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NASA NTRS2003

Automated Serial Sectioning for 3D Reconstruction

Some aspects of an apparatus and method for automated serial sectioning of a specimen of a solder, aluminum, or other relatively soft opaque material are discussed. The apparatus includes a small milling machine (micromiller) that takes precise, shallow cuts (increments of depth as small as 1 micron) to expose successive sections. A microscope equipped with an electronic camera, mounted in a fixed position on the micromiller, takes pictures of the newly exposed specimen surface at each increment of depth. The images are digitized, and the resulting data are subsequently processed to reconstruct three-dimensional (3D) features of the specimen.

Alkemper, Jen↗

DOE OSTI2020

Snapshot multifocal light field microscopy

Light field microscopy (LFM) is an emerging technology for high-speed wide-field 3D imaging by capturing 4D light field of 3D volumes. However, its 3D imaging capability comes at a cost of lateral resolution. In addition, the lateral resolution is not uniform across depth in the light field dconvolution reconstructions. To address these problems, here, we propose a snapshot multifocal light field microscopy (MFLFM) imaging method. The underlying concept of the MFLFM is to collect multiple focal shifted light fields simultaneously. We show that by focal stacking those focal shifted light fields, the depth-of-field (DOF) of the LFM can be further improved but without sacrificing the lateral resolution. Also, if all differently focused light fields are utilized together in the deconvolution, the MFLFM could achieve a high and uniform lateral resolution within a larger DOF. We present a house-built MFLFM system by placing a diffractive optical element at the Fourier plane of a conventional LFM. The optical performance of the MFLFM are analyzed and given. Both simulations and proof-of-principle experimental results are provided to demonstrate the effectiveness and benefits of the MFLFM. We believe that the proposed snapshot MFLFM has potential to enable high-speed and high resolution 3D imaging applications.

He, Kuan↗

DOE OSTI2024

Three-dimensional reconstruction of x-ray emission volumes in magnetized liner inertial fusion from sparse projection data using a learned basis

The ability to visualize x-ray and neutron emission from fusion plasmas in 3D is critical to understand the origin of the complex shapes of the plasmas in experiments. Unfortunately, this remains challenging in experiments that study a fusion concept known as Magnetized Liner Inertial Fusion (MagLIF) due to a small number of available diagnostic views. Here, we present a basis function-expansion approach to reconstruct MagLIF stagnation plasmas from a sparse set of x-ray emission images. A set of natural basis functions is “learned” from training volumes containing quasi-helical structures whose projections are qualitatively similar to those observed in experimental images. Tests on several known volumes demonstrate that the learned basis outperforms both a cylindrical harmonic basis and a simple voxel basis with additional regularization, according to several metrics. Two-view reconstructions with the learned basis can estimate emission volumes to within 11% and those with three views recover morphology to a high degree of accuracy. The technique is applied to experimental data, producing the first 3D reconstruction of a MagLIF stagnation column from multiple views, providing additional indications of liner instabilities imprinting onto the emitting plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1981

Laser electro-optic system for rapid three-dimensional /3-D/ topographic mapping of surfaces

It is pointed out that the generic utility of a robot in a factory/assembly environment could be substantially enhanced by providing a vision capability to the robot. A standard videocamera for robot vision provides a two-dimensional image which contains insufficient information for a detailed three-dimensional reconstruction of an object. Approaches which supply the additional information needed for the three-dimensional mapping of objects with complex surface shapes are briefly considered and a description is presented of a laser-based system which can provide three-dimensional vision to a robot. The system consists of a laser beam array generator, an optical image recorder, and software for controlling the required operations. The projection of a laser beam array onto a surface produces a dot pattern image which is viewed from one or more suitable perspectives. Attention is given to the mathematical method employed, the space coding technique, the approaches used for obtaining the transformation parameters, the optics for laser beam array generation, the hardware for beam array coding, and aspects of image acquisition.

