxillofacial surgery. Copyright © 2015 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Iterative reconstruction of volumetric particle distribution

NASA Astrophysics Data System (ADS)

Wieneke, Bernhard

2013-02-01

For tracking the motion of illuminated particles in space and time several volumetric flow measurement techniques are available like 3D-particle tracking velocimetry (3D-PTV) recording images from typically three to four viewing directions. For higher seeding densities and the same experimental setup, tomographic PIV (Tomo-PIV) reconstructs voxel intensities using an iterative tomographic reconstruction algorithm (e.g. multiplicative algebraic reconstruction technique, MART) followed by cross-correlation of sub-volumes computing instantaneous 3D flow fields on a regular grid. A novel hybrid algorithm is proposed here that similar to MART iteratively reconstructs 3D-particle locations by comparing the recorded images with the projections calculated from the particle distribution in the volume. But like 3D-PTV, particles are represented by 3D-positions instead of voxel-based intensity blobs as in MART. Detailed knowledge of the optical transfer function and the particle image shape is mandatory, which may differ for different positions in the volume and for each camera. Using synthetic data it is shown that this method is capable of reconstructing densely seeded flows up to about 0.05 ppp with similar accuracy as Tomo-PIV. Finally the method is validated with experimental data.

3D morphology reconstruction using linear array CCD binocular stereo vision imaging system

NASA Astrophysics Data System (ADS)

Pan, Yu; Wang, Jinjiang

2018-01-01

Binocular vision imaging system, which has a small field of view, cannot reconstruct the 3-D shape of the dynamic object. We found a linear array CCD binocular vision imaging system, which uses different calibration and reconstruct methods. On the basis of the binocular vision imaging system, the linear array CCD binocular vision imaging systems which has a wider field of view can reconstruct the 3-D morphology of objects in continuous motion, and the results are accurate. This research mainly introduces the composition and principle of linear array CCD binocular vision imaging system, including the calibration, capture, matching and reconstruction of the imaging system. The system consists of two linear array cameras which were placed in special arrangements and a horizontal moving platform that can pick up objects. The internal and external parameters of the camera are obtained by calibrating in advance. And then using the camera to capture images of moving objects, the results are then matched and 3-D reconstructed. The linear array CCD binocular vision imaging systems can accurately measure the 3-D appearance of moving objects, this essay is of great significance to measure the 3-D morphology of moving objects.

Three-dimensional computed tomography reconstruction for operative planning in robotic segmentectomy: a pilot study

PubMed Central

Le Moal, Julien; Peillon, Christophe; Dacher, Jean-Nicolas

2018-01-01

Background The objective of our pilot study was to assess if three-dimensional (3D) reconstruction performed by Visible Patient™ could be helpful for the operative planning, efficiency and safety of robot-assisted segmentectomy. Methods Between 2014 and 2015, 3D reconstructions were provided by the Visible Patient™ online service and used for the operative planning of robotic segmentectomy. To obtain 3D reconstruction, the surgeon uploaded the anonymized computed tomography (CT) image of the patient to the secured Visible Patient™ server and then downloaded the model after completion. Results Nine segmentectomies were performed between 2014 and 2015 using a pre-operative 3D model. All 3D reconstructions met our expectations: anatomical accuracy (bronchi, arteries, veins, tumor, and the thoracic wall with intercostal spaces), accurate delimitation of each segment in the lobe of interest, margin resection, free space rotation, portability (smartphone, tablet) and time saving technique. Conclusions We have shown that operative planning by 3D CT using Visible Patient™ reconstruction is useful in our practice of robot-assisted segmentectomy. The main disadvantage is the high cost. Its impact on reducing complications and improving surgical efficiency is the object of an ongoing study. PMID:29600049

Three-dimensional computed tomography reconstruction for operative planning in robotic segmentectomy: a pilot study.

PubMed

Le Moal, Julien; Peillon, Christophe; Dacher, Jean-Nicolas; Baste, Jean-Marc

2018-01-01

The objective of our pilot study was to assess if three-dimensional (3D) reconstruction performed by Visible Patient™ could be helpful for the operative planning, efficiency and safety of robot-assisted segmentectomy. Between 2014 and 2015, 3D reconstructions were provided by the Visible Patient™ online service and used for the operative planning of robotic segmentectomy. To obtain 3D reconstruction, the surgeon uploaded the anonymized computed tomography (CT) image of the patient to the secured Visible Patient™ server and then downloaded the model after completion. Nine segmentectomies were performed between 2014 and 2015 using a pre-operative 3D model. All 3D reconstructions met our expectations: anatomical accuracy (bronchi, arteries, veins, tumor, and the thoracic wall with intercostal spaces), accurate delimitation of each segment in the lobe of interest, margin resection, free space rotation, portability (smartphone, tablet) and time saving technique. We have shown that operative planning by 3D CT using Visible Patient™ reconstruction is useful in our practice of robot-assisted segmentectomy. The main disadvantage is the high cost. Its impact on reducing complications and improving surgical efficiency is the object of an ongoing study.

A new methodology for automatic detection of reference points in 3D cephalometry: A pilot study.

PubMed

Ed-Dhahraouy, Mohammed; Riri, Hicham; Ezzahmouly, Manal; Bourzgui, Farid; El Moutaoukkil, Abdelmajid

2018-04-05

The aim of this study was to develop a new method for an automatic detection of reference points in 3D cephalometry to overcome the limits of 2D cephalometric analyses. A specific application was designed using the C++ language for automatic and manual identification of 21 (reference) points on the craniofacial structures. Our algorithm is based on the implementation of an anatomical and geometrical network adapted to the craniofacial structure. This network was constructed based on the anatomical knowledge of the 3D cephalometric (reference) points. The proposed algorithm was tested on five CBCT images. The proposed approach for the automatic 3D cephalometric identification was able to detect 21 points with a mean error of 2.32mm. In this pilot study, we propose an automated methodology for the identification of the 3D cephalometric (reference) points. A larger sample will be implemented in the future to assess the method validity and reliability. Copyright © 2018 CEO. Published by Elsevier Masson SAS. All rights reserved.

Reconstruction of quadratic curves in 3D using two or more perspective views: simulation studies

NASA Astrophysics Data System (ADS)

Kumar, Sanjeev; Sukavanam, N.; Balasubramanian, R.

2006-01-01

The shapes of many natural and man-made objects have planar and curvilinear surfaces. The images of such curves usually do not have sufficient distinctive features to apply conventional feature-based reconstruction algorithms. In this paper, we describe a method of reconstruction of a quadratic curve in 3-D space as an intersection of two cones containing the respective projected curve images. The correspondence between this pair of projections of the curve is assumed to be established in this work. Using least-square curve fitting, the parameters of a curve in 2-D space are found. From this we are reconstructing the 3-D quadratic curve. Relevant mathematical formulations and analytical solutions for obtaining the equation of reconstructed curve are given. The result of the described reconstruction methodology are studied by simulation studies. This reconstruction methodology is applicable to LBW decision in cricket, path of the missile, Robotic Vision, path lanning etc.

Accuracy Assessment of a Complex Building 3d Model Reconstructed from Images Acquired with a Low-Cost Uas

NASA Astrophysics Data System (ADS)

Oniga, E.; Chirilă, C.; Stătescu, F.

2017-02-01

Nowadays, Unmanned Aerial Systems (UASs) are a wide used technique for acquisition in order to create buildings 3D models, providing the acquisition of a high number of images at very high resolution or video sequences, in a very short time. Since low-cost UASs are preferred, the accuracy of a building 3D model created using this platforms must be evaluated. To achieve results, the dean's office building from the Faculty of "Hydrotechnical Engineering, Geodesy and Environmental Engineering" of Iasi, Romania, has been chosen, which is a complex shape building with the roof formed of two hyperbolic paraboloids. Seven points were placed on the ground around the building, three of them being used as GCPs, while the remaining four as Check points (CPs) for accuracy assessment. Additionally, the coordinates of 10 natural CPs representing the building characteristic points were measured with a Leica TCR 405 total station. The building 3D model was created as a point cloud which was automatically generated based on digital images acquired with the low-cost UASs, using the image matching algorithm and different software like 3DF Zephyr, Visual SfM, PhotoModeler Scanner and Drone2Map for ArcGIS. Except for the PhotoModeler Scanner software, the interior and exterior orientation parameters were determined simultaneously by solving a self-calibrating bundle adjustment. Based on the UAS point clouds, automatically generated by using the above mentioned software and GNSS data respectively, the parameters of the east side hyperbolic paraboloid were calculated using the least squares method and a statistical blunder detection. Then, in order to assess the accuracy of the building 3D model, several comparisons were made for the facades and the roof with reference data, considered with minimum errors: TLS mesh for the facades and GNSS mesh for the roof. Finally, the front facade of the building was created in 3D based on its characteristic points using the PhotoModeler Scanner software, resulting a CAD (Computer Aided Design) model. The results showed the high potential of using low-cost UASs for building 3D model creation and if the building 3D model is created based on its characteristic points the accuracy is significantly improved.

UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data

NASA Astrophysics Data System (ADS)

Zhang, Hanqing; Stangner, Tim; Wiklund, Krister; Rodriguez, Alvaro; Andersson, Magnus

2017-10-01

We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the 2D lateral positions of particles with an algorithm based on the isosceles triangle transform, and reconstructs their 3D axial positions by a fast implementation of the Rayleigh-Sommerfeld model using a radial intensity profile. To validate the accuracy and performance of our program, we first track the 2D position of polystyrene particles using bright field and digital holographic microscopy. Second, we determine the 3D particle position by analyzing synthetic and experimentally acquired holograms. Finally, to highlight the full program features, we profile the microfluidic flow in a 100 μm high flow chamber. This result agrees with computational fluid dynamic simulations. On a regular desktop computer UmUTracker can detect, analyze, and track multiple particles at 5 frames per second for a template size of 201 ×201 in a 1024 × 1024 image. To enhance usability and to make it easy to implement new functions we used object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement. Program Files doi : http://dx.doi.org/10.17632/fkprs4s6xp.1 Licensing provisions : Creative Commons by 4.0 (CC by 4.0) Programming language : MATLAB Nature of problem: 3D multi-particle tracking is a common technique in physics, chemistry and biology. However, in terms of accuracy, reliable particle tracking is a challenging task since results depend on sample illumination, particle overlap, motion blur and noise from recording sensors. Additionally, the computational performance is also an issue if, for example, a computationally expensive process is executed, such as axial particle position reconstruction from digital holographic microscopy data. Versatile robust tracking programs handling these concerns and providing a powerful post-processing option are significantly limited. Solution method: UmUTracker is a multi-functional tool to extract particle positions from long video sequences acquired with either light microscopy or digital holographic microscopy. The program provides an easy-to-use graphical user interface (GUI) for both tracking and post-processing that does not require any programming skills to analyze data from particle tracking experiments. UmUTracker first conduct automatic 2D particle detection even under noisy conditions using a novel circle detector based on the isosceles triangle sampling technique with a multi-scale strategy. To reduce the computational load for 3D tracking, it uses an efficient implementation of the Rayleigh-Sommerfeld light propagation model. To analyze and visualize the data, an efficient data analysis step, which can for example show 4D flow visualization using 3D trajectories, is included. Additionally, UmUTracker is easy to modify with user-customized modules due to the object-oriented programming style Additional comments: Program obtainable from https://sourceforge.net/projects/umutracker/

An ROI multi-resolution compression method for 3D-HEVC

NASA Astrophysics Data System (ADS)

Ti, Chunli; Guan, Yudong; Xu, Guodong; Teng, Yidan; Miao, Xinyuan

2017-09-01

3D High Efficiency Video Coding (3D-HEVC) provides a significant potential on increasing the compression ratio of multi-view RGB-D videos. However, the bit rate still rises dramatically with the improvement of the video resolution, which will bring challenges to the transmission network, especially the mobile network. This paper propose an ROI multi-resolution compression method for 3D-HEVC to better preserve the information in ROI on condition of limited bandwidth. This is realized primarily through ROI extraction and compression multi-resolution preprocessed video as alternative data according to the network conditions. At first, the semantic contours are detected by the modified structured forests to restrain the color textures inside objects. The ROI is then determined utilizing the contour neighborhood along with the face region and foreground area of the scene. Secondly, the RGB-D videos are divided into slices and compressed via 3D-HEVC under different resolutions for selection by the audiences and applications. Afterwards, the reconstructed low-resolution videos from 3D-HEVC encoder are directly up-sampled via Laplace transformation and used to replace the non-ROI areas of the high-resolution videos. Finally, the ROI multi-resolution compressed slices are obtained by compressing the ROI preprocessed videos with 3D-HEVC. The temporal and special details of non-ROI are reduced in the low-resolution videos, so the ROI will be better preserved by the encoder automatically. Experiments indicate that the proposed method can keep the key high-frequency information with subjective significance while the bit rate is reduced.

[3D bioprinting of cartilage: challenges concerning the reconstruction of a burned ear].

PubMed

Visscher, Dafydd O; Bos, Ernst J; van Zuijlen, Paul P M

2015-01-01

Reconstruction of a severely maimed ear is a major challenge. The ear is highly flexible yet tough, and has a very complex three-dimensional shape. Reconstruction of a patient's burned ear is even more complex due to surrounding tissue damage. Not only does this hamper reconstruction options, it also increases the likelihood of issues when using synthetic implant materials. In such cases, rib cartilage is the preferred option, but this tissue has practical limitations too. For these reasons, tissue engineering and 3D bioprinting may have the potential to create personalized cartilage implants for burns patients. However, 3D bioprinting is a tool to facilitate the reconstruction, and not by itself the Holy Grail. The clinical application of this technique is still at a very early stage. Nevertheless, we expect that 3D bioprinting can be utilised for facial reconstruction following burns come 2020.

Objective and subjective quality assessment of geometry compression of reconstructed 3D humans in a 3D virtual room

NASA Astrophysics Data System (ADS)

Mekuria, Rufael; Cesar, Pablo; Doumanis, Ioannis; Frisiello, Antonella

2015-09-01

Compression of 3D object based video is relevant for 3D Immersive applications. Nevertheless, the perceptual aspects of the degradation introduced by codecs for meshes and point clouds are not well understood. In this paper we evaluate the subjective and objective degradations introduced by such codecs in a state of art 3D immersive virtual room. In the 3D immersive virtual room, users are captured with multiple cameras, and their surfaces are reconstructed as photorealistic colored/textured 3D meshes or point clouds. To test the perceptual effect of compression and transmission, we render degraded versions with different frame rates in different contexts (near/far) in the scene. A quantitative subjective study with 16 users shows that negligible distortion of decoded surfaces compared to the original reconstructions can be achieved in the 3D virtual room. In addition, a qualitative task based analysis in a full prototype field trial shows increased presence, emotion, user and state recognition of the reconstructed 3D Human representation compared to animated computer avatars.

2D to 3D conversion implemented in different hardware

NASA Astrophysics Data System (ADS)

Ramos-Diaz, Eduardo; Gonzalez-Huitron, Victor; Ponomaryov, Volodymyr I.; Hernandez-Fragoso, Araceli

2015-02-01

Conversion of available 2D data for release in 3D content is a hot topic for providers and for success of the 3D applications, in general. It naturally completely relies on virtual view synthesis of a second view given by original 2D video. Disparity map (DM) estimation is a central task in 3D generation but still follows a very difficult problem for rendering novel images precisely. There exist different approaches in DM reconstruction, among them manually and semiautomatic methods that can produce high quality DMs but they demonstrate hard time consuming and are computationally expensive. In this paper, several hardware implementations of designed frameworks for an automatic 3D color video generation based on 2D real video sequence are proposed. The novel framework includes simultaneous processing of stereo pairs using the following blocks: CIE L*a*b* color space conversions, stereo matching via pyramidal scheme, color segmentation by k-means on an a*b* color plane, and adaptive post-filtering, DM estimation using stereo matching between left and right images (or neighboring frames in a video), adaptive post-filtering, and finally, the anaglyph 3D scene generation. Novel technique has been implemented on DSP TMS320DM648, Matlab's Simulink module over a PC with Windows 7, and using graphic card (NVIDIA Quadro K2000) demonstrating that the proposed approach can be applied in real-time processing mode. The time values needed, mean Similarity Structural Index Measure (SSIM) and Bad Matching Pixels (B) values for different hardware implementations (GPU, Single CPU, and DSP) are exposed in this paper.

[Application of Fourier transform profilometry in 3D-surface reconstruction].

PubMed

Shi, Bi'er; Lu, Kuan; Wang, Yingting; Li, Zhen'an; Bai, Jing

2011-08-01

With the improvement of system frame and reconstruction methods in fluorescent molecules tomography (FMT), the FMT technology has been widely used as an important experimental tool in biomedical research. It is necessary to get the 3D-surface profile of the experimental object as the boundary constraints of FMT reconstruction algorithms. We proposed a new 3D-surface reconstruction method based on Fourier transform profilometry (FTP) method under the blue-purple light condition. The slice images were reconstructed using proper image processing methods, frequency spectrum analysis and filtering. The results of experiment showed that the method properly reconstructed the 3D-surface of objects and has the mm-level accuracy. Compared to other methods, this one is simple and fast. Besides its well-reconstructed, the proposed method could help monitor the behavior of the object during the experiment to ensure the correspondence of the imaging process. Furthermore, the method chooses blue-purple light section as its light source to avoid the interference towards fluorescence imaging.

