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Sample records for 3d confocal datasets

  1. Lifting Object Detection Datasets into 3D.

    PubMed

    Carreira, Joao; Vicente, Sara; Agapito, Lourdes; Batista, Jorge

    2016-07-01

    While data has certainly taken the center stage in computer vision in recent years, it can still be difficult to obtain in certain scenarios. In particular, acquiring ground truth 3D shapes of objects pictured in 2D images remains a challenging feat and this has hampered progress in recognition-based object reconstruction from a single image. Here we propose to bypass previous solutions such as 3D scanning or manual design, that scale poorly, and instead populate object category detection datasets semi-automatically with dense, per-object 3D reconstructions, bootstrapped from:(i) class labels, (ii) ground truth figure-ground segmentations and (iii) a small set of keypoint annotations. Our proposed algorithm first estimates camera viewpoint using rigid structure-from-motion and then reconstructs object shapes by optimizing over visual hull proposals guided by loose within-class shape similarity assumptions. The visual hull sampling process attempts to intersect an object's projection cone with the cones of minimal subsets of other similar objects among those pictured from certain vantage points. We show that our method is able to produce convincing per-object 3D reconstructions and to accurately estimate cameras viewpoints on one of the most challenging existing object-category detection datasets, PASCAL VOC. We hope that our results will re-stimulate interest on joint object recognition and 3D reconstruction from a single image. PMID:27295458

  2. 3D imaging of neutron tracks using confocal microscopy

    NASA Astrophysics Data System (ADS)

    Gillmore, Gavin; Wertheim, David; Flowers, Alan

    2016-04-01

    Neutron detection and neutron flux assessment are important aspects in monitoring nuclear energy production. Neutron flux measurements can also provide information on potential biological damage from exposure. In addition to the applications for neutron measurement in nuclear energy, neutron detection has been proposed as a method of enhancing neutrino detectors and cosmic ray flux has also been assessed using ground-level neutron detectors. Solid State Nuclear Track Detectors (or SSNTDs) have been used extensively to examine cosmic rays, long-lived radioactive elements, radon concentrations in buildings and the age of geological samples. Passive SSNTDs consisting of a CR-39 plastic are commonly used to measure radon because they respond to incident charged particles such as alpha particles from radon gas in air. They have a large dynamic range and a linear flux response. We have previously applied confocal microscopy to obtain 3D images of alpha particle tracks in SSNTDs from radon track monitoring (1). As a charged particle traverses through the polymer it creates an ionisation trail along its path. The trail or track is normally enhanced by chemical etching to better expose radiation damage, as the damaged area is more sensitive to the etchant than the bulk material. Particle tracks in CR-39 are usually assessed using 2D optical microscopy. In this study 6 detectors were examined using an Olympus OLS4100 LEXT 3D laser scanning confocal microscope (Olympus Corporation, Japan). The detectors had been etched for 2 hours 50 minutes at 85 °C in 6.25M NaOH. Post etch the plastics had been treated with a 10 minute immersion in a 2% acetic acid stop bath, followed by rinsing in deionised water. The detectors examined had been irradiated with a 2mSv neutron dose from an Am(Be) neutron source (producing roughly 20 tracks per mm2). We were able to successfully acquire 3D images of neutron tracks in the detectors studied. The range of track diameter observed was between 4

  3. Comparison of 3D orientation distribution functions measured with confocal microscopy and diffusion MRI.

    PubMed

    Schilling, Kurt; Janve, Vaibhav; Gao, Yurui; Stepniewska, Iwona; Landman, Bennett A; Anderson, Adam W

    2016-04-01

    The ability of diffusion MRI (dMRI) fiber tractography to non-invasively map three-dimensional (3D) anatomical networks in the human brain has made it a valuable tool in both clinical and research settings. However, there are many assumptions inherent to any tractography algorithm that can limit the accuracy of the reconstructed fiber tracts. Among them is the assumption that the diffusion-weighted images accurately reflect the underlying fiber orientation distribution (FOD) in the MRI voxel. Consequently, validating dMRI's ability to assess the underlying fiber orientation in each voxel is critical for its use as a biomedical tool. Here, using post-mortem histology and confocal microscopy, we present a method to perform histological validation of orientation functions in 3D, which has previously been limited to two-dimensional analysis of tissue sections. We demonstrate the ability to extract the 3D FOD from confocal z-stacks, and quantify the agreement between the MRI estimates of orientation information obtained using constrained spherical deconvolution (CSD) and the true geometry of the fibers. We find an orientation error of approximately 6° in voxels containing nearly parallel fibers, and 10-11° in crossing fiber regions, and note that CSD was unable to resolve fibers crossing at angles below 60° in our dataset. This is the first time that the 3D white matter orientation distribution is calculated from histology and compared to dMRI. Thus, this technique serves as a gold standard for dMRI validation studies - providing the ability to determine the extent to which the dMRI signal is consistent with the histological FOD, and to establish how well different dMRI models can predict the ground truth FOD. PMID:26804781

  4. Comparing multiple 3D magnetotelluric inversions of the same dataset

    NASA Astrophysics Data System (ADS)

    Walter, C.; Jones, A. G.

    2013-12-01

    The Taupo Volcanic Zone (TVZ) hosts the majority of the geothermal systems in New Zealand and is a valuable source for power generation and tourism. It is important for the sustainable exploitation of this area to fully understand the processes and structures in the TVZ. As part of the 'Hotter and Deeper' project of the Foundation for Research, Science and Technology (FRST), a dataset of 200 broadband magnetotelluric (MT) stations has been collected in the TVZ of New Zealand in 2009 and 2010. Combined with a smaller dataset from Reporoa, a total of 230 stations are available for 3D inversion to image the deeper structures of the TVZ. For the study presented in this paper, multiple 3D inversions of this dataset using different control parameters have been undertaken to study the influence of the choice of parameters on the inversion result. The parameters that have been varied include; the type of responses used in the inversion, the use of topography and bathymetry, and varying vertical grid spacings. All inversions commenced with a uniform half-space so that there was no preconceived structures to begin with. The results show that the main structures in the model are robust in that they are independent of the choice of parameters and become introduced in every inversion. The only differences are in the shape and exact location of the structures, which vary between the models. Furthermore, different ways to get a measure for the differences between models have been explored.

  5. 3-D reconstruction of neurons from multichannel confocal laser scanning image series.

    PubMed

    Wouterlood, Floris G

    2014-01-01

    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. PMID:24723320

  6. Comparison of global 3-D aviation emissions datasets

    NASA Astrophysics Data System (ADS)

    Olsen, S. C.; Wuebbles, D. J.; Owen, B.

    2013-01-01

    Aviation emissions are unique from other transportation emissions, e.g., from road transportation and shipping, in that they occur at higher altitudes as well as at the surface. Aviation emissions of carbon dioxide, soot, and water vapor have direct radiative impacts on the Earth's climate system while emissions of nitrogen oxides (NOx), sulfur oxides, carbon monoxide (CO), and hydrocarbons (HC) impact air quality and climate through their effects on ozone, methane, and clouds. The most accurate estimates of the impact of aviation on air quality and climate utilize three-dimensional chemistry-climate models and gridded four dimensional (space and time) aviation emissions datasets. We compare five available aviation emissions datasets currently and historically used to evaluate the impact of aviation on climate and air quality: NASA-Boeing 1992, NASA-Boeing 1999, QUANTIFY 2000, Aero2k 2002, and AEDT 2006 and aviation fuel usage estimates from the International Energy Agency. Roughly 90% of all aviation emissions are in the Northern Hemisphere and nearly 60% of all fuelburn and NOx emissions occur at cruise altitudes in the Northern Hemisphere. While these datasets were created by independent methods and are thus not strictly suitable for analyzing trends they suggest that commercial aviation fuelburn and NOx emissions increased over the last two decades while HC emissions likely decreased and CO emissions did not change significantly. The bottom-up estimates compared here are consistently lower than International Energy Agency fuelburn statistics although the gap is significantly smaller in the more recent datasets. Overall the emissions distributions are quite similar for fuelburn and NOx with regional peaks over the populated land masses of North America, Europe, and East Asia. For CO and HC there are relatively larger differences. There are however some distinct differences in the altitude distribution of emissions in certain regions for the Aero2k dataset.

  7. Richardson-Lucy algorithm with total variation regularization for 3D confocal microscope deconvolution.

    PubMed

    Dey, Nicolas; Blanc-Feraud, Laure; Zimmer, Christophe; Roux, Pascal; Kam, Zvi; Olivo-Marin, Jean-Christophe; Zerubia, Josiane

    2006-04-01

    Confocal laser scanning microscopy is a powerful and popular technique for 3D imaging of biological specimens. Although confocal microscopy images are much sharper than standard epifluorescence ones, they are still degraded by residual out-of-focus light and by Poisson noise due to photon-limited detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes maximum likelihood estimation adapted to Poisson statistics. As this algorithm tends to amplify noise, regularization constraints based on some prior knowledge on the data have to be applied to stabilize the solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularization constraint based on Total Variation, which suppresses unstable oscillations while preserving object edges. We show on simulated and real images that this constraint improves the deconvolution results as compared with the unregularized Richardson-Lucy algorithm, both visually and quantitatively. PMID:16586486

  8. Ultrafast superpixel segmentation of large 3D medical datasets

    NASA Astrophysics Data System (ADS)

    Leblond, Antoine; Kauffmann, Claude

    2016-03-01

    Even with recent hardware improvements, superpixel segmentation of large 3D medical images at interactive speed (<500 ms) remains a challenge. We will describe methods to achieve such performances using a GPU based hybrid framework implementing wavefront propagation and cellular automata resolution. Tasks will be scheduled in blocks (work units) using a wavefront propagation strategy, therefore allowing sparse scheduling. Because work units has been designed as spatially cohesive, the fast Thread Group Shared Memory can be used and reused through a Gauss-Seidel like acceleration. The work unit partitioning scheme will however vary on odd- and even-numbered iterations to reduce convergence barriers. Synchronization will be ensured by an 8-step 3D variant of the traditional Red Black Ordering scheme. An attack model and early termination will also be described and implemented as additional acceleration techniques. Using our hybrid framework and typical operating parameters, we were able to compute the superpixels of a high-resolution 512x512x512 aortic angioCT scan in 283 ms using a AMD R9 290X GPU. We achieved a 22.3X speed-up factor compared to the published reference GPU implementation.

  9. Correlative Confocal and 3D Electron Microscopy of a Specific Sensory Cell

    PubMed Central

    Bohórquez, Diego; Haque, Fariha; Medicetty, Satish; Liddle, Rodger A.

    2015-01-01

    Delineation of a cell’s ultrastructure is important for understanding its function. This can be a daunting project for rare cell types diffused throughout tissues made of diverse cell types, such as enteroendocrine cells of the intestinal epithelium. These gastrointestinal sensors of food and bacteria have been difficult to study because they are dispersed among other epithelial cells at a ratio of 1:1,000. Recently, transgenic reporter mice have been generated to identify enteroendocrine cells by means of fluorescence. One of those is the peptide YY-GFP mouse. Using this mouse, we developed a method to correlate confocal and serial block-face scanning electron microscopy. We named the method cocem3D and applied it to identify a specific enteroendocrine cell in tissue and unveil the cell’s ultrastructure in 3D. The resolution of cocem3D is sufficient to identify organelles as small as secretory vesicles and to distinguish cell membranes for volume rendering. Cocem3D can be easily adapted to study the 3D ultrastructure of other specific cell types in their native tissue. PMID:26273796

  10. Spectral mapping of 3D multi-cellular tumor spheroids: time-resolved confocal microscopy.

    PubMed

    Mohapatra, Saswat; Nandi, Somen; Chowdhury, Rajdeep; Das, Gaurav; Ghosh, Surajit; Bhattacharyya, Kankan

    2016-07-21

    A tumor-like multi-cellular spheroid (3D) differs from a 2D cell in a number of ways. This is demonstrated using time resolved confocal microscopy. Two different tumor spheroids - HeLa (cervical cancer) and A549 (lung cancer) - are studied using 3 different fluorescent dyes - C153 (non-covalent), CPM (covalent) and doxorubicin (non-covalent, anti-cancer drug). The pattern of localization of these three fluorescent probes in the 3D tumor cell exhibits significant differences from that in the conventional 2D cells. For both the cells (HeLa and A549), the total uptake of doxorubicin in the 3D cell is much lower than that in the 2D cell. The uptake of doxorubicin molecules in the A549 spheroid is significantly different compared to the HeLa spheroid. The local polarity (i.e. emission maxima) and solvation dynamics in the 3D tumor cell differ from those in 2D cells. The covalent probe CPM exhibits intermittent fluorescence oscillations in the 1-2 s time scale. This is attributed to redox processes. These results may provide new insights into 3D tumors. PMID:27336201

  11. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  12. 3D optical sectioning with a new hyperspectral confocal fluorescence imaging system.

    SciTech Connect

    Nieman, Linda T.; Sinclair, Michael B.; Davidson, George S.; Van Benthem, Mark Hilary; Haaland, David Michael; Timlin, Jerilyn Ann; Sasaki, Darryl Yoshio; Bachand, George David; Jones, Howland D. T.

    2007-02-01

    A novel hyperspectral fluorescence microscope for high-resolution 3D optical sectioning of cells and other structures has been designed, constructed, and used to investigate a number of different problems. We have significantly extended new multivariate curve resolution (MCR) data analysis methods to deconvolve the hyperspectral image data and to rapidly extract quantitative 3D concentration distribution maps of all emitting species. The imaging system has many advantages over current confocal imaging systems including simultaneous monitoring of numerous highly overlapped fluorophores, immunity to autofluorescence or impurity fluorescence, enhanced sensitivity, and dramatically improved accuracy, reliability, and dynamic range. Efficient data compression in the spectral dimension has allowed personal computers to perform quantitative analysis of hyperspectral images of large size without loss of image quality. We have also developed and tested software to perform analysis of time resolved hyperspectral images using trilinear multivariate analysis methods. The new imaging system is an enabling technology for numerous applications including (1) 3D composition mapping analysis of multicomponent processes occurring during host-pathogen interactions, (2) monitoring microfluidic processes, (3) imaging of molecular motors and (4) understanding photosynthetic processes in wild type and mutant Synechocystis cyanobacteria.

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

    PubMed

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

    2009-01-01

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

  14. Estimation of single cell volume from 3D confocal images using automatic data processing

    NASA Astrophysics Data System (ADS)

    Chorvatova, A.; Cagalinec, M.; Mateasik, A.; Chorvat, D., Jr.

    2012-06-01

    Cardiac cells are highly structured with a non-uniform morphology. Although precise estimation of their volume is essential for correct evaluation of hypertrophic changes of the heart, simple and unified techniques that allow determination of the single cardiomyocyte volume with sufficient precision are still limited. Here, we describe a novel approach to assess the cell volume from confocal microscopy 3D images of living cardiac myocytes. We propose a fast procedure based on segementation using active deformable contours. This technique is independent on laser gain and/or pinhole settings and it is also applicable on images of cells stained with low fluorescence markers. Presented approach is a promising new tool to investigate changes in the cell volume during normal, as well as pathological growth, as we demonstrate in the case of cell enlargement during hypertension in rats.

  15. Comparing GPU Implementations of Bilateral and Anisotropic Diffusion Filters for 3D Biomedical Datasets

    SciTech Connect

    Howison, Mark

    2010-05-06

    We compare the performance of hand-tuned CUDA implementations of bilateral and anisotropic diffusion filters for denoising 3D MRI datasets. Our tests sweep comparable parameters for the two filters and measure total runtime, memory bandwidth, computational throughput, and mean squared errors relative to a noiseless reference dataset.

  16. Performance and sensitivity evaluation of 3D spot detection methods in confocal microscopy.

    PubMed

    Štěpka, Karel; Matula, Pavel; Matula, Petr; Wörz, Stefan; Rohr, Karl; Kozubek, Michal

    2015-08-01

    Reliable 3D detection of diffraction-limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non-specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the F1 score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the F1 score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high-quality images, and for situations in which detailed parameter tuning might be deemed expensive. PMID:26033916

  17. Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

    PubMed Central

    Grocott, Timothy; Thomas, Paul; Münsterberg, Andrea E.

    2016-01-01

    Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states. PMID:26864723

  18. Mars US rover traverse co-registration using multi-resolution Orbital 3D imaging datasets

    NASA Astrophysics Data System (ADS)

    Poole, W. D.

    2013-09-01

    Co-registered 3D Digital terrain Models (DTMs) and orthorectified imaging (ORI) orbital datasets have been produced of all the major US Mars landing sites. These have been sourced from HiRise, HRSC and MOLA. Co-registration was achieved using manual tiepointing within ARCgis v10. These DTM and ORI products were sourced from publicly available datasets or from EU-FP7-PRoViSG partners or generated using internal UCL 3D-RPIF [1] resources. For rover traverses, this results in substantial transformations which implies that all the SPICE kernels will need to be recomputed.

  19. Confocal fluorometer for diffusion tracking in 3D engineered tissue constructs

    NASA Astrophysics Data System (ADS)

    Daly, D.; Zilioli, A.; Tan, N.; Buttenschoen, K.; Chikkanna, B.; Reynolds, J.; Marsden, B.; Hughes, C.

    2016-03-01

    We present results of the development of a non-contacting instrument, called fScan, based on scanning confocal fluorometry for assessing the diffusion of materials through a tissue matrix. There are many areas in healthcare diagnostics and screening where it is now widely accepted that the need for new quantitative monitoring technologies is a major pinch point in patient diagnostics and in vitro testing. With the increasing need to interpret 3D responses this commonly involves the need to track the diffusion of compounds, pharma-active species and cells through a 3D matrix of tissue. Methods are available but to support the advances that are currently only promised, this monitoring needs to be real-time, non-invasive, and economical. At the moment commercial meters tend to be invasive and usually require a sample of the medium to be removed and processed prior to testing. This methodology clearly has a number of significant disadvantages. fScan combines a fiber based optical arrangement with a compact, free space optical front end that has been integrated so that the sample's diffusion can be measured without interference. This architecture is particularly important due to the "wet" nature of the samples. fScan is designed to measure constructs located within standard well plates and a 2-D motion stage locates the required sample with respect to the measurement system. Results are presented that show how the meter has been used to evaluate movements of samples through collagen constructs in situ without disturbing their kinetic characteristics. These kinetics were little understood prior to these measurements.

  20. Efficient segmentation of 3D fluoroscopic datasets from mobile C-arm

    NASA Astrophysics Data System (ADS)

    Styner, Martin A.; Talib, Haydar; Singh, Digvijay; Nolte, Lutz-Peter

    2004-05-01

    The emerging mobile fluoroscopic 3D technology linked with a navigation system combines the advantages of CT-based and C-arm-based navigation. The intra-operative, automatic segmentation of 3D fluoroscopy datasets enables the combined visualization of surgical instruments and anatomical structures for enhanced planning, surgical eye-navigation and landmark digitization. We performed a thorough evaluation of several segmentation algorithms using a large set of data from different anatomical regions and man-made phantom objects. The analyzed segmentation methods include automatic thresholding, morphological operations, an adapted region growing method and an implicit 3D geodesic snake method. In regard to computational efficiency, all methods performed within acceptable limits on a standard Desktop PC (30sec-5min). In general, the best results were obtained with datasets from long bones, followed by extremities. The segmentations of spine, pelvis and shoulder datasets were generally of poorer quality. As expected, the threshold-based methods produced the worst results. The combined thresholding and morphological operations methods were considered appropriate for a smaller set of clean images. The region growing method performed generally much better in regard to computational efficiency and segmentation correctness, especially for datasets of joints, and lumbar and cervical spine regions. The less efficient implicit snake method was able to additionally remove wrongly segmented skin tissue regions. This study presents a step towards efficient intra-operative segmentation of 3D fluoroscopy datasets, but there is room for improvement. Next, we plan to study model-based approaches for datasets from the knee and hip joint region, which would be thenceforth applied to all anatomical regions in our continuing development of an ideal segmentation procedure for 3D fluoroscopic images.

  1. 3D Printing of CT Dataset: Validation of an Open Source and Consumer-Available Workflow.

    PubMed

    Bortolotto, Chandra; Eshja, Esmeralda; Peroni, Caterina; Orlandi, Matteo A; Bizzotto, Nicola; Poggi, Paolo

    2016-02-01

    The broad availability of cheap three-dimensional (3D) printing equipment has raised the need for a thorough analysis on its effects on clinical accuracy. Our aim is to determine whether the accuracy of 3D printing process is affected by the use of a low-budget workflow based on open source software and consumer's commercially available 3D printers. A group of test objects was scanned with a 64-slice computed tomography (CT) in order to build their 3D copies. CT datasets were elaborated using a software chain based on three free and open source software. Objects were printed out with a commercially available 3D printer. Both the 3D copies and the test objects were measured using a digital professional caliper. Overall, the objects' mean absolute difference between test objects and 3D copies is 0.23 mm and the mean relative difference amounts to 0.55 %. Our results demonstrate that the accuracy of 3D printing process remains high despite the use of a low-budget workflow. PMID:26175139

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

    PubMed Central

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

    2013-01-01

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

  3. Points based reconstruction and rendering of 3D shapes from large volume dataset

    NASA Astrophysics Data System (ADS)

    Zhao, Mingchang; Tian, Jie; He, Huiguang; Li, Guangming

    2003-05-01

    In the field of medical imaging, researchers often need visualize lots of 3D datasets to get the informaiton contained in these datasets. But the huge data genreated by modern medical imaging device challenge the real time processing and rendering algorithms at all the time. Spurring by the great achievement of Points Based Rendering (PBR) in the fields of computer graphics to render very large meshes, we propose a new algorithm to use the points as basic primitive of surface reconstruction and rendering to interactively reconstruct and render very large volume dataset. By utilizing the special characteristics of medical image datasets, we obtain a fast and efficient points-based reconstruction and rendering algorithm in common PC. The experimental results show taht this algorithm is feasible and efficient.

  4. Lacunarity analysis of raster datasets and 1D, 2D, and 3D point patterns

    NASA Astrophysics Data System (ADS)

    Dong, Pinliang

    2009-10-01

    Spatial scale plays an important role in many fields. As a scale-dependent measure for spatial heterogeneity, lacunarity describes the distribution of gaps within a set at multiple scales. In Earth science, environmental science, and ecology, lacunarity has been increasingly used for multiscale modeling of spatial patterns. This paper presents the development and implementation of a geographic information system (GIS) software extension for lacunarity analysis of raster datasets and 1D, 2D, and 3D point patterns. Depending on the application requirement, lacunarity analysis can be performed in two modes: global mode or local mode. The extension works for: (1) binary (1-bit) and grey-scale datasets in any raster format supported by ArcGIS and (2) 1D, 2D, and 3D point datasets as shapefiles or geodatabase feature classes. For more effective measurement of lacunarity for different patterns or processes in raster datasets, the extension allows users to define an area of interest (AOI) in four different ways, including using a polygon in an existing feature layer. Additionally, directionality can be taken into account when grey-scale datasets are used for local lacunarity analysis. The methodology and graphical user interface (GUI) are described. The application of the extension is demonstrated using both simulated and real datasets, including Brodatz texture images, a Spaceborne Imaging Radar (SIR-C) image, simulated 1D points on a drainage network, and 3D random and clustered point patterns. The options of lacunarity analysis and the effects of polyline arrangement on lacunarity of 1D points are also discussed. Results from sample data suggest that the lacunarity analysis extension can be used for efficient modeling of spatial patterns at multiple scales.

  5. 3D Quantitative Confocal Laser Microscopy of Ilmenite Volume Distribution in Alpe Arami Olivine

    NASA Astrophysics Data System (ADS)

    Bozhilov, K. N.

    2001-12-01

    The deep origin of the Alpe Arami garnet lherzolite massif in the Swiss Alps proposed by Dobrzhinetskaya et al. (Science, 1996) has been a focus of heated debate. One of the lines of evidence supporting an exhumation from more than 200 km depth includes the abundance, distribution, and orientation of magnesian ilmenite rods in the oldest generation of olivine. This argument has been disputed in terms of the abundance of ilmenite and consequently the maximum TiO2 content in the discussed olivine. In order to address this issue, we have directly measured the volume fraction of ilmenite of the oldest generation of olivine by applying confocal laser scanning microscopy (CLSM). CLSM is a method which allows for three-dimensional imaging and quantitative volume determination by optical sectioning of the objects. The images for 3D reconstruction and measurements were acquired from petrographic thin sections in reflected laser light with 488 nm wavelength. Measurements of more than 80 olivine grains in six thin sections of our material yielded an average volume fraction of 0.31% ilmenite in the oldest generation of olivine from Alpe Arami. This translates into 0.23 wt.% TiO2 in olivine with error in determination of ±0.097 wt.%, a value significantly different from that of 0.02 to 0.03 wt.% TiO2 determined by Hacker et al. (Science, 1997) by a broad-beam microanalysis technique. During the complex geological history of the Alpe Arami massif, several events of metamorphism are recorded which all could have caused increased mobility of the mineral components. Evidence for loss of TiO2 from olivine is the tendency for high densities of ilmenite to be restricted to cores of old grains, the complete absence of ilmenite inclusions from the younger, recrystallized, generation of olivine, and reduction in ilmenite size and abundance in more serpentinized specimens. These observations suggest that only olivine grains with the highest concentrations of ilmenite are close to the

  6. Computational Graph Model for 3D Cells Tracking in Zebra Fish Datasets

    NASA Astrophysics Data System (ADS)

    Zhang, Lelin; Xiong, Hongkai; Zhao, Yang; Zhang, Kai; Zhou, Xiaobo

    2007-11-01

    This paper leads to a novel technique for tracking and identification of zebra-fish cells in 3D image sequences, extending graph-based multi-objects tracking algorithm to 3D applications. As raised in previous work of 2D graph-based method, separated cells are modeled as vertices that connected by edges. Then the tracking work is simplified to that of vertices matching between graphs generated from consecutive frames. Graph-based tracking is composed of three steps: graph generation, initial source vertices selection and graph saturation. To satisfy demands in this work separated cell records are segmented from original datasets using 3D level-set algorithms. Besides, advancements are achieved in each of the step including graph regulations, multi restrictions on source vertices and enhanced flow quantifications. Those strategies make a good compensation for graph-based multi-objects tracking method in 2D space. Experiments are carried out in 3D datasets sampled from zebra fish, results of which shows that this enhanced method could be potentially applied to tracking of objects with diverse features.

  7. Nondestructive 3D confocal laser imaging with deconvolution of seven whole stardust tracks with complementary XRF and quantitative analysis

    SciTech Connect

    Greenberg, M.; Ebel, D.S.

    2009-03-19

    We present a nondestructive 3D system for analysis of whole Stardust tracks, using a combination of Laser Confocal Scanning Microscopy and synchrotron XRF. 3D deconvolution is used for optical corrections, and results of quantitative analyses of several tracks are presented. The Stardust mission to comet Wild 2 trapped many cometary and ISM particles in aerogel, leaving behind 'tracks' of melted silica aerogel on both sides of the collector. Collected particles and their tracks range in size from submicron to millimeter scale. Interstellar dust collected on the obverse of the aerogel collector is thought to have an average track length of {approx}15 {micro}m. It has been our goal to perform a total non-destructive 3D textural and XRF chemical analysis on both types of tracks. To that end, we use a combination of Laser Confocal Scanning Microscopy (LCSM) and X Ray Florescence (XRF) spectrometry. Utilized properly, the combination of 3D optical data and chemical data provides total nondestructive characterization of full tracks, prior to flattening or other destructive analysis methods. Our LCSM techniques allow imaging at 0.075 {micro}m/pixel, without the use of oil-based lenses. A full textural analysis on track No.82 is presented here as well as analysis of 6 additional tracks contained within 3 keystones (No.128, No.129 and No.140). We present a method of removing the axial distortion inherent in LCSM images, by means of a computational 3D Deconvolution algorithm, and present some preliminary experiments with computed point spread functions. The combination of 3D LCSM data and XRF data provides invaluable information, while preserving the integrity of the samples for further analysis. It is imperative that these samples, the first extraterrestrial solids returned since the Apollo era, be fully mapped nondestructively in 3D, to preserve the maximum amount of information prior to other, destructive analysis.

  8. Confocal Microscopy of thick tissue sections: 3D Visualization of rat kidney glomeruli

    EPA Science Inventory

    Confocal laser scanning microscopy (CLSM) as a technique capable of generating serial sections of whole-mount tissue and then reassembling the computer-acquired images as a virtual 3-dimentional structure. In many ways CLSM offers an alternative to traditional sectioning approac...

  9. Confocal microscopy of thick tissue sections: 3D visualizaiton of rat kidney glomeruli

    EPA Science Inventory

    Confocal laser scanning microscopy (CLSM) as a technique capable of generating serial sections of whole-mount tissue and then reassembling the computer-acquired images as a virtual 3-dimentional structure. In many ways CLSM offers an alternative to traditional sectioning approac...

  10. Quantification of fluorescent spots in time series of 3D confocal microscopy images of endoplasmic reticulum exit sites based on the HMAX transform

    NASA Astrophysics Data System (ADS)

    Matula, Petr; Verissimo, Fatima; Wörz, Stefan; Eils, Roland; Pepperkok, Rainer; Rohr, Karl

    2010-03-01

    We present an approach for the quantification of fluorescent spots in time series of 3-D confocal microscopy images of endoplasmic reticulum exit sites of dividing cells. Fluorescent spots are detected based on extracted image regions of highest response using the HMAX transform and prior convolution of the 3-D images with a Gaussian kernel. The sensitivity of the involved parameters was studied and a quantitative evaluation using both 3-D synthetic and 3-D real data was performed. The approach was successfully applied to more than one thousand 3-D confocal microscopy images.

  11. New results from a 3D seismic academic dataset across the west Galicia margin

    NASA Astrophysics Data System (ADS)

    Lymer, Gaël; Cresswell, Derren; Reston, Tim; Stevenson, Carl; Sawyer, Dale

    2016-04-01

    The west Galicia margin (western Spain) is a magma-poor margin and has limited sedimentary cover, providing ideal conditions to study the processes of continental extension and break-up through seismic imaging. The margin is characterised by hyper-extended continental crust, well defined rotated faults blocks with associated syn-kinematic sedimentary wedges, and exhumed serpentinized continental mantle. Faulted blocks overlie a bright reflection, the S reflector, generally interpreted as both a detachment and the crust-mantle boundary. But open questions remain concerning the role of the S detachment in extension leading to breakup. To study further the S reflection and its role in continental breakup, a new 3D high-resolution multi-channel seismic dataset has been acquired over the Galicia margin during summer 2013. It consists in 800 inlines and 5000 crosslines distributed on a ~680 km2 areal. This 3D dataset is thus the largest academic one of its kind. It extends across the edge of the continental crust and captures the 3D nature of extension and break-up of the northern Atlantic continental margins. Here we present some results from our interpretations of the 3D volume, which allow various horizons, including the base of the post-rift sedimentary cover, the top basement and the S reflector, to be mapped out in 3D. These maps provide 3D views of the margin structure and also reveal the texture of each horizon. We also focus on the internal structure of some of the faulted blocks through interpretation of the crustal normal faults. The main normal faults are generally connected downward on the S reflector, revealing strong interactions between crustal thinning and the S. The half-grabens and the fault blocks are dominantly N-S oriented, but the crustal structures vary both along strike and cross strike. We particularly observe an intriguingly NW-SE trend, highlighted by a pronounced low within the crest of the fault blocks. We also observe this trend from

  12. XuvTools: free, fast and reliable stitching of large 3D datasets.

    PubMed

    Emmenlauer, M; Ronneberger, O; Ponti, A; Schwarb, P; Griffa, A; Filippi, A; Nitschke, R; Driever, W; Burkhardt, H

    2009-01-01

    Current biomedical research increasingly requires imaging large and thick 3D structures at high resolution. Prominent examples are the tracking of fine filaments over long distances in brain slices, or the localization of gene expression or cell migration in whole animals like Caenorhabditis elegans or zebrafish. To obtain both high resolution and a large field of view (FOV), a combination of multiple recordings ('tiles') is one of the options. Although hardware solutions exist for fast and reproducible acquisition of multiple 3D tiles, generic software solutions are missing to assemble ('stitch') these tiles quickly and accurately. In this paper, we present a framework that achieves fully automated recombination of tiles recorded at arbitrary positions in 3D space, as long as some small overlap between tiles is provided. A fully automated 3D correlation between all tiles is achieved such that no manual interaction or prior knowledge about tile positions is needed. We use (1) phase-only correlation in a multi-scale approach to estimate the coarse positions, (2) normalized cross-correlation of small patches extracted at salient points to obtain the precise matches, (3) find the globally optimal placement for all tiles by a singular value decomposition and (4) accomplish a nearly seamless stitching by a bleaching correction at the tile borders. If the dataset contains multiple channels, all channels are used to obtain the best matches between tiles. For speedup we employ a heuristic method to prune unneeded correlations, and compute all correlations via the fast Fourier transform (FFT), thereby achieving very good runtime performance. We demonstrate the successful application of the proposed framework to a wide range of different datasets from whole zebrafish embryos and C. elegans, mouse and rat brain slices and fine plant hairs (trichome). Further, we compare our stitching results to those of other commercially and freely available software solutions. The

  13. 3D image restoration for confocal microscopy: toward a wavelet deconvolution for the study of complex biological structures

    NASA Astrophysics Data System (ADS)

    Boutet de Monvel, Jacques; Le Calvez, Sophie; Ulfendahl, Mats

    2000-05-01

    Image restoration algorithms provide efficient tools for recovering part of the information lost in the imaging process of a microscope. We describe recent progress in the application of deconvolution to confocal microscopy. The point spread function of a Biorad-MRC1024 confocal microscope was measured under various imaging conditions, and used to process 3D-confocal images acquired in an intact preparation of the inner ear developed at Karolinska Institutet. Using these experiments we investigate the application of denoising methods based on wavelet analysis as a natural regularization of the deconvolution process. Within the Bayesian approach to image restoration, we compare wavelet denoising with the use of a maximum entropy constraint as another natural regularization method. Numerical experiments performed with test images show a clear advantage of the wavelet denoising approach, allowing to `cool down' the image with respect to the signal, while suppressing much of the fine-scale artifacts appearing during deconvolution due to the presence of noise, incomplete knowledge of the point spread function, or undersampling problems. We further describe a natural development of this approach, which consists of performing the Bayesian inference directly in the wavelet domain.

  14. Unlocking the scientific potential of complex 3D point cloud dataset : new classification and 3D comparison methods

    NASA Astrophysics Data System (ADS)

    Lague, D.; Brodu, N.; Leroux, J.

    2012-12-01

    Ground based lidar and photogrammetric techniques are increasingly used to track the evolution of natural surfaces in 3D at an unprecedented resolution and precision. The range of applications encompass many type of natural surfaces with different geometries and roughness characteristics (landslides, cliff erosion, river beds, bank erosion,....). Unravelling surface change in these contexts requires to compare large point clouds in 2D or 3D. The most commonly used method in geomorphology is based on a 2D difference of the gridded point clouds. Yet this is hardly adapted to many 3D natural environments such as rivers (with horizontal beds and vertical banks), while gridding complex rough surfaces is a complex task. On the other hand, tools allowing to perform 3D comparison are scarce and may require to mesh the point clouds which is difficult on rough natural surfaces. Moreover, existing 3D comparison tools do not provide an explicit calculation of confidence intervals that would factor in registration errors, roughness effects and instrument related position uncertainties. To unlock this problem, we developed the first algorithm combining a 3D measurement of surface change directly on point clouds with an estimate of spatially variable confidence intervals (called M3C2). The method has two steps : (1) surface normal estimation and orientation in 3D at a scale consistent with the local roughness ; (2) measurement of mean surface change along the normal direction with explicit calculation of a local confidence interval. Comparison with existing 3D methods based on a closest-point calculation demonstrates the higher precision of the M3C2 method when mm changes needs to be detected. The M3C2 method is also simple to use as it does not require surface meshing or gridding, and is not sensitive to missing data or change in point density. We also present a 3D classification tool (CANUPO) for vegetation removal based on a new geometrical measure: the multi

  15. Improved 3D density modelling of the Central Andes from combining terrestrial datasets with satellite based datasets

    NASA Astrophysics Data System (ADS)

    Schaller, Theresa; Sobiesiak, Monika; Götze, Hans-Jürgen; Ebbing, Jörg

    2015-04-01

    As horizontal gravity gradients are proxies for large stresses, the uniquely high gravity gradients of the South American continental margin seem to be indicative for the frequently occurring large earthquakes at this plate boundary. It has been observed that these earthquakes can break repeatedly the same respective segment but can also combine to form M>9 earthquakes at the end of longer seismic cycles. A large seismic gap left behind by the 1877 M~9 earthquake existed in the northernmost part of Chile. This gap has partially been ruptured in the Mw 7.7 2007 Tocopilla earthquake and the Mw 8.2 2014 Pisagua earthquake. The nature of this seismological segmentation and the distribution of energy release in an earthquake is part of ongoing research. It can be assumed that both features are related to thickness variations of high density bodies located in the continental crust of the coastal area. These batholiths produce a clear maximum in the gravity signal. Those maxima also show a good spatial correlation with seismic asperity structures and seismological segment boundaries. Understanding of the tectonic situation can be improved through 3D forward density modelling of the gravity field. Problems arise in areas with less ground measurements. Especially in the high Andes severe gaps exist due to the inaccessibility of some regions. Also the transition zone between on and offshore date data displays significant problems, particularly since this is the area that is most interesting in terms of seismic hazard. We modelled the continental and oceanic crust and upper mantle using different gravity datasets. The first one includes terrestrial data measured at a station spacing of 5 km or less along all passable roads combined with satellite altimetry data offshore. The second data set is the newly released EIGEN-6C4 which combines the latest satellite data with ground measurements. The spherical harmonics maximum degree of EIGEN-6C4 is 2190 which corresponds to a

  16. Parallel deconvolution of large 3D images obtained by confocal laser scanning microscopy.

    PubMed

    Pawliczek, Piotr; Romanowska-Pawliczek, Anna; Soltys, Zbigniew

    2010-03-01

    Various deconvolution algorithms are often used for restoration of digital images. Image deconvolution is especially needed for the correction of three-dimensional images obtained by confocal laser scanning microscopy. Such images suffer from distortions, particularly in the Z dimension. As a result, reliable automatic segmentation of these images may be difficult or even impossible. Effective deconvolution algorithms are memory-intensive and time-consuming. In this work, we propose a parallel version of the well-known Richardson-Lucy deconvolution algorithm developed for a system with distributed memory and implemented with the use of Message Passing Interface (MPI). It enables significantly more rapid deconvolution of two-dimensional and three-dimensional images by efficiently splitting the computation across multiple computers. The implementation of this algorithm can be used on professional clusters provided by computing centers as well as on simple networks of ordinary PC machines. PMID:19725070

  17. Influences of edges and steep slopes in 3D interference and confocal microscopy

    NASA Astrophysics Data System (ADS)

    Xie, Weichang; Hagemeier, Sebastian; Woidt, Carsten; Hillmer, Harmut; Lehmann, Peter

    2016-04-01

    Optical measurement techniques are widely applied in high-resolution contour, topography and roughness measurement. In this context vertical scanning white-light interferometers and confocal microscopes have become mature instruments over the last decades. The accuracy of measurement results is highly related not only to the type and physical properties of the measuring instruments, but also to the measurement object itself. This contribution focuses on measurement effects occurring at edges and height steps using white-light interferometers of different numerical apertures. If the edge is perfectly perpendicular, batwing effects appear at height steps. These batwings show maximum height if the height-to-wavelength-ratio (HWR) is about one forth or three forth, and they disappear if the HWR value is about an integer multiple of one half. The wavelength that is relevant in this context is the effective wavelength, i.e. the center wavelength of the illuminating light multiplied by a correction factor known as the numerical aperture correction. However, in practice the edges are usually not perfectly perpendicular. In this case, the measurement results depend also on the derivative of the surface height function and they may differ from theory and the prediction according to the HWR value. Measurements of such steps show systematical effects depending on the lateral resolution of the instrument. In this context, a Linnik interferometer with a magnification of 100x and NA = 0.9 is used to characterize the three dimensional topography of more or less rectangular calibration specimens and quasi-perpendicular structures produced by the nanoimprint technology. The Linnik interferometer is equipped with LED light sources emitting at different wavelengths, so that the HWR value can be changed. This is possible since the high NA objective lenses show a rather limited depth of focus such that the temporal coherence gating may be replaced by focal gating in this

  18. Analyzing Remodeling of Cardiac Tissue: A Comprehensive Approach Based on Confocal Microscopy and 3D Reconstructions.

    PubMed

    Seidel, Thomas; Edelmann, J-C; Sachse, Frank B

    2016-05-01

    Microstructural characterization of cardiac tissue and its remodeling in disease is a crucial step in many basic research projects. We present a comprehensive approach for three-dimensional characterization of cardiac tissue at the submicrometer scale. We developed a compression-free mounting method as well as labeling and imaging protocols that facilitate acquisition of three-dimensional image stacks with scanning confocal microscopy. We evaluated the approach with normal and infarcted ventricular tissue. We used the acquired image stacks for segmentation, quantitative analysis and visualization of important tissue components. In contrast to conventional mounting, compression-free mounting preserved cell shapes, capillary lumens and extracellular laminas. Furthermore, the new approach and imaging protocols resulted in high signal-to-noise ratios at depths up to 60 µm. This allowed extensive analyzes revealing major differences in volume fractions and distribution of cardiomyocytes, blood vessels, fibroblasts, myofibroblasts and extracellular space in control vs. infarct border zone. Our results show that the developed approach yields comprehensive data on microstructure of cardiac tissue and its remodeling in disease. In contrast to other approaches, it allows quantitative assessment of all major tissue components. Furthermore, we suggest that the approach will provide important data for physiological models of cardiac tissue at the submicrometer scale. PMID:26399990

  19. Remote web-based 3D visualization of hydrological forecasting datasets.

    NASA Astrophysics Data System (ADS)

    van Meersbergen, Maarten; Drost, Niels; Blower, Jon; Griffiths, Guy; Hut, Rolf; van de Giesen, Nick

    2015-04-01

    As the possibilities for larger and more detailed simulations of geoscientific data expand, the need for smart solutions in data visualization grow as well. Large volumes of data should be quickly accessible from anywhere in the world without the need for transferring the simulation results. We aim to provide tools for both processing and the handling of these large datasets. As an example, the eWaterCycle project (www.ewatercycle.org) aims to provide a running 14-day ensemble forecast to predict water related stress around the globe. The large volumes of simulation results with uncertainty data that are generated through ensemble hydrological predictions provide a challenge for existing visualization solutions. One possible solution for this challenge lies in the use of web-enabled technology for visualization and analysis of these datasets. Web-based visualization provides an additional benefit in that it eliminates the need for any software installation and configuration and allows for the easy communication of research results between collaborating research parties. Providing interactive tools for the exploration of these datasets will not only help in the analysis of the data by researchers, it can also aid in the dissemination of the research results to the general public. In Vienna, we will present a working open source solution for remote visualization of large volumes of global geospatial data based on the proven open-source 3D web visualization software package Cesium (cesiumjs.org), the ncWMS software package provided by the Reading e-Science Centre and the WebGL and NetCDF standards.

  20. Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids

    PubMed Central

    Barbier, Michaël; Jaensch, Steffen; Cornelissen, Frans; Vidic, Suzana; Gjerde, Kjersti; de Hoogt, Ronald; Graeser, Ralph; Gustin, Emmanuel; Chong, Yolanda T.

    2016-01-01

    In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation. PMID:27303813

  1. Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids.

    PubMed

    Barbier, Michaël; Jaensch, Steffen; Cornelissen, Frans; Vidic, Suzana; Gjerde, Kjersti; de Hoogt, Ronald; Graeser, Ralph; Gustin, Emmanuel; Chong, Yolanda T

    2016-01-01

    In oncology, two-dimensional in-vitro culture models are the standard test beds for the discovery and development of cancer treatments, but in the last decades, evidence emerged that such models have low predictive value for clinical efficacy. Therefore they are increasingly complemented by more physiologically relevant 3D models, such as spheroid micro-tumor cultures. If suitable fluorescent labels are applied, confocal 3D image stacks can characterize the structure of such volumetric cultures and, for example, cell proliferation. However, several issues hamper accurate analysis. In particular, signal attenuation within the tissue of the spheroids prevents the acquisition of a complete image for spheroids over 100 micrometers in diameter. And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors. We present a robust, computationally inexpensive 2.5D method for the segmentation of spheroid cultures and for counting proliferating cells within them. The spheroids are assumed to be approximately ellipsoid in shape. They are identified from information present in the Maximum Intensity Projection (MIP) and the corresponding height view, also known as Z-buffer. It alerts the user when potential bias-introducing factors cannot be compensated for and includes a compensation for signal attenuation. PMID:27303813

  2. Confocal (micro)-XRF for 3D anlaysis of elements distribution in hot environmental particles

    SciTech Connect

    Bielewski, M; Eriksson, M; Himbert, J; Simon, R; Betti, M; Hamilton, T F

    2007-11-27

    Studies on the fate and transport of radioactive contaminates in the environment are often constrained by a lack of knowledge on the elemental distribution and general behavior of particulate bound radionuclides contained in hot particles. A number of hot particles were previously isolated from soil samples collected at former U.S. nuclear test sites in the Marshall Islands and characterized using non-destructive techniques [1]. The present investigation at HASYLAB is a part of larger research program at ITU regarding the characterization of environmental radioactive particles different locations and source-terms. Radioactive particles in the environment are formed under a number of different release scenarios and, as such, their physicochemical properties may provide a basis for identifying source-term specific contamination regimes. Consequently, studies on hot particles are not only important in terms of studying the elemental composition and geochemical behavior of hot particles but may also lead to advances in assessing the long-term impacts of radioactive contamination on the environment. Six particles isolated from soil samples collected at the Marshall Islands were studied. The element distribution in the particles was determined by confocal {micro}-XRF analysis using the ANKA FLUO beam line. The CRL (compound refractive lens) was used to focus the exciting beam and the polycapillary half lens to collimate the detector. The dimensions of confocal spot were measured by 'knife edge scanning' method with thin gold structure placed at Si wafer. The values of 3.1 x 1.4 x 18.4 {micro}m were achieved if defined as FWHMs of measured L?intensity profiles and when the19.1 keV exciting radiation was used. The collected XRF spectra were analyzed offline with AXIL [2] software to obtain net intensities of element characteristic lines.Further data processing and reconstruction of element distribution was done with the software 'R' [3] dedicated for statistical

  3. Automatic Detection, Segmentation and Classification of Retinal Horizontal Neurons in Large-scale 3D Confocal Imagery

    SciTech Connect

    Karakaya, Mahmut; Kerekes, Ryan A; Gleason, Shaun Scott; Martins, Rodrigo; Dyer, Michael

    2011-01-01

    Automatic analysis of neuronal structure from wide-field-of-view 3D image stacks of retinal neurons is essential for statistically characterizing neuronal abnormalities that may be causally related to neural malfunctions or may be early indicators for a variety of neuropathies. In this paper, we study classification of neuron fields in large-scale 3D confocal image stacks, a challenging neurobiological problem because of the low spatial resolution imagery and presence of intertwined dendrites from different neurons. We present a fully automated, four-step processing approach for neuron classification with respect to the morphological structure of their dendrites. In our approach, we first localize each individual soma in the image by using morphological operators and active contours. By using each soma position as a seed point, we automatically determine an appropriate threshold to segment dendrites of each neuron. We then use skeletonization and network analysis to generate the morphological structures of segmented dendrites, and shape-based features are extracted from network representations of each neuron to characterize the neuron. Based on qualitative results and quantitative comparisons, we show that we are able to automatically compute relevant features that clearly distinguish between normal and abnormal cases for postnatal day 6 (P6) horizontal neurons.

  4. Integrating airborne LiDAR dataset and photographic images towards the construction of 3D building model

    NASA Astrophysics Data System (ADS)

    Idris, R.; Latif, Z. A.; Hamid, J. R. A.; Jaafar, J.; Ahmad, M. Y.

    2014-02-01

    A 3D building model of man-made objects is an important tool for various applications such as urban planning, flood mapping and telecommunication. The reconstruction of 3D building models remains difficult. No universal algorithms exist that can extract all objects in an image successfully. At present, advances in remote sensing such as airborne LiDAR (Light Detection and Ranging) technology have changed the conventional method of topographic mapping and increased the interest of these valued datasets towards 3D building model construction. Airborne LiDAR has proven accordingly that it can provide three dimensional (3D) information of the Earth surface with high accuracy. In this study, with the availability of open source software such as Sketch Up, LiDAR datasets and photographic images could be integrated towards the construction of a 3D building model. In order to realize the work an area comprising residential areas situated at Putrajaya in the Klang Valley region, Malaysia, covering an area of two square kilometer was chosen. The accuracy of the derived 3D building model is assessed quantitatively. It is found that the difference between the vertical height (z) of the 3D building models derived from LiDAR dataset and ground survey is approximately ± 0.09 centimeter (cm). For the horizontal component (RMSExy), the accuracy estimates derived for the 3D building models were ± 0.31m. The result also shows that the qualitative assessment of the 3D building models constructed seems feasible for the depiction in the standard of LOD 3 (Level of details).

  5. 3-D laser confocal microscopy study of the oxidation of NdFeB magnets in atmospheric conditions

    NASA Astrophysics Data System (ADS)

    Meakin, J. P.; Speight, J. D.; Sheridan, R. S.; Bradshaw, A.; Harris, I. R.; Williams, A. J.; Walton, A.

    2016-08-01

    Neodymium iron boron (NdFeB) magnets are used in a number of important applications, such as generators in gearless wind turbines, motors in electric vehicles and electronic goods (e.g.- computer hard disk drives, HDD). Hydrogen can be used as a processing gas to separate and recycle scrap sintered Nd-Fe-B magnets from end-of-life products to form a powder suitable for recycling. However, the magnets are likely to have been exposed to atmospheric conditions prior to processing, and any oxidation could lead to activation problems for the hydrogen decrepitation reaction. Many previous studies on the oxidation of NdFeB magnets have been performed at elevated temperatures; however, few studies have been formed under atmospheric conditions. In this paper a combination of 3-D laser confocal microscopy and Raman spectroscopy have been used to assess the composition, morphology and rate of oxidation/corrosion on scrap sintered NdFeB magnets. Confocal microscopy has been employed to measure the growth of surface reaction products at room temperature, immediately after exposure to air. The results showed that there was a significant height increase at the triple junctions of the Nd-rich grain boundaries. Using Raman spectroscopy, the product was shown to consist of Nd2O3 and formed only on the Nd-rich triple junctions. The diffusion coefficient of the triple junction reaction product growth at 20 °C was determined to be approximately 4 × 10-13 cm2/sec. This value is several orders of magnitude larger than values derived from the diffusion controlled oxide growth observations at elevated temperatures in the literature. This indicates that the growth of the room temperature oxidation products are likely defect enhanced processes at the NdFeB triple junctions.

  6. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  7. Enhancing 3-D cell structures in confocal and STED microscopy: a joint model for interpolation, deblurring and anisotropic smoothing

    NASA Astrophysics Data System (ADS)

    Persch, Nico; Elhayek, Ahmed; Welk, Martin; Bruhn, Andrés; Grewenig, Sven; Böse, Katharina; Kraegeloh, Annette; Weickert, Joachim

    2013-12-01

    This paper proposes an advanced image enhancement method that is specifically tailored towards 3-D confocal and STED microscopy imagery. Our approach unifies image denoising, deblurring and interpolation in one joint method to handle the typical weaknesses of these advanced microscopy techniques: out-of-focus blur, Poisson noise and low axial resolution. In detail, we propose the combination of (i) Richardson-Lucy deconvolution, (ii) image restoration and (iii) anisotropic inpainting in one single scheme. To this end, we develop a novel PDE-based model that realizes these three ideas. First we consider a basic variational image restoration functional that is turned into a joint interpolation scheme by extending the regularization domain. Next, we integrate the variational representation of Richardson-Lucy deconvolution into our model, and illustrate its relation to Poisson distributed noise. In the following step, we supplement the components of our model with sub-quadratic penalization strategies that increase the robustness of the overall method. Finally, we consider the associated minimality conditions, where we exchange the occurring scalar-valued diffusivity function by a so-called diffusion tensor. This leads to an anisotropic regularization that is aligned with structures in the evolving image. As a further contribution of this paper, we propose a more efficient and faster semi-implicit iteration scheme that also increases the stability. Our experiments on real data sets demonstrate that this joint model achieves a superior reconstruction quality of the recorded cell.

  8. An interface for precise and comfortable 3D work with volumetric medical datasets.

    PubMed

    Serra, L; Hern, N; Guan, C G; Lee, E; Lee, Y H; Yeo, T T; Chan, C; Kockro, R A

    1999-01-01

    We have developed a 3D/2D paradigm of interaction that combines manipulation of precise 3D volumetric data with unambiguous widget interaction. Precise 3D interaction is ensured by a combination of resting the lower arms on an armrest and pivoting the hands around the wrist. Unambiguous 2D interaction is achieved by providing passive haptic feedback by means of a virtual control panel whose position coincides with the physical surfaces encasing the system. We have tested this interface with a neurosurgical planning application that has been clinically used for 17 skull-base cases at two local hospitals. PMID:10538381

  9. Compression of medical volumetric datasets: physical and psychovisual performance comparison of the emerging JP3D standard and JPEG2000

    NASA Astrophysics Data System (ADS)

    Kimpe, T.; Bruylants, T.; Sneyders, Y.; Deklerck, R.; Schelkens, P.

    2007-03-01

    The size of medical data has increased significantly over the last few years. This poses severe problems for the rapid transmission of medical data across the hospital network resulting into longer access times of the images. Also longterm storage of data becomes more and more a problem. In an attempt to overcome the increasing data size often lossless or lossy compression algorithms are being used. This paper compares the existing JPEG2000 compression algorithm and the new emerging JP3D standard for compression of volumetric datasets. The main benefit of JP3D is that this algorithm truly is a 3D compression algorithm that exploits correlation not only within but also in between slices of a dataset. We evaluate both lossless and lossy modes of these algorithms. As a first step we perform an objective evaluation. Using RMSE and PSNR metrics we determine which compression algorithm performs best and this for multiple compression ratios and for several clinically relevant medical datasets. It is well known that RMSE and PSNR often do not correlate well with subjectively perceived image quality. Therefore we also perform a psycho visual analysis by means of a numerical observer. With this observer model we analyze how compression artifacts actually are perceived by a human observer. Results show superior performance of the new JP3D algorithm compared to the existing JPEG2000 algorithm.

  10. 3-D QSARS FOR RANKING AND PRIORITIZATION OF LARGE CHEMICAL DATASETS: AN EDC CASE STUDY

    EPA Science Inventory

    The COmmon REactivity Pattern (COREPA) approach is a three-dimensional structure activity (3-D QSAR) technique that permits identification and quantification of specific global and local steroelectronic characteristics associated with a chemical's biological activity. It goes bey...

  11. Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

    SciTech Connect

    Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.; Fournier, Marcia V.

    2008-10-20

    One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasets having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds prognostic

  12. Detection of latent fingerprints using high-resolution 3D confocal microscopy in non-planar acquisition scenarios

    NASA Astrophysics Data System (ADS)

    Kirst, Stefan; Vielhauer, Claus

    2015-03-01

    In digitized forensics the support of investigators in any manner is one of the main goals. Using conservative lifting methods, the detection of traces is done manually. For non-destructive contactless methods, the necessity for detecting traces is obvious for further biometric analysis. High resolutional 3D confocal laser scanning microscopy (CLSM) grants the possibility for a detection by segmentation approach with improved detection results. Optimal scan results with CLSM are achieved on surfaces orthogonal to the sensor, which is not always possible due to environmental circumstances or the surface's shape. This introduces additional noise, outliers and a lack of contrast, making a detection of traces even harder. Prior work showed the possibility of determining angle-independent classification models for the detection of latent fingerprints (LFP). Enhancing this approach, we introduce a larger feature space containing a variety of statistical-, roughness-, color-, edge-directivity-, histogram-, Gabor-, gradient- and Tamura features based on raw data and gray-level co-occurrence matrices (GLCM) using high resolutional data. Our test set consists of eight different surfaces for the detection of LFP in four different acquisition angles with a total of 1920 single scans. For each surface and angles in steps of 10, we capture samples from five donors to introduce variance by a variety of sweat compositions and application influences such as pressure or differences in ridge thickness. By analyzing the present test set with our approach, we intend to determine angle- and substrate-dependent classification models to determine optimal surface specific acquisition setups and also classification models for a general detection purpose for both, angles and substrates. The results on overall models with classification rates up to 75.15% (kappa 0.50) already show a positive tendency regarding the usability of the proposed methods for LFP detection on varying surfaces in non

  13. HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database

    NASA Astrophysics Data System (ADS)

    Pollastro, Pasquale; Rampone, Salvatore

    The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

  14. Summary of work on shock wave feature extraction in 3-D datasets

    NASA Technical Reports Server (NTRS)

    Hesselink, Lambertus (Principal Investigator)

    1996-01-01

    A method for extracting and visualizing shock waves from three dimensional data-sets is discussed. Issues concerning computation time, robustness to numerical perturbations, and noise introduction are considered and compared with other methods. Finally, results using this method are discussed.

  15. FluoRender: An Application of 2D Image Space Methods for 3D and 4D Confocal Microscopy Data Visualization in Neurobiology Research

    PubMed Central

    Wan, Yong; Otsuna, Hideo; Chien, Chi-Bin; Hansen, Charles

    2013-01-01

    2D image space methods are processing methods applied after the volumetric data are projected and rendered into the 2D image space, such as 2D filtering, tone mapping and compositing. In the application domain of volume visualization, most 2D image space methods can be carried out more efficiently than their 3D counterparts. Most importantly, 2D image space methods can be used to enhance volume visualization quality when applied together with volume rendering methods. In this paper, we present and discuss the applications of a series of 2D image space methods as enhancements to confocal microscopy visualizations, including 2D tone mapping, 2D compositing, and 2D color mapping. These methods are easily integrated with our existing confocal visualization tool, FluoRender, and the outcome is a full-featured visualization system that meets neurobiologists’ demands for qualitative analysis of confocal microscopy data. PMID:23584131

  16. Automatic 3d Building Reconstruction from a Dense Image Matching Dataset

    NASA Astrophysics Data System (ADS)

    McClune, Andrew P.; Mills, Jon P.; Miller, Pauline E.; Holland, David A.

    2016-06-01

    Over the last 20 years the demand for three dimensional (3D) building models has resulted in a vast amount of research being conducted in attempts to automate the extraction and reconstruction of models from airborne sensors. Recent results have shown that current methods tend to favour planar fitting procedures from lidar data, which are able to successfully reconstruct simple roof structures automatically but fail to reconstruct more complex structures or roofs with small artefacts. Current methods have also not fully explored the potential of recent developments in digital photogrammetry. Large format digital aerial cameras can now capture imagery with increased overlap and a higher spatial resolution, increasing the number of pixel correspondences between images. Every pixel in each stereo pair can also now be matched using per-pixel algorithms, which has given rise to the approach known as dense image matching. This paper presents an approach to 3D building reconstruction to try and overcome some of the limitations of planar fitting procedures. Roof vertices, extracted from true-orthophotos using edge detection, are refined and converted to roof corner points. By determining the connection between extracted corner points, a roof plane can be defined as a closed-cycle of points. Presented results demonstrate the potential of this method for the reconstruction of complex 3D building models at CityGML LoD2 specification.

  17. A new gold-standard dataset for 2D/3D image registration evaluation

    NASA Astrophysics Data System (ADS)

    Pawiro, Supriyanto; Markelj, Primoz; Gendrin, Christelle; Figl, Michael; Stock, Markus; Bloch, Christoph; Weber, Christoph; Unger, Ewald; Nöbauer, Iris; Kainberger, Franz; Bergmeister, Helga; Georg, Dietmar; Bergmann, Helmar; Birkfellner, Wolfgang

    2010-02-01

    In this paper, we propose a new gold standard data set for the validation of 2D/3D image registration algorithms for image guided radiotherapy. A gold standard data set was calculated using a pig head with attached fiducial markers. We used several imaging modalities common in diagnostic imaging or radiotherapy which include 64-slice computed tomography (CT), magnetic resonance imaging (MRI) using T1, T2 and proton density (PD) sequences, and cone beam CT (CBCT) imaging data. Radiographic data were acquired using kilovoltage (kV) and megavoltage (MV) imaging techniques. The image information reflects both anatomy and reliable fiducial marker information, and improves over existing data sets by the level of anatomical detail and image data quality. The markers of three dimensional (3D) and two dimensional (2D) images were segmented using Analyze 9.0 (AnalyzeDirect, Inc) and an in-house software. The projection distance errors (PDE) and the expected target registration errors (TRE) over all the image data sets were found to be less than 1.7 mm and 1.3 mm, respectively. The gold standard data set, obtained with state-of-the-art imaging technology, has the potential to improve the validation of 2D/3D registration algorithms for image guided therapy.

  18. Robust Adaptive 3-D Segmentation of Vessel Laminae From Fluorescence Confocal Microscope Images and Parallel GPU Implementation

    PubMed Central

    Narayanaswamy, Arunachalam; Dwarakapuram, Saritha; Bjornsson, Christopher S.; Cutler, Barbara M.; Shain, William

    2010-01-01

    This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8× speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1–1.6) voxels per mesh face for peak signal-to-noise ratios from (110–28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively. PMID:20199906

  19. A 3-D mixed-reality system for stereoscopic visualization of medical dataset.

    PubMed

    Ferrari, Vincenzo; Megali, Giuseppe; Troia, Elena; Pietrabissa, Andrea; Mosca, Franco

    2009-11-01

    We developed a simple, light, and cheap 3-D visualization device based on mixed reality that can be used by physicians to see preoperative radiological exams in a natural way. The system allows the user to see stereoscopic "augmented images," which are created by mixing 3-D virtual models of anatomies obtained by processing preoperative volumetric radiological images (computed tomography or MRI) with real patient live images, grabbed by means of cameras. The interface of the system consists of a head-mounted display equipped with two high-definition cameras. Cameras are mounted in correspondence of the user's eyes and allow one to grab live images of the patient with the same point of view of the user. The system does not use any external tracker to detect movements of the user or the patient. The movements of the user's head and the alignment of virtual patient with the real one are done using machine vision methods applied on pairs of live images. Experimental results, concerning frame rate and alignment precision between virtual and real patient, demonstrate that machine vision methods used for localization are appropriate for the specific application and that systems based on stereoscopic mixed reality are feasible and can be proficiently adopted in clinical practice. PMID:19651551

  20. Visualizing and Tracking Evolving Features in 3D Unstructured and Adaptive Datasets

    SciTech Connect

    Silver, D.; Zabusky, N.

    2002-08-01

    The massive amounts of time-varying datasets being generated demand new visualization and quantification techniques. Visualization alone is not sufficient. Without proper measurement information/computations real science cannot be done. Our focus is this work was to combine visualization with quantification of the data to allow for advanced querying and searching. As part of this proposal, we have developed a feature extraction adn tracking methodology which allows researcher to identify features of interest and follow their evolution over time. The implementation is distributed and operates over data In-situ: where it is stored and when it was computed.

  1. 3D Imaging of Porous Media Using Laser Scanning Confocal Microscopy with Application to Microscale Transport Processes

    SciTech Connect

    Fredrich, J.T.

    1999-02-10

    We present advances in the application of laser scanning confocal microscopy (LSCM) to image, reconstruct, and characterize statistically the microgeometry of porous geologic and engineering materials. We discuss technical and practical aspects of this imaging technique, including both its advantages and limitations. Confocal imaging can be used to optically section a material, with sub-micron resolution possible in the lateral and axial planes. The resultant volumetric image data, consisting of fluorescence intensities for typically {approximately}50 million voxels in XYZ space, can be used to reconstruct the three-dimensional structure of the two-phase medium. We present several examples of this application, including studying pore geometry in sandstone, characterizing brittle failure processes in low-porosity rock deformed under triaxial loading conditions in the laboratory, and analyzing the microstructure of porous ceramic insulations. We then describe approaches to extract statistical microgeometric descriptions from volumetric image data, and present results derived from confocal volumetric data sets. Finally, we develop the use of confocal image data to automatically generate a three-dimensional mesh for numerical pore-scale flow simulations.

  2. Using 3D Geologic Models to Synthesize Large and Disparate Datasets for Site Characterization and Verification Purposes

    NASA Astrophysics Data System (ADS)

    Hillesheim, M. B.; Rautman, C. A.; Johnson, P. B.; Powers, D. W.

    2008-12-01

    As we are all aware, increases in computing power and efficiency have allowed for the development of many modeling codes capable of processing large and sometimes disparate datasets (e.g., geological, hydrological, geochemical, etc). Because people sometimes have difficulty visualizing in three dimensions (3D) or understanding how multiple figures of various geologic features relate as a whole, 3D geologic models can be excellent tools to illustrate key concepts and findings, especially to lay persons, such as stakeholders, customers, and other concerned parties. In this presentation, we will show examples of 3D geologic modeling efforts using data collected during site characterization and verification work at the Waste Isolation Pilot Plant (WIPP). The WIPP is a U.S. Department of Energy (DOE) facility located in southeastern New Mexico, designed for the safe disposal of transuranic wastes resulting from U.S. defense programs. The 3D geologic modeling efforts focused on refining our understanding of the WIPP site by integrating a variety of geologic data. Examples include: overlaying isopach surfaces of unit thickness and overburden thickness, a map of geologic facies changes, and a transmissivity field onto a 3D structural map of a geologic unit of interest. In addition, we also present a 4D hydrogeologic model of the effects of a large-scale pumping test on water levels. All these efforts have provided additional insights into the controls on transmissivity and flow in the WIPP vicinity. Ultimately, by combining these various types of data we have increased our understanding of the WIPP site's hydrogeologic system, which is a key aspect of continued certification. Sandia is a multi program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04- 94AL85000. This research is funded by WIPP programs administered by the Office of Environmental

  3. 3D Inversion of a Self-Potential Dataset for Contaminant Detection and Mapping

    NASA Astrophysics Data System (ADS)

    Minsley, B. J.; Sogade, J.; Briggs, V.; Lambert, M.; Reppert, P.; Coles, D.; Morgan, F.; Rossabi, J.; Riha, B.; Shi, W.

    2003-12-01

    Due to the complicated nature of subsurface contaminant migration, it is difficult to determine the spatial extent and severity of contamination, which can provide essential information for efficient remediation efforts. Self-potential (SP) geophysics is employed to provide a minimally invasive, fast, and inexpensive method for remote in-situ detection and three-dimensional mapping of subsurface DNAPL (Dense Non-Aqueous Phase Liquid) in conjunction with inverse methods. The self-potential method is commonly used to detect a variety of phenomena that are typically related to thermoelectric, electrochemical, or electrokinetic coupling processes. Surface self-potential surveys have been documented to show anomalies over areas known to be contaminated, but interpretation of these datasets is often mostly qualitative, and can be plagued with problems of non-uniqueness. In this study, oxidation-reduction (redox) reactions, one of the mechanisms associated with the attenuation of chemicals released into the environment, provide an electrochemical source for the SP signal. Electrochemical potentials associated with subsurface zones of redox activity are analogous to localized 'batteries' buried within native earth materials, and produce an electric field that is remotely detected using electrodes placed at the surface and in nearby boreholes. Three-dimensional inversion of the self-potential data incorporating resistivity information is the necessary step in characterizing the source parameters, which are directly related to the redox activity, and therefore to the contaminant itself. Surface and borehole SP data are collected in order to help constrain the solution in depth, and resistivity information is taken from an induced polarization survey performed over the same area during this field excursion. Inversion results are correlated with contaminant concentration data sampled from a series of ground-truth boreholes within the region of interest.

  4. Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets

    PubMed Central

    2010-01-01

    Background Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks. Results We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de. Conclusions The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics. PMID:20064262

  5. 3D granulometry: grain-scale shape and size distribution from point cloud dataset of river environments

    NASA Astrophysics Data System (ADS)

    Steer, Philippe; Lague, Dimitri; Gourdon, Aurélie; Croissant, Thomas; Crave, Alain

    2016-04-01

    The grain-scale morphology of river sediments and their size distribution are important factors controlling the efficiency of fluvial erosion and transport. In turn, constraining the spatial evolution of these two metrics offer deep insights on the dynamics of river erosion and sediment transport from hillslopes to the sea. However, the size distribution of river sediments is generally assessed using statistically-biased field measurements and determining the grain-scale shape of river sediments remains a real challenge in geomorphology. Here we determine, with new methodological approaches based on the segmentation and geomorphological fitting of 3D point cloud dataset, the size distribution and grain-scale shape of sediments located in river environments. Point cloud segmentation is performed using either machine-learning algorithms or geometrical criterion, such as local plan fitting or curvature analysis. Once the grains are individualized into several sub-clouds, each grain-scale morphology is determined using a 3D geometrical fitting algorithm applied on the sub-cloud. If different geometrical models can be conceived and tested, only ellipsoidal models were used in this study. A phase of results checking is then performed to remove grains showing a best-fitting model with a low level of confidence. The main benefits of this automatic method are that it provides 1) an un-biased estimate of grain-size distribution on a large range of scales, from centimeter to tens of meters; 2) access to a very large number of data, only limited by the number of grains in the point-cloud dataset; 3) access to the 3D morphology of grains, in turn allowing to develop new metrics characterizing the size and shape of grains. The main limit of this method is that it is only able to detect grains with a characteristic size greater than the resolution of the point cloud. This new 3D granulometric method is then applied to river terraces both in the Poerua catchment in New-Zealand and

  6. Visualising the 3D Structure of Fine-Grained Estuarine Sediments; Preliminary Interpretations of a Novel Dataset Obtained via Volume Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Spencer, Kate; Carr, Simon

    2014-05-01

    Accurate measurement of the physical characteristics of sediment are critical to determining sediment transport behaviour and the stability of settled deposits. The properties (e.g. particle size, density, and settling velocity) of coarse-grained sediments (> 63 μm φ) can be easily characterised, hence their behaviour is relatively simple to predict and model. However, due to their small size and tendency to interact with their surrounding medium, the characteristics of fine sediments (< 63 μm φ) and their behaviour during transportation, deposition and consolidation is poorly understood. Recent studies have used correlative microscopy, a multi-method technique combining scanning confocal laser microscopy (SCLM), conventional optical microscopy (COM), and transmission electron microscopy (TEM), to characterise fine sediments at both the gross (> 1 μm) and sub-micron scale (Droppo et al., 1996). Whilst this technique has proven insightful, the measurement of geometric properties (e.g. the shape of primary particles and their spatial arrangement) can only be achieved by three-dimensional (3D) analysis and the scale of observation for e.g. TEM does not overlap with those techniques used to characterise sediments at larger scales (100s to 1000s microns) (e.g. video analysis). Volume electron microscopy [or focused ion beam scanning electron microscopy (FIB-SEM)] provides 3D analysis at scales of 10s to 1000s microns and though widely used in cell biology, has not been used to observe sediment. FIB-SEM requires samples that are vacuum stable and a key challenge will be to capture fragile, hydrated sediment samples whilst preserving their structural integrity. The aims of this work are therefore: 1) to modify preparation techniques currently used in cell biology for the stabilization of sedimentary materials; 2) to acquire 3D datasets for both fragile suspended sediments (flocs) and consolidated bed sediments and 3) to interpret the 3D structure of these samples. In

  7. Development and verification of a novel device for dental intra-oral 3D scanning using chromatic confocal technology

    NASA Astrophysics Data System (ADS)

    Zint, M.; Stock, K.; Graser, R.; Ertl, T.; Brauer, E.; Heyninck, J.; Vanbiervliet, J.; Dhondt, S.; De Ceuninck, P.; Hibst, R.

    2015-03-01

    The presented work describes the development and verification of a novel optical, powder-free intra-oral scanner based on chromatic confocal technology combined with a multifocal approach. The proof of concept for a chromatic confocal area scanner for intra-oral scanning is given. Several prototype scanners passed a verification process showing an average accuracy (distance deviation on flat surfaces) of less than 31μm +/- 21μm and a reproducibility of less than 4μm +/- 3μm. Compared to a tactile measurement on a full jaw model fitted with 4mm ceramic spheres the measured average distance deviation between the spheres was 49μm +/- 12μm for scans of up to 8 teeth (3- unit bridge, single Quadrant) and 104μm +/- 82μm for larger scans and full jaws. The average deviation of the measured sphere diameter compared to the tactile measurement was 27μm +/- 14μm. Compared to μCT scans of plaster models equipped with human teeth the average standard deviation on up to 3 units was less than 55μm +/- 49μm whereas the reproducibility of the scans was better than 22μm +/- 10μm.

  8. High-speed 3-D measurement with a large field of view based on direct-view confocal microscope with an electrically tunable lens.

    PubMed

    Jeong, Hyeong-jun; Yoo, Hongki; Gweon, DaeGab

    2016-02-22

    We propose a new structure of confocal imaging system based on a direct-view confocal microscope (DVCM) with an electrically tunable lens (ETL). Since it has no mechanical moving parts to scan both the lateral (x-y) and axial (z) directions, the DVCM with an ETL allows for high-speed 3-dimensional (3-D) imaging. Axial response and signal intensity of the DVCM were analyzed theoretically according to the pinhole characteristics. The system was designed to have an isotropic spatial resolution of 20 µm in both lateral and axial direction with a large field of view (FOV) of 10 × 10 mm. The FOV was maintained according to the various focal shifts as a result of an integrated design of an objective lens with the ETL. The developed system was calibrated to have linear focal shift over a range of 9 mm with an applied current to the ETL. The system performance of 3-D volume imaging was demonstrated using standard height specimens and a dental plaster. PMID:26907034

  9. Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains.

    PubMed

    Lam, Shing Chun Benny; Ruan, Zongcai; Zhao, Ting; Long, Fuhui; Jenett, Arnim; Simpson, Julie; Myers, Eugene W; Peng, Hanchuan

    2010-02-01

    Automatic alignment (registration) of 3D images of adult fruit fly brains is often influenced by the significant displacement of the relative locations of the two optic lobes (OLs) and the center brain (CB). In one of our ongoing efforts to produce a better image alignment pipeline of adult fruit fly brains, we consider separating CB and OLs and align them independently. This paper reports our automatic method to segregate CB and OLs, in particular under conditions where the signal to noise ratio (SNR) is low, the variation of the image intensity is big, and the relative displacement of OLs and CB is substantial. We design an algorithm to find a minimum-cost 3D surface in a 3D image stack to best separate an OL (of one side, either left or right) from CB. This surface is defined as an aggregation of the respective minimum-cost curves detected in each individual 2D image slice. Each curve is defined by a list of control points that best segregate OL and CB. To obtain the locations of these control points, we derive an energy function that includes an image energy term defined by local pixel intensities and two internal energy terms that constrain the curve's smoothness and length. Gradient descent method is used to optimize this energy function. To improve both the speed and robustness of the method, for each stack, the locations of optimized control points in a slice are taken as the initialization prior for the next slice. We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties. PMID:19698789

  10. Study of the collagen structure in the superficial zone and physiological state of articular cartilage using a 3D confocal imaging technique

    PubMed Central

    Wu, Jian P; Kirk, Thomas B; Zheng, Ming H

    2008-01-01

    superficial zone during early physiological alteration of articular cartilage. The fibre confocal imaging technology used in this study has allowed developing confocal arthroscopy for in vivo studying the chondrocytes in different depth of articular cartilage. Therefore, the current study has potential to develop an in vivo 3D histology for diagnosis of early osteoarthritis. PMID:18637164

  11. 3-D visualisation and interpretation of seismic attributes extracted from large 3-D seismic datasets: Subregional and prospect evaluation, deepwater Nigeria

    SciTech Connect

    Sola, M.; Haakon Nordby, L.; Dailey, D.V.; Duncan, E.A. )

    1996-01-01

    High resolution 3-D visualization of horizon interpretation and seismic attributes from large 3-D seismic surveys in deepwater Nigeria has greatly enhanced the exploration team's ability to quickly recognize prospective segments of subregional and prospect specific scale areas. Integrated workstation generated structure, isopach and extracted horizon consistent, interval and windowed attributes are particularly useful in illustrating the complex structural and stratigraphical prospectivity of deepwater Nigeria. Large 3-D seismic volumes acquired over 750 square kilometers can be manipulated within the visualization system with attribute tracking capability that allows for real time data interrogation and interpretation. As in classical seismic stratigraphic studies, pattern recognition is fundamental to effective depositions facies interpretation and reservoir model construction. The 3-D perspective enhances the data interpretation through clear representation of relative scale, spatial distribution and magnitude of attributes. In deepwater Nigeria, many prospective traps rely on an interplay between syndepositional structure and slope turbidite depositional systems. Reservoir systems in many prospects appear to be dominated by unconfined to moderately focused slope feeder channel facies. These units have spatially complex facies architecture with feeder channel axes separated by extensive interchannel areas. Structural culminations generally have a history of initial compressional folding with late in extensional collapse and accommodation faulting. The resulting complex trap configurations often have stacked reservoirs over intervals as thick as 1500 meters. Exploration, appraisal and development scenarios in these settings can be optimized by taking full advantage of integrating high resolution 3-D visualization and seismic workstation interpretation.

  12. 3-D visualisation and interpretation of seismic attributes extracted from large 3-D seismic datasets: Subregional and prospect evaluation, deepwater Nigeria

    SciTech Connect

    Sola, M.; Haakon Nordby, L.; Dailey, D.V.; Duncan, E.A.

    1996-12-31

    High resolution 3-D visualization of horizon interpretation and seismic attributes from large 3-D seismic surveys in deepwater Nigeria has greatly enhanced the exploration team`s ability to quickly recognize prospective segments of subregional and prospect specific scale areas. Integrated workstation generated structure, isopach and extracted horizon consistent, interval and windowed attributes are particularly useful in illustrating the complex structural and stratigraphical prospectivity of deepwater Nigeria. Large 3-D seismic volumes acquired over 750 square kilometers can be manipulated within the visualization system with attribute tracking capability that allows for real time data interrogation and interpretation. As in classical seismic stratigraphic studies, pattern recognition is fundamental to effective depositions facies interpretation and reservoir model construction. The 3-D perspective enhances the data interpretation through clear representation of relative scale, spatial distribution and magnitude of attributes. In deepwater Nigeria, many prospective traps rely on an interplay between syndepositional structure and slope turbidite depositional systems. Reservoir systems in many prospects appear to be dominated by unconfined to moderately focused slope feeder channel facies. These units have spatially complex facies architecture with feeder channel axes separated by extensive interchannel areas. Structural culminations generally have a history of initial compressional folding with late in extensional collapse and accommodation faulting. The resulting complex trap configurations often have stacked reservoirs over intervals as thick as 1500 meters. Exploration, appraisal and development scenarios in these settings can be optimized by taking full advantage of integrating high resolution 3-D visualization and seismic workstation interpretation.

  13. Highlighting the impact of aging on type I collagen: label-free investigation using confocal reflectance microscopy and diffuse reflectance spectroscopy in 3D matrix model

    PubMed Central

    Terryn, Christine; Garnotel, Roselyne; Jeannesson, Pierre; Sockalingum, Ganesh D.; Manfait, Michel; Perraut, François; Dinten, Jean-Marc; Koenig, Anne; Piot, Olivier

    2016-01-01

    During aging, alterations of extracellular matrix proteins contribute to various pathological phenotypes. Among these alterations, type I collagen cross-linking and associated glycation products accumulation over time detrimentally affects its physico-chemical properties, leading to alterations of tissue biomechanical stability. Here, different-age collagen 3D matrices using non-destructive and label-free biophotonic techniques were analysed to highlight the impact of collagen I aging on 3D constructs, at macroscopic and microscopic levels. Matrices were prepared with collagens extracted from tail tendons of rats (newborns, young and old adults) to be within the physiological aging process. The data of diffuse reflectance spectroscopy reveal that aging leads to an inhibition of fibril assembly and a resulting decrease of gel density. Investigations by confocal reflectance microscopy highlight poor-fibrillar structures in oldest collagen networks most likely related to the glycation products accumulation. Complementarily, an infrared analysis brings out marked spectral variations in the Amide I profile, specific of the peptidic bond conformation and for carbohydrates vibrations as function of collagen-age. Interestingly, we also highlight an unexpected behavior for newborn collagen, exhibiting poorly-organized networks and microscopic features close to the oldest collagen. These results demonstrate that changes in collagen optical properties are relevant for investigating the incidence of aging in 3D matrix models. PMID:26885896

  14. Cell-selective knockout and 3D confocal image analysis reveals separate roles for astrocyte-and endothelial-derived CCL2 in neuroinflammation

    PubMed Central

    2014-01-01

    Background Expression of chemokine CCL2 in the normal central nervous system (CNS) is nearly undetectable, but is significantly upregulated and drives neuroinflammation during experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis which is considered a contributing factor in the human disease. As astrocytes and brain microvascular endothelial cells (BMEC) forming the blood–brain barrier (BBB) are sources of CCL2 in EAE and other neuroinflammatory conditions, it is unclear if one or both CCL2 pools are critical to disease and by what mechanism(s). Methods Mice with selective CCL2 gene knockout (KO) in astrocytes (Astro KO) or endothelial cells (Endo KO) were used to evaluate the respective contributions of these sources to neuroinflammation, i.e., clinical disease progression, BBB damage, and parenchymal leukocyte invasion in a myelin oligodendrocyte glycoprotein peptide (MOG35-55)-induced EAE model. High-resolution 3-dimensional (3D) immunofluorescence confocal microscopy and colloidal gold immuno-electron microscopy were employed to confirm sites of CCL2 expression, and 3D immunofluorescence confocal microscopy utilized to assess inflammatory responses along the CNS microvasculature. Results Cell-selective loss of CCL2 immunoreactivity was demonstrated in the respective KO mice. Compared to wild-type (WT) mice, Astro KO mice showed reduced EAE severity but similar onset, while Endo KO mice displayed near normal severity but significantly delayed onset. Neither of the KO mice showed deficits in T cell proliferation, or IL-17 and IFN-γ production, following MOG35-55 exposure in vitro, or altered MOG-major histocompatibility complex class II tetramer binding. 3D confocal imaging further revealed distinct actions of the two CCL2 pools in the CNS. Astro KOs lacked the CNS leukocyte penetration and disrupted immunostaining of CLN-5 at the BBB seen during early EAE in WT mice, while Endo KOs uniquely displayed leukocytes stalled in the

  15. 3D digital image processing for biofilm quantification from confocal laser scanning microscopy: Multidimensional statistical analysis of biofilm modeling

    NASA Astrophysics Data System (ADS)

    Zielinski, Jerzy S.

    The dramatic increase in number and volume of digital images produced in medical diagnostics, and the escalating demand for rapid access to these relevant medical data, along with the need for interpretation and retrieval has become of paramount importance to a modern healthcare system. Therefore, there is an ever growing need for processed, interpreted and saved images of various types. Due to the high cost and unreliability of human-dependent image analysis, it is necessary to develop an automated method for feature extraction, using sophisticated mathematical algorithms and reasoning. This work is focused on digital image signal processing of biological and biomedical data in one- two- and three-dimensional space. Methods and algorithms presented in this work were used to acquire data from genomic sequences, breast cancer, and biofilm images. One-dimensional analysis was applied to DNA sequences which were presented as a non-stationary sequence and modeled by a time-dependent autoregressive moving average (TD-ARMA) model. Two-dimensional analyses used 2D-ARMA model and applied it to detect breast cancer from x-ray mammograms or ultrasound images. Three-dimensional detection and classification techniques were applied to biofilm images acquired using confocal laser scanning microscopy. Modern medical images are geometrically arranged arrays of data. The broadening scope of imaging as a way to organize our observations of the biophysical world has led to a dramatic increase in our ability to apply new processing techniques and to combine multiple channels of data into sophisticated and complex mathematical models of physiological function and dysfunction. With explosion of the amount of data produced in a field of biomedicine, it is crucial to be able to construct accurate mathematical models of the data at hand. Two main purposes of signal modeling are: data size conservation and parameter extraction. Specifically, in biomedical imaging we have four key problems

  16. Quantitative 3D elemental analysis inside plant roots by means of synchrotron confocal micro X-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Terzano, R.; Vekemans, B.; Tomasi, N.; Spagnuolo, M.; Schoonjans, T.; Vincze, L.; Pinton, R.; Cesco, S.; Ruggiero, P.

    2009-04-01

    The knowledge of the distribution and concentration of elements within plants is a fundamental step to better understand how these plants uptake specific elements from the medium of growth and how they manage acquisition and compartmentalisation of nutrients as well as toxic metals. For some elements, either nutrients or toxicants, it can be of relevance to know their concentration level within microscopic volumes in plant organs, where they are stored or accumulated. Usually, this type of microscopic analysis requires complex cutting procedures and extensive sample manipulations. In this research, the technique of synchrotron micro X-ray fluorescence in the confocal mode was applied to image the distribution of elements in selected key-planes of tomato roots without the need of any sample preparation, except washing and freeze-drying. Using this method, a first polycapillary lens focussed the X-ray beam with an energy of 12.4 keV down to a 20 µm beam that is penetrating the sample, and a second polycapillary half-lens, that was positioned at the detection side at 90 degrees to the first polycapillary, could then restrict further the view on this irradiated volume to a defined microscopic volume (typically 20x20x20 µm3) from which the induced fluorescent radiation is finally collected by the energy dispersive detector. In this way, it was possible to investigate the concentration levels of some elements such as K, Ca, Mn, Fe, Cu and Zn within the roots of tomato plants. The quantification was performed by means of a dedicated XRF Fundamental Parameter (FP) method in order to calculate the concentrations of trace elements within the analysed plants. Utilizing fundamental atomic parameters, the applied FP method is taking into account the influence of sample self-absorption and especially the specific detection processes by the polycapillary lens. Quantification was assessed and validated by using different standards: NIST SRM 1573a (trace elements in tomato leaves

  17. 3D modelling of the Austroalpine-Penninic collisional wedge of the NW Alps: dataset management and preliminary results

    NASA Astrophysics Data System (ADS)

    Monopoli, Bruno; Bistacchi, Andrea; Bertolo, Davide; Dal Piaz, Giovanni; Gouffon, Yves; Massironi, Matteo; Sartori, Mario; Vittorio Dal Piaz, Giorgio

    2016-04-01

    We know since the beginning of the 20th century, thanks to mapping and structural studies by the Italian Regio Servizio Geologico (Franchi et al., 1908) and Argand's work (1909; 1911; 1916), that the Austroalpine-Penninic collisional wedge of the NW Alps is spectacularly exposed across the Aosta Valley and Valais ranges (Italy and Switzerland). In the 150th anniversary of the first ascent to Ruskin's "most noble cliff in Europe" - the Cervino/Matterhorn (Whymper, July 14th 1865), first described in a geological profile by Giordano (1869) and in a detailed map by Gerlach (1869; 1871), we have seen the conclusion of very detailed mapping projects carried out in the last years over the two regions, with collaborative efforts across the Italy-Switzerland border, constellated by 4000 m-high peaks. These projects have pictured with an unprecedented detail (up to 1:10.000 scale) the geology of this complex region, resulting from pre-Alpine events, Alpine subduction- and collision-related ductile deformations, and finally late-Alpine brittle deformations from the Oligocene to the Present. Based on this dataset, we use up-to-date technology and software to undertake a 3D modelling study aimed at: i) reconstructing the 3D geometry of the principal tectonic units, ii) detecting and unravelling problems and incongruences in the 2D geometrical models, iii) modelling the kinematics of the Oligocene and Miocene brittle fault network using 2D and 3D balancing and palinspastic restoration techniques. In this contribution we mainly discuss the prerequisites of the project. Common geomodelling paradigms (mainly developed for the hydrocarbon industry) cannot be applied in this project due to (i) the little scale, (ii) the source of the data - fieldwork, and (iii) the polyphase ductile and brittle deformations in the metamorphic nappe stack. Our goals at the moment are to model the post-metamorphic fault network and the boundaries of the principal tectonic units, which will be

  18. Multi-sourced, 3D geometric characterization of volcanogenic karst features: Integrating lidar, sonar, and geophysical datasets (Invited)

    NASA Astrophysics Data System (ADS)

    Sharp, J. M.; Gary, M. O.; Reyes, R.; Halihan, T.; Fairfield, N.; Stone, W. C.

    2009-12-01

    Karstic aquifers can form very complex hydrogeological systems and 3-D mapping has been difficult, but Lidar, phased array sonar, and improved earth resistivity techniques show promise in this and in linking metadata to models. Zacatón, perhaps the Earth’s deepest cenote, has a sub-aquatic void space exceeding 7.5 x 106 cubic m3. It is the focus of this study which has created detailed 3D maps of the system. These maps include data from above and beneath the the water table and within the rock matrix to document the extent of the immense karst features and to interpret the geologic processes that formed them. Phase 1 used high resolution (20 mm) Lidar scanning of surficial features of four large cenotes. Scan locations, selected to achieve full feature coverage once registered, were established atop surface benchmarks with UTM coordinates established using GPS and Total Stations. The combined datasets form a geo-registered mesh of surface features down to water level in the cenotes. Phase 2 conducted subsurface imaging using Earth Resistivity Imaging (ERI) geophysics. ERI identified void spaces isolated from open flow conduits. A unique travertine morphology exists in which some cenotes are dry or contain shallow lakes with flat travertine floors; some water-filled cenotes have flat floors without the cone of collapse material; and some have collapse cones. We hypothesize that the floors may have large water-filled voids beneath them. Three separate flat travertine caps were imaged: 1) La Pilita, which is partially open, exposing cap structure over a deep water-filled shaft; 2) Poza Seca, which is dry and vegetated; and 3) Tule, which contains a shallow (<1 m) lake. A fourth line was run adjacent to cenote Verde. La Pilita ERI, verified by SCUBA, documented the existence of large water-filled void zones ERI at Poza Seca showed a thin cap overlying a conductive zone extending to at least 25 m depth beneath the cap with no lower boundary of this zone evident

  19. The Three-Dimensional Micro- and Nanostructure of the Aortic Medial Lamellar Unit Measured Using 3D Confocal & Electron Microscopy Imaging

    PubMed Central

    O’Connell, Mary K; Murthy, Sushila; Phan, Samson; Xu, Chengpei; Buchanan, JoAnn; Spilker, Ryan; Dalman, Ronald L; Zarins, Christopher K; Denk, Winfried; Taylor, Charles A

    2009-01-01

    Changes in arterial wall composition and function underlie all forms of vascular disease. The fundamental structural and functional unit of the aortic wall is the medial lamellar unit (MLU). While the basic composition and organization of the MLU is known, three-dimensional (3D) microstructural details are tenuous, due (in part) to lack of three-dimensional data at micro- and nano-scales. We applied novel electron and confocal microscopy techniques to obtain 3D volumetric information of aortic medial microstructure at micro- and nano-scales with all constituents present. For the rat abdominal aorta, we show that medial elastin has three primary forms: with approximately 71% of total elastin as thick, continuous lamellar sheets, 27% as thin, protruding interlamellar elastin fibers (IEFs), and 2% as thick radial struts. Elastin pores are not simply holes in lamellar sheets, but are indented and gusseted openings in lamellae. Smooth Muscle Cells (SMCs) weave throughout the interlamellar elastin framework, with cytoplasmic extensions abutting IEFs, resulting in approximately 20° radial tilt (relative to the lumen surface) of elliptical SMC nuclei. Collagen fibers are organized as large, parallel bundles tightly enveloping SMC nuclei. Quantification of the orientation of collagen bundles, SMC nuclei, and IEFs reveal that all three primary medial constituents have predominantly circumferential orientation, correlating with reported circumferentially dominant values of physiological stress, collagen fiber recruitment, and tissue stiffness. This high resolution three-dimensional view of the aortic media reveals MLU microstructure details that suggest a highly complex and integrated mural organization that correlates with aortic mechanical properties. PMID:18248974

  20. Monitoring UVR induced damage in single cells and isolated nuclei using SR-FTIR microspectroscopy and 3D confocal Raman imaging.

    PubMed

    Lipiec, Ewelina; Bambery, Keith R; Heraud, Philip; Kwiatek, Wojciech M; McNaughton, Don; Tobin, Mark J; Vogel, Christian; Wood, Bayden R

    2014-09-01

    SR-FTIR in combination with Principal Component Analysis (PCA) was applied to investigate macromolecular changes in a population of melanocytes and their extracted nuclei induced by environmentally relevant fluxes of UVR (Ultraviolet Radiation). Living cells and isolated cellular nuclei were investigated post-irradiation for three different irradiation dosages (130, 1505, 15,052 Jm(-2) UVR, weighted) after either 24 or 48 hours of incubation. DNA conformational changes were observed in cells exposed to an artificial UVR solar-simulator source as evidenced by a shift in the DNA asymmetric phosphodiester vibration from 1236 cm(-1) to 1242 cm(-1) in the case of the exposed cells and from 1225 cm(-1) to 1242 cm(-1) for irradiated nuclei. PCA Scores plots revealed distinct clustering of spectra from irradiated cells and nuclei from non-irradiated controls in response to the range of applied UVR radiation doses. 3D Raman confocal imaging in combination with k-means cluster analysis was applied to study the effect of the UVR radiation exposure on cellular nuclei. Chemical changes associated with apoptosis were detected and included intra-nuclear lipid deposition along with chromatin condensation. The results reported here demonstrate the utility of SR-FTIR and Raman spectroscopy to probe in situ DNA damage in cell nuclei resulting from UVR exposure. These results are in agreement with the increasing body of evidence that lipid accumulation is a characteristic of aggressive cancer cells, and are involved in the production of membranes for rapid cell proliferation. PMID:24995477

  1. Normal-mode function representation of global 3-D datasets: an open-access software for atmospheric research community

    NASA Astrophysics Data System (ADS)

    Žagar, N.; Kasahara, A.; Terasaki, K.; Tribbia, J.; Tanaka, H.

    2014-12-01

    The paper presents new software for the analysis of global dynamical fields in (re)analyses, weather forecasts and climate models. A new diagnostic tool, developed within the MODES project, allows one to diagnose properties of balanced and inertio-gravity (IG) circulation across many scales. In particular, the IG spectrum, which has only recently become observable, can be studied simultaneously in the mass field and wind field and considering the whole model depth in contrary to majority of studies. The paper presentation includes the theory of normal-mode function expansion, technical details of the Fortran 90 code, examples of namelists which control the software execution and outputs of the software application on the reanalysis dataset ERA Interim. The applied libraries and default compiler are from the open-source domain. A limited understanding of Fortran suffices for the successful implementation of the software. The presented application of the software to the ERA Interim dataset show some features of the large-scale circulation after it has been split into the balanced and IG components. The global energy distribution is dominated by the balanced energy with IG modes making less than 10% of the total wave energy. However, on subsynoptic scales IG energy dominates and it is associated with the main features of tropical variability on all scales. The presented energy distribution and features of the zonally-averaged and equatorial circulation provide a reference for the validation of climate models.

  2. 3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity.

    PubMed

    Wongrattanakamon, Pathomwat; Lee, Vannajan Sanghiran; Nimmanpipug, Piyarat; Jiranusornkul, Supat

    2016-12-01

    The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R (2)=0.927, [Formula: see text], SEE=0.197, F=33.849 and q (2)=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion. PMID:27626051

  3. Early Pleistocene glaciations of the North Sea basin revealed by geomorphic evidence from 3D seismic datasets

    NASA Astrophysics Data System (ADS)

    Stewart, Margaret A.; Graham, Alastair G. C.; Lonergan, Lidia

    2013-04-01

    The record of the last major glaciation across northwest Europe is increasingly well understood, but the extent, timing, and palaeoenvironmental significance of earlier Pleistocene glaciations is still poorly known. Here, two sets of iceberg ploughmarks and a buried tunnel valley, all well-imaged within 3D seismic data, provide direct geomorphic evidence for glacial conditions in the central North Sea during periods of the Early to Middle Pleistocene. Each set of geomorphic features is mapped within separate stratigraphic intervals and constrained using seismic-borehole ties to the Bruhnes-Matuyama [B-M] palaeomagnetic reversal, dated in NW Europe at approximately 0.79 Ma B.P (Funnell, 1995). The first set of iceberg ploughmarks mapped within the Witch Ground Basin at approximately 0°30'W, 58°10N comprises 423 scours within a package of relatively disturbed seismic reflectors approximately 130-170m below seabed. Scours are sub-parallel, cross-cutting, and occasionally sinuous, with widths of 40-60m and lengths between 1km and 10km+. The ploughmarked surface is extensively incised by multiple generations of younger tunnel valleys imaged within the same 3D seismic data, and lies above the older B-M horizon. A second set of ploughmarks are buried approximately 250-430m beneath seabed at 2 °40'E 56 °30'N approximately180km SE of the Witch Ground Basin scours. More than 1800 individual scours are observed with widths between 50m and 100m, and lengths from 1km to 17km. The buried scours are observed within three horizons, and their stratigraphic position indicates they pre-date the B-M reversal, lying within a unit traditionally associated with times of non-glacial deposition. A single buried tunnel valley, c.60km in length, is observed towards the NW of the study area at approximately 0°30'W and 58°30'N. The main channel of the tunnel valley is curvilinear and trends approximately NE-SW with two significant tributary channels trending NW-SE. The tunnel valley

  4. The next chapter in experimental petrology: Metamorphic dehydration of polycrystalline gypsum captured in 3D microtomographic time series datasets

    NASA Astrophysics Data System (ADS)

    Bedford, John; Fusseis, Florian; Leclere, Henry; Wheeler, John; Faulkner, Dan

    2016-04-01

    Nucleation and growth of new minerals in response to disequilibrium is the most fundamental metamorphic process. However, our current kinetic models of metamorphic reactions are largely based on inference from fossil mineral assemblages, rather than from direct observation. The experimental investigation of metamorphism has also been limited, typically to concealed vessels that restrict the possibility of direct microstructural monitoring. Here we present one of the first time series datasets that captures a metamorphic reaction, dehydration of polycrystalline gypsum to form hemihydrate, in a series of three dimensional x-ray microtomographic datasets. We achieved this by installing an x-ray transparent hydrothermal cell (Fusseis et al., 2014, J. Synchrotron Rad. 21, 251-253) in the microtomography beamline 2BM at the Advanced Photon Source (USA). In the cell, we heated a millimetre-sized sample of Volterra Alabaster to 388 K while applying an effective pressure of 5 MPa. Using hard x-rays that penetrate the pressure vessel, we imaged the specimen 40 times while it reacted for approximately 10 hours. Each microtomographic dataset was acquired in 300 seconds without interrupting the reaction. Our absorption microtomographic data have a voxel size of 1.3 μm, which suffices to analyse the reaction progress in 4D. Gypsum can clearly be distinguished from hemihydrate and pores, which form due to the large negative solid volume change. On the resolved scale, the first hemihydrate needles appear after about 2 hours. Our data allow tracking of individual needles throughout the entire experiment. We quantified their growth rates by measuring their circumference. While individual grains grow at different rates, they all start slowly during the initial nucleation stage, then accelerate and grow steadily between about 200 and 400 minutes before reaction rate decelerates again. Hemihydrate needles are surrounded by porous haloes, which grow with the needles, link up and

  5. Confocal scanning laser microscopy with complementary 3D image analysis allows quantitative studies of functional state of ionoregulatory cells in the Nile tilapia (Oreochromis niloticus) following salinity challenge.

    PubMed

    Fridman, Sophie; Rana, Krishen J; Bron, James E

    2013-04-01

    The development of a novel three-dimensional image analysis technique of stacks generated by confocal laser scanning microscopy is described allowing visualization of mitochondria-rich cells (MRCs) in the seawater-adapted Nile tilapia in relation to their spatial location. This method permits the assessment and classification of both active and nonactive MRCs based on the distance of the top of the immunopositive cell from the epithelial surface. In addition, this technique offers the potential for informative and quantitative studies, for example, densitometric and morphometric measurements based on MRC functional state. Confocal scanning laser microscopy used with triple staining whole-mount immunohistochemistry was used to detect integumental MRCs in the yolk-sac larvae tail of the Nile tilapia following transfer from freshwater to elevated salinities, that is, 12.5 and 20 ppt. Mean active MRC volume was always significantly larger and displayed a greater staining intensity (GLM; P<0.05) than nonactive MRCs. Following transfer, the percentage of active MRCs was seen to increase as did MRC volume (GLM; P<0.05). PMID:23390074

  6. Non-destructive 3D Imaging of Extraterrestrial Materials by Synchrotron X-ray Micro- tomography (XR-CMT) and Laser Confocal Scanning Microscopy (LCSM): Beyond Pretty Pictures

    NASA Astrophysics Data System (ADS)

    Ebel, D. S.; Greenberg, M.

    2009-05-01

    We report scientific results made possible only by the use these two non-destructive 3D imaging techniques. XR-CMT provides 3D image reconstructions at spatial resolutions of 1 to 17 micron/voxel edge. We use XR- CMT to locate potential melt-inclusion-bearing phenocrysts in batches of 100-200 micron lunar fire-fountain spherules; to locate and visualize the morphology of 1-2mm size, irregular, unmelted Ca-, Al-rich inclusions (CAIs) and to quantify chondrule/matrix ratios and chondrule size distributions in 6x6x20mm chunks of carbonaceous chondrites; to quantify the modal abundance of opaque phases in similar sized Martian meteorite fragments, and in individual 1-2mm diameter chondrules from chondrites. LCSM provides 3D image stacks at resolutions < 100 nm/pixel. We are the only group creating deconvolved image stacks of 100 to over 1000 micron long comet particle tracks in aerogel keystones from the Stardust mission. We present measurements of track morphology in 3D, and locate high-value particles using complementary synchrotron x- ray fluorescence (XRF) examination. We show that bench-top LCSM extracts maximum information about tracks and particles rapidly and cheaply prior to destructive disassembly. Using XR-CMT we quantify, for the first time, the volumetric abundances of metal grains in 1-2 mm diameter CR chondrite chondrules. Metal abundances vary from 1 to 37 vol.% between 8 chondrules (and more by inspection), in a meteorite with solar (chondritic) Fe/Si ratio, indicating that chondrules formed and accreted locally from bulk solar composition material. They are 'complementary' to each other in Fe/Si ratios. Void spaces in chondritic CAIs and chondrules are shown to be a primary feature, not due to plucking during sectioning. CAI morphology in 3D reveals pre-accretionary impact features, and various types of mineralogical layering, seen in 3D, reveal the formation history of these building blocks of planets and asteroids. We also quantify the x

  7. Novel Application of Confocal Laser Scanning Microscopy and 3D Volume Rendering toward Improving the Resolution of the Fossil Record of Charcoal

    PubMed Central

    Belcher, Claire M.; Punyasena, Surangi W.; Sivaguru, Mayandi

    2013-01-01

    Variations in the abundance of fossil charcoals between rocks and sediments are assumed to reflect changes in fire activity in Earth’s past. These variations in fire activity are often considered to be in response to environmental, ecological or climatic changes. The role that fire plays in feedbacks to such changes is becoming increasingly important to understand and highlights the need to create robust estimates of variations in fossil charcoal abundance. The majority of charcoal based fire reconstructions quantify the abundance of charcoal particles and do not consider the changes in the morphology of the individual particles that may have occurred due to fragmentation as part of their transport history. We have developed a novel application of confocal laser scanning microscopy coupled to image processing that enables the 3-dimensional reconstruction of individual charcoal particles. This method is able to measure the volume of both microfossil and mesofossil charcoal particles and allows the abundance of charcoal in a sample to be expressed as total volume of charcoal. The method further measures particle surface area and shape allowing both relationships between different size and shape metrics to be analysed and full consideration of variations in particle size and size sorting between different samples to be studied. We believe application of this new imaging approach could allow significant improvement in our ability to estimate variations in past fire activity using fossil charcoals. PMID:23977267

  8. Combining depth analysis with surface morphology analysis to analyse the prehistoric painted pottery from Majiayao Culture by confocal 3D-XRF

    NASA Astrophysics Data System (ADS)

    Yi, Longtao; Liu, Zhiguo; Wang, Kai; Lin, Xue; Chen, Man; Peng, Shiqi; Yang, Kui; Wang, Jinbang

    2016-04-01

    The Majiayao Culture (3300 BC-2900 BC) formed one of the three painted pottery centres of the Yellow River basin, China, in prehistoric times. Painted pottery from this period is famous for its exquisite workmanship and meticulous painting. Studying the layer structure and element distribution of the paint on the pottery is conducive to investigating its workmanship, which is important for archaeological research. However, the most common analysis methods are destructive. To investigate the layers of paint on the pottery nondestructively, a confocal three-dimensional micro-X-ray fluorescence set-up combined with two individual polycapillary lenses has been used to analyse two painted pottery fragments. Nondestructive elemental depth analyses and surface topographic analysis were performed. The elemental depth profiles of Mn, Fe and Ca obtained from these measurements were consistent with those obtained using an optical microscope. The depth profiles show that there are layer structures in two samples. The images show that the distribution of Ca is approximately homogeneous in both painted and unpainted regions. In contrast, Mn appeared only in the painted regions. Meanwhile, the distributions of Fe in the painted and unpainted regions were not the same. The surface topographic shows that the pigment of dark-brown region was coated above the brown region. These conclusions allowed the painting process to be inferred.

  9. A clearer view of the insect brain—combining bleaching with standard whole-mount immunocytochemistry allows confocal imaging of pigment-covered brain areas for 3D reconstruction

    PubMed Central

    Stöckl, Anna L.; Heinze, Stanley

    2015-01-01

    In the study of insect neuroanatomy, three-dimensional (3D) reconstructions of neurons and neuropils have become a standard technique. As images have to be obtained from whole-mount brain preparations, pigmentation on the brain surface poses a serious challenge to imaging. In insects, this is a major problematic in the first visual neuropil of the optic lobe, the lamina, which is obstructed by the pigment of the retina as well as by the pigmented fenestration layer. This has prevented inclusion of this major processing center of the insect visual system into most neuroanatomical brain atlases and hinders imaging of neurons within the lamina by confocal microscopy. It has recently been shown that hydrogen peroxide bleaching is compatible with immunohistochemical labeling in insect brains, and we therefore developed a simple technique for removal of pigments on the surface of insect brains by chemical bleaching. We show that our technique enables imaging of the pigment-obstructed regions of insect brains when combined with standard protocols for both anti-synapsin-labeled as well as neurobiotin-injected samples. This method can be combined with different fixation procedures, as well as different fluorophore excitation wavelengths without negative effects on staining quality. It can therefore serve as an effective addition to most standard histology protocols used in insect neuroanatomy. PMID:26441552

  10. A clearer view of the insect brain-combining bleaching with standard whole-mount immunocytochemistry allows confocal imaging of pigment-covered brain areas for 3D reconstruction.

    PubMed

    Stöckl, Anna L; Heinze, Stanley

    2015-01-01

    In the study of insect neuroanatomy, three-dimensional (3D) reconstructions of neurons and neuropils have become a standard technique. As images have to be obtained from whole-mount brain preparations, pigmentation on the brain surface poses a serious challenge to imaging. In insects, this is a major problematic in the first visual neuropil of the optic lobe, the lamina, which is obstructed by the pigment of the retina as well as by the pigmented fenestration layer. This has prevented inclusion of this major processing center of the insect visual system into most neuroanatomical brain atlases and hinders imaging of neurons within the lamina by confocal microscopy. It has recently been shown that hydrogen peroxide bleaching is compatible with immunohistochemical labeling in insect brains, and we therefore developed a simple technique for removal of pigments on the surface of insect brains by chemical bleaching. We show that our technique enables imaging of the pigment-obstructed regions of insect brains when combined with standard protocols for both anti-synapsin-labeled as well as neurobiotin-injected samples. This method can be combined with different fixation procedures, as well as different fluorophore excitation wavelengths without negative effects on staining quality. It can therefore serve as an effective addition to most standard histology protocols used in insect neuroanatomy. PMID:26441552

  11. Virtual pinhole confocal microscope

    SciTech Connect

    George, J.S.; Rector, D.M.; Ranken, D.M.; Peterson, B.; Kesteron, J.

    1999-06-01

    Scanned confocal microscopes enhance imaging capabilities, providing improved contrast and image resolution in 3-D, but existing systems have significant technical shortcomings and are expensive. Researchers at Los Alamos National Laboratory have developed a novel approach--virtual pinhole confocal microscopy--that uses state of the art illumination, detection, and data processing technologies to produce an imager with a number of advantages: reduced cost, faster imaging, improved efficiency and sensitivity, improved reliability and much greater flexibility. Work at Los Alamos demonstrated proof of principle; prototype hardware and software have been used to demonstrate technical feasibility of several implementation strategies. The system uses high performance illumination, patterned in time and space. The authors have built functional confocal imagers using video display technologies (LCD or DLP) and novel scanner based on a micro-lens array. They have developed a prototype system for high performance data acquisition and processing, designed to support realtime confocal imaging. They have developed algorithms to reconstruct confocal images from a time series of spatially sub-sampled images; software development remains an area of active development. These advances allow the collection of high quality confocal images (in fluorescence, reflectance and transmission modes) with equipment that can inexpensively retrofit to existing microscopes. Planned future extensions to these technologies will significantly enhance capabilities for microscopic imaging in a variety of applications, including confocal endoscopy, and confocal spectral imaging.

  12. 3-D Modeling for Upper Mantle Anisotropy Beneath Idaho-Oregon (IDOR) Region Using Sks Splitting Intensity Measurements from IDOR Passive Seismic Project Dataset

    NASA Astrophysics Data System (ADS)

    Hongsresawat, S.; Panning, M. P.; Russo, R. M.; Mocanu, V. I.; Stanciu, A. C.; Bremner, P. M.; Torpey, M. E.; VanDecar, J. C.

    2014-12-01

    We used data recorded at 86 broadband seismic stations of the IDOR Passive Seismic Project to determine upper mantle anisotropy across the suture along which Blue Mountain island-arc terranes accreted to North America during Cretaceous. This suture is currently associated with the Western Idaho Shear Zone (WISZ), a narrow, highly-deformed ductile fault that was the locus of both dextral strike-slip along, and subduction beneath, the Paleozoic margin of the North American craton. We measured shear wave splitting intensity (SI), a seismic observable that is suitable for use in 3-D inversions of upper mantle seismic anisotropy, to determine these fabrics beneath the IDOR network. SI fast-polarization directions are spatially coherent across the region, and fall into three main groups: a group with fast azimuths trending ENE-WSW, observed at stations in eastern Oregon and the NW-SE-striking western Snake River Plain; a group with E-W trending fast azimuths observed at stations along the WISZ and the Idaho Batholith, which outcrops immediately east of the suture zone; and a group with ENE-WSW trending fast azimuths observed at stations situated in the Basin-and-Range extended region of southeastern Idaho. SI delay times range from 0.46 to 1.85 seconds, with a mean of 1.1 s. We also used backazimuthal variations of SI at all stations to invert for for 3-D anisotropic fabric using the finite-frequency approach called vectorial tomography (Chevrot and Monteiller, 2009). Our preliminary results are consistent with alignment of upper mantle fabrics in the extension direction as Basin-and-Range extension propagates northward into less-extended regions of Idaho and Oregon.

  13. How 3D immersive visualization is changing medical diagnostics

    NASA Astrophysics Data System (ADS)

    Koning, Anton H. J.

    2011-03-01

    Originally the only way to look inside the human body without opening it up was by means of two dimensional (2D) images obtained using X-ray equipment. The fact that human anatomy is inherently three dimensional leads to ambiguities in interpretation and problems of occlusion. Three dimensional (3D) imaging modalities such as CT, MRI and 3D ultrasound remove these drawbacks and are now part of routine medical care. While most hospitals 'have gone digital', meaning that the images are no longer printed on film, they are still being viewed on 2D screens. However, this way valuable depth information is lost, and some interactions become unnecessarily complex or even unfeasible. Using a virtual reality (VR) system to present volumetric data means that depth information is presented to the viewer and 3D interaction is made possible. At the Erasmus MC we have developed V-Scope, an immersive volume visualization system for visualizing a variety of (bio-)medical volumetric datasets, ranging from 3D ultrasound, via CT and MRI, to confocal microscopy, OPT and 3D electron-microscopy data. In this talk we will address the advantages of such a system for both medical diagnostics as well as for (bio)medical research.

  14. ShowMe3D

    SciTech Connect

    Sinclair, Michael B

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from the displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.

  15. ShowMe3D

    Energy Science and Technology Software Center (ESTSC)

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from themore » displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.« less

  16. Arena3D: visualization of biological networks in 3D

    PubMed Central

    Pavlopoulos, Georgios A; O'Donoghue, Seán I; Satagopam, Venkata P; Soldatos, Theodoros G; Pafilis, Evangelos; Schneider, Reinhard

    2008-01-01

    Background Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run. PMID:19040715

  17. Fully automatic and robust 3D registration of serial-section microscopic images

    PubMed Central

    Wang, Ching-Wei; Budiman Gosno, Eric; Li, Yen-Sheng

    2015-01-01

    Robust and fully automatic 3D registration of serial-section microscopic images is critical for detailed anatomical reconstruction of large biological specimens, such as reconstructions of dense neuronal tissues or 3D histology reconstruction to gain new structural insights. However, robust and fully automatic 3D image registration for biological data is difficult due to complex deformations, unbalanced staining and variations on data appearance. This study presents a fully automatic and robust 3D registration technique for microscopic image reconstruction, and we demonstrate our method on two ssTEM datasets of drosophila brain neural tissues, serial confocal laser scanning microscopic images of a drosophila brain, serial histopathological images of renal cortical tissues and a synthetic test case. The results show that the presented fully automatic method is promising to reassemble continuous volumes and minimize artificial deformations for all data and outperforms four state-of-the-art 3D registration techniques to consistently produce solid 3D reconstructed anatomies with less discontinuities and deformations. PMID:26449756

  18. Fully automatic and robust 3D registration of serial-section microscopic images.

    PubMed

    Wang, Ching-Wei; Budiman Gosno, Eric; Li, Yen-Sheng

    2015-01-01

    Robust and fully automatic 3D registration of serial-section microscopic images is critical for detailed anatomical reconstruction of large biological specimens, such as reconstructions of dense neuronal tissues or 3D histology reconstruction to gain new structural insights. However, robust and fully automatic 3D image registration for biological data is difficult due to complex deformations, unbalanced staining and variations on data appearance. This study presents a fully automatic and robust 3D registration technique for microscopic image reconstruction, and we demonstrate our method on two ssTEM datasets of drosophila brain neural tissues, serial confocal laser scanning microscopic images of a drosophila brain, serial histopathological images of renal cortical tissues and a synthetic test case. The results show that the presented fully automatic method is promising to reassemble continuous volumes and minimize artificial deformations for all data and outperforms four state-of-the-art 3D registration techniques to consistently produce solid 3D reconstructed anatomies with less discontinuities and deformations. PMID:26449756

  19. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

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

  20. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. Digital differential confocal microscopy based on spatial shift transformation.

    PubMed

    Liu, J; Wang, Y; Liu, C; Wilson, T; Wang, H; Tan, J

    2014-11-01

    Differential confocal microscopy is a particularly powerful surface profilometry technique in industrial metrology due to its high axial sensitivity and insensitivity to noise. However, the practical implementation of the technique requires the accurate positioning of point detectors in three-dimensions. We describe a simple alternative based on spatial transformation of a through-focus series of images obtained from a homemade beam scanning confocal microscope. This digital differential confocal microscopy approach is described and compared with the traditional Differential confocal microscopy approach. The ease of use of the digital differential confocal microscopy system is illustrated by performing measurements on a 3D standard specimen. PMID:25303106

  2. Magmatic Systems in 3-D

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  3. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

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

  4. 3D-HST results and prospects

    NASA Astrophysics Data System (ADS)

    Van Dokkum, Pieter G.

    2015-01-01

    The 3D-HST survey is providing a comprehensive census of the distant Universe, combining HST WFC3 imaging and grism spectroscopy with a myriad of other ground- and space-based datasets. This talk constitutes an overview of science results from the survey, with a focus on ongoing work and ways to exploit the rich public release of the 3D-HST data.

  5. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

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

  6. Confocal microscopy in microgravity research

    NASA Astrophysics Data System (ADS)

    Goede, A. P. H.; Brakenhoff, G. J.; Woldringh, C. L.; Aalders, J. W. G.; Imhof, J. P.; van Kralingen, P.; Mels, W. A.; Schreinemakers, P.; Zegers, A.

    We have studied the application and the feasibility of confocal scanning laser microscopy (CSLM) in microgravity research. Its superior spatial resolution and 3D imaging capabilities and its use of light as a probe, render this instrument ideally suited for the study of living biological material on a (sub-)cellular level. In this paper a number of pertinent biological microgravity experiments is listed, concentrating on the direct observation of developing cells and cellular structures under microgravity condition. A conceptual instrument design is also presented, aimed at sounding rocket application followed by Biorack/Biolab application at a later stage.

  7. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

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

  8. RAG-3D: a search tool for RNA 3D substructures.

    PubMed

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-10-30

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  9. bioWeb3D: an online webGL 3D data visualisation tool

    PubMed Central

    2013-01-01

    Background Data visualization is critical for interpreting biological data. However, in practice it can prove to be a bottleneck for non trained researchers; this is especially true for three dimensional (3D) data representation. Whilst existing software can provide all necessary functionalities to represent and manipulate biological 3D datasets, very few are easily accessible (browser based), cross platform and accessible to non-expert users. Results An online HTML5/WebGL based 3D visualisation tool has been developed to allow biologists to quickly and easily view interactive and customizable three dimensional representations of their data along with multiple layers of information. Using the WebGL library Three.js written in Javascript, bioWeb3D allows the simultaneous visualisation of multiple large datasets inputted via a simple JSON, XML or CSV file, which can be read and analysed locally thanks to HTML5 capabilities. Conclusions Using basic 3D representation techniques in a technologically innovative context, we provide a program that is not intended to compete with professional 3D representation software, but that instead enables a quick and intuitive representation of reasonably large 3D datasets. PMID:23758781

  10. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

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

  11. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  12. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGESBeta

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  13. RAG-3D: A search tool for RNA 3D substructures

    SciTech Connect

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

  14. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  15. Vasculogenesis and angiogenesis in the first trimester human placenta: an innovative 3D study using an immersive Virtual Reality system.

    PubMed

    van Oppenraaij, R H F; Koning, A H J; Lisman, B A; Boer, K; van den Hoff, M J B; van der Spek, P J; Steegers, E A P; Exalto, N

    2009-03-01

    First trimester human villous vascularization is mainly studied by conventional two-dimensional (2D) microscopy. With this (2D) technique it is not possible to observe the spatial arrangement of the haemangioblastic cords and vessels, transition of cords into vessels and the transition of vasculogenesis to angiogenesis. The Confocal Laser Scanning Microscopy (CLSM) allows for a three-dimensional (3D) reconstruction of images of early pregnancy villous vascularization. These 3D reconstructions, however, are normally analyzed on a 2D medium, lacking depth perception. We performed a descriptive morphologic study, using an immersive Virtual Reality system to utilize the full third dimension completely. This innovative 3D technique visualizes 3D datasets as enlarged 3D holograms and provided detailed insight in the spatial arrangement of first trimester villous vascularization, the beginning of lumen formation within various junctions of haemangioblastic cords between 5 and 7 weeks gestational age and in the gradual transition of vasculogenesis to angiogenesis. This innovative immersive Virtual Reality system enables new perspectives for vascular research and will be implemented for future investigation. PMID:19185915

  16. Non-destructive investigations of a copper and argon doped sputtered beryllium capsule using x-rays in 3d

    SciTech Connect

    Patterson, Brian M; Defriend, Kimberly A; Havrilla, George J; Nikroo, Abbas

    2008-01-01

    The combination of 3D computed micro x-ray tomography (micro CT) and 3D confocal micro x-ray fluorescence (confocal MXRF) are very useful nondestructive metrology techniques for determining the unique compositional and morphological information of fusion targets and target materials.

  17. 3D object retrieval using salient views

    PubMed Central

    Shapiro, Linda G.

    2013-01-01

    This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223–232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223–232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

  18. 3D object retrieval using salient views.

    PubMed

    Atmosukarto, Indriyati; Shapiro, Linda G

    2013-06-01

    This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223-232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223-232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

  19. 3D Cell Culture Imaging with Digital Holographic Microscopy

    NASA Astrophysics Data System (ADS)

    Dimiduk, Thomas; Nyberg, Kendra; Almeda, Dariela; Koshelva, Ekaterina; McGorty, Ryan; Kaz, David; Gardel, Emily; Auguste, Debra; Manoharan, Vinothan

    2011-03-01

    Cells in higher organisms naturally exist in a three dimensional (3D) structure, a fact sometimes ignored by in vitro biological research. Confinement to a two dimensional culture imposes significant deviations from the native 3D state. One of the biggest obstacles to wider use of 3D cultures is the difficulty of 3D imaging. The confocal microscope, the dominant 3D imaging instrument, is expensive, bulky, and light-intensive; live cells can be observed for only a short time before they suffer photodamage. We present an alternative 3D imaging techinque, digital holographic microscopy, which can capture 3D information with axial resolution better than 2 μm in a 100 μm deep volume. Capturing a 3D image requires only a single camera exposure with a sub-millisecond laser pulse, allowing us to image cell cultures using five orders of magnitude less light energy than with confocal. This can be done with hardware costing ~ 1000. We use the instrument to image growth of MCF7 breast cancer cells and p. pastoras yeast. We acknowledge support from NSF GRFP.

  20. LOTT RANCH 3D PROJECT

    SciTech Connect

    Larry Lawrence; Bruce Miller

    2004-09-01

    The Lott Ranch 3D seismic prospect located in Garza County, Texas is a project initiated in September of 1991 by the J.M. Huber Corp., a petroleum exploration and production company. By today's standards the 126 square mile project does not seem monumental, however at the time it was conceived it was the most intensive land 3D project ever attempted. Acquisition began in September of 1991 utilizing GEO-SEISMIC, INC., a seismic data contractor. The field parameters were selected by J.M. Huber, and were of a radical design. The recording instruments used were GeoCor IV amplifiers designed by Geosystems Inc., which record the data in signed bit format. It would not have been practical, if not impossible, to have processed the entire raw volume with the tools available at that time. The end result was a dataset that was thought to have little utility due to difficulties in processing the field data. In 1997, Yates Energy Corp. located in Roswell, New Mexico, formed a partnership to further develop the project. Through discussions and meetings with Pinnacle Seismic, it was determined that the original Lott Ranch 3D volume could be vastly improved upon reprocessing. Pinnacle Seismic had shown the viability of improving field-summed signed bit data on smaller 2D and 3D projects. Yates contracted Pinnacle Seismic Ltd. to perform the reprocessing. This project was initiated with high resolution being a priority. Much of the potential resolution was lost through the initial summing of the field data. Modern computers that are now being utilized have tremendous speed and storage capacities that were cost prohibitive when this data was initially processed. Software updates and capabilities offer a variety of quality control and statics resolution, which are pertinent to the Lott Ranch project. The reprocessing effort was very successful. The resulting processed data-set was then interpreted using modern PC-based interpretation and mapping software. Production data, log data

  1. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

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

  2. Anisotropy effects on 3D waveform inversion

    NASA Astrophysics Data System (ADS)

    Stekl, I.; Warner, M.; Umpleby, A.

    2010-12-01

    In the recent years 3D waveform inversion has become achievable procedure for seismic data processing. A number of datasets has been inverted and presented (Warner el al 2008, Ben Hadj at all, Sirgue et all 2010) using isotropic 3D waveform inversion. However the question arises will the results be affected by isotropic assumption. Full-wavefield inversion techniques seek to match field data, wiggle-for-wiggle, to synthetic data generated by a high-resolution model of the sub-surface. In this endeavour, correctly matching the travel times of the principal arrivals is a necessary minimal requirement. In many, perhaps most, long-offset and wide-azimuth datasets, it is necessary to introduce some form of p-wave velocity anisotropy to match the travel times successfully. If this anisotropy is not also incorporated into the wavefield inversion, then results from the inversion will necessarily be compromised. We have incorporated anisotropy into our 3D wavefield tomography codes, characterised as spatially varying transverse isotropy with a tilted axis of symmetry - TTI anisotropy. This enhancement approximately doubles both the run time and the memory requirements of the code. We show that neglect of anisotropy can lead to significant artefacts in the recovered velocity models. We will present inversion results of inverting anisotropic 3D dataset by assuming isotropic earth and compare them with anisotropic inversion result. As a test case Marmousi model extended to 3D with no velocity variation in third direction and with added spatially varying anisotropy is used. Acquisition geometry is assumed as OBC with sources and receivers everywhere at the surface. We attempted inversion using both 2D and full 3D acquisition for this dataset. Results show that if no anisotropy is taken into account although image looks plausible most features are miss positioned in depth and space, even for relatively low anisotropy, which leads to incorrect result. This may lead to

  3. 3D visualisation and analysis of single and coalescing tracks in Solid state Nuclear Track Detectors

    NASA Astrophysics Data System (ADS)

    Wertheim, David; Gillmore, Gavin; Brown, Louise; Petford, Nick

    2010-05-01

    Exposure to radon gas (222Rn) and associated ionising decay products can cause lung cancer in humans (1). Solid state Nuclear Track Detectors (SSNTDs) can be used to monitor radon concentrations (2). Radon particles form tracks in the detectors and these tracks can be etched in order to enable 2D surface image analysis. We have previously shown that confocal microscopy can be used for 3D visualisation of etched SSNTDs (3). The aim of the study was to further investigate track angles and patterns in SSNTDs. A 'LEXT' confocal laser scanning microscope (Olympus Corporation, Japan) was used to acquire 3D image datasets of five CR-39 plastic SSNTD's. The resultant 3D visualisations were analysed by eye and inclination angles assessed on selected tracks. From visual assessment, single isolated tracks as well as coalescing tracks were observed on the etched detectors. In addition varying track inclination angles were observed. Several different patterns of track formation were seen such as single isolated and double coalescing tracks. The observed track angles of inclination may help to assess the angle at which alpha particles hit the detector. Darby, S et al. Radon in homes and risk of lung cancer : collaborative analysis of individual data from 13 European case-control studies. British Medical Journal 2005; 330, 223-226. Phillips, P.S., Denman, A.R., Crockett, R.G.M., Gillmore, G., Groves-Kirkby, C.J., Woolridge, A., Comparative Analysis of Weekly vs. Three monthly radon measurements in dwellings. DEFRA Report No., DEFRA/RAS/03.006. (2004). Wertheim D, Gillmore G, Brown L, and Petford N. A new method of imaging particle tracks in Solid State Nuclear Track Detectors. Journal of Microscopy 2010; 237: 1-6.

  4. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

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

  5. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

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

    1998-09-01

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

  6. Dual side transparent OLED 3D display using Gabor super-lens

    NASA Astrophysics Data System (ADS)

    Chestak, Sergey; Kim, Dae-Sik; Cho, Sung-Woo

    2015-03-01

    We devised dual side transparent 3D display using transparent OLED panel and two lenticular arrays. The OLED panel is sandwiched between two parallel confocal lenticular arrays, forming Gabor super-lens. The display provides dual side stereoscopic 3D imaging and floating image of the object, placed behind it. The floating image can be superimposed with the displayed 3D image. The displayed autostereoscopic 3D images are composed of 4 views, each with resolution 64x90 pix.

  7. 3D Surgical Simulation

    PubMed Central

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

    2009-01-01

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

  8. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

  9. 3D field harmonics

    SciTech Connect

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

    1991-03-30

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

  10. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

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

  11. A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

    PubMed

    Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl

    2016-08-01

    The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci. PMID:27037463

  12. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data.

    PubMed

    Spiegel, M; Redel, T; Struffert, T; Hornegger, J; Doerfler, A

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling. PMID:21908904

  13. A 2D driven 3D vessel segmentation algorithm for 3D digital subtraction angiography data

    NASA Astrophysics Data System (ADS)

    Spiegel, M.; Redel, T.; Struffert, T.; Hornegger, J.; Doerfler, A.

    2011-10-01

    Cerebrovascular disease is among the leading causes of death in western industrial nations. 3D rotational angiography delivers indispensable information on vessel morphology and pathology. Physicians make use of this to analyze vessel geometry in detail, i.e. vessel diameters, location and size of aneurysms, to come up with a clinical decision. 3D segmentation is a crucial step in this pipeline. Although a lot of different methods are available nowadays, all of them lack a method to validate the results for the individual patient. Therefore, we propose a novel 2D digital subtraction angiography (DSA)-driven 3D vessel segmentation and validation framework. 2D DSA projections are clinically considered as gold standard when it comes to measurements of vessel diameter or the neck size of aneurysms. An ellipsoid vessel model is applied to deliver the initial 3D segmentation. To assess the accuracy of the 3D vessel segmentation, its forward projections are iteratively overlaid with the corresponding 2D DSA projections. Local vessel discrepancies are modeled by a global 2D/3D optimization function to adjust the 3D vessel segmentation toward the 2D vessel contours. Our framework has been evaluated on phantom data as well as on ten patient datasets. Three 2D DSA projections from varying viewing angles have been used for each dataset. The novel 2D driven 3D vessel segmentation approach shows superior results against state-of-the-art segmentations like region growing, i.e. an improvement of 7.2% points in precision and 5.8% points for the Dice coefficient. This method opens up future clinical applications requiring the greatest vessel accuracy, e.g. computational fluid dynamic modeling.

  14. 3D quantitative phase imaging of neural networks using WDT

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Liu, S. C.; Iyer, Raj; Gillette, Martha U.; Popescu, Gabriel

    2015-03-01

    White-light diffraction tomography (WDT) is a recently developed 3D imaging technique based on a quantitative phase imaging system called spatial light interference microscopy (SLIM). The technique has achieved a sub-micron resolution in all three directions with high sensitivity granted by the low-coherence of a white-light source. Demonstrations of the technique on single cell imaging have been presented previously; however, imaging on any larger sample, including a cluster of cells, has not been demonstrated using the technique. Neurons in an animal body form a highly complex and spatially organized 3D structure, which can be characterized by neuronal networks or circuits. Currently, the most common method of studying the 3D structure of neuron networks is by using a confocal fluorescence microscope, which requires fluorescence tagging with either transient membrane dyes or after fixation of the cells. Therefore, studies on neurons are often limited to samples that are chemically treated and/or dead. WDT presents a solution for imaging live neuron networks with a high spatial and temporal resolution, because it is a 3D imaging method that is label-free and non-invasive. Using this method, a mouse or rat hippocampal neuron culture and a mouse dorsal root ganglion (DRG) neuron culture have been imaged in order to see the extension of processes between the cells in 3D. Furthermore, the tomogram is compared with a confocal fluorescence image in order to investigate the 3D structure at synapses.

  15. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

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

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

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

  16. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

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

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

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

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

  17. A near-infrared confocal scanner

    NASA Astrophysics Data System (ADS)

    Lee, Seungwoo; Yoo, Hongki

    2014-06-01

    In the semiconductor industry, manufacturing of three-dimensional (3D) packages or 3D integrated circuits is a high-performance technique that requires combining several functions in a small volume. Through-silicon vias, which are vertical electrical connections extending through a wafer, can be used to direct signals between stacked chips, thus increasing areal density by stacking and connecting multiple patterned chips. While defect detection is essential in the semiconductor manufacturing process, it is difficult to identify defects within a wafer or to monitor the bonding results between bonded surfaces because silicon and many other semiconductor materials are opaque to visible wavelengths. In this context, near-infrared (NIR) imaging is a promising non-destructive method to detect defects within silicon chips, to inspect bonding between chips and to monitor the chip alignment since NIR transmits through silicon. In addition, a confocal scanner provides high-contrast, optically-sectioned images of the specimen due to its ability to reject out-of-focus noise. In this study, we report an NIR confocal scanner that rapidly acquires high-resolution images with a large field of view through silicon. Two orthogonal line-scanning images can be acquired without rotating the system or the specimen by utilizing two orthogonally configured resonant scanning mirrors. This NIR confocal scanner can be efficiently used as an in-line inspection system when manufacturing semiconductor devices by rapidly detecting defects on and beneath the surface.

  18. The Galicia 3D experiment: an Introduction.

    NASA Astrophysics Data System (ADS)

    Reston, Timothy; Martinez Loriente, Sara; Holroyd, Luke; Merry, Tobias; Sawyer, Dale; Morgan, Julia; Jordan, Brian; Tesi Sanjurjo, Mari; Alexanian, Ara; Shillington, Donna; Gibson, James; Minshull, Tim; Karplus, Marianne; Bayracki, Gaye; Davy, Richard; Klaeschen, Dirk; Papenberg, Cord; Ranero, Cesar; Perez-Gussinye, Marta; Martinez, Miguel

    2014-05-01

    In June and July 2013, scientists from 8 institutions took part in the Galicia 3D seismic experiment, the first ever crustal -scale academic 3D MCS survey over a rifted margin. The aim was to determine the 3D structure of a critical portion of the west Galicia rifted margin. At this margin, well-defined tilted fault blocks, bound by west-dipping faults and capped by synrift sediments are underlain by a bright reflection, undulating on time sections, termed the S reflector and thought to represent a major detachment fault of some kind. Moving west, the crust thins to zero thickness and mantle is unroofed, as evidence by the "Peridotite Ridge" first reported at this margin, but since observed at many other magma-poor margins. By imaging such a margin in detail, the experiment aimed to resolve the processes controlling crustal thinning and mantle unroofing at a type example magma poor margin. The experiment set out to collect several key datasets: a 3D seismic reflection volume measuring ~20x64km and extending down to ~14s TWT, a 3D ocean bottom seismometer dataset suitable for full wavefield inversion (the recording of the complete 3D seismic shots by 70 ocean bottom instruments), the "mirror imaging" of the crust using the same grid of OBS, a single 2D combined reflection/refraction profile extending to the west to determine the transition from unroofed mantle to true oceanic crust, and the seismic imaging of the water column, calibrated by regular deployment of XBTs to measure the temperature structure of the water column. We collected 1280 km2 of seismic reflection data, consisting of 136533 shots recorded on 1920 channels, producing 260 million seismic traces, each ~ 14s long. This adds up to ~ 8 terabytes of data, representing, we believe, the largest ever academic 3D MCS survey in terms of both the area covered and the volume of data. The OBS deployment was the largest ever within an academic 3D survey.

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

    PubMed

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

    2015-12-01

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

  20. Confocal stereology: an efficient tool for measurement of microscopic structures.

    PubMed

    Kubínová, Lucie; Janáček, Jiří

    2015-04-01

    Quantitative measurements of geometric forms or counting of objects in microscopic specimens is an essential tool in studies of microstructure. Confocal stereology represents a contemporary approach to the evaluation of microscopic structures by using a combination of stereological methods and confocal microscopy. 3-D images acquired by confocal microscopy can be used for the estimation of geometrical characteristics of microscopic structures by stereological methods, based on the evaluation of optical sections within a thick slice and using computer-generated virtual test probes. Such methods can be used for estimating volume, number, surface area and length using relevant spatial probes, which are generated by specific software. The interactions of the probes with the structure under study are interactively evaluated. An overview of the methods of confocal stereology developed during the past 30 years is presented. Their advantages and pitfalls in comparison with other methods for measurement of geometrical characteristics of microscopic structures are discussed. PMID:25743691

  1. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  2. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  3. 3D microscopy - new powerful tools in geomaterials characterization

    NASA Astrophysics Data System (ADS)

    Mauko Pranjić, Alenka; Mladenovič, Ana; Turk, Janez; Šajna, Aljoša; Čretnik, Janko

    2016-04-01

    Microtomography (microCT) is becoming more and more widely recognized in geological sciences as a powerful tool for the spatial characterization of rock and other geological materials. Together with 3D image analysis and other complementary techniques, it has the characteristics of an innovative and non-destructive 3D microscopical technique. On the other hand its main disadvantages are low availability (only a few geological laboratories are equipped with high resolution tomographs), the relatively high prices of testing connected with the use of an xray source, technical limitations connected to the resolution and imaging of certain materials, as well as timeconsuming and complex 3D image analysis, necessary for quantification of 3D tomographic data sets. In this work three examples are presented of optimal 3D microscopy analysis of geomaterials in construction such as porosity characterization of impregnated sandstone, aerated concrete and marble prone to bowing. Studies include processes of microCT imaging, 3D data analysis and fitting of data with complementary analysis, such as confocal microscopy, mercury porosimetry, gas sorption, optical/fluorescent microscopy and scanning electron microscopy. Present work has been done in the frame of national research project 3D and 4D microscopy development of new powerful tools in geosciences (ARRS J1-7148) funded by Slovenian Research Agency.

  4. Texture splats for 3D vector and scalar field visualization

    SciTech Connect

    Crawfis, R.A.; Max, N.

    1993-04-06

    Volume Visualization is becoming an important tool for understanding large 3D datasets. A popular technique for volume rendering is known as splatting. With new hardware architectures offering substantial improvements in the performance of rendering texture mapped objects, we present textured splats. An ideal reconstruction function for 3D signals is developed which can be used as a texture map for a splat. Extensions to the basic splatting technique are then developed to additionally represent vector fields.

  5. 3-D Perspective Pasadena, California

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This perspective view shows the western part of the city of Pasadena, California, looking north towards the San Gabriel Mountains. Portions of the cities of Altadena and La Canada, Flintridge are also shown. The image was created from three datasets: the Shuttle Radar Topography Mission (SRTM) supplied the elevation data; Landsat data from November 11, 1986 provided the land surface color (not the sky) and U.S. Geological Survey digital aerial photography provides the image detail. The Rose Bowl, surrounded by a golf course, is the circular feature at the bottom center of the image. The Jet Propulsion Laboratory is the cluster of large buildings north of the Rose Bowl at the base of the mountains. A large landfill, Scholl Canyon, is the smooth area in the lower left corner of the scene. This image shows the power of combining data from different sources to create planning tools to study problems that affect large urban areas. In addition to the well-known earthquake hazards, Southern California is affected by a natural cycle of fire and mudflows. Wildfires strip the mountains of vegetation, increasing the hazards from flooding and mudflows for several years afterwards. Data such as shown on this image can be used to predict both how wildfires will spread over the terrain and also how mudflows will be channeled down the canyons. The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, uses the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, an additional C-band imaging antenna and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Imagery and Mapping Agency

  6. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  7. Modular 3-D Transport model

    EPA Science Inventory

    MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...

  8. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

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

  9. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  10. 3D World Building System

    ScienceCinema

    None

    2014-02-26

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  11. LLNL-Earth3D

    Energy Science and Technology Software Center (ESTSC)

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  12. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  13. 3D image of protein visualization in a whole rice grain using an automatic precision microtome system

    NASA Astrophysics Data System (ADS)

    Ogawa, Yukiharu; Ohtani, Toshio; Sugiyama, Junichi; Hagiwara, Shoji; Tanaka, Kunisuke; Kudoh, Ken-ichi; Higuchi, Toshiro

    2000-05-01

    The 3D image formation technique using confocal microscopy has allows visualization of the 3D chemical structure in small parts of the bio-body. However, the large-scale 3D structure such as the distribution of chemical components throughout the whole body has not been shown. To allow such large scale visualization of the 3D internal analysis technique for bio-body has been developed.

  14. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery. PMID:26657435

  15. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  16. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  17. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  18. Scanning computed confocal imager

    DOEpatents

    George, John S.

    2000-03-14

    There is provided a confocal imager comprising a light source emitting a light, with a light modulator in optical communication with the light source for varying the spatial and temporal pattern of the light. A beam splitter receives the scanned light and direct the scanned light onto a target and pass light reflected from the target to a video capturing device for receiving the reflected light and transferring a digital image of the reflected light to a computer for creating a virtual aperture and outputting the digital image. In a transmissive mode of operation the invention omits the beam splitter means and captures light passed through the target.

  19. Bioprinting of 3D hydrogels.

    PubMed

    Stanton, M M; Samitier, J; Sánchez, S

    2015-08-01

    Three-dimensional (3D) bioprinting has recently emerged as an extension of 3D material printing, by using biocompatible or cellular components to build structures in an additive, layer-by-layer methodology for encapsulation and culture of cells. These 3D systems allow for cell culture in a suspension for formation of highly organized tissue or controlled spatial orientation of cell environments. The in vitro 3D cellular environments simulate the complexity of an in vivo environment and natural extracellular matrices (ECM). This paper will focus on bioprinting utilizing hydrogels as 3D scaffolds. Hydrogels are advantageous for cell culture as they are highly permeable to cell culture media, nutrients, and waste products generated during metabolic cell processes. They have the ability to be fabricated in customized shapes with various material properties with dimensions at the micron scale. 3D hydrogels are a reliable method for biocompatible 3D printing and have applications in tissue engineering, drug screening, and organ on a chip models. PMID:26066320

  20. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  1. SOAX: A software for quantification of 3D biopolymer networks

    PubMed Central

    Xu, Ting; Vavylonis, Dimitrios; Tsai, Feng-Ching; Koenderink, Gijsje H.; Nie, Wei; Yusuf, Eddy; I-Ju Lee; Wu, Jian-Qiu; Huang, Xiaolei

    2015-01-01

    Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called “SOAX”, which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint. PMID:25765313

  2. 3D Microperiodic Hydrogel Scaffolds for Robust Neuronal Cultures

    PubMed Central

    Hanson Shepherd, Jennifer N.; Parker, Sara T.; Shepherd, Robert F.; Gillette, Martha U.; Lewis, Jennifer A.; Nuzzo, Ralph G.

    2011-01-01

    Three-dimensional (3D) microperiodic scaffolds of poly(2-hydroxyethyl methacrylate) (pHEMA) have been fabricated by direct-write assembly of a photopolymerizable hydrogel ink. The ink is initially composed of physically entangled pHEMA chains dissolved in a solution of HEMA monomer, comonomer, photoinitiator and water. Upon printing 3D scaffolds of varying architecture, the ink filaments are exposed to UV light, where they are transformed into an interpenetrating hydrogel network of chemically cross-linked and physically entangled pHEMA chains. These 3D microperiodic scaffolds are rendered growth compliant for primary rat hippocampal neurons by absorption of polylysine. Neuronal cells thrive on these scaffolds, forming differentiated, intricately branched networks. Confocal laser scanning microscopy reveals that both cell distribution and extent of neuronal process alignment depend upon scaffold architecture. This work provides an important step forward in the creation of suitable platforms for in vitro study of sensitive cell types. PMID:21709750

  3. Fdf in US3D

    NASA Astrophysics Data System (ADS)

    Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman

    2013-11-01

    The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.

  4. Validation of 3D multimodality roadmapping in interventional neuroradiology

    NASA Astrophysics Data System (ADS)

    Ruijters, Daniel; Homan, Robert; Mielekamp, Peter; van de Haar, Peter; Babic, Drazenko

    2011-08-01

    Three-dimensional multimodality roadmapping is entering clinical routine utilization for neuro-vascular treatment. Its purpose is to navigate intra-arterial and intra-venous endovascular devices through complex vascular anatomy by fusing pre-operative computed tomography (CT) or magnetic resonance (MR) with the live fluoroscopy image. The fused image presents the real-time position of the intra-vascular devices together with the patient's 3D vascular morphology and its soft-tissue context. This paper investigates the effectiveness, accuracy, robustness and computation times of the described methods in order to assess their suitability for the intended clinical purpose: accurate interventional navigation. The mutual information-based 3D-3D registration proved to be of sub-voxel accuracy and yielded an average registration error of 0.515 mm and the live machine-based 2D-3D registration delivered an average error of less than 0.2 mm. The capture range of the image-based 3D-3D registration was investigated to characterize its robustness, and yielded an extent of 35 mm and 25° for >80% of the datasets for registration of 3D rotational angiography (3DRA) with CT, and 15 mm and 20° for >80% of the datasets for registration of 3DRA with MR data. The image-based 3D-3D registration could be computed within 8 s, while applying the machine-based 2D-3D registration only took 1.5 µs, which makes them very suitable for interventional use.

  5. Validation of 3D multimodality roadmapping in interventional neuroradiology.

    PubMed

    Ruijters, Daniel; Homan, Robert; Mielekamp, Peter; van de Haar, Peter; Babic, Drazenko

    2011-08-21

    Three-dimensional multimodality roadmapping is entering clinical routine utilization for neuro-vascular treatment. Its purpose is to navigate intra-arterial and intra-venous endovascular devices through complex vascular anatomy by fusing pre-operative computed tomography (CT) or magnetic resonance (MR) with the live fluoroscopy image. The fused image presents the real-time position of the intra-vascular devices together with the patient's 3D vascular morphology and its soft-tissue context. This paper investigates the effectiveness, accuracy, robustness and computation times of the described methods in order to assess their suitability for the intended clinical purpose: accurate interventional navigation. The mutual information-based 3D-3D registration proved to be of sub-voxel accuracy and yielded an average registration error of 0.515 mm and the live machine-based 2D-3D registration delivered an average error of less than 0.2 mm. The capture range of the image-based 3D-3D registration was investigated to characterize its robustness, and yielded an extent of 35 mm and 25° for >80% of the datasets for registration of 3D rotational angiography (3DRA) with CT, and 15 mm and 20° for >80% of the datasets for registration of 3DRA with MR data. The image-based 3D-3D registration could be computed within 8 s, while applying the machine-based 2D-3D registration only took 1.5 µs, which makes them very suitable for interventional use. PMID:21799235

  6. Holography, tomography and 3D microscopy as linear filtering operations

    NASA Astrophysics Data System (ADS)

    Coupland, J. M.; Lobera, J.

    2008-07-01

    In this paper, we characterize 3D optical imaging techniques as 3D linear shift-invariant filtering operations. From the Helmholtz equation that is the basis of scalar diffraction theory, we show that the scattered field, or indeed a holographic reconstruction of this field, can be considered to be the result of a linear filtering operation applied to a source distribution. We note that if the scattering is weak, the source distribution is independent of the scattered field and a holographic reconstruction (or in fact any far-field optical imaging system) behaves as a 3D linear shift-invariant filter applied to the refractive index contrast (which effectively defines the object). We go on to consider tomographic techniques that synthesize images from recordings of the scattered field using different illumination conditions. In our analysis, we compare the 3D response of monochromatic optical tomography with the 3D imagery offered by confocal microscopy and scanning white light interferometry (using quasi-monochromatic illumination) and explain the circumstances under which these approaches are equivalent. Finally, we consider the 3D response of polychromatic optical tomography and in particular the response of spectral optical coherence tomography and scanning white light interferometry.

  7. Heterodyne 3D ghost imaging

    NASA Astrophysics Data System (ADS)

    Yang, Xu; Zhang, Yong; Yang, Chenghua; Xu, Lu; Wang, Qiang; Zhao, Yuan

    2016-06-01

    Conventional three dimensional (3D) ghost imaging measures range of target based on pulse fight time measurement method. Due to the limit of data acquisition system sampling rate, range resolution of the conventional 3D ghost imaging is usually low. In order to take off the effect of sampling rate to range resolution of 3D ghost imaging, a heterodyne 3D ghost imaging (HGI) system is presented in this study. The source of HGI is a continuous wave laser instead of pulse laser. Temporal correlation and spatial correlation of light are both utilized to obtain the range image of target. Through theory analysis and numerical simulations, it is demonstrated that HGI can obtain high range resolution image with low sampling rate.

  8. Wavefront construction in 3-D

    SciTech Connect

    Chilcoat, S.R. Hildebrand, S.T.

    1995-12-31

    Travel time computation in inhomogeneous media is essential for pre-stack Kirchhoff imaging in areas such as the sub-salt province in the Gulf of Mexico. The 2D algorithm published by Vinje, et al, has been extended to 3D to compute wavefronts in complicated inhomogeneous media. The 3D wavefront construction algorithm provides many advantages over conventional ray tracing and other methods of computing travel times in 3D. The algorithm dynamically maintains a reasonably consistent ray density without making a priori guesses at the number of rays to shoot. The determination of caustics in 3D is a straight forward geometric procedure. The wavefront algorithm also enables the computation of multi-valued travel time surfaces.

  9. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  10. Met.3D - a new open-source tool for interactive 3D visualization of ensemble weather forecasts

    NASA Astrophysics Data System (ADS)

    Rautenhaus, Marc; Kern, Michael; Schäfler, Andreas; Westermann, Rüdiger

    2015-04-01

    We introduce Met.3D, a new open-source tool for the interactive 3D visualization of numerical ensemble weather predictions. The tool has been developed to support weather forecasting during aircraft-based atmospheric field campaigns, however, is applicable to further forecasting, research and teaching activities. Our work approaches challenging topics related to the visual analysis of numerical atmospheric model output -- 3D visualisation, ensemble visualization, and how both can be used in a meaningful way suited to weather forecasting. Met.3D builds a bridge from proven 2D visualization methods commonly used in meteorology to 3D visualization by combining both visualization types in a 3D context. It implements methods that address the issue of spatial perception in the 3D view as well as approaches to using the ensemble in order to assess forecast uncertainty. Interactivity is key to the Met.3D approach. The tool uses modern graphics hardware technology to achieve interactive visualization of present-day numerical weather prediction datasets on standard consumer hardware. Met.3D supports forecast data from the European Centre for Medium Range Weather Forecasts and operates directly on ECMWF hybrid sigma-pressure level grids. In this presentation, we provide an overview of the software --illustrated with short video examples--, and give information on its availability.

  11. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  12. The 3D widgets for exploratory scientific visualization

    NASA Technical Reports Server (NTRS)

    Herndon, Kenneth P.; Meyer, Tom

    1995-01-01

    Computational fluid dynamics (CFD) techniques are used to simulate flows of fluids like air or water around such objects as airplanes and automobiles. These techniques usually generate very large amounts of numerical data which are difficult to understand without using graphical scientific visualization techniques. There are a number of commercial scientific visualization applications available today which allow scientists to control visualization tools via textual and/or 2D user interfaces. However, these user interfaces are often difficult to use. We believe that 3D direct-manipulation techniques for interactively controlling visualization tools will provide opportunities for powerful and useful interfaces with which scientists can more effectively explore their datasets. A few systems have been developed which use these techniques. In this paper, we will present a variety of 3D interaction techniques for manipulating parameters of visualization tools used to explore CFD datasets, and discuss in detail various techniques for positioning tools in a 3D scene.

  13. 3-D segmentation of human sternum in lung MDCT images.

    PubMed

    Pazokifard, Banafsheh; Sowmya, Arcot

    2013-01-01

    A fully automatic novel algorithm is presented for accurate 3-D segmentation of the human sternum in lung multi detector computed tomography (MDCT) images. The segmentation result is refined by employing active contours to remove calcified costal cartilage that is attached to the sternum. For each dataset, costal notches (sternocostal joints) are localized in 3-D by using a sternum mask and positions of the costal notches on it as reference. The proposed algorithm for sternum segmentation was tested on 16 complete lung MDCT datasets and comparison of the segmentation results to the reference delineation provided by a radiologist, shows high sensitivity (92.49%) and specificity (99.51%) and small mean distance (dmean=1.07 mm). Total average of the Euclidean distance error for costal notches positioning in 3-D is 4.2 mm. PMID:24110446

  14. Hyperspectral confocal microscope

    NASA Astrophysics Data System (ADS)

    Sinclair, Michael B.; Haaland, David M.; Timlin, Jerilyn A.; Jones, Howland D. T.

    2006-08-01

    We have developed a new, high performance, hyperspectral microscope for biological and other applications. For each voxel within a three-dimensional specimen, the microscope simultaneously records the emission spectrum from 500 nm to 800 nm, with better than 3 nm spectral resolution. The microscope features a fully confocal design to ensure high spatial resolution and high quality optical sectioning. Optical throughput and detection efficiency are maximized through the use of a custom prism spectrometer and a backside thinned electron multiplying charge coupled device (EMCCD) array. A custom readout mode and synchronization scheme enable 512-point spectra to be recorded at a rate of 8300 spectra per second. In addition, the EMCCD readout mode eliminates curvature and keystone artifacts that often plague spectral imaging systems. The architecture of the new microscope is described in detail, and hyperspectral images from several specimens are presented.

  15. Hyperspectral confocal microscope.

    PubMed

    Sinclair, Michael B; Haaland, David M; Timlin, Jerilyn A; Jones, Howland D T

    2006-08-20

    We have developed a new, high performance, hyperspectral microscope for biological and other applications. For each voxel within a three-dimensional specimen, the microscope simultaneously records the emission spectrum from 500 nm to 800 nm, with better than 3 nm spectral resolution. The microscope features a fully confocal design to ensure high spatial resolution and high quality optical sectioning. Optical throughput and detection efficiency are maximized through the use of a custom prism spectrometer and a backside thinned electron multiplying charge coupled device (EMCCD) array. A custom readout mode and synchronization scheme enable 512-point spectra to be recorded at a rate of 8300 spectra per second. In addition, the EMCCD readout mode eliminates curvature and keystone artifacts that often plague spectral imaging systems. The architecture of the new microscope is described in detail, and hyperspectral images from several specimens are presented. PMID:16892134

  16. Confocal coded aperture imaging

    DOEpatents

    Tobin, Jr., Kenneth William; Thomas, Jr., Clarence E.

    2001-01-01

    A method for imaging a target volume comprises the steps of: radiating a small bandwidth of energy toward the target volume; focusing the small bandwidth of energy into a beam; moving the target volume through a plurality of positions within the focused beam; collecting a beam of energy scattered from the target volume with a non-diffractive confocal coded aperture; generating a shadow image of said aperture from every point source of radiation in the target volume; and, reconstructing the shadow image into a 3-dimensional image of the every point source by mathematically correlating the shadow image with a digital or analog version of the coded aperture. The method can comprise the step of collecting the beam of energy scattered from the target volume with a Fresnel zone plate.

  17. Improving 3d Spatial Queries Search: Newfangled Technique of Space Filling Curves in 3d City Modeling

    NASA Astrophysics Data System (ADS)

    Uznir, U.; Anton, F.; Suhaibah, A.; Rahman, A. A.; Mioc, D.

    2013-09-01

    The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc.. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using web standards. However, these 3D city models consume much more storage compared to two dimensional (2D) spatial data. They involve extra geometrical and topological information together with semantic data. Without a proper spatial data clustering method and its corresponding spatial data access method, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban objects. In this research, we propose an opponent data constellation technique of space-filling curves (3D Hilbert curves) for 3D city model data representation. Unlike previous methods, that try to project 3D or n-dimensional data down to 2D or 3D using Principal Component Analysis (PCA) or Hilbert mappings, in this research, we extend the Hilbert space-filling curve to one higher dimension for 3D city model data implementations. The query performance was tested using a CityGML dataset of 1,000 building blocks and the results are presented in this paper. The advantages of implementing space-filling curves in 3D city modeling will improve data retrieval time by means of optimized 3D adjacency, nearest neighbor information and 3D indexing. The Hilbert mapping, which maps a subinterval of the [0, 1] interval to the corresponding portion of the d-dimensional Hilbert's curve, preserves the Lebesgue measure and is Lipschitz continuous. Depending on the applications, several alternatives are possible in order to cluster spatial data together in the third dimension compared to its

  18. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

  19. Rapid high-fidelity visualisation of multispectral 3D mapping

    NASA Astrophysics Data System (ADS)

    Tudor, Philip M.; Christy, Mark

    2011-06-01

    Mobile LIDAR scanning typically provides captured 3D data in the form of 3D 'Point Clouds'. Combined with colour imagery these data produce coloured point clouds or, if further processed, polygon-based 3D models. The use of point clouds is simple and rapid, but visualisation can appear ghostly and diffuse. Textured 3D models provide high fidelity visualisation, but their creation is time consuming, difficult to automate and can modify key terrain details. This paper describes techniques for the visualisation of fused multispectral 3D data that approach the visual fidelity of polygon-based models with the rapid turnaround and detail of 3D point clouds. The general approaches to data capture and data fusion are identified as well as the central underlying mathematical transforms, data management and graphics processing techniques used to support rapid, interactive visualisation of very large multispectral 3D datasets. Performance data with respect to real-world 3D mapping as well as illustrations of visualisation outputs are included.

  20. Bringing 3D Printing to Geophysical Science Education

    NASA Astrophysics Data System (ADS)

    Boghosian, A.; Turrin, M.; Porter, D. F.

    2014-12-01

    3D printing technology has been embraced by many technical fields, and is rapidly making its way into peoples' homes and schools. While there is a growing educational and hobbyist community engaged in the STEM focused technical and intellectual challenges associated with 3D printing, there is unrealized potential for the earth science community to use 3D printing to communicate scientific research to the public. Moreover, 3D printing offers scientists the opportunity to connect students and the public with novel visualizations of real data. As opposed to introducing terrestrial measurements through the use of colormaps and gradients, scientists can represent 3D concepts with 3D models, offering a more intuitive education tool. Furthermore, the tactile aspect of models make geophysical concepts accessible to a wide range of learning styles like kinesthetic or tactile, and learners including both visually impaired and color-blind students.We present a workflow whereby scientists, students, and the general public will be able to 3D print their own versions of geophysical datasets, even adding time through layering to include a 4th dimension, for a "4D" print. This will enable scientists with unique and expert insights into the data to easily create the tools they need to communicate their research. It will allow educators to quickly produce teaching aids for their students. Most importantly, it will enable the students themselves to translate the 2D representation of geophysical data into a 3D representation of that same data, reinforcing spatial reasoning.

  1. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

    Welch, Greg; Sonnenwald, Diane H.; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Krishnan, Srinivas; Söderholm, Hanna M.

    Two-dimensional (2D) video-based telemedical consultation has been explored widely in the past 15-20 years. Two issues that seem to arise in most relevant case studies are the difficulty associated with obtaining the desired 2D camera views, and poor depth perception. To address these problems we are exploring the use of a small array of cameras to synthesize a spatially continuous range of dynamic three-dimensional (3D) views of a remote environment and events. The 3D views can be sent across wired or wireless networks to remote viewers with fixed displays or mobile devices such as a personal digital assistant (PDA). The viewpoints could be specified manually or automatically via user head or PDA tracking, giving the remote viewer virtual head- or hand-slaved (PDA-based) remote cameras for mono or stereo viewing. We call this idea remote 3D medical consultation (3DMC). In this article we motivate and explain the vision for 3D medical consultation; we describe the relevant computer vision/graphics, display, and networking research; we present a proof-of-concept prototype system; and we present some early experimental results supporting the general hypothesis that 3D remote medical consultation could offer benefits over conventional 2D televideo.

  2. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  3. 3D-Printed Microfluidics.

    PubMed

    Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert

    2016-03-14

    The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia. PMID:26854878

  4. 3D Computations and Experiments

    SciTech Connect

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

    2004-04-05

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

  5. 3D Computations and Experiments

    SciTech Connect

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

    2003-05-12

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

  6. Confocal microscopy and exfoliative cytology

    PubMed Central

    Reddy, Shyam Prasad; Ramani, Pratibha; Nainani, Purshotam

    2013-01-01

    Context: Early detection of potentially malignant lesions and invasive squamous-cell carcinoma in the oral cavity could be greatly improved through techniques that permit visualization of subtle cellular changes indicative of the neoplastic transformation process. One such technique is confocal microscopy. Combining rapidity with reliability, an innovative idea has been put forward using confocal microscope in exfoliative cytology. Aims: The main objective of this study was to assess confocal microscopy for cytological diagnosis and the results were compared with that of the standard PAP stain. Settings and Design: Confocal microscope, acridine orange (AO) stain, PAP (Papanicolaou) stain. The study was designed to assess confocal microscopy for cytological diagnosis. In the process, smears of patients with (clinically diagnosed and/or suspected) oral squamous cell carcinoma as well as those of controls (normal people) were stained with acridine orange and observed under confocal microscope. The results were compared with those of the standard PAP method. Materials and Methods: Samples of buccal mucosa smears from normal patients and squamous cell carcinoma patients were made, fixed in 100% alcohol, followed by AO staining. The corresponding set of smears was stained with PAP stain using rapid PAP stain kit. The results obtained were compared with those obtained with AO confocal microscopy. Results: The study had shown nuclear changes (malignant cells) in the smears of squamous cell carcinoma patients as increased intensity of fluorescence of the nucleus, when observed under confocal microscope. Acridine orange confocal microscopy showed good amount of sensitivity and specificity (93%) in identifying malignant cells in exfoliative cytological smears. Conclusion: Confocal microscopy was found to have good sensitivity in the identification of cancer (malignant) cells in exfoliative cytology, at par with the PAP method. The rapidity of processing and screening a

  7. SNL3dFace

    Energy Science and Technology Software Center (ESTSC)

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial featuresmore » of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.« less

  8. 3D Printing: Exploring Capabilities

    ERIC Educational Resources Information Center

    Samuels, Kyle; Flowers, Jim

    2015-01-01

    As 3D printers become more affordable, schools are using them in increasing numbers. They fit well with the emphasis on product design in technology and engineering education, allowing students to create high-fidelity physical models to see and test different iterations in their product designs. They may also help students to "think in three…

  9. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  10. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  11. High precision radially-polarized-light pupil-filtering differential confocal measurement

    NASA Astrophysics Data System (ADS)

    Wang, Yun; Qiu, Lirong; Zhao, Weiqian

    2016-08-01

    A new method, high precision radially-polarized light pupil-filtering differential confocal measurement (RPDCM), is proposed to improve the 3D measurement resolution of confocal system. SPDCM uses the property that the radially-polarized-light can produce a strong longitudinal field component after being focused by a high numerical aperture objective to reduce the lateral size of the focus spot, and relies on the pupil-filtering technique to optimize the pupil function of the optical system by the designed pupil filter, which therefore improves the lateral resolution of confocal system, and it uses the differential confocal technology to improve the axial measurement resolution of the confocal system, thereby improves the 3D measurement resolution of the confocal system. Based on RPDCM, we developed a high precision radially-polarized light pupil-filtering differential confocal setup, and use it to verify the effectiveness of RPDCM by experiments. The theoretical analysis and experimental results show that the RPDCM can reach the lateral and axial measurement resolutions of 150 nm and 1 nm, respectively, which are an improvement of 20-32% and 3.7 times compared with a confocal system.

  12. Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization

    PubMed Central

    Chaumeil, Julie; Micsinai, Mariann; Skok, Jane A.

    2013-01-01

    Fluorescent in situ hybridization using DNA probes on 3-dimensionally preserved nuclei followed by 3D confocal microscopy (3D DNA FISH) represents the most direct way to visualize the location of gene loci, chromosomal sub-regions or entire territories in individual cells. This type of analysis provides insight into the global architecture of the nucleus as well as the behavior of specific genomic loci and regions within the nuclear space. Immunofluorescence, on the other hand, permits the detection of nuclear proteins (modified histones, histone variants and modifiers, transcription machinery and factors, nuclear sub-compartments, etc). The major challenge in combining immunofluorescence and 3D DNA FISH is, on the one hand to preserve the epitope detected by the antibody as well as the 3D architecture of the nucleus, and on the other hand, to allow the penetration of the DNA probe to detect gene loci or chromosome territories 1-5. Here we provide a protocol that combines visualization of chromatin modifications with genomic loci in 3D preserved nuclei. PMID:23407477

  13. TACO3D. 3-D Finite Element Heat Transfer Code

    SciTech Connect

    Mason, W.E.

    1992-03-04

    TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.

  14. Comparison of 2D and 3D gamma analyses

    SciTech Connect

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F.; Bosca, Ryan; O’Daniel, Jennifer

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  15. Automated cellular pathology in noninvasive confocal microscopy

    NASA Astrophysics Data System (ADS)

    Ting, Monica; Krueger, James; Gareau, Daniel

    2014-03-01

    A computer algorithm was developed to automatically identify and count melanocytes and keratinocytes in 3D reflectance confocal microscopy (RCM) images of the skin. Computerized pathology increases our understanding and enables prevention of superficial spreading melanoma (SSM). Machine learning involved looking at the images to measure the size of cells through a 2-D Fourier transform and developing an appropriate mask with the erf() function to model the cells. Implementation involved processing the images to identify cells whose image segments provided the least difference when subtracted from the mask. With further simplification of the algorithm, the program may be directly implemented on the RCM images to indicate the presence of keratinocytes in seconds and to quantify the keratinocytes size in the en face plane as a function of depth. Using this system, the algorithm can identify any irregularities in maturation and differentiation of keratinocytes, thereby signaling the possible presence of cancer.

  16. 3D Printing of Biocompatible Supramolecular Polymers and their Composites.

    PubMed

    Hart, Lewis R; Li, Siwei; Sturgess, Craig; Wildman, Ricky; Jones, Julian R; Hayes, Wayne

    2016-02-10

    A series of polymers capable of self-assembling into infinite networks via supramolecular interactions have been designed, synthesized, and characterized for use in 3D printing applications. The biocompatible polymers and their composites with silica nanoparticles were successfully utilized to deposit both simple cubic structures, as well as a more complex twisted pyramidal feature. The polymers were found to be not toxic to a chondrogenic cell line, according to ISO 10993-5 and 10993-12 standard tests and the cells attached to the supramolecular polymers as demonstrated by confocal microscopy. Silica nanoparticles were then dispersed within the polymer matrix, yielding a composite material which was optimized for inkjet printing. The hybrid material showed promise in preliminary tests to facilitate the 3D deposition of a more complex structure. PMID:26766139

  17. 3D light scanning macrography.

    PubMed

    Huber, D; Keller, M; Robert, D

    2001-08-01

    The technique of 3D light scanning macrography permits the non-invasive surface scanning of small specimens at magnifications up to 200x. Obviating both the problem of limited depth of field inherent to conventional close-up macrophotography and the metallic coating required by scanning electron microscopy, 3D light scanning macrography provides three-dimensional digital images of intact specimens without the loss of colour, texture and transparency information. This newly developed technique offers a versatile, portable and cost-efficient method for the non-invasive digital and photographic documentation of small objects. Computer controlled device operation and digital image acquisition facilitate fast and accurate quantitative morphometric investigations, and the technique offers a broad field of research and educational applications in biological, medical and materials sciences. PMID:11489078

  18. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikawa, K.-I.; Frank, J.; Koide, S.; Sakai, J.-I.; Christodoulou, D. M.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W = 4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure.

  19. Forensic 3D Scene Reconstruction

    SciTech Connect

    LITTLE,CHARLES Q.; PETERS,RALPH R.; RIGDON,J. BRIAN; SMALL,DANIEL E.

    1999-10-12

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a feasible prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  20. Forensic 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Little, Charles Q.; Small, Daniel E.; Peters, Ralph R.; Rigdon, J. B.

    2000-05-01

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a fieldable prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  1. 360-degree 3D profilometry

    NASA Astrophysics Data System (ADS)

    Song, Yuanhe; Zhao, Hong; Chen, Wenyi; Tan, Yushan

    1997-12-01

    A new method of 360 degree turning 3D shape measurement in which light sectioning and phase shifting techniques are both used is presented in this paper. A sine light field is applied in the projected light stripe, meanwhile phase shifting technique is used to calculate phases of the light slit. Thereafter wrapped phase distribution of the slit is formed and the unwrapping process is made by means of the height information based on the light sectioning method. Therefore phase measuring results with better precision can be obtained. At last the target 3D shape data can be produced according to geometric relationships between phases and the object heights. The principles of this method are discussed in detail and experimental results are shown in this paper.

  2. Optoplasmonics: hybridization in 3D

    NASA Astrophysics Data System (ADS)

    Rosa, L.; Gervinskas, G.; Žukauskas, A.; Malinauskas, M.; Brasselet, E.; Juodkazis, S.

    2013-12-01

    Femtosecond laser fabrication has been used to make hybrid refractive and di ractive micro-optical elements in photo-polymer SZ2080. For applications in micro- uidics, axicon lenses were fabricated (both single and arrays), for generation of light intensity patterns extending through the entire depth of a typically tens-of-micrometers deep channel. Further hybridisation of an axicon with a plasmonic slot is fabricated and demonstrated nu- merically. Spiralling chiral grooves were inscribed into a 100-nm-thick gold coating sputtered over polymerized micro-axicon lenses, using a focused ion beam. This demonstrates possibility of hybridisation between optical and plasmonic 3D micro-optical elements. Numerical modelling of optical performance by 3D-FDTD method is presented.

  3. 3D Printed Robotic Hand

    NASA Technical Reports Server (NTRS)

    Pizarro, Yaritzmar Rosario; Schuler, Jason M.; Lippitt, Thomas C.

    2013-01-01

    Dexterous robotic hands are changing the way robots and humans interact and use common tools. Unfortunately, the complexity of the joints and actuations drive up the manufacturing cost. Some cutting edge and commercially available rapid prototyping machines now have the ability to print multiple materials and even combine these materials in the same job. A 3D model of a robotic hand was designed using Creo Parametric 2.0. Combining "hard" and "soft" materials, the model was printed on the Object Connex350 3D printer with the purpose of resembling as much as possible the human appearance and mobility of a real hand while needing no assembly. After printing the prototype, strings where installed as actuators to test mobility. Based on printing materials, the manufacturing cost of the hand was $167, significantly lower than other robotic hands without the actuators since they have more complex assembly processes.

  4. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  5. 3D Printable Graphene Composite.

    PubMed

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being's history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today's personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite's linear thermal coefficient is below 75 ppm·°C(-1) from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  6. 3D/3D registration of coronary CTA and biplane XA reconstructions for improved image guidance

    SciTech Connect

    Dibildox, Gerardo Baka, Nora; Walsum, Theo van; Punt, Mark; Aben, Jean-Paul; Schultz, Carl; Niessen, Wiro

    2014-09-15

    Purpose: The authors aim to improve image guidance during percutaneous coronary interventions of chronic total occlusions (CTO) by providing information obtained from computed tomography angiography (CTA) to the cardiac interventionist. To this end, the authors investigate a method to register a 3D CTA model to biplane reconstructions. Methods: The authors developed a method for registering preoperative coronary CTA with intraoperative biplane x-ray angiography (XA) images via 3D models of the coronary arteries. The models are extracted from the CTA and biplane XA images, and are temporally aligned based on CTA reconstruction phase and XA ECG signals. Rigid spatial alignment is achieved with a robust probabilistic point set registration approach using Gaussian mixture models (GMMs). This approach is extended by including orientation in the Gaussian mixtures and by weighting bifurcation points. The method is evaluated on retrospectively acquired coronary CTA datasets of 23 CTO patients for which biplane XA images are available. Results: The Gaussian mixture model approach achieved a median registration accuracy of 1.7 mm. The extended GMM approach including orientation was not significantly different (P > 0.1) but did improve robustness with regards to the initialization of the 3D models. Conclusions: The authors demonstrated that the GMM approach can effectively be applied to register CTA to biplane XA images for the purpose of improving image guidance in percutaneous coronary interventions.

  7. [Real time 3D echocardiography].

    PubMed

    Bauer, F; Shiota, T; Thomas, J D

    2001-07-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630

  8. [Real time 3D echocardiography

    NASA Technical Reports Server (NTRS)

    Bauer, F.; Shiota, T.; Thomas, J. D.

    2001-01-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

  9. GPU-Accelerated Denoising in 3D (GD3D)

    Energy Science and Technology Software Center (ESTSC)

    2013-10-01

    The raw computational power GPU Accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. This software addresses two facets of this promising application: what tuning is necessary to achieve optimal performance on a modern GPU? And what parameters yield the best denoising results in practice? To answer the first question, the software performs an autotuning step to empirically determine optimal memory blocking on the GPU. To answer themore » second, it performs a sweep of algorithm parameters to determine the combination that best reduces the mean squared error relative to a noiseless reference image.« less

  10. Developing 3D SEM in a broad biological context

    PubMed Central

    Kremer, A; Lippens, S; Bartunkova, S; Asselbergh, B; Blanpain, C; Fendrych, M; Goossens, A; Holt, M; Janssens, S; Krols, M; Larsimont, J-C; Mc Guire, C; Nowack, MK; Saelens, X; Schertel, A; Schepens, B; Slezak, M; Timmerman, V; Theunis, C; Van Brempt, R; Visser, Y; GuÉRin, CJ

    2015-01-01

    When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions. Lay Description Life happens in three dimensions. For many years, first light, and then EM struggled to image the smallest parts of cells in 3D. With recent advances in technology and corresponding improvements in computing, scientists can now see the 3D world of the cell at the nanoscale. In this paper we present the

  11. Multivariate 3D modelling of Scottish soil properties

    NASA Astrophysics Data System (ADS)

    Poggio, Laura; Gimona, Alessandro

    2015-04-01

    Information regarding soil properties across landscapes at national or continental scales is critical for better soil and environmental management and for climate regulation and adaptation policy. The prediction of soil properties variation in space and time and their uncertainty is an important part of environmental modelling. Soil properties, and in particular the 3 fractions of soil texture, exhibit strong co-variation among themselves and therefore taking into account this correlation leads to spatially more accurate results. In this study the continuous vertical and lateral distributions of relevant soil properties in Scottish soils were modelled with a multivariate 3D-GAM+GS approach. The approach used involves 1) modelling the multivariate trend with full 3D spatial correlation, i.e., exploiting the values of the neighbouring pixels in 3D-space, and 2) 3D kriging to interpolate the residuals. The values at each cell for each of the considered depth layers were defined using a hybrid GAM-geostatistical 3D model, combining the fitting of a GAM (generalised Additive Models) to estimate multivariate trend of the variables, using a 3D smoother with related covariates. Gaussian simulations of the model residuals were used as spatial component to account for local details. A dataset of about 26,000 horizons (7,800 profiles) was used for this study. A validation set was randomly selected as 25% of the full dataset. Numerous covariates derived from globally available data, such as MODIS and SRTM, are considered. The results of the 3D-GAM+kriging showed low RMSE values, good R squared and an accurate reproduction of the spatial structure of the data for a range of soil properties. The results have an out-of-sample RMSE between 10 to 15% of the observed range when taking into account the whole profile. The approach followed allows the assessment of the uncertainty of both the trend and the residuals.

  12. Automatic generation of alignments for 3D QSAR analyses.

    PubMed

    Jewell, N E; Turner, D B; Willett, P; Sexton, G J

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a program for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments. PMID:11774998

  13. 3D medical volume reconstruction using web services.

