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All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

3D Integration of Sensors and Electronics

A three dimensional integrated circuit is composed of multiple tiers of integrated electronics and sensors integrated vertically by wafer bonding, thinning and insertion of through-silicon-vias. The technologies associated with three dimensional integrated circuits can provide new capabilities for high energy physics and x-ray imaging experiments. These include finer pixel pitch, lower interconnect capacitance, the ability to separate analog and digital functions, and better power distribution and connectivity. In this paper we review the status of 3DIC demonstration projects at Fermilab, discuss several possible applications, and summarize the current availability of commercial processes. Results of a three-tier demonstration project that includes designs for x-ray imaging, CMS track triggering, and ILC vertex are described. We discuss the status of several ongoing 3D projects and prospects for future evolution of the technology.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Automated Aerial Triangulation for UAV-Based Mapping

Accurate 3D reconstruction/modelling from unmanned aerial vehicle (UAV)-based imagery has become the key prerequisite in various applications. Although current commercial software has automated the process of image-based reconstruction, a transparent system, which can be incorporated with different user-defined constraints, is still preferred by the photogrammetric research community. In this regard, this paper presents a transparent framework for the automated aerial triangulation of UAV images. The proposed framework is conducted in three steps. In the first step, two approaches, which take advantage of prior information regarding the flight trajectory, are implemented for reliable relative orientation recovery. Then, initial recovery of image exterior orientation parameters (EOPs) is achieved through either an incremental or global approach. Finally, a global bundle adjustment involving Ground Control Points (GCPs) and check points is carried out to refine all estimated parameters in the defined mapping coordinate system. Four real image datasets, which are acquired by two different UAV platforms, have been utilized to evaluate the feasibility of the proposed framework. In addition, a comparative analysis between the proposed framework and the existing commercial software is performed. The derived experimental results demonstrate the superior performance of the proposed framework in providing an accurate 3D model, especially when dealing with acquired UAV images containing repetitive pattern and significant image distortions.

3D reconstruction↗
DOE OSTI2022

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement

Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Adaptive Machine Learning for Bragg Coherent Diffraction Imaging (BCDI) of 3D Electron Density Maps with Application to La 2-x Ba x CuO 4 (LBCO) High Temperature Superconductor Studies [PowerPoint]

Understanding mesoscale heterogeneity is important for evaluating fatigue and failure of structural materials and for manufacturing processes. Data-driven tools can facilitate in guiding effort investment (measurements and computations) at various stages of the materials development. Our 3D reconstruction approach is to find a set of coefficients which define a bounding surface of the electron density. Data for training the 3D CNN was generated by sampling coefficients from uniform distributions. Test vs. prediction values are shown for the 28 even-valued coefficients for 1000 test structures, with the best and worst performers highlighted. The adaptive part of this work utilized a model independent extremum seeking (ES). The predictions of the CNN were used as the starting point for the ES algorithm. The convergence of the ES algorithm for 3 different structures is illustrated, and the robustness of the adaptive ML approach was demonstrated on experimentally measured 3D crystal from high energy diffraction microscopy. Reconstruction of a non-uniform density volume with different levels of Poisson noise is also shown. Preliminary attempts at reconstructing measured La 2-x Ba x CuO 4 diffraction patterns have so far failed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

MO-F-CAMPUS-J-05: Toward MRI-Only Radiotherapy: Novel Tissue Segmentation and Pseudo-CT Generation Techniques Based On T1 MRI Sequences

Purpose: To develop and validate a 4 class tissue segmentation approach (air cavities, background, bone and soft-tissue) on T1 -weighted brain MRI and to create a pseudo-CT for MRI-only radiation therapy verification. Methods: Contrast-enhanced T1-weighted fast-spin-echo sequences (TR = 756ms, TE= 7.152ms), acquired on a 1.5T GE MRI-Simulator, are used.MRIs are firstly pre-processed to correct for non uniformity using the non parametric, non uniformity intensity normalization algorithm. Subsequently, a logarithmic inverse scaling log(1/image) is applied, prior to segmentation, to better differentiate bone and air from soft-tissues. Finally, the following method is enrolled to classify intensities into air cavities, background, bone and soft-tissue:Thresholded region growing with seed points in image corners is applied to get a mask of Air+Bone+Background. The background is, afterward, separated by the scan-line filling algorithm. The air mask is extracted by morphological opening followed by a post-processing based on knowledge about air regions geometry. The remaining rough bone pre-segmentation is refined by applying 3D geodesic active contours; bone segmentation evolves by the sum of internal forces from contour geometry and external force derived from image gradient magnitude.Pseudo-CT is obtained by assigning −1000HU to air and background voxels, performing linear mapping of soft-tissue MR intensities in [-400HU, 200HU] and inverse linear mapping of bone MR intensities in [200HU, 1000HU]. Results: Three brain patients having registered MRI and CT are used for validation. CT intensities classification into 4 classes is performed by thresholding. Dice and misclassification errors are quantified. Correct classifications for soft-tissue, bone, and air are respectively 89.67%, 77.8%, and 64.5%. Dice indices are acceptable for bone (0.74) and soft-tissue (0.91) but low for air regions (0.48). Pseudo-CT produces DRRs with acceptable clinical visual agreement to CT-based DRR. Conclusion: The proposed approach makes it possible to use T1-weighted MRI to generate accurate pseudo-CT from 4-class segmentation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Tomographic Volumetric Additive Manufacturing of Silica Glass with In Situ Error Calculation and Projection Tiling

The optical, thermal, and chemical properties of glass make it an ideal material for use in a wide range of applications, from optics and chemistry reactionware to consumer products. Tomographic volumetric additive manufacturing (tVAM) creates 3D objects by selectively gelling material within a rotating vial of photo-sensitive material by exposure to a series of tomographically-determined images. Here, in this study, tVAM is investigated for fabrication of complex, centimeter-scale, 3D silica glass parts. By optimizing the post-processing procedure, fully-dense glass parts with up to 2 cm 2 cross sectional area are achieved. The changes in optical properties during printing are leveraged for in situ metrology during printing, and the non-Newtonian nature of the glass-filled photoresin system to facilitate larger fabrication volumes via tiled projections. Printed structures are finally demonstrated for applications as MEMS components, optics, fluidics, and consumer products.

Materials science↗
DOE OSTI2013

Single Molecule and Nanoparticle Imaging in Biophysical, Surface, and Photocatalysis Studies

A differential interference contrast (DIC) polarization anisotropy is reported that was successfully used for rotational tracking of gold nanorods attached onto a kinesin-driven microtubule. A dual-wavelength detection of single gold nanorods rotating on a live cell membrane is described. Both transverse and longitudinal surface plasmon resonance (SPR) modes were used for tracking the rotational motions during a fast dynamic process under a DIC microscope. A novel method is presented to determine the full three-dimensional (3D) orientation of single plasmonic gold nanorods rotating on live cell membranes by combining DIC polarization anisotropy with an image pattern recognition technique. Polarization- and wavelength-sensitive DIC microscopy imaging of 2- m long gold nanowires as optical probes in biological studies is reported. A new method is demonstrated to track 3D orientation of single gold nanorods supported on a gold film without angular degeneracy. The idea is to use the interaction (or coupling) of gold nanorods with gold film, yielding characteristic scattering patterns such as a doughnut shape. Imaging of photocatalytic activity, polarity and selectivity on single Au-CdS hybrid nanocatalysts using a high-resolution superlocalization fluorescence imaging technique is described.

36 MATERIALS SCIENCE↗
DOE OSTI2017

What can we learn from in-soil imaging of a live plant: X-ray Computed Tomography and 3D numerical simulation of root-soil system

