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Results for “3D image processing”

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At least 109 records · Page 6

Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching

An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.

3D imaging↗

Processing-in-Memory Enabled Graphics Processors for 3D Rendering

The performance of 3D rendering of Graphics Processing Unit that convents 3D vector stream into 2D frame with 3D image effects significantly impact users’ gaming experience on modern computer systems. Due to the high texture throughput in 3D rendering, main memory bandwidth becomes a critical obstacle for improving the overall rendering performance. 3D stacked memory systems such as Hybrid Memory Cube (HMC) provide opportunities to significantly overcome the memory wall by directly connecting logic controllers to DRAM dies. Based on the observation that texel fetches significantly impact off-chip memory traffic, we propose two architectural designs to enable Processing-In-Memory based GPU for efficient 3D rendering.

Innovative hardware/software co-design↗

Real-Time Simultaneous 3D Volumetric Imaging and Mapping of Gamma-ray and Neutron Sources

The invention combines radiation detection instrumentation, data processing algorithms, and visualization software to enable, for the first time ever, simultaneous, real-time imaging of both gamma ray and neutron sources (fast and slow). Radiation detectors sensitive to gamma rays and neutrons are integrated with readout electronics that allow discriminated particles to be incorporated into real-time 3D volumetric reconstructions as two separate data streams. Using the Scene Data Fusion (SDF) conceptual framework and contextual sensors from the Localization and Mapping Platform (LAMP) developed at LBNL, gamma-ray and neutron data are fused onto contextual information from the environment around the detection system. The invention is compatible with radiation detection media capable of detecting and discriminating between gamma rays and neutrons or the pairing of multiple detectors separately capable of detecting gamma rays and/or neutrons. It can be integrated into a compact, lightweight imaging platform for operation as a hand-carry device, on unmanned aerial systems, and with unmanned vehicles. The ability to measure neutron enables the detection and 3D localization of shielded nuclear materials such as Pu-239 which is not possible with means of gamma-ray detection and spectroscopy overcoming of major limitation in the detection of such materials to-date.

Cates, Joshua↗

Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation

Abnormal tau inclusions are hallmarks of Alzheimer's disease and predictors of clinical decline. Several tau PET tracers are available for neurodegenerative disease research, opening avenues for molecular diagnosis in vivo. However, few have been approved for clinical use. Understanding the neurobiological basis of PET signal validation remains problematic because it requires a large-scale, voxel-to-voxel correlation between PET and (immuno) histological signals. Large dimensionality of whole human brains, tissue deformation impacting co-registration, and computing requirements to process terabytes of information preclude proper validation. We developed a computational pipeline to identify and segment particles of interest in billion-pixel digital pathology images to generate quantitative, 3D density maps. The proposed convolutional neural network for immunohistochemistry samples, IHCNet, is at the pipeline's core. We have successfully processed and immunostained over 500 slides from two whole human brains with three phospho-tau antibodies (AT100, AT8, and MC1), spanning several terabytes of images. Our artificial neural network estimated tau inclusion from brain images, which performs with ROC AUC of 0.87, 0.85, and 0.91 for AT100, AT8, and MC1, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. We present an end-to-end pipeline to create terabytes-large 3D tau inclusion density maps co-registered to MRI as a means to facilitate validation of PET tracers.

60 APPLIED LIFE SCIENCES↗

MO-G-BRF-07: Anomalously Fast Diffusion of Carbon Nanotubes Carriers in 3D Tissue Model

Purpose: We aim to investigate and understand diffusion process of carbon nanotubes (CNTs) and other nanoscale particles in tissue and organs. Methods: In this research, we utilized a 3D model tissue of hepatocellular carcinoma (HCC)cultured in inverted colloidal crystal (ICC) scaffolds to compare the diffusivity of CNTs with small molecules such as Rhodamine and FITC in vitro, and further investigated the transportation of CNTs with and without targeting ligand, TGFβ1. The real-time permeation profiles of CNTs in HCC tissue model with high temporal and spatial resolution was demonstrated by using standard confocal microscopy. Quantitative analysis of the diffusion process in 3D was carried out using luminescence intensity in a series of Z-stack images obtained for different time points of the diffusion process after initial addition of CNTs or small molecules to the cell culture and the image data was analyzed by software ImageJ and Mathematica. Results: CNTs display diffusion rate in model tissues substantially faster than small molecules of the similar charge such as FITC, and the diffusion rate of CNTs are significantly enhanced with targeting ligand, TGFβ1. Conclusion: In terms of the advantages of in-vitro model, we were able to have access to measuring the rate of CNT penetration at designed conditions with variable parameters. And the findings by using this model, changed our understanding about advantages of CNTs as nanoscale drug carriers and provides design principles for making new drug carriers for both treatment and diagnostics. Additionally the fast diffusion opens the discussion of the best possible drug carriers to reach deep parts of cancerous tissues, which is often a prerequisite for successful cancer treatment. This work was supported by the Center for Photonic and Multiscale Nanomaterials funded by National Science Foundation Materials Research Science and Engineering Center program DMR 1120923. The work was also partially supported by NSF grant ECS-0601345; EFRI-BSBA 0938019; CBET 0933384; CBET 0932823; CBET 1036672, AFOSR MURI 444286-P061716 and NIH 1R21CA121841-01A2.

60 APPLIED LIFE SCIENCES↗

Extending Hypersonic Diagnostics to the Third Dimension

The design, construction, and initial testing of a high-magnification, long working-distance plenoptic camera is reported. A plenoptic camera uses a microlens array to enable resolution of the spatial and angular information of the incoming light field. With this, instantaneous images can be numerically refocused and perspective shifted in post-processing to enable instantaneous three-dimensional (3D) resolution of a scene. Prior to this work, most applications of plenoptic imaging were limited to relatively low magnifications (1× or less) or small working distances. Here, a unique system is developed with enables 5× magnification at a working distance of over a quarter meter. Experimental results demonstrate ~25 m spatial resolution with 3D imaging capabilities. This technology is demonstrated on two practical applications. First, burning aluminum particles on the order of 100 m in diameter are imaged near the reacting surface of a combusting solid rocket propellant. The long working distance is particularly advantageous for protection of the experimental hardware in this extremely hazardous environment. Next, background oriented schlieren is used to resolve the 3D structure of an underexpanded free jet. This demonstrates the ability to resolve index-of-refraction gradients at the working distances and spatial scales necessary to meet our ultimate goal of resolving 3D turbulent transition in the boundary layer of Sandia’s Hypersonic Wind Tunnel (HWT).

47 OTHER INSTRUMENTATION↗

3-D advanced gas-cooled nuclear reactor fuel channel reconstruction using structure-from-motion - 110

During planned, periodic outages, a selection of fuel channels within the UK fleet of Advanced Gas-cooled Reactor (AGR) cores are inspected using specialist tools which record video footage and other sensory data for each channel which undergoes inspection. Current visualization techniques comprise of manually produced montages by inspection engineers of points of interest (i.e. structural defects) and 2-D panoramic images of the fuel channels automatically produced using bespoke image stitching software. Both techniques however provide limited structural information due to the loss of depth data as a result of the image formation process. By recovering the depth information from the footage, a 3D model could be constructed and subsequently, allow for more accurate profiling of specific defects observed during inspection in addition to obtaining the fuel channels structure using existing footage. This work explores the preliminary application of a 3-D visualization technique known as Structure-from-Motion (SfM) which aims to obtain 3-D information by exploiting image correspondences across multiple viewpoints of the same scene in the RVI footage. This paper investigates the difficulties of applying state-of-the-art SfM to RVI footage and we present new techniques to improve feature correspondence searching in repetitive, nondescript environments. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

A synchrotron study of defect and strain inhomogeneity in laser-assisted three-dimensionally-printed Ni-based superalloy

Synchrotron X-ray microdiffraction was employed to investigate the inhomogeneous distribution of defect and residual strain in the transitional region between the dendritic and stray grains in a laser-assisted 3D printed Ni-based superalloy. The dendritic region was found to be under tensile strain transversely to the primary dendrite arm directions. The dendrite edges, where high level of strains and geometrically necessary dislocations were detected, were discerned as low angle grain boundaries. Lastly, high angle grain boundaries were observed in the stray grain region, and the orientation of the strain tensor in this region varied dramatically at the micron scale, in contrast with the more or less homogeneous distribution in the dendritic region.

36 MATERIALS SCIENCE↗

A Two-Tier Convolutional Neural Network for Combined Detection and Segmentation in Biological Imagery

Deep learning techniques have been useful for modern microscopy imaging techniques to further study and analyze biological structures and organs. Convolutional neural networks (CNN) have improved 2D object detection, localization, and segmentation. For imagery containing biological structures with depth, it is especially desirable to perform these tasks in 3D. Traditionally, performing these tasks simultaneously in 3D has proven to be computationally expensive. Currently available methodologies thus largely work to segment 3D objects from 2D images (without context from captured 3D volumes). In this work, we present a novel approach to perform fast and accurate localization, detection, and segmentation of volumes containing cells. Specifically, in our method, we modify and tune two state-of-the-art CNNs, namely 2D YOLOv2 and 3D U-Net, and combine them with a new fusion and image processing algorithms. Annotated volumes in this space are limited, and we have created synthetic data that mimics actual structures for training and testing our proposed approach. Promising results on this test data demonstrate the value of the technique and offers a methodology for 3D cell analysis in real microscopy imagery.

Ziabari, Amir↗

Neutron tomography of porous aluminum electrodes used in electrocoagulation of groundwater

In this work, neutron computed tomography (CT) is employed to investigate the dissolution of porous aluminum electrodes during electrocoagulation (EC). Porous electrodes were chosen in efforts to reduce electric power requirements by using larger surface-area electrodes, having both inner and outer surface, for the EC process. Neutron CT allowed 3D reconstruction of the porous electrodes, and image analysis provided the volume of each electrode vs. thickness, which can indicate whether the inner surface is effectively involved in EC reactions. For the anode, the volume decreased uniformly throughout the thickness of the electrode, indicating that both the outer and inner surface participated in electrochemical dissolution, while the volume of the cathode increased uniformly vs. thickness, indicating deposition of material on both the outer and inner surface. The attenuation coefficient vs. thickness, increased for both anode and cathode, indicating surface chemistry changes. For the anode, the attenuation coefficient increased slightly but uniformly, probably due to aluminum oxide formation on the surface of the anode. For the cathode, the attenuation coefficient increased more than for the anode and nonuniformly. The higher increase in the attenuation coefficient for the cathode is due to precipitation of aluminum hydroxide on the electrode surface, which added hydrogen. Image analysis also showed that, although the attenuation coefficient increased throughout the thickness of the electrode, most of the hydroxide deposition occurred on the outer surface. Energy analysis showed that porous electrodes can be used to reduce process energy requirements by as much as 4 times compared to solid electrodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

3D nanolithography with metalens arrays and spatially adaptive illumination

The growing demand for advanced materials, miniaturized devices and integrated microsystems calls for the reliable fabrication of complex, multiscale, three-dimensional (3D) architectures, a need increasingly addressed through light-based and laser-based processes. However, owing to the field-of-view (FOV) limitations of conventional imaging optics, existing 3D laser nanofabrication techniques face fundamental challenges in throughput, proximity error and stitching defects on the path to scaling. Here, in this study, we present a scalable 3D nanofabrication platform that uses a metalens-generated focal spot array to parallelize two-photon lithography (TPL) beyond centimetre-scale write field areas. Metalenses are ideally suited for producing submicron-scale focal spots for high-throughput nanolithography, as they uniquely feature large numerical apertures (NAs), immersion media compatibility and large-scale manufacturability. We experimentally demonstrate a printing system that uses a 12-cm 2 metalens array to produce more than 120,000 cooperative focal spots, corresponding to a throughput exceeding 10 8 voxels s −1 . By programmatically patterning the focal spot array using a spatial light modulator (SLM), an adaptive parallel printing strategy is developed for precise greyscale linewidth modulation and choreographed printing of semiperiodic and fully aperiodic 3D geometries. We demonstrate parallel printing of replicated microstructures (>50 M microparticles per day), centimetre-scale 3D architectures with feature sizes down to 113 nm, and photonic and mechanical metamaterials. This work demonstrates the potential of 3D nanolithography towards wafer-scale production, showing how TPL could be used at scale for applications in microelectronics, biomedicine, quantum technology and high-energy laser targets.

Materials science↗

Online coupled camera pose estimation and dense reconstruction from video

A product may receive each image in a stream of video image of a scene, and before processing the next image, generate information indicative of the position and orientation of an image capture device that captured the image at the time of capturing the image. The product may do so by identifying distinguishable image feature points in the image; determining a coordinate for each identified image feature point; and for each identified image feature point, attempting to identify one or more distinguishable model feature points in a three dimensional (3D) model of at least a portion of the scene that appears likely to correspond to the identified image feature point. Thereafter, the product may find each of the following that, in combination, produce a consistent projection transformation of the 3D model onto the image: a subset of the identified image feature points for which one or more corresponding model feature points were identified; and, for each image feature point that has multiple likely corresponding model feature points, one of the corresponding model feature points. The product may update a 3D model of at least a portion of the scene following the receipt of each video image and before processing the next video image base on the generated information indicative of the position and orientation of the image capture device at the time of capturing the received image. The product may display the updated 3D model after each update to the model.

97 MATHEMATICS AND COMPUTING↗

Imaging mechanism for hyperspectral scanning probe microscopy via Gaussian process modelling

We investigate the ability to reconstruct and derive spatial structure from sparsely sampled 3D piezoresponse force microcopy data, captured using the band-excitation (BE) technique, via Gaussian Process (GP) methods. Even for weakly informative priors, GP methods allow unambiguous determination of the characteristic length scales of the imaging process both in spatial and frequency domains. We further show that BE data set tends to be oversampled in the spatial domains, with ~30% of original data set sufficient for high-quality reconstruction, potentially enabling faster BE imaging. At the same time, reliable reconstruction along the frequency domain requires the resonance peak to be within the measured band. This behavior suggests the optimal strategy for the BE imaging on unknown samples. Finally, we discuss how GP can be used for automated experimentation in SPM, by combining GP regression with non-rectangular scans.

47 OTHER INSTRUMENTATION↗

Application of Plasma FIB to Analyze a Single Oxide Inclusion in Steel

We demonstrate that Plasma Dual Beam focused ion beam (PFIB) milling can be used for high-resolution three-dimensional chemical study of a single non-metallic inclusion in steel. A CaO-Al{sub 2}O{sub 3}-MgO inclusion (~ 10 μm) on a polished cross-section of steel sample was located and milled using a Xe{sup +} ion beam. A secondary electron image and EDS map of every section were recorded and subsequently processed to show the 3D chemistry and morphology of the inclusion.

36 MATERIALS SCIENCE↗

Shared autonomy for low–cost underwater vehicles

This field report presents an overview of the development and testing of a semi-autonomous underwater vehicle (sAUV). The work presented here is aimed at bridging the gap between current remotely operated vehicles and autonomous research platforms by developing shared autonomy capabilities for low-cost underwater vehicles. We use commercially available components and open-source software interfaces to provide a wider range of capabilities for underwater autonomy research at a lower cost than previously available systems. We describe the overall structure of the system, discuss its capabilities, and provide results demonstrating system performance. We place particular emphasis on shared autonomy, where a human operator is assisted in controlling an underwater tethered vehicle. We present three capabilities developed for the sAUV: (a) an assisted control mode that provides a variable level of assistance using an on-line estimate of user skill level, (b) a planner to generate paths that avoid tether entanglement, and (c) a sonar processing algorithm that identifies informative sonar images for selecting features for 3D scene reconstruction. Here, the vehicle has been deployed on five off-shore and near-shore marine field deployments since 2015, and this report includes selected results from four of those trials to demonstrate the capabilities and limitations of the sAUV system.

16 TIDAL AND WAVE POWER↗

Optical super-resolution microscopy in polymer science

The advent of optical super-resolution microscopy (OSRM) over two decades ago has transformed light-mediated interrogation of systems down to the nanoscale. This innovative set of approaches to optics breaks the so-called diffraction limit of light (~200 nm), allowing for the first time to use optics in the far field to visualize behavior on nanoscopic length scales. While these visualization tools have rapidly found widespread use in biology and related fields, their implementation in materials and, more specifically, in polymer science has been far slower. To overcome possible barriers and highlight possible future directions, we present in this paper an introduction to OSRM for polymer scientists, beginning with an overview of relevant techniques and existing optical probes. We then show and examine the first examples of OSRM adaptation across major areas of polymer science, including: polymerization and structural characterization, self-assembly and solution behavior, bulk structure and behavior, crystallization, gel structure and behavior, phase transitions, and biofunctionality. We hope and anticipate that the discussions provided in this review will draw the attention of the polymer community to the capacities of these hitherto underexplored optical visualization techniques to further transform polymer science.

36 MATERIALS SCIENCE↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II

X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation ( i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Finally, two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.

36 MATERIALS SCIENCE↗

Real-time X-ray phase-contrast imaging using SPINNet—a speckle-based phase-contrast imaging neural network

X-ray phase-contrast imaging has become indispensable for visualizing samples with low absorption contrast. In this regard, speckle-based techniques have shown significant advantages in spatial resolution, phase sensitivity, and implementation flexibility compared with traditional methods. However, the computational cost associated with data inversion has hindered their wider adoption. By exploiting the power of deep learning, we developed a speckle-based phase-contrast imaging neural network (SPINNet) that significantly improves the imaging quality and boosts the phase retrieval speed by at least 2 orders of magnitude compared to existing methods. To achieve this performance, we combined SPINNet with a coded-mask-based technique, an enhanced version of the speckle-based method. Using this scheme, we demonstrate the simultaneous reconstruction of absorption and phase images on the order of 100 ms, where a traditional correlation-based analysis would take several minutes even with a cluster. In addition to significant improvement in speed, our experimental results show that the imaging and phase retrieval quality of SPINNet outperform existing single-shot speckle-based methods. Furthermore, we successfully demonstrate SPINNet application in x-ray optics metrology and 3D x-ray phase-contrast tomography. Our result shows that SPINNet could enable many applications requiring high-resolution and fast data acquisition and processing, such as in situ and in operando 2D and 3D phase-contrast imaging and real-time at-wavelength metrology and wavefront sensing.

36 MATERIALS SCIENCE↗