Analysis of acetabular orientation and femoral anteversion using images of three-dimensional reconstructed bone models.

PubMed

Park, Jaeyeong; Kim, Jun-Young; Kim, Hyun Deok; Kim, Young Cheol; Seo, Anna; Je, Minkyu; Mun, Jong Uk; Kim, Bia; Park, Il Hyung; Kim, Shin-Yoon

2017-05-01

Radiographic measurements using two-dimensional (2D) plain radiographs or planes from computed tomography (CT) scans have several drawbacks, while measurements using images of three-dimensional (3D) reconstructed bone models can provide more consistent anthropometric information. We compared the consistency of results using measurements based on images of 3D reconstructed bone models (3D measurements) with those using planes from CT scans (measurements using 2D slice images). Ninety-six of 561 patients who had undergone deep vein thrombosis-CT between January 2013 and November 2014 were randomly selected. We evaluated measurements using 2D slice images and 3D measurements. The images used for 3D reconstruction of bone models were obtained and measured using [Formula: see text] and [Formula: see text] (Materialize, Leuven, Belgium). The mean acetabular inclination, acetabular anteversion and femoral anteversion values on 2D slice images were 42.01[Formula: see text], 18.64[Formula: see text] and 14.44[Formula: see text], respectively, while those using images of 3D reconstructed bone models were 52.80[Formula: see text], 14.98[Formula: see text] and 17.26[Formula: see text]. Intra-rater reliabilities for acetabular inclination, acetabular anteversion, and femoral anteversion on 2D slice images were 0.55, 0.81, and 0.85, respectively, while those for 3D measurements were 0.98, 0.99, and 0.98. Inter-rater reliabilities for acetabular inclination, acetabular anteversion and femoral anteversion on 2D slice images were 0.48, 0.86, and 0.84, respectively, while those for 3D measurements were 0.97, 0.99, and 0.97. The differences between the two measurements are explained by the use of different tools. However, more consistent measurements were possible using the images of 3D reconstructed bone models. Therefore, 3D measurement can be a good alternative to measurement using 2D slice images.

Evaluation of a Fully 3-D Bpf Method for Small Animal PET Images on Mimd Architectures

NASA Astrophysics Data System (ADS)

Bevilacqua, A.

Positron Emission Tomography (PET) images can be reconstructed using Fourier transform methods. This paper describes the performance of a fully 3-D Backprojection-Then-Filter (BPF) algorithm on the Cray T3E machine and on a cluster of workstations. PET reconstruction of small animals is a class of problems characterized by poor counting statistics. The low-count nature of these studies necessitates 3-D reconstruction in order to improve the sensitivity of the PET system: by including axially oblique Lines Of Response (LORs), the sensitivity of the system can be significantly improved by the 3-D acquisition and reconstruction. The BPF method is widely used in clinical studies because of its speed and easy implementation. Moreover, the BPF method is suitable for on-time 3-D reconstruction as it does not need any sinogram or rearranged data. In order to investigate the possibility of on-line processing, we reconstruct a phantom using the data stored in the list-mode format by the data acquisition system. We show how the intrinsically parallel nature of the BPF method makes it suitable for on-line reconstruction on a MIMD system such as the Cray T3E. Lastly, we analyze the performance of this algorithm on a cluster of workstations.

Efficient hybrid monocular-stereo approach to on-board video-based traffic sign detection and tracking

NASA Astrophysics Data System (ADS)

Marinas, Javier; Salgado, Luis; Arróspide, Jon; Camplani, Massimo

2012-01-01

In this paper we propose an innovative method for the automatic detection and tracking of road traffic signs using an onboard stereo camera. It involves a combination of monocular and stereo analysis strategies to increase the reliability of the detections such that it can boost the performance of any traffic sign recognition scheme. Firstly, an adaptive color and appearance based detection is applied at single camera level to generate a set of traffic sign hypotheses. In turn, stereo information allows for sparse 3D reconstruction of potential traffic signs through a SURF-based matching strategy. Namely, the plane that best fits the cloud of 3D points traced back from feature matches is estimated using a RANSAC based approach to improve robustness to outliers. Temporal consistency of the 3D information is ensured through a Kalman-based tracking stage. This also allows for the generation of a predicted 3D traffic sign model, which is in turn used to enhance the previously mentioned color-based detector through a feedback loop, thus improving detection accuracy. The proposed solution has been tested with real sequences under several illumination conditions and in both urban areas and highways, achieving very high detection rates in challenging environments, including rapid motion and significant perspective distortion.

Equilibrium reconstruction with 3D eddy currents in the Lithium Tokamak eXperiment

DOE PAGES

Hansen, C.; Boyle, D. P.; Schmitt, J. C.; ...

2017-04-18

Axisymmetric free-boundary equilibrium reconstructions of tokamak plasmas in the Lithium Tokamak eXperiment (LTX) are performed using the PSI-Tri equilibrium code. Reconstructions in LTX are complicated by the presence of long-lived non-axisymmetric eddy currents generated by a vacuum vessel and first wall structures. To account for this effect, reconstructions are performed with additional toroidal current sources in these conducting regions. The eddy current sources are fixed in their poloidal distributions, but their magnitude is adjusted as part of the full reconstruction. Eddy distributions are computed by toroidally averaging currents, generated by coupling to vacuum field coils, from a simplified 3D filamentmore » model of important conducting structures. The full 3D eddy current fields are also used to enable the inclusion of local magnetic field measurements, which have strong 3D eddy current pick-up, as reconstruction constraints. Using this method, equilibrium reconstruction yields good agreement with all available diagnostic signals. Here, an accompanying field perturbation produced by 3D eddy currents on the plasma surface with a primarily n = 2, m = 1 character is also predicted for these equilibria.« less

Reconstruction of three-dimensional ultrasound images based on cyclic Savitzky-Golay filters

NASA Astrophysics Data System (ADS)

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

2011-01-01

We present a new algorithm for reconstructing a three-dimensional (3-D) ultrasound image from a series of two-dimensional B-scan ultrasound slices acquired in the mechanical linear scanning framework. Unlike most existing 3-D ultrasound reconstruction algorithms, which have been developed and evaluated in the freehand scanning framework, the new algorithm has been designed to capitalize the regularity pattern of the mechanical linear scanning, where all the B-scan slices are precisely parallel and evenly spaced. The new reconstruction algorithm, referred to as the cyclic Savitzky-Golay (CSG) reconstruction filter, is an improvement on the original Savitzky-Golay filter in two respects: First, it is extended to accept a 3-D array of data as the filter input instead of a one-dimensional data sequence. Second, it incorporates the cyclic indicator function in its least-squares objective function so that the CSG algorithm can simultaneously perform both smoothing and interpolating tasks. The performance of the CSG reconstruction filter compared to that of most existing reconstruction algorithms in generating a 3-D synthetic test image and a clinical 3-D carotid artery bifurcation in the mechanical linear scanning framework are also reported.

High Density Aerial Image Matching: State-Of and Future Prospects

NASA Astrophysics Data System (ADS)

Haala, N.; Cavegn, S.

2016-06-01

Ongoing innovations in matching algorithms are continuously improving the quality of geometric surface representations generated automatically from aerial images. This development motivated the launch of the joint ISPRS/EuroSDR project "Benchmark on High Density Aerial Image Matching", which aims on the evaluation of photogrammetric 3D data capture in view of the current developments in dense multi-view stereo-image matching. Originally, the test aimed on image based DSM computation from conventional aerial image flights for different landuse and image block configurations. The second phase then put an additional focus on high quality, high resolution 3D geometric data capture in complex urban areas. This includes both the extension of the test scenario to oblique aerial image flights as well as the generation of filtered point clouds as additional output of the respective multi-view reconstruction. The paper uses the preliminary outcomes of the benchmark to demonstrate the state-of-the-art in airborne image matching with a special focus of high quality geometric data capture in urban scenarios.

Feasibility of intra-acquisition motion correction for 4D DSA reconstruction for applications in the thorax and abdomen

NASA Astrophysics Data System (ADS)

Wagner, Martin; Laeseke, Paul; Harari, Colin; Schafer, Sebastian; Speidel, Michael; Mistretta, Charles

2018-03-01

The recently proposed 4D DSA technique enables reconstruction of time resolved 3D volumes from two C-arm CT acquisitions. This provides information on the blood flow in neurovascular applications and can be used for the diagnosis and treatment of vascular diseases. For applications in the thorax and abdomen, respiratory motion can prevent successful 4D DSA reconstruction and cause severe artifacts. The purpose of this work is to propose a novel technique for motion compensated 4D DSA reconstruction to enable applications in the thorax and abdomen. The approach uses deformable 2D registration to align the projection images of a non-contrast and a contrast enhanced scan. A subset of projection images is then selected, which are acquired in a similar respiratory state and an iterative simultaneous multiplicative algebraic reconstruction is applied to determine a 3D constraint volume. A 2D-3D registration step then aligns the remaining projection images with the 3D constraint volume. Finally, a constrained back-projection is performed to create a 3D volume for each projection image. A pig study has been performed, where 4D DSA acquisitions were performed with and without respiratory motion to evaluate the feasibility of the approach. The dice similarity coefficient between the reference 3D constraint volume and the motion compensated reconstruction was 51.12 % compared to 35.99 % without motion compensation. This technique could improve the workflow for procedures in interventional radiology, e.g. liver embolizations, where changes in blood flow have to be monitored carefully.

Use of reconstructed 3D VMEC equilibria to match effects of toroidally rotating discharges in DIII-D

DOE PAGES

Wingen, Andreas; Wilcox, Robert S.; Cianciosa, Mark R.; ...

2016-10-13

Here, a technique for tokamak equilibrium reconstructions is used for multiple DIII-D discharges, including L-mode and H-mode cases when weakly 3D fieldsmore » $$\\left(\\delta B/B\\sim {{10}^{-3}}\\right)$$ are applied. The technique couples diagnostics to the non-linear, ideal MHD equilibrium solver VMEC, using the V3FIT code, to find the most likely 3D equilibrium based on a suite of measurements. It is demonstrated that V3FIT can be used to find non-linear 3D equilibria that are consistent with experimental measurements of the plasma response to very weak 3D perturbations, as well as with 2D profile measurements. Observations at DIII-D show that plasma rotation larger than 20 krad s –1 changes the relative phase between the applied 3D fields and the measured plasma response. Discharges with low averaged rotation (10 krad s –1) and peaked rotation profiles (40 krad s –1) are reconstructed. Similarities and differences to forward modeled VMEC equilibria, which do not include rotational effects, are shown. Toroidal phase shifts of up to $${{30}^{\\circ}}$$ are found between the measured and forward modeled plasma responses at the highest values of rotation. The plasma response phases of reconstructed equilibra on the other hand match the measured ones. This is the first time V3FIT has been used to reconstruct weakly 3D tokamak equilibria.« less

Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images

PubMed Central

Salas, Desirée; Le Gall, Antoine; Fiche, Jean-Bernard; Valeri, Alessandro; Ke, Yonggang; Bron, Patrick; Bellot, Gaetan

2017-01-01

Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions. PMID:28811371

3D range-gated super-resolution imaging based on stereo matching for moving platforms and targets

NASA Astrophysics Data System (ADS)

Sun, Liang; Wang, Xinwei; Zhou, Yan

2017-11-01

3D range-gated superresolution imaging is a novel 3D reconstruction technique for target detection and recognition with good real-time performance. However, for moving targets or platforms such as airborne, shipborne, remote operated vehicle and autonomous vehicle, 3D reconstruction has a large error or failure. In order to overcome this drawback, we propose a method of stereo matching for 3D range-gated superresolution reconstruction algorithm. In experiment, the target is a doll of Mario with a height of 38cm at the location of 34m, and we obtain two successive frame images of the Mario. To confirm our method is effective, we transform the original images with translation, rotation, scale and perspective, respectively. The experimental result shows that our method has a good result of 3D reconstruction for moving targets or platforms.

Limited angle C-arm tomosynthesis reconstruction algorithms

NASA Astrophysics Data System (ADS)

Malalla, Nuhad A. Y.; Xu, Shiyu; Chen, Ying

2015-03-01

In this paper, C-arm tomosynthesis with digital detector was investigated as a novel three dimensional (3D) imaging technique. Digital tomosythses is an imaging technique to provide 3D information of the object by reconstructing slices passing through the object, based on a series of angular projection views with respect to the object. C-arm tomosynthesis provides two dimensional (2D) X-ray projection images with rotation (-/+20 angular range) of both X-ray source and detector. In this paper, four representative reconstruction algorithms including point by point back projection (BP), filtered back projection (FBP), simultaneous algebraic reconstruction technique (SART) and maximum likelihood expectation maximization (MLEM) were investigated. Dataset of 25 projection views of 3D spherical object that located at center of C-arm imaging space was simulated from 25 angular locations over a total view angle of 40 degrees. With reconstructed images, 3D mesh plot and 2D line profile of normalized pixel intensities on focus reconstruction plane crossing the center of the object were studied with each reconstruction algorithm. Results demonstrated the capability to generate 3D information from limited angle C-arm tomosynthesis. Since C-arm tomosynthesis is relatively compact, portable and can avoid moving patients, it has been investigated for different clinical applications ranging from tumor surgery to interventional radiology. It is very important to evaluate C-arm tomosynthesis for valuable applications.

Quantitative 3D high resolution transmission ultrasound tomography: creating clinically relevant images (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wiskin, James; Klock, John; Iuanow, Elaine; Borup, Dave T.; Terry, Robin; Malik, Bilal H.; Lenox, Mark

2017-03-01

There has been a great deal of research into ultrasound tomography for breast imaging over the past 35 years. Few successful attempts have been made to reconstruct high-resolution images using transmission ultrasound. To this end, advances have been made in 2D and 3D algorithms that utilize either time of arrival or full wave data to reconstruct images with high spatial and contrast resolution suitable for clinical interpretation. The highest resolution and quantitative accuracy result from inverse scattering applied to full wave data in 3D. However, this has been prohibitively computationally expensive, meaning that full inverse scattering ultrasound tomography has not been considered clinically viable. Here we show the results of applying a nonlinear inverse scattering algorithm to 3D data in a clinically useful time frame. This method yields Quantitative Transmission (QT) ultrasound images with high spatial and contrast resolution. We reconstruct sound speeds for various 2D and 3D phantoms and verify these values with independent measurements. The data are fully 3D as is the reconstruction algorithm, with no 2D approximations. We show that 2D reconstruction algorithms can introduce artifacts into the QT breast image which are avoided by using a full 3D algorithm and data. We show high resolution gross and microscopic anatomic correlations comparing cadaveric breast QT images with MRI to establish imaging capability and accuracy. Finally, we show reconstructions of data from volunteers, as well as an objective visual grading analysis to confirm clinical imaging capability and accuracy.

Optical cone beam tomography of Cherenkov-mediated signals for fast 3D dosimetry of x-ray photon beams in water.

PubMed

Glaser, Adam K; Andreozzi, Jacqueline M; Zhang, Rongxiao; Pogue, Brian W; Gladstone, David J

2015-07-01

To test the use of a three-dimensional (3D) optical cone beam computed tomography reconstruction algorithm, for estimation of the imparted 3D dose distribution from megavoltage photon beams in a water tank for quality assurance, by imaging the induced Cherenkov-excited fluorescence (CEF). An intensified charge-coupled device coupled to a standard nontelecentric camera lens was used to tomographically acquire two-dimensional (2D) projection images of CEF from a complex multileaf collimator (MLC) shaped 6 MV linear accelerator x-ray photon beam operating at a dose rate of 600 MU/min. The resulting projections were used to reconstruct the 3D CEF light distribution, a potential surrogate of imparted dose, using a Feldkamp-Davis-Kress cone beam back reconstruction algorithm. Finally, the reconstructed light distributions were compared to the expected dose values from one-dimensional diode scans, 2D film measurements, and the 3D distribution generated from the clinical Varian ECLIPSE treatment planning system using a gamma index analysis. A Monte Carlo derived correction was applied to the Cherenkov reconstructions to account for beam hardening artifacts. 3D light volumes were successfully reconstructed over a 400 × 400 × 350 mm(3) volume at a resolution of 1 mm. The Cherenkov reconstructions showed agreement with all comparative methods and were also able to recover both inter- and intra-MLC leaf leakage. Based upon a 3%/3 mm criterion, the experimental Cherenkov light measurements showed an 83%-99% pass fraction depending on the chosen threshold dose. The results from this study demonstrate the use of optical cone beam computed tomography using CEF for the profiling of the imparted dose distribution from large area megavoltage photon beams in water.

Filtering techniques for efficient inversion of two-dimensional Nuclear Magnetic Resonance data

NASA Astrophysics Data System (ADS)

Bortolotti, V.; Brizi, L.; Fantazzini, P.; Landi, G.; Zama, F.

2017-10-01

The inversion of two-dimensional Nuclear Magnetic Resonance (NMR) data requires the solution of a first kind Fredholm integral equation with a two-dimensional tensor product kernel and lower bound constraints. For the solution of this ill-posed inverse problem, the recently presented 2DUPEN algorithm [V. Bortolotti et al., Inverse Problems, 33(1), 2016] uses multiparameter Tikhonov regularization with automatic choice of the regularization parameters. In this work, I2DUPEN, an improved version of 2DUPEN that implements Mean Windowing and Singular Value Decomposition filters, is deeply tested. The reconstruction problem with filtered data is formulated as a compressed weighted least squares problem with multi-parameter Tikhonov regularization. Results on synthetic and real 2D NMR data are presented with the main purpose to deeper analyze the separate and combined effects of these filtering techniques on the reconstructed 2D distribution.