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to farming, forest management and climate change. X-ray computed tomography (XCT) has been proven to be an effective tool for non-invasive root imaging and analysis. A combination of XCT, open-source software, and our own code was used to noninvasively image a prairie dropseed (Sporobolus heterolepis) specimen, segment the root data to obtain a 3D image of the root structure at 31µm resolution, and extract quantitative information (root volume and surface area) from the 3D data, respectively. Based on the mesh generated from the root structure, computational fluid dynamics (CFD) simulations were applied to numerically investigate the root-soil-groundwater system. The plant root conductivity, soil hydraulic conductivity and transpiration rate were shown to control the groundwater distribution. The flow variability and soil water distributions under different scenarios were investigated. Parameterizations were evaluated to show their impacts on the average conductivity. The pore-scale modeling approach provides realistic simulations of rhizosphere flow processes and provides useful information that can be linked to upscaled models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Accuracy of UTE-MRI-based patient setup for brain cancer radiation therapy

Purpose: Radiation therapy simulations solely based on MRI have advantages compared to CT-based approaches. One feature readily available from computed tomography (CT) that would need to be reproduced with MR is the ability to compute digitally reconstructed radiographs (DRRs) for comparison against on-board radiographs commonly used for patient positioning. In this study, the authors generate MR-based bone images using a single ultrashort echo time (UTE) pulse sequence and quantify their 3D and 2D image registration accuracy to CT and radiographic images for treatments in the cranium. Methods: Seven brain cancer patients were scanned at 1.5 T using a radial UTE sequence. The sequence acquired two images at two different echo times. The two images were processed using an in-house software to generate the UTE bone images. The resultant bone images were rigidly registered to simulation CT data and the registration error was determined using manually annotated landmarks as references. DRRs were created based on UTE-MRI and registered to simulated on-board images (OBIs) and actual clinical 2D oblique images from ExacTrac™. Results: UTE-MRI resulted in well visualized cranial, facial, and vertebral bones that quantitatively matched the bones in the CT images with geometric measurement errors of less than 1 mm. The registration error between DRRs generated from 3D UTE-MRI and the simulated 2D OBIs or the clinical oblique x-ray images was also less than 1 mm for all patients. Conclusions: UTE-MRI-based DRRs appear to be promising for daily patient setup of brain cancer radiotherapy with kV on-board imaging.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2020

Image Collection Simulation Using High-Resolution Atmospheric Modeling

A new method is described for simulating the passive remote sensing image collection of ground targets that includes effects from atmospheric physics and dynamics at fine spatial and temporal scales. The innovation in this research is the process of combining a high-resolution weather model with image collection simulation to attempt to account for heterogeneous and high-resolution atmospheric effects on image products. The atmosphere was modeled on a 3D voxel grid by a Large-Eddy Simulation (LES) driven by forcing data constrained by local ground-based and air-based observations. The spatial scale of the atmospheric model (10–100 m) came closer than conventional weather forecast scales (10–100 km) to approaching the scale of typical commercial multispectral imagery (2 m). This approach was demonstrated through a ground truth experiment conducted at the Department of Energy Atmospheric Radiation Measurement Southern Great Plains site. In this experiment, calibrated targets (colored spectral tarps) were placed on the ground, and the scene was imaged with WorldView-3 multispectral imagery at a resolution enabling the tarps to be visible in at least 9–12 image pixels. The image collection was simulated with Digital Imaging and Remote Sensing Image Generation (DIRSIG) software, using the 3D atmosphere from the LES model to generate a high-resolution cloud mask. The high-resolution atmospheric model-predicted cloud coverage was usually within 23% of the measured cloud cover. The simulated image products were comparable to the WorldView-3 satellite imagery in terms of the variations of cloud distributions and spectral properties of the ground targets in clear-sky regions, suggesting the potential utility of the proposed modeling framework in improving simulation capabilities, as well as testing and improving the operation of image collection processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Identifying build orientation of 3D-printed materials using convolutional neural networks

The advent of additive manufacturing (AM) processes brought with it intense research into various materials and manufacturing processes. At the same time, the need for validation of material properties, as well as study and forecasting of aging, has arisen. Modern imaging techniques, like X-ray computed tomography (XCT), are a convenient vehicle for such studies; however, the large datasets they produce require novel analysis techniques to efficiently extract critical information. Here, we present our work on developing a 3D extension of the ResNet architecture to distinguish between two build orientations of tensile bars produced by AM. Using only information from XCT, our method achieves a 99.3% correct classification at a misidentification of 1%.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Real-time kinematic (RTK) Drone-collected Data and Processed Models of Port Arthur Coastal Neighborhood and Pleasure Island Golf Course, June 2024

The Southeast Texas Urban Integrated field lab’s Co-design team captured aerial photos in the Port Arthur Coastal Neighborhood Community and the Golf Course on Pleasure Island, Texas, in June 2024. Aerial photos taken were through autonomous flight, and models were processed through the DroneDeploy engine. All aerial photos are in .JPG format and contained in zipped files for each area. The processed data package includes 3D models, geospatial data, mappings, and point clouds. Please be aware that DTM, Elevation toolbox, Point Cloud, and Orthomosaic use EPSG: 6588. And 3D Model uses EPSG: 3857.For using these data:- The Adobe Suite gives you great software to open .Tif files.- You can use LASUtility (Windows), ESRI ArcGIS Pro (Windows), or Blaze3D (Windows, Linux) to open a LAS file and view the data it contains.- Open an .OBJ file with a large number of free and commercial applications. Some examples include Microsoft 3D Builder, Apple Preview, Blender, and Autodesk.- You may use ArcGIS, Merkaartor, Blender (with the Google Earth Importer plug-in), Global Mapper, and Marble to open .KML files.- The .tfw world file is a text file used to georeference the GeoTIFF raster images, like the orthomosaic and the DSM. You need suitable software like ArcView to open a .TFW file.This dataset provides researchers with sufficient geometric data and the status quo of the land surface at the locations mentioned above. This dataset will support researchers' decision-making processes under uncertainties.

2D mapping↗
DOE OSTI2016

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models

BioSig3D is a computational platform for high-content screening of three-dimensional (3D) cell culture models that are imaged in full 3D volume. It provides an end-to-end solution for designing high content screening assays, based on colony organization that is derived from segmentation of nuclei in each colony. BioSig3D also enables visualization of raw and processed 3D volumetric data for quality control, and integrates advanced bioinformatics analysis. The system consists of multiple computational and annotation modules that are coupled together with a strong use of controlled vocabularies to reduce ambiguities between different users. It is a web-based system that allows users to: design an experiment by defining experimental variables, upload a large set of volumetric images into the system, analyze and visualize the dataset, and either display computed indices as a heatmap, or phenotypic subtypes for heterogeneity analysis, or download computed indices for statistical analysis or integrative biology. BioSig3D has been used to profile baseline colony formations with two experiments: (i) morphogenesis of a panel of human mammary epithelial cell lines (HMEC), and (ii) heterogeneity in colony formation using an immortalized non-transformed cell line. These experiments reveal intrinsic growth properties of well-characterized cell lines that are routinely used for biological studies. BioSig3D is being released with seed datasets and video-based documentation.

Science & Technology - Other Topics↗
DOE OSTI2023

The MIGDAL experiment: Measuring a rare atomic process to aid the search for dark matter

We present the Migdal In Galactic Dark mAtter expLoration (MIGDAL) experiment aiming at the unambiguous observation and study of the so-called Migdal effect induced by fast-neutron scattering. It is hoped that this elusive atomic process can be exploited to enhance the reach of direct dark matter search experiments to lower masses, but it is still lacking experimental confirmation. Our goal is to detect the predicted atomic electron emission which is thought to accompany nuclear scattering with low, but calculable, probability, by deploying an Optical Time Projection Chamber filled with a low-pressure gas based on CF 4 . Initially, pure CF 4 will be used, and then in mixtures containing other elements employed by leading dark matter search technologies — including noble species, plus Si and Ge. High resolution track images generated by a Gas Electron Multiplier stack, together with timing information from scintillation and ionisation readout, will be used for 3D reconstruction of the characteristic event topology expected for this process — an arrangement of two tracks sharing a common vertex, with one belonging to a Migdal electron and the other to a nuclear recoil. Different energy-loss rate distributions along both tracks will be used as a powerful discrimination tool against background events. In this article we present the design of the experiment, informed by extensive particle and track simulations and detailed estimations of signal and background rates. In pure CF 4 we expect to observe 8.9 (29.3) Migdal events per calendar day of exposure to an intense D–D (D–T) neutron generator beam at the NILE facility located at the Rutherford Appleton Laboratory (UK). With our nominal assumptions, 5σ median discovery significance can be achieved in under one day with either generator.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Revealing the aging process of solid electrolyte interphase on SiOx anode

Abstract As one of the most promising alternatives to graphite negative electrodes, silicon oxide (SiO x ) has been hindered by its fast capacity fading. Solid electrolyte interphase (SEI) aging on silicon SiO x has been recognized as the most critical yet least understood facet. Herein, leveraging 3D focused ion beam-scanning electron microscopy (FIB-SEM) tomographic imaging, we reveal an exceptionally characteristic SEI microstructure with an incompact inner region and a dense outer region, which overturns the prevailing belief that SEIs are homogeneous structure and reveals the SEI evolution process. Through combining nanoprobe and electron energy loss spectroscopy (EELS), it is also discovered that the electronic conductivity of thick SEI relies on the percolation network within composed of conductive agents (e.g., carbon black particles), which are embedded into the SEI upon its growth. Therefore, the free growth of SEI will gradually attenuate this electron percolation network, thereby causing capacity decay of SiO x . Based on these findings, a proof-of-concept strategy is adopted to mechanically restrict the SEI growth via applying a confining layer on top of the electrode. Through shedding light on the fundamental understanding of SEI aging for SiO x anodes, this work could potentially inspire viable improving strategies in the future.

25 ENERGY STORAGE↗
DOE OSTI2015

Optimization and evaluation of metal injection molding by using X-ray tomography

6061 aluminum alloy and 316L stainless steel green bodies were obtained by using different injection parameters (injection pressure, speed and temperature). After injection process, the green bodies were scanned by X-ray tomography. The projection and reconstruction images show the different kinds of defects obtained by the improper injection parameters. Then, 3D rendering of the Al alloy green bodies was used to demonstrate the spatial morphology characteristics of the serious defects. Based on the scanned and calculated results, it is convenient to obtain the proper injection parameters for the Al alloy. Then, reasons of the defect formation were discussed. During mold filling, the serious defects mainly formed in the case of low injection temperature and high injection speed. According to the gray value distribution of projection image, a threshold gray value was obtained to evaluate whether the quality of green body can meet the desired standard. The proper injection parameters of 316L stainless steel can be obtained efficiently by using the method of analyzing the Al alloy injection. - Highlights: • Different types of defects in green bodies were scanned by using X-ray tomography. • Reasons of the defect formation were discussed. • Optimization of the injection parameters can be simplified greatly by the way of X-ray tomography. • Evaluation standard of the injection process can be obtained by using the gray value distribution of projection image.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Simulated annealing reconstruction and characterization of the three-dimensional microstructure of a LiCoO{sub 2} Lithium-ion battery cathode

We adapt the simulated annealing approach for reconstruction of the 3D microstructure of a LiCoO{sub 2} cathode from a commercial Li-ion battery. The real size distribution curve of LiCoO{sub 2} particles is applied to regulate the reconstruction process. By discretizing a 40 × 40 × 40 μm cathode volume with 8,000,000 numerical cubes, the cathode involving three individual phases: 1) LiCoO{sub 2} as active material, 2) pores or electrolyte, and 3) additives (polyvinylidene fluoride + carbon black) is reconstructed. The microstructural statistical properties required in the reconstruction process are extracted from 2D focused ion beam/scanning electron microscopy images or obtained by analyzing the powder mixture used to make the cathode. Characterization of the reconstructed cathode gives important structural and transport properties including the two-point correlation functions, volume-specific surface area between phases, tortuosity and geometrical connectivity of individual phase. - Highlights: • Simulated annealing approach is adapted for 3D reconstruction of LiCoO{sub 2} cathode. • Real size distribution of LiCoO{sub 2} particles is applied in reconstruction process. • Reconstructed cathode accords with real one at important statistical properties. • Effective electrode-characterization approaches have been established. • Extensive characterization gives important structural properties, say, tortuosity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ , a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

3D zooming↗