    PubMed

    Kooper, Rob; Shirk, Andrew; Lee, Sang-Chul; Lin, Amy; Folberg, Robert; Bajcsy, Peter

    2008-04-01

    We address the problem of 3D medical volume reconstruction using web services. The use of proposed web services is motivated by the fact that the problem of 3D medical volume reconstruction requires significant computer resources and human expertise in medical and computer science areas. Web services are implemented as an additional layer to a dataflow framework called data to knowledge. In the collaboration between UIC and NCSA, pre-processed input images at NCSA are made accessible to medical collaborators for registration. Every time UIC medical collaborators inspected images and selected corresponding features for registration, the web service at NCSA is contacted and the registration processing query is executed using the image to knowledge library of registration methods. Co-registered frames are returned for verification by medical collaborators in a new window. In this paper, we present 3D volume reconstruction problem requirements and the architecture of the developed prototype system at http://isda.ncsa.uiuc.edu/MedVolume. We also explain the tradeoffs of our system design and provide experimental data to support our system implementation. The prototype system has been used for multiple 3D volume reconstructions of blood vessels and vasculogenic mimicry patterns in histological sections of uveal melanoma studied by fluorescent confocal laser scanning microscope. PMID:18336808

  14. 3D map of the human corneal endothelial cell

    PubMed Central

    He, Zhiguo; Forest, Fabien; Gain, Philippe; Rageade, Damien; Bernard, Aurélien; Acquart, Sophie; Peoc’h, Michel; Defoe, Dennis M.; Thuret, Gilles

    2016-01-01

    Corneal endothelial cells (CECs) are terminally differentiated cells, specialized in regulating corneal hydration and transparency. They are highly polarized flat cells that separate the cornea from the aqueous humor. Their apical surface, in contact with aqueous humor is hexagonal, whereas their basal surface is irregular. We characterized the structure of human CECs in 3D using confocal microscopy of immunostained whole corneas in which cells and their interrelationships remain intact. Hexagonality of the apical surface was maintained by the interaction between tight junctions and a submembraneous network of actomyosin, braced like a drum. Lateral membranes, which support enzymatic pumps, presented complex expansions resembling interdigitated foot processes at the basal surface. Using computer-aided design and drafting software, we obtained a first simplified 3D model of CECs. By comparing their expression with those in epithelial, stromal and trabecular corneal cells, we selected 9 structural or functional proteins for which 3D patterns were specific to CECs. This first 3D map aids our understanding of the morphologic and functional specificity of CECs and could be used as a reference for characterizing future cell therapy products destined to treat endothelial dysfunctions. PMID:27381832

  15. 3D map of the human corneal endothelial cell.

    PubMed

    He, Zhiguo; Forest, Fabien; Gain, Philippe; Rageade, Damien; Bernard, Aurélien; Acquart, Sophie; Peoc'h, Michel; Defoe, Dennis M; Thuret, Gilles

    2016-01-01

    Corneal endothelial cells (CECs) are terminally differentiated cells, specialized in regulating corneal hydration and transparency. They are highly polarized flat cells that separate the cornea from the aqueous humor. Their apical surface, in contact with aqueous humor is hexagonal, whereas their basal surface is irregular. We characterized the structure of human CECs in 3D using confocal microscopy of immunostained whole corneas in which cells and their interrelationships remain intact. Hexagonality of the apical surface was maintained by the interaction between tight junctions and a submembraneous network of actomyosin, braced like a drum. Lateral membranes, which support enzymatic pumps, presented complex expansions resembling interdigitated foot processes at the basal surface. Using computer-aided design and drafting software, we obtained a first simplified 3D model of CECs. By comparing their expression with those in epithelial, stromal and trabecular corneal cells, we selected 9 structural or functional proteins for which 3D patterns were specific to CECs. This first 3D map aids our understanding of the morphologic and functional specificity of CECs and could be used as a reference for characterizing future cell therapy products destined to treat endothelial dysfunctions. PMID:27381832

  16. E3D, the Euro3D visualization tool II: Mosaics, VIMOS data and large IFUs of the future

    NASA Astrophysics Data System (ADS)

    Sánchez, S. F.; Becker, T.; Kelz, A.

    2004-03-01

    In this paper, we describe the capabilities of E3D, the Euro3D visualization tool, to handle and display data created by large Integral Field Units (IFUs) and by mosaics consisting of multiple pointings. The reliability of the software has been tested with real data, originating from the PMAS instrument in mosaic mode and from the VIMOS instrument, which features the largest IFU currently available. The capabilities and limitations of the current software are examined in view of future large IFUs, which will produce extremely large datasets.

  17. Laser scanning confocal microscopy: history, applications, and related optical sectioning techniques.

    PubMed

    Paddock, Stephen W; Eliceiri, Kevin W

    2014-01-01

    Confocal microscopy is an established light microscopical technique for imaging fluorescently labeled specimens with significant three-dimensional structure. Applications of confocal microscopy in the biomedical sciences include the imaging of the spatial distribution of macromolecules in either fixed or living cells, the automated collection of 3D data, the imaging of multiple labeled specimens and the measurement of physiological events in living cells. The laser scanning confocal microscope continues to be chosen for most routine work although a number of instruments have been developed for more specific applications. Significant improvements have been made to all areas of the confocal approach, not only to the instruments themselves, but also to the protocols of specimen preparation, to the analysis, the display, the reproduction, sharing and management of confocal images using bioinformatics techniques. PMID:24052346

  18. Interactive 3D Mars Visualization

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.

    2012-01-01

    The Interactive 3D Mars Visualization system provides high-performance, immersive visualization of satellite and surface vehicle imagery of Mars. The software can be used in mission operations to provide the most accurate position information for the Mars rovers to date. When integrated into the mission data pipeline, this system allows mission planners to view the location of the rover on Mars to 0.01-meter accuracy with respect to satellite imagery, with dynamic updates to incorporate the latest position information. Given this information so early in the planning process, rover drivers are able to plan more accurate drive activities for the rover than ever before, increasing the execution of science activities significantly. Scientifically, this 3D mapping information puts all of the science analyses to date into geologic context on a daily basis instead of weeks or months, as was the norm prior to this contribution. This allows the science planners to judge the efficacy of their previously executed science observations much more efficiently, and achieve greater science return as a result. The Interactive 3D Mars surface view is a Mars terrain browsing software interface that encompasses the entire region of exploration for a Mars surface exploration mission. The view is interactive, allowing the user to pan in any direction by clicking and dragging, or to zoom in or out by scrolling the mouse or touchpad. This set currently includes tools for selecting a point of interest, and a ruler tool for displaying the distance between and positions of two points of interest. The mapping information can be harvested and shared through ubiquitous online mapping tools like Google Mars, NASA WorldWind, and Worldwide Telescope.

  19. An automatic approach for 3D registration of CT scans

    NASA Astrophysics Data System (ADS)

    Hu, Yang; Saber, Eli; Dianat, Sohail; Vantaram, Sreenath Rao; Abhyankar, Vishwas

    2012-03-01

    CT (Computed tomography) is a widely employed imaging modality in the medical field. Normally, a volume of CT scans is prescribed by a doctor when a specific region of the body (typically neck to groin) is suspected of being abnormal. The doctors are required to make professional diagnoses based upon the obtained datasets. In this paper, we propose an automatic registration algorithm that helps healthcare personnel to automatically align corresponding scans from 'Study' to 'Atlas'. The proposed algorithm is capable of aligning both 'Atlas' and 'Study' into the same resolution through 3D interpolation. After retrieving the scanned slice volume in the 'Study' and the corresponding volume in the original 'Atlas' dataset, a 3D cross correlation method is used to identify and register various body parts.

  20. What Lies Ahead (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D cylindrical-perspective mosaic taken by the navigation camera on the Mars Exploration Rover Spirit on sol 82 shows the view south of the large crater dubbed 'Bonneville.' The rover will travel toward the Columbia Hills, seen here at the upper left. The rock dubbed 'Mazatzal' and the hole the rover drilled in to it can be seen at the lower left. The rover's position is referred to as 'Site 22, Position 32.' This image was geometrically corrected to make the horizon appear flat.

  1. A Clean Adirondack (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This is a 3-D anaglyph showing a microscopic image taken of an area measuring 3 centimeters (1.2 inches) across on the rock called Adirondack. The image was taken at Gusev Crater on the 33rd day of the Mars Exploration Rover Spirit's journey (Feb. 5, 2004), after the rover used its rock abrasion tool brush to clean the surface of the rock. Dust, which was pushed off to the side during cleaning, can still be seen to the left and in low areas of the rock.

  2. Vacant Lander in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D image captured by the Mars Exploration Rover Opportunity's rear hazard-identification camera shows the now-empty lander that carried the rover 283 million miles to Meridiani Planum, Mars. Engineers received confirmation that Opportunity's six wheels successfully rolled off the lander and onto martian soil at 3:01 a.m. PST, January 31, 2004, on the seventh martian day, or sol, of the mission. The rover is approximately 1 meter (3 feet) in front of the lander, facing north.

  3. Making Inexpensive 3-D Models

    NASA Astrophysics Data System (ADS)

    Manos, Harry

    2016-03-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the TPT theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity well tailored to specific class lessons. Most of the supplies are readily available in the home or at school: rubbing alcohol, a rag, two colors of spray paint, art brushes, and masking tape. The cost of these supplies, if you don't have them, is less than 20.

  4. Learning the spherical harmonic features for 3-D face recognition.

    PubMed

    Liu, Peijiang; Wang, Yunhong; Huang, Di; Zhang, Zhaoxiang; Chen, Liming

    2013-03-01

    In this paper, a competitive method for 3-D face recognition (FR) using spherical harmonic features (SHF) is proposed. With this solution, 3-D face models are characterized by the energies contained in spherical harmonics with different frequencies, thereby enabling the capture of both gross shape and fine surface details of a 3-D facial surface. This is in clear contrast to most 3-D FR techniques which are either holistic or feature based, using local features extracted from distinctive points. First, 3-D face models are represented in a canonical representation, namely, spherical depth map, by which SHF can be calculated. Then, considering the predictive contribution of each SHF feature, especially in the presence of facial expression and occlusion, feature selection methods are used to improve the predictive performance and provide faster and more cost-effective predictors. Experiments have been carried out on three public 3-D face datasets, SHREC2007, FRGC v2.0, and Bosphorus, with increasing difficulties in terms of facial expression, pose, and occlusion, and which demonstrate the effectiveness of the proposed method. PMID:23060332

  5. 3D web visualization of huge CityGML models

    NASA Astrophysics Data System (ADS)

    Prandi, F.; Devigili, F.; Soave, M.; Di Staso, U.; De Amicis, R.

    2015-08-01

    Nowadays, rapid technological development into acquiring geo-spatial information; joined to the capabilities to process these data in a relative short period of time, allows the generation of detailed 3D textured city models that will become an essential part of the modern city information infrastructure (Spatial Data Infrastructure) and, can be used to integrate various data from different sources for public accessible visualisation and many other applications. One of the main bottlenecks, which at the moment limit the use of these datasets to few experts, is a lack on efficient visualization systems through the web and interoperable frameworks that allow standardising the access to the city models. The work presented in this paper tries to satisfy these two requirements developing a 3D web-based visualization system based on OGC standards and effective visualization concepts. The architectural framework, based on Services Oriented Architecture (SOA) concepts, provides the 3D city data to a web client designed to support the view process in a very effective way. The first part of the work is to design a framework compliant to the 3D Portrayal Service drafted by the of the Open Geospatial Consortium (OGC) 3D standardization working group. The latter is related to the development of an effective web client able to render in an efficient way the 3D city models.

  6. Photothermal Confocal Spectromicroscopy of Multiple Cellular Chromophores and Fluorophores

    PubMed Central

    Nedosekin, D.A.; Galanzha, E.I.; Ayyadevara, Srinivas; Shmookler Reis, Robert J.; Zharov, V.P.

    2012-01-01

    Confocal fluorescence microscopy is a powerful biological tool providing high-resolution, three-dimensional (3D) imaging of fluorescent molecules. Many cellular components are weakly fluorescent, however, and thus their imaging requires additional labeling. As an alternative, label-free imaging can be performed by photothermal (PT) microscopy (PTM), based on nonradiative relaxation of absorbed energy into heat. Previously, little progress has been made in PT spectral identification of cellular chromophores at the 3D microscopic scale. Here, we introduce PTM integrating confocal thermal-lens scanning schematic, time-resolved detection, PT spectral identification, and nonlinear nanobubble-induced signal amplification with a tunable pulsed nanosecond laser. The capabilities of this confocal PTM were demonstrated for high-resolution 3D imaging and spectral identification of up to four chromophores and fluorophores in live cells and Caenorhabditis elegans. Examples include cytochrome c, green fluorescent protein, Mito-Tracker Red, Alexa-488, and natural drug-enhanced or genetically engineered melanin as a PT contrast agent. PTM was able to guide spectral burning of strong absorption background, which masked weakly absorbing chromophores (e.g., cytochromes in the melanin background). PTM provided label-free monitoring of stress-related changes to cytochrome c distribution, in C. elegans at the single-cell level. In nonlinear mode ultrasharp PT spectra from cyt c and the lateral resolution of 120 nm during calibration with 10-nm gold film were observed, suggesting a potential of PTM to break through the spectral and diffraction limits, respectively. Confocal PT spectromicroscopy could provide a valuable alternative or supplement to fluorescence microscopy for imaging of nonfluorescent chromophores and certain fluorophores. PMID:22325291

  7. 3-D Seismic Experimentation and Advanced Processing/Inversion Development for Investigations of the Shallow Subsurface

    SciTech Connect

    Levander, Alan R.

    2004-12-01

    Under ER63662, 3-D Seismic Experimentation and Advanced Processing/Inversion Development for Investigations of the Shallow Subsurface, we have completed a number of subprojects associated with the Hill Air Force Base (HAFB) high resolution 3-D reflection/tomography dataset.

  8. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  9. 3D Printable Graphene Composite

    PubMed Central

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C−1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  10. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikaw, K.-I.; Frank, J.; Christodoulou, D. M.; Koide, S.; Sakai, J.-I.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W=4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure. We also simulate jets with the more realistic initial conditions for injecting jets for helical mangetic field, perturbed density, velocity, and internal energy, which are supposed to be caused in the process of jet generation. Three possible explanations for the observed variability are (i) tidal disruption of a star falling into the black hole, (ii) instabilities in the relativistic accretion disk, and (iii) jet-related PRocesses. New results will be reported at the meeting.

  11. 3D Printable Graphene Composite

    NASA Astrophysics Data System (ADS)

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-07-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C-1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process.

  12. 3D acoustic atmospheric tomography

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Finn, Anthony

    2014-10-01

    This paper presents a method for tomographically reconstructing spatially varying 3D atmospheric temperature profiles and wind velocity fields based. Measurements of the acoustic signature measured onboard a small Unmanned Aerial Vehicle (UAV) are compared to ground-based observations of the same signals. The frequency-shifted signal variations are then used to estimate the acoustic propagation delay between the UAV and the ground microphones, which are also affected by atmospheric temperature and wind speed vectors along each sound ray path. The wind and temperature profiles are modelled as the weighted sum of Radial Basis Functions (RBFs), which also allow local meteorological measurements made at the UAV and ground receivers to supplement any acoustic observations. Tomography is used to provide a full 3D reconstruction/visualisation of the observed atmosphere. The technique offers observational mobility under direct user control and the capacity to monitor hazardous atmospheric environments, otherwise not justifiable on the basis of cost or risk. This paper summarises the tomographic technique and reports on the results of simulations and initial field trials. The technique has practical applications for atmospheric research, sound propagation studies, boundary layer meteorology, air pollution measurements, analysis of wind shear, and wind farm surveys.

  13. 3D Printed Bionic Ears

    PubMed Central

    Mannoor, Manu S.; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A.; Soboyejo, Winston O.; Verma, Naveen; Gracias, David H.; McAlpine, Michael C.

    2013-01-01

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the precise anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  14. 3D Ion Temperature Reconstruction

    NASA Astrophysics Data System (ADS)

    Tanabe, Hiroshi; You, Setthivoine; Balandin, Alexander; Inomoto, Michiaki; Ono, Yasushi

    2009-11-01

    The TS-4 experiment at the University of Tokyo collides two spheromaks to form a single high-beta compact toroid. Magnetic reconnection during the merging process heats and accelerates the plasma in toroidal and poloidal directions. The reconnection region has a complex 3D topology determined by the pitch of the spheromak magnetic fields at the merging plane. A pair of multichord passive spectroscopic diagnostics have been established to measure the ion temperature and velocity in the reconnection volume. One setup measures spectral lines across a poloidal plane, retrieving velocity and temperature from Abel inversion. The other, novel setup records spectral lines across another section of the plasma and reconstructs velocity and temperature from 3D vector and 2D scalar tomography techniques. The magnetic field linking both measurement planes is determined from in situ magnetic probe arrays. The ion temperature is then estimated within the volume between the two measurement planes and at the reconnection region. The measurement is followed over several repeatable discharges to follow the heating and acceleration process during the merging reconnection.

  15. 3D medical thermography device

    NASA Astrophysics Data System (ADS)

    Moghadam, Peyman

    2015-05-01

    In this paper, a novel handheld 3D medical thermography system is introduced. The proposed system consists of a thermal-infrared camera, a color camera and a depth camera rigidly attached in close proximity and mounted on an ergonomic handle. As a practitioner holding the device smoothly moves it around the human body parts, the proposed system generates and builds up a precise 3D thermogram model by incorporating information from each new measurement in real-time. The data is acquired in motion, thus it provides multiple points of view. When processed, these multiple points of view are adaptively combined by taking into account the reliability of each individual measurement which can vary due to a variety of factors such as angle of incidence, distance between the device and the subject and environmental sensor data or other factors influencing a confidence of the thermal-infrared data when captured. Finally, several case studies are presented to support the usability and performance of the proposed system.

  16. 3D printed bionic ears.

    PubMed

    Mannoor, Manu S; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A; Soboyejo, Winston O; Verma, Naveen; Gracias, David H; McAlpine, Michael C

    2013-06-12

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  17. Three-dimensional photoacoustic imaging system in line confocal mode for breast cancer detection

    NASA Astrophysics Data System (ADS)

    Ye, Fei; Yang, Sihua; Xing, Da

    2010-11-01

    We present a three-dimensional (3-D) photoacoustic imaging system (PAIS) in line confocal mode for breast cancer detection. With the line confocal mode, the spatial resolution of the PAIS was tested to be improved about three times compared with the nonconfocal mode PAIS. Furthermore, with a flexible scanning system and no compression on the breast, the PAIS could supply a comfortable and safe diagnosis process for the patient. An ex vivo breast tumor imaging experiment was performed and the tumor was visualized by the 3-D photoacoustic image. The experimental result demonstrated that the system had great potential of application in breast cancer detection.

  18. 3D Printing of Graphene Aerogels.

    PubMed

    Zhang, Qiangqiang; Zhang, Feng; Medarametla, Sai Pradeep; Li, Hui; Zhou, Chi; Lin, Dong

    2016-04-01

    3D printing of a graphene aerogel with true 3D overhang structures is highlighted. The aerogel is fabricated by combining drop-on-demand 3D printing and freeze casting. The water-based GO ink is ejected and freeze-cast into designed 3D structures. The lightweight (<10 mg cm(-3) ) 3D printed graphene aerogel presents superelastic and high electrical conduction. PMID:26861680

  19. 3D Elastic Wavefield Tomography

    NASA Astrophysics Data System (ADS)

    Guasch, L.; Warner, M.; Stekl, I.; Umpleby, A.; Shah, N.

    2010-12-01

    Wavefield tomography, or waveform inversion, aims to extract the maximum information from seismic data by matching trace by trace the response of the solid earth to seismic waves using numerical modelling tools. Its first formulation dates from the early 80's, when Albert Tarantola developed a solid theoretical basis that is still used today with little change. Due to computational limitations, the application of the method to 3D problems has been unaffordable until a few years ago, and then only under the acoustic approximation. Although acoustic wavefield tomography is widely used, a complete solution of the seismic inversion problem requires that we account properly for the physics of wave propagation, and so must include elastic effects. We have developed a 3D tomographic wavefield inversion code that incorporates the full elastic wave equation. The bottle neck of the different implementations is the forward modelling algorithm that generates the synthetic data to be compared with the field seismograms as well as the backpropagation of the residuals needed to form the direction update of the model parameters. Furthermore, one or two extra modelling runs are needed in order to calculate the step-length. Our approach uses a FD scheme explicit time-stepping by finite differences that are 4th order in space and 2nd order in time, which is a 3D version of the one developed by Jean Virieux in 1986. We chose the time domain because an explicit time scheme is much less demanding in terms of memory than its frequency domain analogue, although the discussion of wich domain is more efficient still remains open. We calculate the parameter gradients for Vp and Vs by correlating the normal and shear stress wavefields respectively. A straightforward application would lead to the storage of the wavefield at all grid points at each time-step. We tackled this problem using two different approaches. The first one makes better use of resources for small models of dimension equal

  20. Laser differential confocal radius measurement.

    PubMed

    Zhao, Weiqian; Sun, Ruoduan; Qiu, Lirong; Sha, Dingguo

    2010-02-01

    A new laser differential confocal radius measurement (DCRM) is proposed for high precision measurement of radius. Based on the property of an axial intensity curve that the absolute zero precisely corresponds to the focus of the objective in a differential confocal system (DCS), DCRM uses the zero point of the DCS axial intensity curve to precisely identify the cat's-eye and confocal positions of the test lens, and measures the accurate distance between the two positions to achieve the high-precision measurement of radius of curvature (ROC). In comparison with the existing measurement methods, DCRM proposed has a high measurement precision, a strong environmental anti-interference capability and a low cost. The theoretical analyses and preliminary experimental results indicate that DCRM has a relative measurement error of better than 5 ppm. PMID:20174065

  1. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

  2. 3D multimodality roadmapping in neuroangiography

    NASA Astrophysics Data System (ADS)

    Ruijters, Daniel; Babic, Drazenko; Homan, Robert; Mielekamp, Peter; ter Haar Romeny, Bart M.; Suetens, Paul

    2007-03-01

    In this paper we describe a novel approach to using morphological datasets (such as CT or MR) in the minimally invasive image guidance of intra-arterial and intra-venous endovascular devices in neuroangiography interventions. Minimally invasive X-ray angiography procedures rely on the navigation of endovascular devices, such as guide wires and catheters, through human vessels, using C-arm fluoroscopy. While the bone structure may be visible, and the injection of iodine contrast medium allows to guide endovascular devices through the vasculature, the soft-tissue structures remain invisible in the fluoroscopic images. We intend to present a method for the combined visualization of morphological data, a 3D rotational angiography (3DRA) reconstruction and the live fluoroscopy data stream in a single image. The combination of the fluoroscopic image with the 3DRA vessel tree offers the advantage that endovascular devices can be located with respect to the vasculature, without additional contrast injection, while the position of the C-arm geometry can be altered freely. The additional visualization of the morphological data, adds contextual information to the position of endovascular devices. This article addresses the clinical applications, the real-time aspects of the registration algorithms and fast fused visualization of the proposed method.

  3. Three-dimensional reconstruction of topological deformation in chiral nematic microspheres using fluorescence confocal polarizing microscopy.

    PubMed

    Guo, Jin-Kun; Song, Jang-Kun

    2016-04-01

    Chiral nematic droplets exhibit abundant topological defect structures, which have been intensively studied, both theoretically and experimentally. However, to observe and reconstruct the exact shape of three-dimensional (3D) defect structures has been a challenging task. In this study, we successfully reconstruct the 3D defect structures within a CLC microsphere with long helical pitches by combining polarized optical microscopy (POM) and laser scanning type fluorescence confocal polarizing microscopy (FCPM). The obtained confocal stack images provide us with the vertical location of disclination defects, to allow reconstruction of the full 3D structures. The reconstructed 3D structures can be viewed from different directions, providing a better understanding of the topological structure. Moreover, the defect lines are identified to be + 1 defects, different from the previous prediction. Thus, FCPM provides an excellent tool to study the complex topological configuration in microspheres, and fosters its potential applicability in new devices based on topologically structured soft media. PMID:27137028

  4. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

  5. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  6. 3D flow focusing for microfluidic flow cytometry with ultrasonics

    NASA Astrophysics Data System (ADS)

    Gnyawali, Vaskar; Strohm, Eric M.; Daghighi, Yasaman; van de Vondervoort, Mia; Kolios, Michael C.; Tsai, Scott S. H.

    2015-11-01

    We are developing a flow cytometer that detects unique acoustic signature waves generated from single cells due to interactions between the cells and ultrasound waves. The generated acoustic waves depend on the size and biomechanical properties of the cells and are sufficient for identifying cells in the medium. A microfluidic system capable of focusing cells through a 10 x 10 μm ultrasound beam cross section was developed to facilitate acoustic measurements of single cells. The cells are streamlined in a hydro-dynamically 3D focused flow in a 300 x 300 μm channel made using PDMS. 3D focusing is realized by lateral sheath flows and an inlet needle (inner diameter 100 μm). The accuracy of the 3D flow focusing is measured using a dye and detecting its localization using confocal microscopy. Each flowing cell would be probed by an ultrasound pulse, which has a center frequency of 375 MHz and bandwidth of 250 MHz. The same probe would also be used for recording the scattered waves from the cells, which would be processed to distinguish the physical and biomechanical characteristics of the cells, eventually identifying them. This technique has potential applications in detecting circulating tumor cells, blood cells and blood-related diseases.

  7. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  8. NIF Ignition Target 3D Point Design

    SciTech Connect

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

    2008-11-05

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

  9. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  10. On averaging multiview relations for 3D scan registration.

    PubMed

    Govindu, Venu Madhav; Pooja, A

    2014-03-01

    In this paper, we present an extension of the iterative closest point (ICP) algorithm that simultaneously registers multiple 3D scans. While ICP fails to utilize the multiview constraints available, our method exploits the information redundancy in a set of 3D scans by using the averaging of relative motions. This averaging method utilizes the Lie group structure of motions, resulting in a 3D registration method that is both efficient and accurate. In addition, we present two variants of our approach, i.e., a method that solves for multiview 3D registration while obeying causality and a transitive correspondence variant that efficiently solves the correspondence problem across multiple scans. We present experimental results to characterize our method and explain its behavior as well as those of some other multiview registration methods in the literature. We establish the superior accuracy of our method in comparison to these multiview methods with registration results on a set of well-known real datasets of 3D scans. PMID:23412615