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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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6 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↗
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↗
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↗