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DOE OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Dark matter substructure or source model systematics? A case study of cluster lens Abell S1063

Mapping the small-scale structure of the universe through gravitational lensing is a promising tool for probing the particle nature of dark matter. Curved Arc Basis (CAB) has been proposed as a local lensing formalism in galaxy clusters, with the potential to detect low-mass dark matter substructure. In this work, we analyse the cluster lens Abell S1063 in search of dark matter substructure with the CAB formalism, using multiband imaging data from James Webb Space Telescope ( JWST ). We use two different source modelling methods: shapelets and pixel-based source reconstruction based on Delaunay triangulation. We find that source modelling systematics from shapelets result in a disagreement between CAB parameters measured from different filters. Source modelling with Delaunay significantly alleviates this systematic, as seen in the improvement in agreement across filters. We also find that inadequate complexity in source modelling can result in convincing spurious detections of dark matter substructure from strong gravitational lenses, as seen by our $\Delta \text{BIC} > 20$ measurement of a $M \sim 10^{10}$ ${\rm M}_{\odot }$ subhalo with shapelets, a spurious detection that is not reproduced with Delaunay source modelling. We demonstrate that multiband analysis with different JWST filters is key for disentangling source and lens model systematics from dark matter substructure detections.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Self-supervised physics-informed generative networks for phase retrieval from a single X-ray hologram

X-ray phase contrast imaging significantly improves the visualization of structures with weak or uniform absorption, broadening its applications across a wide range of scientific disciplines. Propagation-based phase contrast is particularly suitable for time- or dose-critical in vivo/in situ/operando (tomography) experiments because it requires only a single intensity measurement. However, the phase information of the wave field is lost during the measurement and must be recovered. Conventional algebraic and iterative methods often rely on specific approximations or boundary conditions that may not be met by many samples or experimental setups. In addition, they require manual tuning of reconstruction parameters by experts, making them less adaptable for complex or variable conditions. Here we present a self-learning approach for solving the inverse problem of phase retrieval in the near-field regime of Fresnel theory using a single intensity measurement (hologram). A physics-informed generative adversarial network is employed to reconstruct both the phase and absorbance of the unpropagated wave field in the sample plane from a single hologram. Unlike most state-of-the-art deep learning approaches for phase retrieval, our approach does not require paired, unpaired, or simulated training data. This significantly broadens the applicability of our approach, as acquiring or generating suitable training data remains a major challenge due to the wide variability in sample types and experimental configurations. The algorithm demonstrates robust and consistent performance across diverse imaging conditions and sample types, delivering quantitative, high-quality reconstructions for both simulated data and experimental datasets acquired at beamline P05 at PETRA III (DESY, Hamburg), operated by Helmholtz-Zentrum Hereon. Furthermore, it enables the simultaneous retrieval of both phase and absorption information.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Quantitative phase measurements of human cell nuclei using X-ray ptychography

The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. Furthermore, the ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Improving High-Energy Particle Detectors with Machine Learning

Microseconds after the Big Bang, the universe existed in a state called the quark-gluon plasma (QGP). To experimentally study its properties, the QGP is recreated in high-energy nuclear collisions at the LHC, and the particles produced from the QGP are reconstructed from their energy deposition in the ATLAS calorimeter. This requires both classifying the particles and calibrating their deposited energy. The objective of this project is to improve the reconstruction by using machine learning techniques, where the energy depositions of clusters of cells, formed by ATLAS topo-clustering methods, are treated as three-dimensional images when inputted to neural networks. This approach significantly improves the calibration of deposited energies when cross-validating while training, and models trained on idealized data predict the calibrated energies of particles in more complex data sets well. