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Results for “missing wedge”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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9 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3–20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.

42 ENGINEERING↗
DOE OSTI2026

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021)View full citation, Nat. Methods, 18, 186–193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, sub­tomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L1/L2 losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.

contrast enhancement↗
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2025

Field-level reconstruction from foreground-contaminated 21-cm maps

Current and upcoming 21-cm experiments will soon be able to map 21-cm spatial fluctuations in three dimensions for a wide range of redshifts. However, bright foreground contamination and the nature of radio interferometry create significant challenges, making it difficult to access rich cosmological information from the Fourier modes that lie within the “foreground wedge”. Here, in this work, we introduce two approaches aiming to reconstruct the full 21-cm density field, including the missing modes in the wedge: (a) a field-level inference under an effective field theory (EFT) framework; (b) a diffusion-based deep generative model trained on simulations. Under the EFT framework, we implement a fully differentiable forward model that maps the initial conditions of matter fluctuations to the observed, foreground-filtered 21-cm maps. This enables a gradient-based sampler to simultaneously sample the initial conditions and bias parameters, allowing a physically motivated mode reconstruction. Alternatively, we apply a variational diffusion model to perform 21-cm density reconstruction at the map level. Our model is trained on semi-numerical simulations over a wide range of astrophysical parameters. Our results from both approaches should provide improved cosmological constraints from the field level and also enable cross-correlation between experiments that have little or no overlapping modes.

cosmological perturbation theory↗
NASA NTRS2010

Materials International Space Station Experiment-6 (MISSE-6) Atomic Oxygen Fluence Monitor Experiment

An atomic oxygen fluence monitor was flown as part of the Materials International Space Station Experiment-6 (MISSE-6). The monitor was designed to measure the accumulation of atomic oxygen fluence with time as it impinged upon the ram surface of the MISSE 6B Passive Experiment Container (PEC). This was an active experiment for which data was to be stored on a battery-powered data logger for post-flight retrieval and analysis. The atomic oxygen fluence measurement was accomplished by allowing atomic oxygen to erode two opposing wedges of pyrolytic graphite that partially covered a photodiode. As the wedges of pyrolytic graphite erode, the area of the photodiode that is illuminated by the Sun increases. The short circuit current, which is proportional to the area of illumination, was to be measured and recorded as a function of time. The short circuit current from a different photodiode, which was oriented in the same direction and had an unobstructed view of the Sun, was also to be recorded as a reference current. The ratio of the two separate recorded currents should bear a linear relationship with the accumulated atomic oxygen fluence and be independent of the intensity of solar illumination. Ground hyperthermal atomic oxygen exposure facilities were used to evaluate the linearity of the ratio of short circuit current to the atomic oxygen fluence. In flight, the current measurement circuitry failed to operate properly, thus the overall atomic oxygen mission fluence could only be estimated based on the physical erosion of the pyrolytic graphite wedges. The atomic oxygen fluence was calculated based on the knowledge of the space atomic oxygen erosion yield of pyrolytic graphite measured from samples on the MISSE 2. The atomic oxygen fluence monitor, the expected result and comparison of mission atomic oxygen fluence based on the erosion of the pyrolytic graphite and Kapton H atomic oxygen fluence witness samples are presented in this paper.

Banks, Bruce A.↗
DOE OSTI2024

Poromechanical cohesive interface element with combined Mode I-II cohesive zone elastoplasticity for simulating fracture in fluid-saturated porous media

A combined Mode I-II cohesive zone (CZ) elasto-plastic constitutive model, and a two-dimensional (2D) cohesive interface element (CIE) are formulated and implemented at small strain within an ABAQUS User Element (UEL) for simulating 2D crack nucleation and propagation in fluid-saturated porous media. Here, the CZ model mitigates problems of convergence for the global Newton-Raphson solver within ABAQUS, which when combined with a viscous stabilization procedure allows for simulation of post-peak response under load control for coupled poromechanical finite element analysis, such as concrete gravity dam stability analysis. Verification examples are presented, along with a more complex ambient limestone-concrete wedge fracture experiment, water-pressurized concrete wedge experiment, and concrete gravity dam stability analyses. A calibration procedure for estimating the CZ parameters is demonstrated with the limestone-concrete wedge fracture process. For the water-pressurized concrete wedge fracture experiment it is shown that the inherent time-dependence of the poromechanical CIE analysis provides a good match with experimental force versus displacement results at various crack mouth opening rates, yet misses the pore water pressure evolution ahead of the crack tip propagation. This is likely a result of the concrete being partially-saturated in the experiment, whereas the finite element analysis assumes fully water saturated concrete. For the concrete gravity dam analysis, it is shown that base crack opening and associated water uplift pressure leads to a reduced Factor of Safety, which is confirmed by separate analytical calculations.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2009

Assessment of the Short-Term Radiometric Stability between Terra MODIS and Landsat 7 ETM+ Sensors

The Landsat 7 (L7) Enhanced Thematic Mapper (ETM+) sensor was launched on April 15th, 1999 and has been in operation for over nine years. It has six reflective solar spectral bands located in the visible and shortwave infrared part of the electromagnetic spectrum (0.5 - 2.5 micron) at a spatial resolution of 30 m. The on-board calibrators are used to monitor the on-orbit sensor system changes. The ETM+ performs solar calibrations using on-board Full Aperture Solar Calibrator (FASC) and the Partial Aperture Solar Calibrator (PASC). The Internal Calibrator Lamp (IC) lamps, a blackbody and shutter optics constitute the on-orbit calibration mechanism for ETM+. On 31 May 2003, a malfunction of the scan-line corrector (SLC) mirror assembly resulted in the loss of approximately 22% of the normal scene area. The missing data affects most of the image with scan gaps varying in width from one pixel or less near the centre of the image to 14 pixels along the east and west edges of the image, creating a wedge-shaped pattern. However, the SLC failure has no impacts on the radiometric performance of the valid pixels. On December 18, 1999, the Moderate Resolution Imaging Spectroradiometer (MODIS) Proto-Flight Model (PFM) was launched on-board the NASA's EOS Terra spacecraft. Terra MODIS has 36 spectral bands with wavelengths ranging from 0.41 to 14.5 micron and collects data over a wide field of view angle (+/-55 deg) at three nadir spatial resolutions of 250 m, 500 in 1 km for bands 1 to 2, 3 to 7, and 8 to 36, respectively. It has 20 reflective solar bands (RSB) with spectral wavelengths from 0.41 to 2.1 micron. The RSB radiometric calibration is performed by using on-board solar diffuser (SD), solar diffuser stability monitor (SDSM), space-view (SV), and spectro-radiometric calibration assembly (SRCA). Through the SV port, periodic lunar observations are used to track radiometric response changes at different angles of incidence (AOI) of the scan mirror. As a part of the AM Constellation satellites, Terra MODIS flies approximately 30 minutes behind L7 ETM+ in the same orbit. The orbit of L7 is repetitive, circular, sunsynchronous, and near polar at a nominal altitude of 705 km (438 miles) at the Equator. The spacecraft crosses the Equator from north to south on a descending node between 10:00 AM and 10:15 AM. Circling the Earth at 7.5 km/sec, each orbit takes nearly 99 minutes. The spacecraft completes just over 14 orbits per day, covering the entire Earth between 81 degrees north and south latitude every 16 days. The longest continuous imaging swath that L7 sensor can collect is for a 14-minute subinterval contact period which is equivalent to 35 full WRS-2 scenes. On the other hand, Terra can provide the entire corresponding orbit with wider swath at any given ETM+ collection without contact time limitation. There are six spectral matching band pairs between MODIS (bands 3, 4, 1, 2, 6, 7) and ETM+ (bands 1, 2, 3, 4, 5, 7) sensor. MODIS has narrower spectral responses than ETM+ in all the bands. A short-term radiometric stability was evaluated using continuous ETM+ scenes within the contact period and the corresponding half orbit MODIS scenes. The near simultaneous earth observations (SNO) were limited by the smaller swath size of ETM+ (187 km) as compared to MODIS (2330 km). Two sets of continuous granules for MODIS and ETM+ were selected and mosaiced based on pixel geolocation information for non cloudy pixels over the North American continent. The Top-of- Atmosphere (TOA) reflectances were computed for the spectrally matching bands between ETM+ and MODIS over the regions of interest (ROI). The matching pixel pairs were aggregated from a finer to a coarser pixel resolution and the TOA reflectance values covering a wide dynamic range of the sensors were compared and analyzed. Considering the uncertainties of the absolute calibration of the both sensors, radiometric stability was verified for the band pairs. The Railroad Valley Playa, Nada (RVPN) was included in the path of this continuous orbit, which served as a verification point between the shortterm and the long-term trending results from previous studies. This work focuses on monitoring the short-term on-orbit stability of MODIS and the ETM+ RSB. It also provides an assessment of the absolute calibration differences between the two sensors over their wide dynamic ranges.

Choi, Taeyoung↗
DOE OSTI2024

Volcanic arc rigidity variations illuminated by coseismic deformation of the 2011 Tohoku-oki M9

Rock strength has long been linked to lithospheric deformation and seismicity. However, independent constraints on the related elastic heterogeneity are missing, yet could provide key information for solid Earth dynamics. Using coseismic Global Navigation Satellite Systems (GNSS) data for the 2011 M9 Tohoku-oki earthquake in Japan, we apply an inverse method to infer elastic structure and fault slip simultaneously. We find compliant material beneath the volcanic arc and in the mantle wedge within the partial melt generation zone inferred to lie above ~100 km slab depth. We also identify low-rigidity material closer to the trench matching seismicity patterns, likely associated with accretionary wedge structure. Along with traditional seismic and electromagnetic methods, our approach opens up avenues for multiphysics inversions. Those have the potential to advance earthquake and volcano science, and in particular once expanded to InSAR type constraints, may lead to a better understanding of transient lithospheric deformation across scales.

58 GEOSCIENCES↗
NASA NTRS2008

The School of Virtual Knocks: Learning from Doing--Without Pain of Mistakes

The present day educational process, as currently practiced, is no longer necessarily synonymous with learning, and the concept of learning is becoming disassociated with knowledge acquisition. True, learning is not accidental, nor is the absence of learning normally by choice. It is the result, intended or otherwise, of decisions made by government, researchers, educators, students, parents, and the wider community. It is underpinned by the quality of teaching, the relevancy of the instruction to the student's world, and the perseverance of the student's desire to learn. It is these choices that are driving the wedge between teaching and learning. The learning outcomes are derived by curriculum developers, educational psychologists, government and industry.Yet as advances in understanding how students learn have been made, the advances in technology, specifically models and simulation, which are able to underpin complex knowledge domains, have been left behind if not ignored. While a majority of stakeholders in education agree that the current educational environment is missing the mark, it is important to underpin those impressions with a basis of knowledge. This paper reviews education in order to foster the conclusion that education must change and that the enabling methodologies and technologies already exist in the form of models and simulation.

Darby, Michael↗