Altschuler, M. D.↗

DOE OSTI2024

LumaCam: a novel class of position-sensitive event mode particle detectors using scintillator screens

A new type of position-sensitive detectors is gaining attention in the neutron community. They are scintillator based detectors that detect the scintillation light on an individual photon basis via an image intensifier and a fast image sensor. Their readout operates in event mode i.e. it produces information about individual neutron interactions, reconstructed from the sensor data, thus enabling to achieve superior spatial and temporal resolutions compared to regular detectors. Although the development of current detectors is focused on neutrons, the concept is also applicable to the detection of other particles such as high-energy photons. This document provides a description on how these detectors are built, how they operate, and what their characteristics are. An example of a detector implementation based on a Timepix3 chip is described to illustrate the detector concept. This includes a detailed description of the algorithm that reconstructs the neutron interactions from the sensor data, one of the core components that sets it apart from established scintillator-based imaging detectors. Energy-resolved epithermal neutron radiography was performed at the ISIS EMMA beamline with this detector, illustrating some of the fundamental differences in the data that can be produced with the new type of detector compared to more established types of scintillator based neutron detectors. The term LumaCam is proposed to refer to this new class of position-sensitive event-mode detectors.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Design and Characterization of an Optically Segmented Single Volume Scatter Camera Module

Here, the optically segmented single volume scatter camera (OS-SVSC) aims to image neutron sources for nuclear nonproliferation applications using the kinematic reconstruction of elastic double-scatter events. We report on the design, construction, and calibration of one module of a new prototype. The module includes 16 EJ-204 organic plastic scintillating bars individually wrapped in Teflon tape, each measuring 0.5cx0.5cmx20cm . The scintillator array is coupled to two custom silicon photomultiplier (SiPM) boards consisting of a 2x8 array of SensL J-Series-60035 SiPMs, which are read out by a custom 16 channel DRS4 based digitizer board. The electrical crosstalk between SiPMs within the electronics chain is measured as 0.76%±0.11% among all 16 channels. We report the detector response of one module including interaction position, time, and energy, using two different optical coupling materials: EJ-560 silicone rubber optical coupling pads and EJ-550 optical coupling grease. We present results in terms of the overall mean and standard deviation of the z -position reconstruction and interaction time resolutions for all 16 bars in the module. We observed the 1σz -position resolution for gamma interactions in the 0.3–0.4 MeVee range to be 2.24 cm ± 1.10 cm and 1.45 cm ± 0.19 cm for silicone optical coupling pad and optical grease, respectively. The observed 1σ interaction time resolution is 265 ps ± 29 ps and 235 ps ± 10 ps for silicone optical coupling pad and optical grease, respectively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Shower Reconstruction for Cross-Section Measurements with Photon(s) in the Final State at SBND

The Short-Baseline Near Detector (SBND) is a 112-ton liquid argon time projection chamber operating in the Booster Neutrino Beam at Fermilab as part of the Short-Baseline Neutrino Program. Precise reconstruction of electromagnetic showers from photons and electrons is essential for searches for neutrino oscillations, cross-section measurements, and rare-process studies in liquid argon. In this poster, we present a unified set of SBND analyses enabled by the SPINE (Scalable Particle Imaging with Neural Embeddings) end-to-end machine-learning–based reconstruction framework, highlighting charged-current neutral pion (CC π⁰) production and neutral-current (NC) Δ radiative decay as complementary physics cases. Charged-current π⁰ interactions provide a high-statistics benchmark for validating photon reconstruction, constraining the electromagnetic energy scale, and modeling backgrounds to other cross-section measurements and BSM searches with one or more photons in the final state. We summarize progress toward the ongoing development of a CC π⁰ selection in SBND and, report on the current status of a search for NC resonant Δ production followed by radiative decay (Δ→Nγ) in SBND. This rare process, previously investigated in MicroBooNE, provides a stringent test of photon-only final-state reconstruction and is of interest in the context of the MiniBooNE low-energy excess. Together, these analyses demonstrate how modern machine-learning–based shower reconstruction enables a diverse and scalable physics program at SBND.