A hybrid 3D region growing and 4D curvature analysis-based automatic abdominal blood vessel segmentation through contrast enhanced CT

NASA Astrophysics Data System (ADS)

Maklad, Ahmed S.; Matsuhiro, Mikio; Suzuki, Hidenobu; Kawata, Yoshiki; Niki, Noboru; Shimada, Mitsuo; Iinuma, Gen

2017-03-01

In abdominal disease diagnosis and various abdominal surgeries planning, segmentation of abdominal blood vessel (ABVs) is a very imperative task. Automatic segmentation enables fast and accurate processing of ABVs. We proposed a fully automatic approach for segmenting ABVs through contrast enhanced CT images by a hybrid of 3D region growing and 4D curvature analysis. The proposed method comprises three stages. First, candidates of bone, kidneys, ABVs and heart are segmented by an auto-adapted threshold. Second, bone is auto-segmented and classified into spine, ribs and pelvis. Third, ABVs are automatically segmented in two sub-steps: (1) kidneys and abdominal part of the heart are segmented, (2) ABVs are segmented by a hybrid approach that integrates a 3D region growing and 4D curvature analysis. Results are compared with two conventional methods. Results show that the proposed method is very promising in segmenting and classifying bone, segmenting whole ABVs and may have potential utility in clinical use.

Evaluation of automatic image quality assessment in chest CT - A human cadaver study.

PubMed

Franck, Caro; De Crop, An; De Roo, Bieke; Smeets, Peter; Vergauwen, Merel; Dewaele, Tom; Van Borsel, Mathias; Achten, Eric; Van Hoof, Tom; Bacher, Klaus

2017-04-01

The evaluation of clinical image quality (IQ) is important to optimize CT protocols and to keep patient doses as low as reasonably achievable. Considering the significant amount of effort needed for human observer studies, automatic IQ tools are a promising alternative. The purpose of this study was to evaluate automatic IQ assessment in chest CT using Thiel embalmed cadavers. Chest CT's of Thiel embalmed cadavers were acquired at different exposures. Clinical IQ was determined by performing a visual grading analysis. Physical-technical IQ (noise, contrast-to-noise and contrast-detail) was assessed in a Catphan phantom. Soft and sharp reconstructions were made with filtered back projection and two strengths of iterative reconstruction. In addition to the classical IQ metrics, an automatic algorithm was used to calculate image quality scores (IQs). To be able to compare datasets reconstructed with different kernels, the IQs values were normalized. Good correlations were found between IQs and the measured physical-technical image quality: noise (ρ=-1.00), contrast-to-noise (ρ=1.00) and contrast-detail (ρ=0.96). The correlation coefficients between IQs and the observed clinical image quality of soft and sharp reconstructions were 0.88 and 0.93, respectively. The automatic scoring algorithm is a promising tool for the evaluation of thoracic CT scans in daily clinical practice. It allows monitoring of the image quality of a chest protocol over time, without human intervention. Different reconstruction kernels can be compared after normalization of the IQs. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

4D-PET reconstruction using a spline-residue model with spatial and temporal roughness penalties

NASA Astrophysics Data System (ADS)

Ralli, George P.; Chappell, Michael A.; McGowan, Daniel R.; Sharma, Ricky A.; Higgins, Geoff S.; Fenwick, John D.

2018-05-01

4D reconstruction of dynamic positron emission tomography (dPET) data can improve the signal-to-noise ratio in reconstructed image sequences by fitting smooth temporal functions to the voxel time-activity-curves (TACs) during the reconstruction, though the optimal choice of function remains an open question. We propose a spline-residue model, which describes TACs as weighted sums of convolutions of the arterial input function with cubic B-spline basis functions. Convolution with the input function constrains the spline-residue model at early time-points, potentially enhancing noise suppression in early time-frames, while still allowing a wide range of TAC descriptions over the entire imaged time-course, thus limiting bias. Spline-residue based 4D-reconstruction is compared to that of a conventional (non-4D) maximum a posteriori (MAP) algorithm, and to 4D-reconstructions based on adaptive-knot cubic B-splines, the spectral model and an irreversible two-tissue compartment (‘2C3K’) model. 4D reconstructions were carried out using a nested-MAP algorithm including spatial and temporal roughness penalties. The algorithms were tested using Monte-Carlo simulated scanner data, generated for a digital thoracic phantom with uptake kinetics based on a dynamic [18F]-Fluromisonidazole scan of a non-small cell lung cancer patient. For every algorithm, parametric maps were calculated by fitting each voxel TAC within a sub-region of the reconstructed images with the 2C3K model. Compared to conventional MAP reconstruction, spline-residue-based 4D reconstruction achieved  >50% improvements for five of the eight combinations of the four kinetics parameters for which parametric maps were created with the bias and noise measures used to analyse them, and produced better results for 5/8 combinations than any of the other reconstruction algorithms studied, while spectral model-based 4D reconstruction produced the best results for 2/8. 2C3K model-based 4D reconstruction generated the most biased parametric maps. Inclusion of a temporal roughness penalty function improved the performance of 4D reconstruction based on the cubic B-spline, spectral and spline-residue models.

Three-Dimensional Reconstruction of Cloud-to-Ground Lightning Using High-Speed Video and VHF Broadband Interferometer

NASA Astrophysics Data System (ADS)

Li, Yun; Qiu, Shi; Shi, Lihua; Huang, Zhengyu; Wang, Tao; Duan, Yantao

2017-12-01

The time resolved three-dimensional (3-D) spatial reconstruction of lightning channels using high-speed video (HSV) images and VHF broadband interferometer (BITF) data is first presented in this paper. Because VHF and optical radiations in step formation process occur with time separation no more than 1 μs, the observation data of BITF and HSV at two different sites provide the possibility of reconstructing the time resolved 3-D channel of lightning. With the proposed procedures for 3-D reconstruction of leader channels, dart leaders as well as stepped leaders with complex multiple branches can be well reconstructed. The differences between 2-D speeds and 3-D speeds of leader channels are analyzed by comparing the development of leader channels in 2-D and 3-D space. Since return stroke (RS) usually follows the path of previous leader channels, the 3-D speeds of the return strokes are first estimated by combination with the 3-D structure of the preceding leaders and HSV image sequences. For the fourth RS, the ratios of the 3-D to 2-D RS speeds increase with height, and the largest ratio of the 3-D to 2-D return stroke speeds can reach 2.03, which is larger than the result of triggered lightning reported by Idone. Since BITF can detect lightning radiation in a 360° view, correlated BITF and HSV observations increase the 3-D detection probability than dual-station HSV observations, which is helpful to obtain more events and deeper understanding of the lightning process.

Using Affordable Data Capturing Devices for Automatic 3d City Modelling

NASA Astrophysics Data System (ADS)

Alizadehashrafi, B.; Abdul-Rahman, A.

2017-11-01

In this research project, many movies from UTM Kolej 9, Skudai, Johor Bahru (See Figure 1) were taken by AR. Drone 2. Since the AR drone 2.0 has liquid lens, while flying there were significant distortions and deformations on the converted pictures of the movies. Passive remote sensing (RS) applications based on image matching and Epipolar lines such as Agisoft PhotoScan have been tested to create the point clouds and mesh along with 3D models and textures. As the result was not acceptable (See Figure 2), the previous Dynamic Pulse Function based on Ruby programming language were enhanced and utilized to create the 3D models automatically in LoD3. The accuracy of the final 3D model is almost 10 to 20 cm. After rectification and parallel projection of the photos based on some tie points and targets, all the parameters were measured and utilized as an input to the system to create the 3D model automatically in LoD3 in a very high accuracy.

Low-cost Method for Obtaining Medical Rapid Prototyping Using Desktop 3D printing: A Novel Technique for Mandibular Reconstruction Planning.

PubMed

Velasco, Ignacio; Vahdani, Soheil; Ramos, Hector

2017-09-01

Three-dimensional (3D) printing is relatively a new technology with clinical applications, which enable us to create rapid accurate prototype of the selected anatomic region, making it possible to plan complex surgery and pre-bend hardware for individual surgical cases. This study aimed to express our experience with the use of medical rapid prototype (MRP) of the maxillofacial region created by desktop 3D printer and its application in maxillofacial reconstructive surgeries. Three patients with benign mandible tumors were included in this study after obtaining informed consent. All patient's maxillofacial CT scan data was processed by segmentation and isolation software and mandible MRP was printed using our desktop 3D printer. These models were used for preoperative surgical planning and prebending of the reconstruction plate. MRP created by desktop 3D printer is a cost-efficient, quick and easily produced appliance for the planning of reconstructive surgery. It can contribute in patient orientation and helping them in a better understanding of their condition and proposed surgical treatment. It helps surgeons for pre-operative planning in the resection or reconstruction cases and represent an excellent tool in academic setting for residents training. The pre-bended reconstruction plate based on MRP, resulted in decreased surgery time, cost and anesthesia risks on the patients. Key words: 3D printing, medical modeling, rapid prototype, mandibular reconstruction, ameloblastoma.

Dense 3D Face Alignment from 2D Video for Real-Time Use

PubMed Central

Jeni, László A.; Cohn, Jeffrey F.; Kanade, Takeo

2018-01-01

To enable real-time, person-independent 3D registration from 2D video, we developed a 3D cascade regression approach in which facial landmarks remain invariant across pose over a range of approximately 60 degrees. From a single 2D image of a person’s face, a dense 3D shape is registered in real time for each frame. The algorithm utilizes a fast cascade regression framework trained on high-resolution 3D face-scans of posed and spontaneous emotion expression. The algorithm first estimates the location of a dense set of landmarks and their visibility, then reconstructs face shapes by fitting a part-based 3D model. Because no assumptions are required about illumination or surface properties, the method can be applied to a wide range of imaging conditions that include 2D video and uncalibrated multi-view video. The method has been validated in a battery of experiments that evaluate its precision of 3D reconstruction, extension to multi-view reconstruction, temporal integration for videos and 3D head-pose estimation. Experimental findings strongly support the validity of real-time, 3D registration and reconstruction from 2D video. The software is available online at http://zface.org. PMID:29731533

Radiation-free quantification of head malformations in craniosynostosis patients from 3D photography

NASA Astrophysics Data System (ADS)

Tu, Liyun; Porras, Antonio R.; Oh, Albert; Lepore, Natasha; Mastromanolis, Manuel; Tsering, Deki; Paniagua, Beatriz; Enquobahrie, Andinet; Keating, Robert; Rogers, Gary F.; Linguraru, Marius George

2018-02-01

The evaluation of cranial malformations plays an essential role both in the early diagnosis and in the decision to perform surgical treatment for craniosynostosis. In clinical practice, both cranial shape and suture fusion are evaluated using CT images, which involve the use of harmful radiation on children. Three-dimensional (3D) photography offers noninvasive, radiation-free, and anesthetic-free evaluation of craniofacial morphology. The aim of this study is to develop an automated framework to objectively quantify cranial malformations in patients with craniosynostosis from 3D photography. We propose a new method that automatically extracts the cranial shape by identifying a set of landmarks from a 3D photograph. Specifically, it registers the 3D photograph of a patient to a reference template in which the position of the landmarks is known. Then, the method finds the closest cranial shape to that of the patient from a normative statistical shape multi-atlas built from 3D photographs of healthy cases, and uses it to quantify objectively cranial malformations. We calculated the cranial malformations on 17 craniosynostosis patients and we compared them with the malformations of the normative population used to build the multi-atlas. The average malformations of the craniosynostosis cases were 2.68 +/- 0.75 mm, which is significantly higher (p<0.001) than the average malformations of 1.70 +/- 0.41 mm obtained from the normative cases. Our approach can support the quantitative assessment of surgical procedures for cranial vault reconstruction without exposing pediatric patients to harmful radiation.

Modeling the Decay in AN Hbim Starting from 3d Point Clouds. a Followed Approach for Cultural Heritage Knowledge

NASA Astrophysics Data System (ADS)

Chiabrando, F.; Lo Turco, M.; Rinaudo, F.

2017-08-01

The recent trends in architectural data management imply the scientific and professional collaborations of several disciplines involved in the design, restoration and maintenance. It seems an achieved concept that, in the next future, all the information connected to new interventions or conservation activities on historical buildings will be managed by using a BIM platform. Nowadays the actual range or image based metric survey techniques (mainly produced by using Terrestrial Laser Scanner or photogrammetric platform today more based on projective geometry) allow to generate 3D point clouds, 3D models, orthophotos and other outputs with assessed accuracy. The subsequent conversion of 3D information into parametric components, especially in an historical environment, is not easy and has a lot of open issues. According to the actual BIM commercial software and to the embedded tools or plugin, the paper deals with the methodology followed for the realization of two parametric 3D models (Palazzo Sarmatoris and Smistamento RoundHouse, two historical building in the north-west part of Italy). The paper describes the proposed workflow according to the employed plug-in for automatic reconstruction and to the solution adopted for the well-known problems connected to the modeling phase such as the vaults realization or the 3D irregular surfaces modeling. Finally, the studied strategy for mapping the decay in a BIM environment and the connected results with the conclusions and future perspectives are critically discussed.

Refocusing-range and image-quality enhanced optical reconstruction of 3-D objects from integral images using a principal periodic δ-function array

NASA Astrophysics Data System (ADS)

Ai, Lingyu; Kim, Eun-Soo

2018-03-01

We propose a method for refocusing-range and image-quality enhanced optical reconstruction of three-dimensional (3-D) objects from integral images only by using a 3 × 3 periodic δ-function array (PDFA), which is called a principal PDFA (P-PDFA). By directly convolving the elemental image array (EIA) captured from 3-D objects with the P-PDFAs whose spatial periods correspond to each object's depth, a set of spatially-filtered EIAs (SF-EIAs) are extracted, and from which 3-D objects can be reconstructed to be refocused on their real depth. convolutional operations are performed directly on each of the minimum 3 × 3 EIs of the picked-up EIA, the capturing and refocused-depth ranges of 3-D objects can be greatly enhanced, as well as 3-D objects much improved in image quality can be reconstructed without any preprocessing operations. Through ray-optical analysis and optical experiments with actual 3-D objects, the feasibility of the proposed method has been confirmed.

Comparison of T1-weighted 2D TSE, 3D SPGR, and two-point 3D Dixon MRI for automated segmentation of visceral adipose tissue at 3 Tesla.

PubMed

Fallah, Faezeh; Machann, Jürgen; Martirosian, Petros; Bamberg, Fabian; Schick, Fritz; Yang, Bin

2017-04-01

To evaluate and compare conventional T1-weighted 2D turbo spin echo (TSE), T1-weighted 3D volumetric interpolated breath-hold examination (VIBE), and two-point 3D Dixon-VIBE sequences for automatic segmentation of visceral adipose tissue (VAT) volume at 3 Tesla by measuring and compensating for errors arising from intensity nonuniformity (INU) and partial volume effects (PVE). The body trunks of 28 volunteers with body mass index values ranging from 18 to 41.2 kg/m 2 (30.02 ± 6.63 kg/m 2 ) were scanned at 3 Tesla using three imaging techniques. Automatic methods were applied to reduce INU and PVE and to segment VAT. The automatically segmented VAT volumes obtained from all acquisitions were then statistically and objectively evaluated against the manually segmented (reference) VAT volumes. Comparing the reference volumes with the VAT volumes automatically segmented over the uncorrected images showed that INU led to an average relative volume difference of -59.22 ± 11.59, 2.21 ± 47.04, and -43.05 ± 5.01 % for the TSE, VIBE, and Dixon images, respectively, while PVE led to average differences of -34.85 ± 19.85, -15.13 ± 11.04, and -33.79 ± 20.38 %. After signal correction, differences of -2.72 ± 6.60, 34.02 ± 36.99, and -2.23 ± 7.58 % were obtained between the reference and the automatically segmented volumes. A paired-sample two-tailed t test revealed no significant difference between the reference and automatically segmented VAT volumes of the corrected TSE (p = 0.614) and Dixon (p = 0.969) images, but showed a significant VAT overestimation using the corrected VIBE images. Under similar imaging conditions and spatial resolution, automatically segmented VAT volumes obtained from the corrected TSE and Dixon images agreed with each other and with the reference volumes. These results demonstrate the efficacy of the signal correction methods and the similar accuracy of TSE and Dixon imaging for automatic volumetry of VAT at 3 Tesla.

Weighted regularized statistical shape space projection for breast 3D model reconstruction.

PubMed

Ruiz, Guillermo; Ramon, Eduard; García, Jaime; Sukno, Federico M; Ballester, Miguel A González

2018-07-01

The use of 3D imaging has increased as a practical and useful tool for plastic and aesthetic surgery planning. Specifically, the possibility of representing the patient breast anatomy in a 3D shape and simulate aesthetic or plastic procedures is a great tool for communication between surgeon and patient during surgery planning. For the purpose of obtaining the specific 3D model of the breast of a patient, model-based reconstruction methods can be used. In particular, 3D morphable models (3DMM) are a robust and widely used method to perform 3D reconstruction. However, if additional prior information (i.e., known landmarks) is combined with the 3DMM statistical model, shape constraints can be imposed to improve the 3DMM fitting accuracy. In this paper, we present a framework to fit a 3DMM of the breast to two possible inputs: 2D photos and 3D point clouds (scans). Our method consists in a Weighted Regularized (WR) projection into the shape space. The contribution of each point in the 3DMM shape is weighted allowing to assign more relevance to those points that we want to impose as constraints. Our method is applied at multiple stages of the 3D reconstruction process. Firstly, it can be used to obtain a 3DMM initialization from a sparse set of 3D points. Additionally, we embed our method in the 3DMM fitting process in which more reliable or already known 3D points or regions of points, can be weighted in order to preserve their shape information. The proposed method has been tested in two different input settings: scans and 2D pictures assessing both reconstruction frameworks with very positive results. Copyright © 2018 Elsevier B.V. All rights reserved.

Use of a Three-Dimensional Model to Optimize a MEDPOR Implant for Delayed Reconstruction of a Suprastructure Maxillectomy Defect

PubMed Central

Echo, Anthony; Wolfswinkel, Erik M.; Weathers, William; McKnight, Aisha; Izaddoost, Shayan

2013-01-01

The use of a three-dimensional (3-D) model has been well described for craniomaxillofacial reconstruction, especially with the preoperative planning of free fibula flaps. This article reports the application of an innovative 3-D model approach for the calculation of the exact contours, angles, length, and general morphology of a prefabricated MEDPOR 2/3 orbital implant for reconstruction of a suprastructure maxillectomy defect. The 3-D model allowed intraoperative modification of the MEDPOR implant which decreased the risk of iatrogenic harm, contamination while also improving aesthetic results and function. With the aid of preoperative 3-D models, porous polypropylene facial implants can be contoured efficiently intraoperatively to precisely reconstruct complex craniomaxillofacial defects. PMID:24436774

Subpixel based defocused points removal in photon-limited volumetric dataset

NASA Astrophysics Data System (ADS)

Muniraj, Inbarasan; Guo, Changliang; Malallah, Ra'ed; Maraka, Harsha Vardhan R.; Ryle, James P.; Sheridan, John T.

2017-03-01

The asymptotic property of the maximum likelihood estimator (MLE) has been utilized to reconstruct three-dimensional (3D) sectional images in the photon counting imaging (PCI) regime. At first, multiple 2D intensity images, known as Elemental images (EI), are captured. Then the geometric ray-tracing method is employed to reconstruct the 3D sectional images at various depth cues. We note that a 3D sectional image consists of both focused and defocused regions, depending on the reconstructed depth position. The defocused portion is redundant and should be removed in order to facilitate image analysis e.g., 3D object tracking, recognition, classification and navigation. In this paper, we present a subpixel level three-step based technique (i.e. involving adaptive thresholding, boundary detection and entropy based segmentation) to discard the defocused sparse-samples from the reconstructed photon-limited 3D sectional images. Simulation results are presented demonstrating the feasibility and efficiency of the proposed method.

Stereo Cameras for Clouds (STEREOCAM) Instrument Handbook

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romps, David; Oktem, Rusen

2017-10-31

The three pairs of stereo camera setups aim to provide synchronized and stereo calibrated time series of images that can be used for 3D cloud mask reconstruction. Each camera pair is positioned at approximately 120 degrees from the other pair, with a 17o-19o pitch angle from the ground, and at 5-6 km distance from the U.S. Department of Energy (DOE) Central Facility at the Atmospheric Radiation Measurement (ARM) Climate Research Facility Southern Great Plains (SGP) observatory to cover the region from northeast, northwest, and southern views. Images from both cameras of the same stereo setup can be paired together tomore » obtain 3D reconstruction by triangulation. 3D reconstructions from the ring of three stereo pairs can be combined together to generate a 3D mask from surrounding views. This handbook delivers all stereo reconstruction parameters of the cameras necessary to make 3D reconstructions from the stereo camera images.« less

Stereoscopic Analysis of 19 May and 31 Aug 2007 Filament Eruptions

NASA Technical Reports Server (NTRS)

Liewer, Paulett; DeJong, E. M.; Hall, J. R.

2008-01-01

The presentation outline includes results from stereoscopic analysis of SECCHI/EUVI data for 19 May 2007 filament eruption, including the determined 3D trajectory of erupting filament, strong evidence for reconnection below erupting filament as consistent with standard model, and comparison of EUVI and H-alpha images during eruption; and results from stereoscopic analytic of 21 August 2007 filament eruption. Slide topics include standard model of filament eruption; 2007 May 19 STEREO A/SECCHI/EUVI 195 and 304 A: CME signatures and filament eruption, 3D reconstruction of erupting prominence; filament's relation to coronal magnetic fields; 3d reconstructions of filament eruption; height-time plot of eruption from 3D reconstructions; detailed pre-eruptions comparison of H-alpha and EUVI 304 at 12:42 UT; comparisons during the eruption; STEREO prominence and CME August 31, 2007; reconstructions of prominence and leading edges of both dark cavity and CME; and 3D reconstructions of prominence and leading edges.

Simultaneous reconstruction of 3D refractive index, temperature, and intensity distribution of combustion flame by double computed tomography technologies based on spatial phase-shifting method

NASA Astrophysics Data System (ADS)

Guo, Zhenyan; Song, Yang; Yuan, Qun; Wulan, Tuya; Chen, Lei

2017-06-01

In this paper, a transient multi-parameter three-dimensional (3D) reconstruction method is proposed to diagnose and visualize a combustion flow field. Emission and transmission tomography based on spatial phase-shifted technology are combined to reconstruct, simultaneously, the various physical parameter distributions of a propane flame. Two cameras triggered by the internal trigger mode capture the projection information of the emission and moiré tomography, respectively. A two-step spatial phase-shifting method is applied to extract the phase distribution in the moiré fringes. By using the filtered back-projection algorithm, we reconstruct the 3D refractive-index distribution of the combustion flow field. Finally, the 3D temperature distribution of the flame is obtained from the refractive index distribution using the Gladstone-Dale equation. Meanwhile, the 3D intensity distribution is reconstructed based on the radiation projections from the emission tomography. Therefore, the structure and edge information of the propane flame are well visualized.

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

Integrated Approach to Reconstruction of Microbial Regulatory Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodionov, Dmitry A; Novichkov, Pavel S

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated inmore » RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.« less

High-order central ENO finite-volume scheme for hyperbolic conservation laws on three-dimensional cubed-sphere grids

NASA Astrophysics Data System (ADS)

Ivan, L.; De Sterck, H.; Susanto, A.; Groth, C. P. T.

2015-02-01

A fourth-order accurate finite-volume scheme for hyperbolic conservation laws on three-dimensional (3D) cubed-sphere grids is described. The approach is based on a central essentially non-oscillatory (CENO) finite-volume method that was recently introduced for two-dimensional compressible flows and is extended to 3D geometries with structured hexahedral grids. Cubed-sphere grids feature hexahedral cells with nonplanar cell surfaces, which are handled with high-order accuracy using trilinear geometry representations in the proposed approach. Varying stencil sizes and slope discontinuities in grid lines occur at the boundaries and corners of the six sectors of the cubed-sphere grid where the grid topology is unstructured, and these difficulties are handled naturally with high-order accuracy by the multidimensional least-squares based 3D CENO reconstruction with overdetermined stencils. A rotation-based mechanism is introduced to automatically select appropriate smaller stencils at degenerate block boundaries, where fewer ghost cells are available and the grid topology changes, requiring stencils to be modified. Combining these building blocks results in a finite-volume discretization for conservation laws on 3D cubed-sphere grids that is uniformly high-order accurate in all three grid directions. While solution-adaptivity is natural in the multi-block setting of our code, high-order accurate adaptive refinement on cubed-sphere grids is not pursued in this paper. The 3D CENO scheme is an accurate and robust solution method for hyperbolic conservation laws on general hexahedral grids that is attractive because it is inherently multidimensional by employing a K-exact overdetermined reconstruction scheme, and it avoids the complexity of considering multiple non-central stencil configurations that characterizes traditional ENO schemes. Extensive numerical tests demonstrate fourth-order convergence for stationary and time-dependent Euler and magnetohydrodynamic flows on cubed-sphere grids, and robustness against spurious oscillations at 3D shocks. Performance tests illustrate efficiency gains that can be potentially achieved using fourth-order schemes as compared to second-order methods for the same error level. Applications on extended cubed-sphere grids incorporating a seventh root block that discretizes the interior of the inner sphere demonstrate the versatility of the spatial discretization method.

Towards 3D crystal orientation reconstruction using automated crystal orientation mapping transmission electron microscopy (ACOM-TEM).

PubMed

Kobler, Aaron; Kübel, Christian

2018-01-01

To relate the internal structure of a volume (crystallite and phase boundaries) to properties (electrical, magnetic, mechanical, thermal), a full 3D reconstruction in combination with in situ testing is desirable. In situ testing allows the crystallographic changes in a material to be followed by tracking and comparing the individual crystals and phases. Standard transmission electron microscopy (TEM) delivers a projection image through the 3D volume of an electron-transparent TEM sample lamella. Only with the help of a dedicated TEM tomography sample holder is an accurate 3D reconstruction of the TEM lamella currently possible. 2D crystal orientation mapping has become a standard method for crystal orientation and phase determination while 3D crystal orientation mapping have been reported only a few times. The combination of in situ testing with 3D crystal orientation mapping remains a challenge in terms of stability and accuracy. Here, we outline a method to 3D reconstruct the crystal orientation from a superimposed diffraction pattern of overlapping crystals without sample tilt. Avoiding the typically required tilt series for 3D reconstruction enables not only faster in situ tests but also opens the possibility for more stable and more accurate in situ mechanical testing. The approach laid out here should serve as an inspiration for further research and does not make a claim to be complete.

Modelling Urban Noise in Citygml Ade: Case of the Netherlands

NASA Astrophysics Data System (ADS)

Kumar, K.; Ledoux, H.; Commandeur, T. J. F.; Stoter, J. E.

2017-10-01

Road traffic and industrial noise has become a major source of discomfort and annoyance among the residents in urban areas. More than 44 % of the EU population is regularly exposed to road traffic noise levels over 55 dB, which is currently the maximum accepted value prescribed by the Environmental Noise Directive for road traffic noise. With continuously increasing population and number of motor vehicles and industries, it is very unlikely to hope for noise levels to diminish in the near future. Therefore, it is necessary to monitor urban noise, so as to make mitigation plans and to deal with its adverse effects. The 2002/49/EC Environmental Noise Directive aims to determine the exposure of an individual to environmental noise through noise mapping. One of the most important steps in noise mapping is the creation of input data for simulation. At present, it is done semi-automatically (and sometimes even manually) by different companies in different ways and is very time consuming and can lead to errors in the data. In this paper, we present our approach for automatically creating input data for noise simulations. Secondly, we focus on using 3D city models for presenting the results of simulation for the noise arising from road traffic and industrial activities in urban areas. We implemented a few noise modelling standards for industrial and road traffic noise in CityGML by extending the existing Noise ADE with new objects and attributes. This research is a steping stone in the direction of standardising the input and output data for noise studies and for reconstructing the 3D data accordingly.

Phase correction for three-dimensional (3D) diffusion-weighted interleaved EPI using 3D multiplexed sensitivity encoding and reconstruction (3D-MUSER).

PubMed

Chang, Hing-Chiu; Hui, Edward S; Chiu, Pui-Wai; Liu, Xiaoxi; Chen, Nan-Kuei

2018-05-01

Three-dimensional (3D) multiplexed sensitivity encoding and reconstruction (3D-MUSER) algorithm is proposed to reduce aliasing artifacts and signal corruption caused by inter-shot 3D phase variations in 3D diffusion-weighted echo planar imaging (DW-EPI). 3D-MUSER extends the original framework of multiplexed sensitivity encoding (MUSE) to a hybrid k-space-based reconstruction, thereby enabling the correction of inter-shot 3D phase variations. A 3D single-shot EPI navigator echo was used to measure inter-shot 3D phase variations. The performance of 3D-MUSER was evaluated by analyses of point-spread function (PSF), signal-to-noise ratio (SNR), and artifact levels. The efficacy of phase correction using 3D-MUSER for different slab thicknesses and b-values were investigated. Simulations showed that 3D-MUSER could eliminate artifacts because of through-slab phase variation and reduce noise amplification because of SENSE reconstruction. All aliasing artifacts and signal corruption in 3D interleaved DW-EPI acquired with different slab thicknesses and b-values were reduced by our new algorithm. A near-whole brain single-slab 3D DTI with 1.3-mm isotropic voxel acquired at 1.5T was successfully demonstrated. 3D phase correction for 3D interleaved DW-EPI data is made possible by 3D-MUSER, thereby improving feasible slab thickness and maximum feasible b-value. Magn Reson Med 79:2702-2712, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Jini service to reconstruct tomographic data

NASA Astrophysics Data System (ADS)

Knoll, Peter; Mirzaei, S.; Koriska, K.; Koehn, H.

2002-06-01

A number of imaging systems rely on the reconstruction of a 3- dimensional model from its projections through the process of computed tomography (CT). In medical imaging, for example magnetic resonance imaging (MRI), positron emission tomography (PET), and Single Computer Tomography (SPECT) acquire two-dimensional projections of a three dimensional projections of a three dimensional object. In order to calculate the 3-dimensional representation of the object, i.e. its voxel distribution, several reconstruction algorithms have been developed. Currently, mainly two reconstruct use: the filtered back projection(FBP) and iterative methods. Although the quality of iterative reconstructed SPECT slices is better than that of FBP slices, such iterative algorithms are rarely used for clinical routine studies because of their low availability and increased reconstruction time. We used Jini and a self-developed iterative reconstructions algorithm to design and implement a Jini reconstruction service. With this service, the physician selects the patient study from a database and a Jini client automatically discovers the registered Jini reconstruction services in the department's Intranet. After downloading the proxy object the this Jini service, the SPECT acquisition data are reconstructed. The resulting transaxial slices are visualized using a Jini slice viewer, which can be used for various imaging modalities.

3D image processing architecture for camera phones

NASA Astrophysics Data System (ADS)

Atanassov, Kalin; Ramachandra, Vikas; Goma, Sergio R.; Aleksic, Milivoje

2011-03-01

Putting high quality and easy-to-use 3D technology into the hands of regular consumers has become a recent challenge as interest in 3D technology has grown. Making 3D technology appealing to the average user requires that it be made fully automatic and foolproof. Designing a fully automatic 3D capture and display system requires: 1) identifying critical 3D technology issues like camera positioning, disparity control rationale, and screen geometry dependency, 2) designing methodology to automatically control them. Implementing 3D capture functionality on phone cameras necessitates designing algorithms to fit within the processing capabilities of the device. Various constraints like sensor position tolerances, sensor 3A tolerances, post-processing, 3D video resolution and frame rate should be carefully considered for their influence on 3D experience. Issues with migrating functions such as zoom and pan from the 2D usage model (both during capture and display) to 3D needs to be resolved to insure the highest level of user experience. It is also very important that the 3D usage scenario (including interactions between the user and the capture/display device) is carefully considered. Finally, both the processing power of the device and the practicality of the scheme needs to be taken into account while designing the calibration and processing methodology.

An efficient global energy optimization approach for robust 3D plane segmentation of point clouds

NASA Astrophysics Data System (ADS)

Dong, Zhen; Yang, Bisheng; Hu, Pingbo; Scherer, Sebastian

2018-03-01

Automatic 3D plane segmentation is necessary for many applications including point cloud registration, building information model (BIM) reconstruction, simultaneous localization and mapping (SLAM), and point cloud compression. However, most of the existing 3D plane segmentation methods still suffer from low precision and recall, and inaccurate and incomplete boundaries, especially for low-quality point clouds collected by RGB-D sensors. To overcome these challenges, this paper formulates the plane segmentation problem as a global energy optimization because it is robust to high levels of noise and clutter. First, the proposed method divides the raw point cloud into multiscale supervoxels, and considers planar supervoxels and individual points corresponding to nonplanar supervoxels as basic units. Then, an efficient hybrid region growing algorithm is utilized to generate initial plane set by incrementally merging adjacent basic units with similar features. Next, the initial plane set is further enriched and refined in a mutually reinforcing manner under the framework of global energy optimization. Finally, the performances of the proposed method are evaluated with respect to six metrics (i.e., plane precision, plane recall, under-segmentation rate, over-segmentation rate, boundary precision, and boundary recall) on two benchmark datasets. Comprehensive experiments demonstrate that the proposed method obtained good performances both in high-quality TLS point clouds (i.e., http://SEMANTIC3D.NET)

A Method for 3D-Reconstruction of a Muscle Thick Filament Using the Tilt Series Images of a Single Filament Electron Tomogram

PubMed Central

Márquez, G.; Pinto, A.; Alamo, L.; Baumann, B.; Ye, F.; Winkler, H.; Taylor, K.; Padrón, R.

2014-01-01

Summary Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament –calculated without any image averaging and/or imposition of helical symmetry- only reveals MIH motifs infrequently. This is –to our knowledge- the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. PMID:24727133

A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

PubMed

Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

2014-05-01

Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. Copyright © 2014 Elsevier Inc. All rights reserved.

Enhancing breast projection in autologous reconstruction using the St Andrew's coning technique and 3D volumetric analysis.

PubMed

Chae, Michael P; Rozen, Warren Matthew; Patel, Nakul Gamanlal; Hunter-Smith, David J; Ramakrishnan, Venkat

2017-12-01

An increasing number of women undergo mastectomy for breast cancer and post-mastectomy autologous breast reconstruction has been shown to significantly improve the psychosexual wellbeing of the patients. A goal of treatment is to achieve symmetry and projection to match the native breast, and/or the contralateral breast in the case of a unilateral reconstruction. Autologous reconstruction, particularly with the deep inferior epigastric artery perforator (DIEP) flap, is particularly advantageous as it can be manipulated to mimic the shape and turgor of the native breast. However, very few techniques of shaping the breast conus when insetting the DIEP flap to enhance aesthetic outcome have been reported to date. With the aide of three-dimension (3D) photography and 3D-printed mirrored image of the contralateral breast as a guide intraoperatively, we describe our St Andrew's coning technique to create a personalized flap projection. We report a prospective case series of 3 delayed unilateral breast reconstructions where symmetrization procedure to the contralateral breast was not indicated. Using a commercial 3D scanner (VECTRA XR, Canfield Scientific), the breast region was imaged. The mirrored image was 3D-printed in-house using a desktop 3D printer. In all cases, projection of the breast mound was able to be safely achieved, with a demonstrated central volume (or 'cone') able to be highlighted on imaging and a 3D printed breast. A 3D print of the contralateral breast was able to be used intraoperatively to guide the operative approach. The St Andrew's coning technique is a useful aesthetic maneuver for achieving breast projection during DIEP flap breast reconstruction, with 3D imaging techniques able to assist in perioperative assessment of breast volume.

Enhancing breast projection in autologous reconstruction using the St Andrew’s coning technique and 3D volumetric analysis

PubMed Central

Chae, Michael P.; Patel, Nakul Gamanlal; Hunter-Smith, David J.; Ramakrishnan, Venkat

2017-01-01

Background An increasing number of women undergo mastectomy for breast cancer and post-mastectomy autologous breast reconstruction has been shown to significantly improve the psychosexual wellbeing of the patients. A goal of treatment is to achieve symmetry and projection to match the native breast, and/or the contralateral breast in the case of a unilateral reconstruction. Autologous reconstruction, particularly with the deep inferior epigastric artery perforator (DIEP) flap, is particularly advantageous as it can be manipulated to mimic the shape and turgor of the native breast. However, very few techniques of shaping the breast conus when insetting the DIEP flap to enhance aesthetic outcome have been reported to date. With the aide of three-dimension (3D) photography and 3D-printed mirrored image of the contralateral breast as a guide intraoperatively, we describe our St Andrew’s coning technique to create a personalized flap projection. Method We report a prospective case series of 3 delayed unilateral breast reconstructions where symmetrization procedure to the contralateral breast was not indicated. Using a commercial 3D scanner (VECTRA XR, Canfield Scientific), the breast region was imaged. The mirrored image was 3D-printed in-house using a desktop 3D printer. Results In all cases, projection of the breast mound was able to be safely achieved, with a demonstrated central volume (or ‘cone’) able to be highlighted on imaging and a 3D printed breast. A 3D print of the contralateral breast was able to be used intraoperatively to guide the operative approach. Conclusions The St Andrew’s coning technique is a useful aesthetic maneuver for achieving breast projection during DIEP flap breast reconstruction, with 3D imaging techniques able to assist in perioperative assessment of breast volume. PMID:29302489

MO-C-18A-01: Advances in Model-Based 3D Image Reconstruction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, G; Pan, X; Stayman, J

2014-06-15

Recent years have seen the emergence of CT image reconstruction techniques that exploit physical models of the imaging system, photon statistics, and even the patient to achieve improved 3D image quality and/or reduction of radiation dose. With numerous advantages in comparison to conventional 3D filtered backprojection, such techniques bring a variety of challenges as well, including: a demanding computational load associated with sophisticated forward models and iterative optimization methods; nonlinearity and nonstationarity in image quality characteristics; a complex dependency on multiple free parameters; and the need to understand how best to incorporate prior information (including patient-specific prior images) within themore » reconstruction process. The advantages, however, are even greater – for example: improved image quality; reduced dose; robustness to noise and artifacts; task-specific reconstruction protocols; suitability to novel CT imaging platforms and noncircular orbits; and incorporation of known characteristics of the imager and patient that are conventionally discarded. This symposium features experts in 3D image reconstruction, image quality assessment, and the translation of such methods to emerging clinical applications. Dr. Chen will address novel methods for the incorporation of prior information in 3D and 4D CT reconstruction techniques. Dr. Pan will show recent advances in optimization-based reconstruction that enable potential reduction of dose and sampling requirements. Dr. Stayman will describe a “task-based imaging” approach that leverages models of the imaging system and patient in combination with a specification of the imaging task to optimize both the acquisition and reconstruction process. Dr. Samei will describe the development of methods for image quality assessment in such nonlinear reconstruction techniques and the use of these methods to characterize and optimize image quality and dose in a spectrum of clinical applications. Learning Objectives: Learn the general methodologies associated with model-based 3D image reconstruction. Learn the potential advantages in image quality and dose associated with model-based image reconstruction. Learn the challenges associated with computational load and image quality assessment for such reconstruction methods. Learn how imaging task can be incorporated as a means to drive optimal image acquisition and reconstruction techniques. Learn how model-based reconstruction methods can incorporate prior information to improve image quality, ease sampling requirements, and reduce dose.« less

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

PubMed

Vollmar, S; Michel, C; Treffert, J T; Newport, D F; Casey, M; Knöss, C; Wienhard, K; Liu, X; Defrise, M; Heiss, W D

2002-08-07

Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

Samba: a real-time motion capture system using wireless camera sensor networks.

PubMed

Oh, Hyeongseok; Cha, Geonho; Oh, Songhwai

2014-03-20

There is a growing interest in 3D content following the recent developments in 3D movies, 3D TVs and 3D smartphones. However, 3D content creation is still dominated by professionals, due to the high cost of 3D motion capture instruments. The availability of a low-cost motion capture system will promote 3D content generation by general users and accelerate the growth of the 3D market. In this paper, we describe the design and implementation of a real-time motion capture system based on a portable low-cost wireless camera sensor network. The proposed system performs motion capture based on the data-driven 3D human pose reconstruction method to reduce the computation time and to improve the 3D reconstruction accuracy. The system can reconstruct accurate 3D full-body poses at 16 frames per second using only eight markers on the subject's body. The performance of the motion capture system is evaluated extensively in experiments.

Samba: A Real-Time Motion Capture System Using Wireless Camera Sensor Networks

PubMed Central

Oh, Hyeongseok; Cha, Geonho; Oh, Songhwai

2014-01-01

There is a growing interest in 3D content following the recent developments in 3D movies, 3D TVs and 3D smartphones. However, 3D content creation is still dominated by professionals, due to the high cost of 3D motion capture instruments. The availability of a low-cost motion capture system will promote 3D content generation by general users and accelerate the growth of the 3D market. In this paper, we describe the design and implementation of a real-time motion capture system based on a portable low-cost wireless camera sensor network. The proposed system performs motion capture based on the data-driven 3D human pose reconstruction method to reduce the computation time and to improve the 3D reconstruction accuracy. The system can reconstruct accurate 3D full-body poses at 16 frames per second using only eight markers on the subject's body. The performance of the motion capture system is evaluated extensively in experiments. PMID:24658618

Computerized Interpretation of Dynamic Breast MRI

DTIC Science & Technology

2006-05-01

correction, tumor segmentation , extraction of computerized features that help distinguish between benign and malignant lesions, and classification. Our...for assessing tumor extent in 3D. The primary feature used for 3D tumor segmentation is the postcontrast enhancement vector. Tumor segmentation is a...Appendix B. 4. Investigation of methods for automatic tumor segmentation We developed an automatic method for assessing tumor extent in 3D. The

Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium.

PubMed

Ginsburg, Hagai

2009-01-01

The functional reconstruction of metabolic pathways from an annotated genome is a tedious and demanding enterprise. Automation of this endeavor using bioinformatics algorithms could cope with the ever-increasing number of sequenced genomes and accelerate the process. Here, the manual reconstruction of metabolic pathways in the functional genomic database of Plasmodium falciparum--Malaria Parasite Metabolic Pathways--is described and compared with pathways generated automatically as they appear in PlasmoCyc, metaSHARK and the Kyoto Encyclopedia for Genes and Genomes. A critical evaluation of this comparison discloses that the automatic reconstruction of pathways generates manifold paths that need an expert manual verification to accept some and reject most others based on manually curated gene annotation.

Thermal Texture Generation and 3d Model Reconstruction Using SFM and Gan

NASA Astrophysics Data System (ADS)

Kniaz, V. V.; Mizginov, V. A.

2018-05-01

Realistic 3D models with textures representing thermal emission of the object are widely used in such fields as dynamic scene analysis, autonomous driving, and video surveillance. Structure from Motion (SfM) methods provide a robust approach for the generation of textured 3D models in the visible range. Still, automatic generation of 3D models from the infrared imagery is challenging due to an absence of the feature points and low sensor resolution. Recent advances in Generative Adversarial Networks (GAN) have proved that they can perform complex image-to-image transformations such as a transformation of day to night and generation of imagery in a different spectral range. In this paper, we propose a novel method for generation of realistic 3D models with thermal textures using the SfM pipeline and GAN. The proposed method uses visible range images as an input. The images are processed in two ways. Firstly, they are used for point matching and dense point cloud generation. Secondly, the images are fed into a GAN that performs the transformation from the visible range to the thermal range. We evaluate the proposed method using real infrared imagery captured with a FLIR ONE PRO camera. We generated a dataset with 2000 pairs of real images captured in thermal and visible range. The dataset is used to train the GAN network and to generate 3D models using SfM. The evaluation of the generated 3D models and infrared textures proved that they are similar to the ground truth model in both thermal emissivity and geometrical shape.

Application of 3-D imaging sensor for tracking minipigs in the open field test.

PubMed

Kulikov, Victor A; Khotskin, Nikita V; Nikitin, Sergey V; Lankin, Vasily S; Kulikov, Alexander V; Trapezov, Oleg V

2014-09-30

The minipig is a promising model in neurobiology and psychopharmacology. However, automated tracking of minipig behavior is still unresolved problem. The study was carried out on white, agouti and black (or spotted) minipiglets (n=108) bred in the Institute of Cytology and Genetics. New method of automated tracking of minipig behavior is based on Microsoft Kinect 3-D image sensor and the 3-D image reconstruction with EthoStudio software. The algorithms of distance run and time in the center evaluation were adapted for 3-D image data and new algorithm of vertical activity quantification was developed. The 3-D imaging system successfully detects white, black, spotted and agouti pigs in the open field test (OFT). No effect of sex or color on horizontal (distance run), vertical activities and time in the center was shown. Agouti pigs explored the arena more intensive than white or black animals, respectively. The OFT behavioral traits were compared with the fear reaction to experimenter. Time in the center of the OFT was positively correlated with fear reaction rank (ρ=0.21, p<0.05). Black pigs were significantly more fearful compared with white or agouti animals. The 3-D imaging system has three advantages over existing automated tracking systems: it avoids perspective distortion, distinguishes animals any color from any background and automatically evaluates vertical activity. The 3-D imaging system can be successfully applied for automated measurement of minipig behavior in neurobiological and psychopharmacological experiments. Copyright © 2014 Elsevier B.V. All rights reserved.

A new OH5 reconstruction with an assessment of its uncertainty.

PubMed

Benazzi, Stefano; Bookstein, Fred L; Strait, David S; Weber, Gerhard W

2011-07-01

The OH5 cranium, holotype of Paranthropus boisei consists of two main portions that do not fit together: the extensively reconstructed face and a portion of the neurocranium. A physical reconstruction of the cranium was carried out by Tobias in 1967, who did not discuss problems related to deformation, although he noted a slight functional asymmetry. Nevertheless, the reconstructed cranium shows some anomalies, mainly due to the right skewed position of the upper calvariofacial fragment and uncertainty of the relative position of the neurocranium to the face, which hamper further quantitative analysis of OH5's cranial geometry. Here, we present a complete virtual reconstruction of OH5, using three-dimensional (3D) digital data, geometric morphometric (GM) methods and computer-aided design (CAD) techniques. Starting from a CT scan of Tobias's reconstruction, a semi-automatic segmentation method was used to remove Tobias's plaster. The upper calvariofacial fragment was separated from the lower facial fragment and re-aligned using superposition of their independent midsagittal planes in a range of feasible positions. The missing parts of the right hemiface were reconstructed using non-uniform rational basis-spline (NURBS) surface and subsequently mirrored using the midsagittal plane to arrive at a symmetrical facial reconstruction. A symmetric neurocranium was obtained as the average of the original shape and its mirrored version. The alignment between the two symmetric shapes (face and neurocranium) used their independent midsagittal plane and a reference shape (KNM-ER 406) to highly reduce their degrees of freedom. From the series of alternative reconstructions, we selected the middle of this rather small feasible range. When reconstructed as a range in this way, the whole cranial form of this unique specimen can be further quantified by comparative coordinate-based methods such as GM or can be used for finite element modeling (FEM) explorations of hypotheses about the mechanics of early hominin feeding and diets. Copyright © 2011 Elsevier Ltd. All rights reserved.

Investigation of iterative image reconstruction in three-dimensional optoacoustic tomography

PubMed Central

Wang, Kun; Su, Richard; Oraevsky, Alexander A; Anastasio, Mark A

2012-01-01

Iterative image reconstruction algorithms for optoacoustic tomography (OAT), also known as photoacoustic tomography, have the ability to improve image quality over analytic algorithms due to their ability to incorporate accurate models of the imaging physics, instrument response, and measurement noise. However, to date, there have been few reported attempts to employ advanced iterative image reconstruction algorithms for improving image quality in three-dimensional (3D) OAT. In this work, we implement and investigate two iterative image reconstruction methods for use with a 3D OAT small animal imager: namely, a penalized least-squares (PLS) method employing a quadratic smoothness penalty and a PLS method employing a total variation norm penalty. The reconstruction algorithms employ accurate models of the ultrasonic transducer impulse responses. Experimental data sets are employed to compare the performances of the iterative reconstruction algorithms to that of a 3D filtered backprojection (FBP) algorithm. By use of quantitative measures of image quality, we demonstrate that the iterative reconstruction algorithms can mitigate image artifacts and preserve spatial resolution more effectively than FBP algorithms. These features suggest that the use of advanced image reconstruction algorithms can improve the effectiveness of 3D OAT while reducing the amount of data required for biomedical applications. PMID:22864062

Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions

PubMed Central

Rose, Johann Christian; Kicherer, Anna; Wieland, Markus; Klingbeil, Lasse; Töpfer, Reinhard; Kuhlmann, Heiner

2016-01-01

In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter. PMID:27983669

Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions.

PubMed

Rose, Johann Christian; Kicherer, Anna; Wieland, Markus; Klingbeil, Lasse; Töpfer, Reinhard; Kuhlmann, Heiner

2016-12-15

In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter.

Fast implementations of reconstruction-based scatter compensation in fully 3D SPECT image reconstruction

NASA Astrophysics Data System (ADS)

Kadrmas, Dan J.; Frey, Eric C.; Karimi, Seemeen S.; Tsui, Benjamin M. W.

1998-04-01

Accurate scatter compensation in SPECT can be performed by modelling the scatter response function during the reconstruction process. This method is called reconstruction-based scatter compensation (RBSC). It has been shown that RBSC has a number of advantages over other methods of compensating for scatter, but using RBSC for fully 3D compensation has resulted in prohibitively long reconstruction times. In this work we propose two new methods that can be used in conjunction with existing methods to achieve marked reductions in RBSC reconstruction times. The first method, coarse-grid scatter modelling, significantly accelerates the scatter model by exploiting the fact that scatter is dominated by low-frequency information. The second method, intermittent RBSC, further accelerates the reconstruction process by limiting the number of iterations during which scatter is modelled. The fast implementations were evaluated using a Monte Carlo simulated experiment of the 3D MCAT phantom with tracer, and also using experimentally acquired data with tracer. Results indicated that these fast methods can reconstruct, with fully 3D compensation, images very similar to those obtained using standard RBSC methods, and in reconstruction times that are an order of magnitude shorter. Using these methods, fully 3D iterative reconstruction with RBSC can be performed well within the realm of clinically realistic times (under 10 minutes for image reconstruction).

Fast assembling of neuron fragments in serial 3D sections.

PubMed

Chen, Hanbo; Iascone, Daniel Maxim; da Costa, Nuno Maçarico; Lein, Ed S; Liu, Tianming; Peng, Hanchuan

2017-09-01

Reconstructing neurons from 3D image-stacks of serial sections of thick brain tissue is very time-consuming and often becomes a bottleneck in high-throughput brain mapping projects. We developed NeuronStitcher, a software suite for stitching non-overlapping neuron fragments reconstructed in serial 3D image sections. With its efficient algorithm and user-friendly interface, NeuronStitcher has been used successfully to reconstruct very large and complex human and mouse neurons.

A new SPECT/CT reconstruction algorithm: reliability and accuracy in clinical routine for non-oncologic bone diseases.

PubMed

Delcroix, Olivier; Robin, Philippe; Gouillou, Maelenn; Le Duc-Pennec, Alexandra; Alavi, Zarrin; Le Roux, Pierre-Yves; Abgral, Ronan; Salaun, Pierre-Yves; Bourhis, David; Querellou, Solène

2018-02-12

xSPECT Bone® (xB) is a new reconstruction algorithm developed by Siemens® in bone hybrid imaging (SPECT/CT). A CT-based tissue segmentation is incorporated into SPECT reconstruction to provide SPECT images with bone anatomy appearance. The objectives of this study were to assess xB/CT reconstruction diagnostic reliability and accuracy in comparison with Flash 3D® (F3D)/CT in clinical routine. Two hundred thirteen consecutive patients referred to the Brest Nuclear Medicine Department for non-oncological bone diseases were evaluated retrospectively. Two hundred seven SPECT/CT were included. All SPECT/CT were independently interpreted by two nuclear medicine physicians (a junior and a senior expert) with xB/CT then with F3D/CT three months later. Inter-observer agreement (IOA) and diagnostic confidence were determined using McNemar test, and unweighted Kappa coefficient. The study objectives were then re-assessed for validation through > 18 months of clinical and paraclinical follow-up. No statistically significant differences between IOA xB and IOA F3D were found (p = 0.532). Agreement for xB after categorical classification of the diagnoses was high (κ xB = 0.89 [95% CI 0.84 -0.93]) but without statistically significant difference F3D (κ F3D = 0.90 [95% CI 0.86 - 0.94]). Thirty-one (14.9%) inter-reconstruction diagnostic discrepancies were observed of which 21 (10.1%) were classified as major. The follow-up confirmed the diagnosis of F3D in 10 cases, xB in 6 cases and was non-contributory in 5 cases. xB reconstruction algorithm was found reliable, providing high interobserver agreement and similar diagnostic confidence to F3D reconstruction in clinical routine.

Facial recognition software success rates for the identification of 3D surface reconstructed facial images: implications for patient privacy and security.

PubMed

Mazura, Jan C; Juluru, Krishna; Chen, Joseph J; Morgan, Tara A; John, Majnu; Siegel, Eliot L

2012-06-01

Image de-identification has focused on the removal of textual protected health information (PHI). Surface reconstructions of the face have the potential to reveal a subject's identity even when textual PHI is absent. This study assessed the ability of a computer application to match research subjects' 3D facial reconstructions with conventional photographs of their face. In a prospective study, 29 subjects underwent CT scans of the head and had frontal digital photographs of their face taken. Facial reconstructions of each CT dataset were generated on a 3D workstation. In phase 1, photographs of the 29 subjects undergoing CT scans were added to a digital directory and tested for recognition using facial recognition software. In phases 2-4, additional photographs were added in groups of 50 to increase the pool of possible matches and the test for recognition was repeated. As an internal control, photographs of all subjects were tested for recognition against an identical photograph. Of 3D reconstructions, 27.5% were matched correctly to corresponding photographs (95% upper CL, 40.1%). All study subject photographs were matched correctly to identical photographs (95% lower CL, 88.6%). Of 3D reconstructions, 96.6% were recognized simply as a face by the software (95% lower CL, 83.5%). Facial recognition software has the potential to recognize features on 3D CT surface reconstructions and match these with photographs, with implications for PHI.

Low-cost Method for Obtaining Medical Rapid Prototyping Using Desktop 3D printing: A Novel Technique for Mandibular Reconstruction Planning

PubMed Central

Vahdani, Soheil; Ramos, Hector

2017-01-01

Background Three-dimensional (3D) printing is relatively a new technology with clinical applications, which enable us to create rapid accurate prototype of the selected anatomic region, making it possible to plan complex surgery and pre-bend hardware for individual surgical cases. This study aimed to express our experience with the use of medical rapid prototype (MRP) of the maxillofacial region created by desktop 3D printer and its application in maxillofacial reconstructive surgeries. Material and Methods Three patients with benign mandible tumors were included in this study after obtaining informed consent. All patient’s maxillofacial CT scan data was processed by segmentation and isolation software and mandible MRP was printed using our desktop 3D printer. These models were used for preoperative surgical planning and prebending of the reconstruction plate. Conclusions MRP created by desktop 3D printer is a cost-efficient, quick and easily produced appliance for the planning of reconstructive surgery. It can contribute in patient orientation and helping them in a better understanding of their condition and proposed surgical treatment. It helps surgeons for pre-operative planning in the resection or reconstruction cases and represent an excellent tool in academic setting for residents training. The pre-bended reconstruction plate based on MRP, resulted in decreased surgery time, cost and anesthesia risks on the patients. Key words:3D printing, medical modeling, rapid prototype, mandibular reconstruction, ameloblastoma. PMID:29075412

A 3D Reconstruction Strategy of Vehicle Outline Based on Single-Pass Single-Polarization CSAR Data.

PubMed

Leping Chen; Daoxiang An; Xiaotao Huang; Zhimin Zhou

2017-11-01

In the last few years, interest in circular synthetic aperture radar (CSAR) acquisitions has arisen as a consequence of the potential achievement of 3D reconstructions over 360° azimuth angle variation. In real-world scenarios, full 3D reconstructions of arbitrary targets need multi-pass data, which makes the processing complex, money-consuming, and time expending. In this paper, we propose a processing strategy for the 3D reconstruction of vehicle, which can avoid using multi-pass data by introducing a priori information of vehicle's shape. Besides, the proposed strategy just needs the single-pass single-polarization CSAR data to perform vehicle's 3D reconstruction, which makes the processing much more economic and efficient. First, an analysis of the distribution of attributed scattering centers from vehicle facet model is presented. And the analysis results show that a smooth and continuous basic outline of vehicle could be extracted from the peak curve of a noncoherent processing image. Second, the 3D location of vehicle roofline is inferred from layover with empirical insets of the basic outline. At last, the basic line and roofline of the vehicle are used to estimate the vehicle's 3D information and constitute the vehicle's 3D outline. The simulated and measured data processing results prove the correctness and effectiveness of our proposed strategy.

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.

Multi Sensor Data Integration for AN Accurate 3d Model Generation

NASA Astrophysics Data System (ADS)

Chhatkuli, S.; Satoh, T.; Tachibana, K.

2015-05-01

The aim of this paper is to introduce a novel technique of data integration between two different data sets, i.e. laser scanned RGB point cloud and oblique imageries derived 3D model, to create a 3D model with more details and better accuracy. In general, aerial imageries are used to create a 3D city model. Aerial imageries produce an overall decent 3D city models and generally suit to generate 3D model of building roof and some non-complex terrain. However, the automatically generated 3D model, from aerial imageries, generally suffers from the lack of accuracy in deriving the 3D model of road under the bridges, details under tree canopy, isolated trees, etc. Moreover, the automatically generated 3D model from aerial imageries also suffers from undulated road surfaces, non-conforming building shapes, loss of minute details like street furniture, etc. in many cases. On the other hand, laser scanned data and images taken from mobile vehicle platform can produce more detailed 3D road model, street furniture model, 3D model of details under bridge, etc. However, laser scanned data and images from mobile vehicle are not suitable to acquire detailed 3D model of tall buildings, roof tops, and so forth. Our proposed approach to integrate multi sensor data compensated each other's weakness and helped to create a very detailed 3D model with better accuracy. Moreover, the additional details like isolated trees, street furniture, etc. which were missing in the original 3D model derived from aerial imageries could also be integrated in the final model automatically. During the process, the noise in the laser scanned data for example people, vehicles etc. on the road were also automatically removed. Hence, even though the two dataset were acquired in different time period the integrated data set or the final 3D model was generally noise free and without unnecessary details.

SU-E-T-154: Establishment and Implement of 3D Image Guided Brachytherapy Planning System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, S; Zhao, S; Chen, Y

2014-06-01

Purpose: Cannot observe the dose intuitionally is a limitation of the existing 2D pre-implantation dose planning. Meanwhile, a navigation module is essential to improve the accuracy and efficiency of the implantation. Hence a 3D Image Guided Brachytherapy Planning System conducting dose planning and intra-operative navigation based on 3D multi-organs reconstruction is developed. Methods: Multi-organs including the tumor are reconstructed in one sweep of all the segmented images using the multiorgans reconstruction method. The reconstructed organs group establishs a three-dimensional visualized operative environment. The 3D dose maps of the three-dimentional conformal localized dose planning are calculated with Monte Carlo method whilemore » the corresponding isodose lines and isodose surfaces are displayed in a stereo view. The real-time intra-operative navigation is based on an electromagnetic tracking system (ETS) and the fusion between MRI and ultrasound images. Applying Least Square Method, the coordinate registration between 3D models and patient is realized by the ETS which is calibrated by a laser tracker. The system is validated by working on eight patients with prostate cancer. The navigation has passed the precision measurement in the laboratory. Results: The traditional marching cubes (MC) method reconstructs one organ at one time and assembles them together. Compared to MC, presented multi-organs reconstruction method has superiorities in reserving the integrality and connectivity of reconstructed organs. The 3D conformal localized dose planning, realizing the 'exfoliation display' of different isodose surfaces, helps make sure the dose distribution has encompassed the nidus and avoid the injury of healthy tissues. During the navigation, surgeons could observe the coordinate of instruments real-timely employing the ETS. After the calibration, accuracy error of the needle position is less than 2.5mm according to the experiments. Conclusion: The speed and quality of 3D reconstruction, the efficiency in dose planning and accuracy in navigation all can be improved simultaneously.« less

Reconstructing White Walls: Multi-View Multi-Shot 3d Reconstruction of Textureless Surfaces

NASA Astrophysics Data System (ADS)

Ley, Andreas; Hänsch, Ronny; Hellwich, Olaf

2016-06-01

The reconstruction of the 3D geometry of a scene based on image sequences has been a very active field of research for decades. Nevertheless, there are still existing challenges in particular for homogeneous parts of objects. This paper proposes a solution to enhance the 3D reconstruction of weakly-textured surfaces by using standard cameras as well as a standard multi-view stereo pipeline. The underlying idea of the proposed method is based on improving the signal-to-noise ratio in weakly-textured regions while adaptively amplifying the local contrast to make better use of the limited numerical range in 8-bit images. Based on this premise, multiple shots per viewpoint are used to suppress statistically uncorrelated noise and enhance low-contrast texture. By only changing the image acquisition and adding a preprocessing step, a tremendous increase of up to 300% in completeness of the 3D reconstruction is achieved.

Case series of 64 slice computed tomography-computed tomographic angiography with 3D reconstruction to diagnose symptomatic cerebral aneurysms: new standard of care?

PubMed Central

Jehle, Dietrich; Chae, Floria; Wai, Jonathan; Cloud, Sam; Pierce, David; Meyer, Michael

2012-01-01

CT angiography (CTA) has improved significantly over the past few years such that the reconstructed images of the cerebral arteries may now be equivalent to conventional digital angiography. The new technology of 64 slice multi-detector CTA can reconstruct detailed images that can reliably identify small cerebral aneurysms, even those <3mm. In addition, it is estimated that CT followed by lumbar puncture (LP) misses up to 4% of symptomatic aneurysms. We present a series of cases that illustrates how CT followed by CTA may be replacing CT-LP as the standard of care in working up patients for symptomatic cerebral aneurysms and the importance of performing three dimensional (3D) reconstructions. A series of seven cases of symptomatic cerebral aneurysms were identified that illustrate the sensitivity of CT-CTA versus CT-LP and the importance of 3D reconstruction in identifying these aneurysms. Surgical treatment was recommended for 6 of the 7 patients with aneurysms and strict hypertension control was recommended for the seventh patient. Some of these patients demonstrated subarachnoid hemorrhage on presentation while others had negative LPs. A number of these patients with negative LPs were clearly symptomatic from their aneurysms. At least one of these cerebral aneurysms was not apparent on CTA without 3D reconstruction. 3D reconstruction of CTA is crucial to adequately identify cerebral aneurysms. This case series helps reinforce the importance of 3D reconstruction. There is some data to suggest that 64 slice CT-CTA may be equivalent or superior to CT-LP in the detection of symptomatic cerebral aneurysms. PMID:22593806

Intermediate view reconstruction using adaptive disparity search algorithm for real-time 3D processing

NASA Astrophysics Data System (ADS)

Bae, Kyung-hoon; Park, Changhan; Kim, Eun-soo

2008-03-01

In this paper, intermediate view reconstruction (IVR) using adaptive disparity search algorithm (ASDA) is for realtime 3-dimensional (3D) processing proposed. The proposed algorithm can reduce processing time of disparity estimation by selecting adaptive disparity search range. Also, the proposed algorithm can increase the quality of the 3D imaging. That is, by adaptively predicting the mutual correlation between stereo images pair using the proposed algorithm, the bandwidth of stereo input images pair can be compressed to the level of a conventional 2D image and a predicted image also can be effectively reconstructed using a reference image and disparity vectors. From some experiments, stereo sequences of 'Pot Plant' and 'IVO', it is shown that the proposed algorithm improves the PSNRs of a reconstructed image to about 4.8 dB by comparing with that of conventional algorithms, and reduces the Synthesizing time of a reconstructed image to about 7.02 sec by comparing with that of conventional algorithms.

Automatic updating and 3D modeling of airport information from high resolution images using GIS and LIDAR data

NASA Astrophysics Data System (ADS)

Lv, Zheng; Sui, Haigang; Zhang, Xilin; Huang, Xianfeng

2007-11-01

As one of the most important geo-spatial objects and military establishment, airport is always a key target in fields of transportation and military affairs. Therefore, automatic recognition and extraction of airport from remote sensing images is very important and urgent for updating of civil aviation and military application. In this paper, a new multi-source data fusion approach on automatic airport information extraction, updating and 3D modeling is addressed. Corresponding key technologies including feature extraction of airport information based on a modified Ostu algorithm, automatic change detection based on new parallel lines-based buffer detection algorithm, 3D modeling based on gradual elimination of non-building points algorithm, 3D change detecting between old airport model and LIDAR data, typical CAD models imported and so on are discussed in detail. At last, based on these technologies, we develop a prototype system and the results show our method can achieve good effects.

A fully automatic three-step liver segmentation method on LDA-based probability maps for multiple contrast MR images.

PubMed

Gloger, Oliver; Kühn, Jens; Stanski, Adam; Völzke, Henry; Puls, Ralf

2010-07-01

Automatic 3D liver segmentation in magnetic resonance (MR) data sets has proven to be a very challenging task in the domain of medical image analysis. There exist numerous approaches for automatic 3D liver segmentation on computer tomography data sets that have influenced the segmentation of MR images. In contrast to previous approaches to liver segmentation in MR data sets, we use all available MR channel information of different weightings and formulate liver tissue and position probabilities in a probabilistic framework. We apply multiclass linear discriminant analysis as a fast and efficient dimensionality reduction technique and generate probability maps then used for segmentation. We develop a fully automatic three-step 3D segmentation approach based upon a modified region growing approach and a further threshold technique. Finally, we incorporate characteristic prior knowledge to improve the segmentation results. This novel 3D segmentation approach is modularized and can be applied for normal and fat accumulated liver tissue properties. Copyright 2010 Elsevier Inc. All rights reserved.

3D-MSCT imaging of bullet trajectory in 3D crime scene reconstruction: two case reports.

PubMed

Colard, T; Delannoy, Y; Bresson, F; Marechal, C; Raul, J S; Hedouin, V

2013-11-01

Postmortem investigations are increasingly assisted by three-dimensional multi-slice computed tomography (3D-MSCT) and have become more available to forensic pathologists over the past 20years. In cases of ballistic wounds, 3D-MSCT can provide an accurate description of the bullet location, bone fractures and, more interestingly, a clear visual of the intracorporeal trajectory (bullet track). These forensic medical examinations can be combined with tridimensional bullet trajectory reconstructions created by forensic ballistic experts. These case reports present the implementation of tridimensional methods and the results of 3D crime scene reconstruction in two cases. The authors highlight the value of collaborations between police forensic experts and forensic medicine institutes through the incorporation of 3D-MSCT data in a crime scene reconstruction, which is of great interest in forensic science as a clear visual communication tool between experts and the court. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Virtual rough samples to test 3D nanometer-scale scanning electron microscopy stereo photogrammetry.

PubMed

Villarrubia, J S; Tondare, V N; Vladár, A E

2016-01-01

The combination of scanning electron microscopy for high spatial resolution, images from multiple angles to provide 3D information, and commercially available stereo photogrammetry software for 3D reconstruction offers promise for nanometer-scale dimensional metrology in 3D. A method is described to test 3D photogrammetry software by the use of virtual samples-mathematical samples from which simulated images are made for use as inputs to the software under test. The virtual sample is constructed by wrapping a rough skin with any desired power spectral density around a smooth near-trapezoidal line with rounded top corners. Reconstruction is performed with images simulated from different angular viewpoints. The software's reconstructed 3D model is then compared to the known geometry of the virtual sample. Three commercial photogrammetry software packages were tested. Two of them produced results for line height and width that were within close to 1 nm of the correct values. All of the packages exhibited some difficulty in reconstructing details of the surface roughness.

Photogrammetry in 3d Modelling of Human Bone Structures from Radiographs

NASA Astrophysics Data System (ADS)

Hosseinian, S.; Arefi, H.