Chung, Seokju [Nevis Labs, Columbia U.]↗

DOE OSTI2021

Visualizing defects and pore connectivity within metal–organic frameworks by X-ray transmission tomography

Metal–Organic Frameworks (MOFs) have the potential to change the landscape of molecular separations in chemical processes owing to their ability of selectively binding molecules. Their molecular sorting properties generally rely on the micro- and meso-pore structure, as well as on the presence of coordinatively unsaturated sites that interact with the different chemical species present in the feed. In this work, we show a first-of-its-kind tomographic imaging of the crystal morphology of a metal– organic framework by means of transmission X-ray microscopy (TXM), including a detailed data reconstruction and processing approach. Corroboration with Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) images shows the potential of this strategy for further (non-destructively) assessing the inner architecture of MOF crystals. By doing this, we have unraveled the presence of large voids in the internal structure of a MIL-47(V) crystal, which are typically thought of as rather homogeneous lattices. This challenges the established opinion that hydrothermal syntheses yield relatively defect-free material and sheds further light on the internal morphology of crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1977

DKDP /potassium dideuterium phosphate/ light valves

The use of potassium dideuterium phosphate (DKDP) light valves for optical data processing is discussed. The operating principles and structure of optically and electron beam addressed DKDPs are compared, and specifications for both devices given. Optically addressed DKDPs are capable of higher resolution and contrast, but both systems represent viable real time spatial light modulators adaptable to optical processing. Examples of real time data processing performed by the DKDPs include: image addition and subtraction; reduction of noise introduced by scattered light in recording media; reconstruction of computer generated and acoustic holograms; reconstruction of synthetic aperture radar data; retrieval of three-dimensional information in X-ray diagnoses; radar signal processing and display; and optical pattern recognition and correlation of images, which has applications for missile guidance systems.

Casasent, D.↗

NASA NTRS2010

Self-Referencing Hartmann Test for Large-Aperture Telescopes

A method is proposed for end-to-end, full aperture testing of large-aperture telescopes using an innovative variation of a Hartmann mask. This technique is practical for telescopes with primary mirrors tens of meters in diameter and of any design. Furthermore, it is applicable to the entire optical band (near IR, visible, ultraviolet), relatively insensitive to environmental perturbations, and is suitable for ambient laboratory as well as thermal-vacuum environments. The only restriction is that the telescope optical axis must be parallel to the local gravity vector during testing. The standard Hartmann test utilizes an array of pencil beams that are cut out of a well-corrected wavefront using a mask. The pencil beam array is expanded to fill the full aperture of the telescope. The detector plane of the telescope is translated back and forth along the optical axis in the vicinity of the nominal focal plane, and the centroid of each pencil beam image is recorded. Standard analytical techniques are then used to reconstruct the telescope wavefront from the centroid data. The expansion of the array of pencil beams is usually accomplished by double passing the beams through the telescope under test. However, this requires a well-corrected, autocollimation flat, the diameter or which is approximately equal to that of the telescope aperture. Thus, the standard Hartmann method does not scale well because of the difficulty and expense of building and mounting a well-corrected, large aperture flat. The innovation in the testing method proposed here is to replace the large aperture, well-corrected, monolithic autocollimation flat with an array of small-aperture mirrors. In addition to eliminating the need for a large optic, the surface figure requirement for the small mirrors is relaxed compared to that required of the large autocollimation flat. The key point that allows this method to work is that the small mirrors need to operate as a monolithic flat only with regard to tip/tilt and not piston because in collimated space piston has no effect on the image centroids. The problem of aligning the small mirrors in tip/tilt requires a two-part solution. First, each mirror is suspended from a two-axis gimbal. The orientation of the gimbal is maintained by gravity. Second, the mirror is aligned such that the mirror normal is parallel to gravity vector. This is accomplished interferometrically in a test fixture. Of course, the test fixture itself needs to be calibrated with respect to gravity.

Korechoff, Robert P.↗

DOE OSTI2020

Real-time sparse-sampled Ptychographic imaging through deep neural networks

Ptychography has rapidly grown in the fields of X-ray and electron imaging for its unprecedented ability to achieve nano or atomic scale resolution while simultaneously retrieving chemical or magnetic information from a sample. A ptychographic reconstruction is achieved by means of solving a complex inverse problem that imposes constraints both on the acquisition and on the analysis of the data, which typically precludes real-time imaging due to computational cost involved in solving this inverse problem. In this work we propose PtychoNN, a novel approach to solve the ptychography reconstruction problem based on deep convolutional neural networks. We demonstrate how the proposed method can be used to predict real-space structure and phase at each scan point solely from the corresponding far-field diffraction data. The presented results demonstrate how PtychoNN can effectively be used on experimental data, being able to generate high quality reconstructions of a sample up to hundreds of times faster than state-of-the-art ptychography reconstruction solutions once trained. By surpassing the typical constraints of iterative model-based methods, we can significantly relax the data acquisition sampling conditions and produce equally satisfactory reconstructions. Besides drastically accelerating acquisition and analysis, this capability can enable new imaging scenarios that were not possible before, in cases of dose sensitive, dynamic and extremely voluminous samples.

Cherukara, Mathew J↗

DOE OSTI2024

Extraction of Vibration Data with Imaging

To date, the primary sensing technology used to measure the vibration response has been accelerometers and strain gages mounted directly to the structure and using either wired or, more recently, wireless telemetry. Cost issues with these sensors and the associated data acquisition systems typically limit the numbers that are deployed on in situ structures. Although there are a few structures with larger sensing counts that in some cases exceed over 1000 sensors, more typical numbers range from ten to one hundred sensors resulting in low spatial resolution when they are applied to physically large systems. When one considers that nuclear power plant structures usually have complex geometries, material properties, connectivity and boundary conditions, it is clear these current approaches to vibration measurements can only provide limited information about a system’s dynamics response characteristics. As an alternative, many non-contact measurement technologies have emerged, including point wise measurement methods such as Global Positioning System (GPS), microwave interferometry, and laser Doppler vibrometry (LDV), as well as simultaneous full-field measurement methods such as electronic speckle pattern interferometry, holography interferometry, and muon tomography, some of which can provide high spatial resolution measurements. Among these methods, digital video imaging techniques have emerged as a feasible solution for full-field vibration measurements that provide significantly more detailed dynamic response information because every pixel becomes a measurement point. Furthermore, recent advances in image processing and computer vision algorithms have been successfully used to process video data for experimental and operational modal analysis. Such full-field measurements have the potential to significantly improve many current structural assessment procedures including system identification (modal parameter estimation), structural health monitoring, load reconstruction, model validation, and model updating. Furthermore, more recent full-field imaging techniques can be accomplished with relatively low-cost, commercially-available off-the-shelf cameras. However, these measurement procedures have other limitations that must be considered such as the ability to only measure visibly accessible points on a structure and a more limited dynamic range and bandwidth than can be achieved with accelerometers or strain gages.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1976

Space communication system for compressed data with a concatenated Reed-Solomon-Viterbi coding channel

A space communication system incorporating a concatenated Reed Solomon Viterbi coding channel is discussed for transmitting compressed and uncompressed data from a spacecraft to a data processing center on Earth. Imaging (and other) data are first compressed into source blocks which are then coded by a Reed Solomon coder and interleaver, followed by a convolutional encoder. The received data is first decoded by a Viterbi decoder, followed by a Reed Solomon decoder and deinterleaver. The output of the latter is then decompressed, based on the compression criteria used in compressing the data in the spacecraft. The decompressed data is processed to reconstruct an approximation of the original data-producing condition or images.

Rice, R. F.↗

DOE OSTI2023

Physics-Informed Deep Learning for Reconstruction of Spatial Missing Climate Information in the Antarctic

Understanding the influence of the Antarctic on the global climate is crucial for the prediction of global warming. However, due to very few observation sites, it is difficult to reconstruct the rational spatial pattern by filling in the missing values from the limited site observations. To tackle this challenge, regional spatial gap-filling methods, such as Kriging and inverse distance weighted (IDW), are regularly used in geoscience. Nevertheless, the reconstructing credibility of these methods is undesirable when the spatial structure has massive missing pieces. Inspired by image inpainting, we propose a novel deep learning method that demonstrates a good effect by embedding the physics-aware initialization of deep learning methods for rapid learning and capturing the spatial dependence for the high-fidelity imputation of missing areas. We create the benchmark dataset that artificially masks the Antarctic region with ratios of 30%, 50% and 70%. The reconstructing monthly mean surface temperature using the deep learning image inpainting method RFR (Recurrent Feature Reasoning) exhibits an average of 63% and 71% improvement of accuracy over Kriging and IDW under different missing rates. With regard to wind speed, there are still 36% and 50% improvements. In particular, the achieved improvement is even better for the larger missing ratio, such as under the 70% missing rate, where the accuracy of RFR is 68% and 74% higher than Kriging and IDW for temperature and also 38% and 46% higher for wind speed. In addition, the PI-RFR (Physics-Informed Recurrent Feature Reasoning) method we proposed is initialized using the spatial pattern data simulated by the numerical climate model instead of the unified average. Compared with RFR, PI-RFR has an average accuracy improvement of 10% for temperature and 9% for wind speed. When applied to reconstruct the spatial pattern based on the Antarctic site observations, where the missing rate is over 90%, the proposed method exhibits more spatial characteristics than Kriging and IDW.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1991

Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.

NASA Program Space Biology↗

DOE OSTI2025

Measurement of interfacial thermal resistance in high-energy-density matter

Heat transport across interfaces is a ubiquitous phenomenon with many unresolved aspects. In particular, it is unknown if an interfacial thermal resistance (ITR) occurs in matter with high-energy-density where free electrons dominate the heat conduction. Here, we report on the first experimental evidence that a significant heat barrier is present between two different regions of high-energy-density matter: a strongly heated tungsten wire and a surrounding plastic layer that stays relatively cold. We use diffraction-enhanced imaging to track the time evolution of density discontinuities and reconstruct the temperature evolution in the quasi-stationary stage. The clear signatures of a temperature jump demonstrate the importance of the ITR for strongly heated systems with far-reaching implications for interpreting experiments and applications like inertial confinement fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Fourier method for 3-dimensional data fusion of X-ray Computed Tomography and ultrasound

X-ray Computed Tomography (CT) is essential for nondestructive inspection of many manufactured components but is susceptible to various forms of artifacts and noise. In particular, multi-detector row cone-beam CT systems can suffer from so called “cone-beam” artifacts and partial volume effects, particularly on planar edges at the periphery of the field of view in the cone angle dimension. Uni-directional ultrasonic testing methods generally have extremely accurate in-plane depth resolution but poorer lateral resolution due to physical and geometric constraints. This paper presents a novel technique called Computed Tomographic Fusion (CT-F) which uses three-dimensional Fourier filtering to combine x-ray cone-beam CT reconstructions and ultrasound data in the frequency space. The result is a single image with improved accuracy and quality. CT-F mitigates artifacts while allowing for rapid, accurate characterization of large three-dimensional CT volumes. Finally, using simulations and experiments, we demonstrate artifact reduction and edge contrast improvement in volumetric reconstructions.

42 ENGINEERING↗