2017-05-01

Photogrammetry can have great impact on the success of medical processes for diagnosis, treatment and surgeries. Precise 3D models which can be achieved by photogrammetry improve considerably the results of orthopedic surgeries and processes. Usual 3D imaging techniques, computed tomography (CT) and magnetic resonance imaging (MRI), have some limitations such as being used only in non-weight-bearing positions, costs and high radiation dose(for CT) and limitations of MRI for patients with ferromagnetic implants or objects in their bodies. 3D reconstruction of bony structures from biplanar X-ray images is a reliable and accepted alternative for achieving accurate 3D information with low dose radiation in weight-bearing positions. The information can be obtained from multi-view radiographs by using photogrammetry. The primary step for 3D reconstruction of human bone structure from medical X-ray images is calibration which is done by applying principles of photogrammetry. After the calibration step, 3D reconstruction can be done using efficient methods with different levels of automation. Because of the different nature of X-ray images from optical images, there are distinct challenges in medical applications for calibration step of stereoradiography. In this paper, after demonstrating the general steps and principles of 3D reconstruction from X-ray images, a comparison will be done on calibration methods for 3D reconstruction from radiographs and they are assessed from photogrammetry point of view by considering various metrics such as their camera models, calibration objects, accuracy, availability, patient-friendly and cost.

Multiview 3D sensing and analysis for high quality point cloud reconstruction

NASA Astrophysics Data System (ADS)

Satnik, Andrej; Izquierdo, Ebroul; Orjesek, Richard

2018-04-01

Multiview 3D reconstruction techniques enable digital reconstruction of 3D objects from the real world by fusing different viewpoints of the same object into a single 3D representation. This process is by no means trivial and the acquisition of high quality point cloud representations of dynamic 3D objects is still an open problem. In this paper, an approach for high fidelity 3D point cloud generation using low cost 3D sensing hardware is presented. The proposed approach runs in an efficient low-cost hardware setting based on several Kinect v2 scanners connected to a single PC. It performs autocalibration and runs in real-time exploiting an efficient composition of several filtering methods including Radius Outlier Removal (ROR), Weighted Median filter (WM) and Weighted Inter-Frame Average filtering (WIFA). The performance of the proposed method has been demonstrated through efficient acquisition of dense 3D point clouds of moving objects.

Automatic extraction of via in the CT image of PCB

NASA Astrophysics Data System (ADS)

Liu, Xifeng; Hu, Yuwei

2018-04-01

In modern industry, the nondestructive testing of printed circuit board (PCB) can prevent effectively the system failure and is becoming more and more important. In order to detect the via in the PCB base on the CT image automatically accurately and reliably, a novel algorithm for via extraction based on weighting stack combining the morphologic character of via is designed. Every slice data in the vertical direction of the PCB is superimposed to enhanced vias target. The OTSU algorithm is used to segment the slice image. OTSU algorithm of thresholding gray level images is efficient for separating an image into two classes where two types of fairly distinct classes exist in the image. Randomized Hough Transform was used to locate the region of via in the segmented binary image. Then the 3D reconstruction of via based on sequence slice images was done by volume rendering. The accuracy of via positioning and detecting from a CT images of PCB was demonstrated by proposed algorithm. It was found that the method is good in veracity and stability for detecting of via in three dimensional.

Fast multiview three-dimensional reconstruction method using cost volume filtering

NASA Astrophysics Data System (ADS)

Lee, Seung Joo; Park, Min Ki; Jang, In Yeop; Lee, Kwan H.

2014-03-01

As the number of customers who want to record three-dimensional (3-D) information using a mobile electronic device increases, it becomes more and more important to develop a method which quickly reconstructs a 3-D model from multiview images. A fast multiview-based 3-D reconstruction method is presented, which is suitable for the mobile environment by constructing a cost volume of the 3-D height field. This method consists of two steps: the construction of a reliable base surface and the recovery of shape details. In each step, the cost volume is constructed using photoconsistency and then it is filtered according to the multiscale. The multiscale-based cost volume filtering allows the 3-D reconstruction to maintain the overall shape and to preserve the shape details. We demonstrate the strength of the proposed method in terms of computation time, accuracy, and unconstrained acquisition environment.

Applications of Computer Technology in Complex Craniofacial Reconstruction.

PubMed

Day, Kristopher M; Gabrick, Kyle S; Sargent, Larry A

2018-03-01

To demonstrate our use of advanced 3-dimensional (3D) computer technology in the analysis, virtual surgical planning (VSP), 3D modeling (3DM), and treatment of complex congenital and acquired craniofacial deformities. We present a series of craniofacial defects treated at a tertiary craniofacial referral center utilizing state-of-the-art 3D computer technology. All patients treated at our center using computer-assisted VSP, prefabricated custom-designed 3DMs, and/or 3D printed custom implants (3DPCI) in the reconstruction of craniofacial defects were included in this analysis. We describe the use of 3D computer technology to precisely analyze, plan, and reconstruct 31 craniofacial deformities/syndromes caused by: Pierre-Robin (7), Treacher Collins (5), Apert's (2), Pfeiffer (2), Crouzon (1) Syndromes, craniosynostosis (6), hemifacial microsomia (2), micrognathia (2), multiple facial clefts (1), and trauma (3). In select cases where the available bone was insufficient for skeletal reconstruction, 3DPCIs were fabricated using 3D printing. We used VSP in 30, 3DMs in all 31, distraction osteogenesis in 16, and 3DPCIs in 13 cases. Utilizing these technologies, the above complex craniofacial defects were corrected without significant complications and with excellent aesthetic results. Modern 3D technology allows the surgeon to better analyze complex craniofacial deformities, precisely plan surgical correction with computer simulation of results, customize osteotomies, plan distractions, and print 3DPCI, as needed. The use of advanced 3D computer technology can be applied safely and potentially improve aesthetic and functional outcomes after complex craniofacial reconstruction. These techniques warrant further study and may be reproducible in various centers of care.

A hierarchical structure for automatic meshing and adaptive FEM analysis

NASA Technical Reports Server (NTRS)

Kela, Ajay; Saxena, Mukul; Perucchio, Renato

1987-01-01

A new algorithm for generating automatically, from solid models of mechanical parts, finite element meshes that are organized as spatially addressable quaternary trees (for 2-D work) or octal trees (for 3-D work) is discussed. Because such meshes are inherently hierarchical as well as spatially addressable, they permit efficient substructuring techniques to be used for both global analysis and incremental remeshing and reanalysis. The global and incremental techniques are summarized and some results from an experimental closed loop 2-D system in which meshing, analysis, error evaluation, and remeshing and reanalysis are done automatically and adaptively are presented. The implementation of 3-D work is briefly discussed.

Immediate breast reconstruction with anatomical implants following mastectomy: The radiation perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben-David, Merav, E-mail: Merav.ben-david@sheba.health.gov.il; Sackler School of Medicine, Tel Aviv University, Tel Aviv; Granot, Hila

2016-07-01

Immediate implant-based breast reconstruction followed by postmastectomy radiation therapy (PMRT) is controversial because of the risk of compromised treatment plans and concerns regarding cosmetic outcomes. We evaluated the effects of immediate direct-to-implant breast reconstruction with anatomical implants on the quality of PMRT delivered by 3-dimensional conformal radiotherapy (3D-CRT). In this retrospective, single-institution study, patients who had undergone reconstruction with direct anatomic implant, performed by a single surgeon, received 3D-CRT between 2008 and 2013. For each patient, 2 plans (including or excluding internal mammary nodes [IMN]) were created and calculated. The primary end point was the dose distribution among reconstructed breasts,more » heart, lungs, and IMNs, and between right and left breasts. Of 29 consecutive patients, 11 received right-sided and 18 received left-sided PMRT to a total dose of 50 Gy. For plans excluding IMN coverage, mean D{sub mean} for right and left reconstructed breasts was 49.09 Gy (98.2% of the prescribed dose) and 48.51 Gy (97.0%), respectively. For plans including IMNs, mean D{sub mean} was 49.15 Gy (98.3%) for right and 48.46 Gy (96.9%) for left reconstructed breasts; the mean IMN D{sub mean} was 47.27 Gy (right) and 47.89 Gy (left). Heart D{sub mean} was below 1.56 Gy for all plans. Mean total lung volume receiving a dose of ≥ 20 Gy was 13.80% to 19.47%. PMRT can be delivered effectively and safely by 3D-CRT after direct-to-implant breast reconstruction with anatomical implants, even if patients require IMN treatment.« less

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging.

PubMed

Kolehmainen, Ville; Vanne, Antti; Siltanen, Samuli; Järvenpää, Seppo; Kaipio, Jari P; Lassas, Matti; Kalke, Martti

2006-02-01

Diagnostic and operational tasks based on dental radiology often require three-dimensional (3-D) information that is not available in a single X-ray projection image. Comprehensive 3-D information about tissues can be obtained by computerized tomography (CT) imaging. However, in dental imaging a conventional CT scan may not be available or practical because of high radiation dose, low-resolution or the cost of the CT scanner equipment. In this paper, we consider a novel type of 3-D imaging modality for dental radiology. We consider situations in which projection images of the teeth are taken from a few sparsely distributed projection directions using the dentist's regular (digital) X-ray equipment and the 3-D X-ray attenuation function is reconstructed. A complication in these experiments is that the reconstruction of the 3-D structure based on a few projection images becomes an ill-posed inverse problem. Bayesian inversion is a well suited framework for reconstruction from such incomplete data. In Bayesian inversion, the ill-posed reconstruction problem is formulated in a well-posed probabilistic form in which a priori information is used to compensate for the incomplete information of the projection data. In this paper we propose a Bayesian method for 3-D reconstruction in dental radiology. The method is partially based on Kolehmainen et al. 2003. The prior model for dental structures consist of a weighted l1 and total variation (TV)-prior together with the positivity prior. The inverse problem is stated as finding the maximum a posteriori (MAP) estimate. To make the 3-D reconstruction computationally feasible, a parallelized version of an optimization algorithm is implemented for a Beowulf cluster computer. The method is tested with projection data from dental specimens and patient data. Tomosynthetic reconstructions are given as reference for the proposed method.

Modelisation de l'architecture des forets pour ameliorer la teledetection des attributs forestiers

NASA Astrophysics Data System (ADS)

Cote, Jean-Francois

The quality of indirect measurements of canopy structure, from in situ and satellite remote sensing, is based on knowledge of vegetation canopy architecture. Technological advances in ground-based, airborne or satellite remote sensing can now significantly improve the effectiveness of measurement programs on forest resources. The structure of vegetation canopy describes the position, orientation, size and shape of elements of the canopy. The complexity of the canopy in forest environments greatly limits our ability to characterize forest structural attributes. Architectural models have been developed to help the interpretation of canopy structural measurements by remote sensing. Recently, the terrestrial LiDAR systems, or TLiDAR (Terrestrial Light Detection and Ranging), are used to gather information on the structure of individual trees or forest stands. The TLiDAR allows the extraction of 3D structural information under the canopy at the centimetre scale. The methodology proposed in my Ph.D. thesis is a strategy to overcome the weakness in the structural sampling of vegetation cover. The main objective of the Ph.D. is to develop an architectural model of vegetation canopy, called L-Architect (LiDAR data to vegetation Architecture), and to focus on the ability to document forest sites and to get information on canopy structure from remote sensing tools. Specifically, L-Architect reconstructs the architecture of individual conifer trees from TLiDAR data. Quantitative evaluation of L-Architect consisted to investigate (i) the structural consistency of the reconstructed trees and (ii) the radiative coherence by the inclusion of reconstructed trees in a 3D radiative transfer model. Then, a methodology was developed to quasi-automatically reconstruct the structure of individual trees from an optimization algorithm using TLiDAR data and allometric relationships. L-Architect thus provides an explicit link between the range measurements of TLiDAR and structural attributes of individual trees. L-Architect has finally been applied to model the architecture of forest canopy for better characterization of vertical and horizontal structure with airborne LiDAR data. This project provides a mean to answer requests of detailed canopy architectural data, difficult to obtain, to reproduce a variety of forest covers. Because of the importance of architectural models, L-Architect provides a significant contribution for improving the capacity of parameters' inversion in vegetation cover for optical and lidar remote sensing. Mots-cles: modelisation architecturale, lidar terrestre, couvert forestier, parametres structuraux, teledetection.

A novel three-dimensional image reconstruction method for near-field coded aperture single photon emission computerized tomography

PubMed Central

Mu, Zhiping; Hong, Baoming; Li, Shimin; Liu, Yi-Hwa

2009-01-01

Coded aperture imaging for two-dimensional (2D) planar objects has been investigated extensively in the past, whereas little success has been achieved in imaging 3D objects using this technique. In this article, the authors present a novel method of 3D single photon emission computerized tomography (SPECT) reconstruction for near-field coded aperture imaging. Multiangular coded aperture projections are acquired and a stack of 2D images is reconstructed separately from each of the projections. Secondary projections are subsequently generated from the reconstructed image stacks based on the geometry of parallel-hole collimation and the variable magnification of near-field coded aperture imaging. Sinograms of cross-sectional slices of 3D objects are assembled from the secondary projections, and the ordered subset expectation and maximization algorithm is employed to reconstruct the cross-sectional image slices from the sinograms. Experiments were conducted using a customized capillary tube phantom and a micro hot rod phantom. Imaged at approximately 50 cm from the detector, hot rods in the phantom with diameters as small as 2.4 mm could be discerned in the reconstructed SPECT images. These results have demonstrated the feasibility of the authors’ 3D coded aperture image reconstruction algorithm for SPECT, representing an important step in their effort to develop a high sensitivity and high resolution SPECT imaging system. PMID:19544769

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters.

PubMed

Galavis, Paulina E; Hollensen, Christian; Jallow, Ngoneh; Paliwal, Bhudatt; Jeraj, Robert

2010-10-01

Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45-60 minutes post-injection of 10 mCi of [(18)F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor segmentation.

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters

PubMed Central

GALAVIS, PAULINA E.; HOLLENSEN, CHRISTIAN; JALLOW, NGONEH; PALIWAL, BHUDATT; JERAJ, ROBERT

2014-01-01

Background Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Material and methods Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45–60 minutes post-injection of 10 mCi of [18F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Results Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Conclusion Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor segmentation. PMID:20831489

Three-Dimensional Printing: Custom-Made Implants for Craniomaxillofacial Reconstructive Surgery

PubMed Central

Matias, Mariana; Zenha, Horácio; Costa, Horácio

2017-01-01

Craniomaxillofacial reconstructive surgery is a challenging field. First it aims to restore primary functions and second to preserve craniofacial anatomical features like symmetry and harmony. Three-dimensional (3D) printed biomodels have been widely adopted in medical fields by providing tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. Craniomaxillofacial reconstructive surgery was one of the first areas to implement 3D printing technology in their practice. Biomodeling has been used in craniofacial reconstruction of traumatic injuries, congenital disorders, tumor removal, iatrogenic injuries (e.g., decompressive craniectomies), orthognathic surgery, and implantology. 3D printing has proven to improve and enable an optimization of preoperative planning, develop intraoperative guidance tools, reduce operative time, and significantly improve the biofunctional and the aesthetic outcome. This technology has also shown great potential in enriching the teaching of medical students and surgical residents. The aim of this review is to present the current status of 3D printing technology and its practical and innovative applications, specifically in craniomaxillofacial reconstructive surgery, illustrated with two clinical cases where the 3D printing technology was successfully used. PMID:28523082

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

PubMed Central

Ross, James D.; Cullen, D. Kacy; Harris, James P.; LaPlaca, Michelle C.; DeWeerth, Stephen P.

2015-01-01

Three-dimensional (3-D) image analysis techniques provide a powerful means to rapidly and accurately assess complex morphological and functional interactions between neural cells. Current software-based identification methods of neural cells generally fall into two applications: (1) segmentation of cell nuclei in high-density constructs or (2) tracing of cell neurites in single cell investigations. We have developed novel methodologies to permit the systematic identification of populations of neuronal somata possessing rich morphological detail and dense neurite arborization throughout thick tissue or 3-D in vitro constructs. The image analysis incorporates several novel automated features for the discrimination of neurites and somata by initially classifying features in 2-D and merging these classifications into 3-D objects; the 3-D reconstructions automatically identify and adjust for over and under segmentation errors. Additionally, the platform provides for software-assisted error corrections to further minimize error. These features attain very accurate cell boundary identifications to handle a wide range of morphological complexities. We validated these tools using confocal z-stacks from thick 3-D neural constructs where neuronal somata had varying degrees of neurite arborization and complexity, achieving an accuracy of ≥95%. We demonstrated the robustness of these algorithms in a more complex arena through the automated segmentation of neural cells in ex vivo brain slices. These novel methods surpass previous techniques by improving the robustness and accuracy by: (1) the ability to process neurites and somata, (2) bidirectional segmentation correction, and (3) validation via software-assisted user input. This 3-D image analysis platform provides valuable tools for the unbiased analysis of neural tissue or tissue surrogates within a 3-D context, appropriate for the study of multi-dimensional cell-cell and cell-extracellular matrix interactions. PMID:26257609

3D SAPIV particle field reconstruction method based on adaptive threshold.

PubMed

Qu, Xiangju; Song, Yang; Jin, Ying; Li, Zhenhua; Wang, Xuezhen; Guo, ZhenYan; Ji, Yunjing; He, Anzhi

2018-03-01

Particle image velocimetry (PIV) is a necessary flow field diagnostic technique that provides instantaneous velocimetry information non-intrusively. Three-dimensional (3D) PIV methods can supply the full understanding of a 3D structure, the complete stress tensor, and the vorticity vector in the complex flows. In synthetic aperture particle image velocimetry (SAPIV), the flow field can be measured with large particle intensities from the same direction by different cameras. During SAPIV particle reconstruction, particles are commonly reconstructed by manually setting a threshold to filter out unfocused particles in the refocused images. In this paper, the particle intensity distribution in refocused images is analyzed, and a SAPIV particle field reconstruction method based on an adaptive threshold is presented. By using the adaptive threshold to filter the 3D measurement volume integrally, the three-dimensional location information of the focused particles can be reconstructed. The cross correlations between images captured from cameras and images projected by the reconstructed particle field are calculated for different threshold values. The optimal threshold is determined by cubic curve fitting and is defined as the threshold value that causes the correlation coefficient to reach its maximum. The numerical simulation of a 16-camera array and a particle field at two adjacent time events quantitatively evaluates the performance of the proposed method. An experimental system consisting of a camera array of 16 cameras was used to reconstruct the four adjacent frames in a vortex flow field. The results show that the proposed reconstruction method can effectively reconstruct the 3D particle fields.

In vivo bioluminescence tomography based on multi-view projection and 3D surface reconstruction

NASA Astrophysics Data System (ADS)

Zhang, Shuang; Wang, Kun; Leng, Chengcai; Deng, Kexin; Hu, Yifang; Tian, Jie

2015-03-01

Bioluminescence tomography (BLT) is a powerful optical molecular imaging modality, which enables non-invasive realtime in vivo imaging as well as 3D quantitative analysis in preclinical studies. In order to solve the inverse problem and reconstruct inner light sources accurately, the prior structural information is commonly necessary and obtained from computed tomography or magnetic resonance imaging. This strategy requires expensive hybrid imaging system, complicated operation protocol and possible involvement of ionizing radiation. The overall robustness highly depends on the fusion accuracy between the optical and structural information. In this study we present a pure optical bioluminescence tomographic system (POBTS) and a novel BLT method based on multi-view projection acquisition and 3D surface reconstruction. The POBTS acquired a sparse set of white light surface images and bioluminescent images of a mouse. Then the white light images were applied to an approximate surface model to generate a high quality textured 3D surface reconstruction of the mouse. After that we integrated multi-view luminescent images based on the previous reconstruction, and applied an algorithm to calibrate and quantify the surface luminescent flux in 3D.Finally, the internal bioluminescence source reconstruction was achieved with this prior information. A BALB/C mouse with breast tumor of 4T1-fLuc cells mouse model were used to evaluate the performance of the new system and technique. Compared with the conventional hybrid optical-CT approach using the same inverse reconstruction method, the reconstruction accuracy of this technique was improved. The distance error between the actual and reconstructed internal source was decreased by 0.184 mm.

2D image classification for 3D anatomy localization: employing deep convolutional neural networks

NASA Astrophysics Data System (ADS)

de Vos, Bob D.; Wolterink, Jelmer M.; de Jong, Pim A.; Viergever, Max A.; Išgum, Ivana

2016-03-01

Localization of anatomical regions of interest (ROIs) is a preprocessing step in many medical image analysis tasks. While trivial for humans, it is complex for automatic methods. Classic machine learning approaches require the challenge of hand crafting features to describe differences between ROIs and background. Deep convolutional neural networks (CNNs) alleviate this by automatically finding hierarchical feature representations from raw images. We employ this trait to detect anatomical ROIs in 2D image slices in order to localize them in 3D. In 100 low-dose non-contrast enhanced non-ECG synchronized screening chest CT scans, a reference standard was defined by manually delineating rectangular bounding boxes around three anatomical ROIs -- heart, aortic arch, and descending aorta. Every anatomical ROI was automatically identified using a combination of three CNNs, each analyzing one orthogonal image plane. While single CNNs predicted presence or absence of a specific ROI in the given plane, the combination of their results provided a 3D bounding box around it. Classification performance of each CNN, expressed in area under the receiver operating characteristic curve, was >=0.988. Additionally, the performance of ROI localization was evaluated. Median Dice scores for automatically determined bounding boxes around the heart, aortic arch, and descending aorta were 0.89, 0.70, and 0.85 respectively. The results demonstrate that accurate automatic 3D localization of anatomical structures by CNN-based 2D image classification is feasible.

Comparing a novel automatic 3D method for LGE-CMR quantification of scar size with established methods.

PubMed

Woie, Leik; Måløy, Frode; Eftestøl, Trygve; Engan, Kjersti; Edvardsen, Thor; Kvaløy, Jan Terje; Ørn, Stein

2014-02-01

Current methods for the estimation of infarct size by late-enhanced cardiac magnetic imaging are based upon 2D analysis that first determines the size of the infarction in each slice, and thereafter adds the infarct sizes from each slice to generate a volume. We present a novel, automatic 3D method that estimates infarct size by a simultaneous analysis of all pixels from all slices. In a population of 54 patients with ischemic scars, the infarct size estimated by the automatic 3D method was compared with four established 2D methods. The new 3D method defined scar as the sum of all pixels with signal intensity (SI) ≥35 % of max SI from the complete myocardium, border zone: SI 35-50 % of max SI and core as SI ≥50 % of max SI. The 3D method yielded smaller infarct size (-2.8 ± 2.3 %) and core size (-3.0 ± 1.7 %) than the 2D method most similar to ours. There was no difference in the size of the border zone (0.2 ± 1.4 %). The 3D method demonstrated stronger correlations between scar size and left ventricular (LV) remodelling parameters (LV ejection fraction: r = -0.71, p < 0.0005, LV end-diastolic index: r = 0.54, p < 0.0005, and LV end-systolic index: r = 0.59, p < 0.0005) compared with conventional 2D methods. Infarct size estimation by our novel 3D automatic method is without the need for manual demarcation of the scar; it is less time-consuming and has a stronger correlation with remodelling parameters compared with existing methods.

Is Unilateral Implant or Autologous Breast Reconstruction Better in Obtaining Breast Symmetry?

PubMed

Cohen, Oriana; Small, Kevin; Lee, Christina; Petruolo, Oriana; Karp, Nolan; Choi, Mihye

2016-01-01

Unilateral breast reconstruction poses a special set of challenges to the reconstructive breast surgeon compared to bilateral reconstructions. No studies to date provide an objective comparison between autologous and implant based reconstructions in matching the contralateral breast. This study compares the quantitative postoperative results between unilateral implant and autologous flap reconstructions in matching the native breast in shape, size, and projection using three-dimensional (3D) imaging. Sixty-four patients who underwent unilateral mastectomy with tissue expander (TE)-implant (n = 34) or autologous microvascular free transverse rectus abdominus myocutaneous (TRAM; n = 18) or deep inferior epigastric artery perforator (DIEP; n = 12) flap (n = 30) reconstruction from 2007 to 2010 were analyzed. Key patient demographics and risk factors were collected. Using 3D scans of patients obtained during pre and postoperative visits including over 1 year follow-ups for both groups, 3D models were constructed and analyzed for total breast volume, anterior-posterior projection from the chest wall, and 3D comparison. No significant differences in mean age, body mass index, or total number of reconstructive surgeries were observed between the two groups (TE-implant: 52.2 ± 10, 23.9 ± 3.7, 3 ± 0.9; autologous: 50.7 ± 9.4, 25.4 ± 3.9, 2.9 ± 1.3; p > 0.05). The total volume difference between the reconstructed and contralateral breasts in the TE-implant group was insignificant: 27.1 ± 22.2 cc, similar to the autologous group: 29.5 ± 24.7 cc, as was the variance of breast volume from the mean. In both groups, the reconstructed breast had a larger volume. A-P projections were similar between the contralateral and the reconstructed breasts in the TE-implant group: 72.5 ± 3.21 mm versus 71.7 ± 3.5 mm (p > 0.05). The autologous reconstructed breast had statistically insignificant but less A-P projection compared to the contralateral breast (81.9 ± 16.1 mm versus 61.5 ± 9.5 mm; p > 0.05). Variance of A-P projection from the mean was additionally insignificant between the contralateral and reconstructed breasts. Both groups produced similar asymmetry scores based on global 3D comparison (TE-implant: 2.24 ± 0.3 mm; autologous: 1.96 ± 0.2 mm; p > 0.05). Lastly, when the autologous group was further subdivided into TRAM and DIEP cohorts, no significant differences in breast volume, A-P projection or symmetry existed. Using 3D imaging, we demonstrate that both TE-implant and autologous reconstruction can achieve symmetrical surgical results with the same number of operations. This study demonstrates that breast symmetry, while an important consideration in the breast reconstruction algorithm, should not be the sole consideration in a patient' decision to proceed with autologous versus TE-implant reconstruction. © 2015 Wiley Periodicals, Inc.

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, J; Yang, D

2015-06-15

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets,more » and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from Varian Medical System.« less

Picture grammars in classification and semantic interpretation of 3D coronary vessels visualisations

NASA Astrophysics Data System (ADS)

Ogiela, M. R.; Tadeusiewicz, R.; Trzupek, M.

2009-09-01

The work presents the new opportunity for making semantic descriptions and analysis of medical structures, especially coronary vessels CT spatial reconstructions, with the use of AI graph-based linguistic formalisms. In the paper there will be discussed the manners of applying methods of computational intelligence to the development of a syntactic semantic description of spatial visualisations of the heart's coronary vessels. Such descriptions may be used for both smart ordering of images while archiving them and for their semantic searches in medical multimedia databases. Presented methodology of analysis can furthermore be used for attaining other goals related performance of computer-assisted semantic interpretation of selected elements and/or the entire 3D structure of the coronary vascular tree. These goals are achieved through the use of graph-based image formalisms based on IE graphs generating grammars that allow discovering and automatic semantic interpretation of irregularities visualised on the images obtained during diagnostic examinations of the heart muscle. The basis for the construction of 3D reconstructions of biological objects used in this work are visualisations obtained from helical CT scans, yet the method itself may be applied also for other methods of medical 3D images acquisition. The obtained semantic information makes it possible to make a description of the structure focused on the semantics of various morphological forms of the visualised vessels from the point of view of the operation of coronary circulation and the blood supply of the heart muscle. Thanks to these, the analysis conducted allows fast and — to a great degree — automated interpretation of the semantics of various morphological changes in the coronary vascular tree, and especially makes it possible to detect these stenoses in the lumen of the vessels that can cause critical decrease in blood supply to extensive or especially important fragments of the heart muscle.

Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions

PubMed Central

Capurso, Daniel; Bengtsson, Henrik; Segal, Mark R.

2016-01-01

The spatial organization of the genome influences cellular function, notably gene regulation. Recent studies have assessed the three-dimensional (3D) co-localization of functional annotations (e.g. centromeres, long terminal repeats) using 3D genome reconstructions from Hi-C (genome-wide chromosome conformation capture) data; however, corresponding assessments for continuous functional genomic data (e.g. chromatin immunoprecipitation-sequencing (ChIP-seq) peak height) are lacking. Here, we demonstrate that applying bump hunting via the patient rule induction method (PRIM) to ChIP-seq data superposed on a Saccharomyces cerevisiae 3D genome reconstruction can discover ‘functional 3D hotspots’, regions in 3-space for which the mean ChIP-seq peak height is significantly elevated. For the transcription factor Swi6, the top hotspot by P-value contains MSB2 and ERG11 – known Swi6 target genes on different chromosomes. We verify this finding in a number of ways. First, this top hotspot is relatively stable under PRIM across parameter settings. Second, this hotspot is among the top hotspots by mean outcome identified by an alternative algorithm, k-Nearest Neighbor (k-NN) regression. Third, the distance between MSB2 and ERG11 is smaller than expected (by resampling) in two other 3D reconstructions generated via different normalization and reconstruction algorithms. This analytic approach can discover functional 3D hotspots and potentially reveal novel regulatory interactions. PMID:26869583

Simultaneous motion estimation and image reconstruction (SMEIR) for 4D cone-beam CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jing; Gu, Xuejun

2013-10-15

Purpose: Image reconstruction and motion model estimation in four-dimensional cone-beam CT (4D-CBCT) are conventionally handled as two sequential steps. Due to the limited number of projections at each phase, the image quality of 4D-CBCT is degraded by view aliasing artifacts, and the accuracy of subsequent motion modeling is decreased by the inferior 4D-CBCT. The objective of this work is to enhance both the image quality of 4D-CBCT and the accuracy of motion model estimation with a novel strategy enabling simultaneous motion estimation and image reconstruction (SMEIR).Methods: The proposed SMEIR algorithm consists of two alternating steps: (1) model-based iterative image reconstructionmore » to obtain a motion-compensated primary CBCT (m-pCBCT) and (2) motion model estimation to obtain an optimal set of deformation vector fields (DVFs) between the m-pCBCT and other 4D-CBCT phases. The motion-compensated image reconstruction is based on the simultaneous algebraic reconstruction technique (SART) coupled with total variation minimization. During the forward- and backprojection of SART, measured projections from an entire set of 4D-CBCT are used for reconstruction of the m-pCBCT by utilizing the updated DVF. The DVF is estimated by matching the forward projection of the deformed m-pCBCT and measured projections of other phases of 4D-CBCT. The performance of the SMEIR algorithm is quantitatively evaluated on a 4D NCAT phantom. The quality of reconstructed 4D images and the accuracy of tumor motion trajectory are assessed by comparing with those resulting from conventional sequential 4D-CBCT reconstructions (FDK and total variation minimization) and motion estimation (demons algorithm). The performance of the SMEIR algorithm is further evaluated by reconstructing a lung cancer patient 4D-CBCT.Results: Image quality of 4D-CBCT is greatly improved by the SMEIR algorithm in both phantom and patient studies. When all projections are used to reconstruct a 3D-CBCT by FDK, motion-blurring artifacts are present, leading to a 24.4% relative reconstruction error in the NACT phantom. View aliasing artifacts are present in 4D-CBCT reconstructed by FDK from 20 projections, with a relative error of 32.1%. When total variation minimization is used to reconstruct 4D-CBCT, the relative error is 18.9%. Image quality of 4D-CBCT is substantially improved by using the SMEIR algorithm and relative error is reduced to 7.6%. The maximum error (MaxE) of tumor motion determined from the DVF obtained by demons registration on a FDK-reconstructed 4D-CBCT is 3.0, 2.3, and 7.1 mm along left–right (L-R), anterior–posterior (A-P), and superior–inferior (S-I) directions, respectively. From the DVF obtained by demons registration on 4D-CBCT reconstructed by total variation minimization, the MaxE of tumor motion is reduced to 1.5, 0.5, and 5.5 mm along L-R, A-P, and S-I directions. From the DVF estimated by SMEIR algorithm, the MaxE of tumor motion is further reduced to 0.8, 0.4, and 1.5 mm along L-R, A-P, and S-I directions, respectively.Conclusions: The proposed SMEIR algorithm is able to estimate a motion model and reconstruct motion-compensated 4D-CBCT. The SMEIR algorithm improves image reconstruction accuracy of 4D-CBCT and tumor motion trajectory estimation accuracy as compared to conventional sequential 4D-CBCT reconstruction and motion estimation.« less

Three-dimensional proximal flow convergence automatic calculation for determining mitral valve area in rheumatic mitral stenosis.

PubMed

Sampaio, Francisco; Ladeiras-Lopes, Ricardo; Almeida, João; Fonseca, Paulo; Fontes-Carvalho, Ricardo; Ribeiro, José; Gama, Vasco

2017-07-01

Management of patients with mitral stenosis (MS) depends heavily on the accurate quantification of mitral valve area (MVA) using echocardiography. All currently used two-dimensional (2D) methods have limitations. Estimation of MVA using the proximal isovelocity surface area (PISA) method with real time three-dimensional (3D) echocardiography may circumvent those limitations. We aimed to evaluate the accuracy of 3D direct measurement of PISA in the estimation of MVA. Twenty-seven consecutive patients (median age of 63 years; 77.8% females) with rheumatic MS were prospectively studied. Transthoracic and transesophageal echocardiography with 2D and 3D acquisitions were performed on the same day. The reference method for MVA quantification was valve planimetry after 3D-volume multiplanar reconstruction. A semi-automated software was used to calculate the 3D flow convergence volume. Compared to MVA estimation using 3D planimetry, 3D PISA showed the best correlation (rho=0.78, P<.0001), followed by pressure half-time (PHT: rho=0.66, P<.001), continuity equation (CE: rho=0.61, P=.003), and 2D PISA (rho=0.26, P=.203). Bland-Altman analysis revealed a good agreement for MVA estimation with 3D PISA (mean difference -0.03 cm 2 ; limits of agreement (LOA) -0.40-0.35), in contrast to wider LOA for 2D methods: CE (mean difference 0.02 cm 2 , LOA -0.56-0.60); PHT (mean difference 0.31 cm 2 , LOA -0.32-0.95); 2D PISA (mean difference -0.03 cm 2 , LOA -0.92-0.86). MVA estimation using 3D PISA was feasible and more accurate than 2D methods. Its introduction in daily clinical practice seems possible and may overcome technical limitations of 2D methods. © 2017, Wiley Periodicals, Inc.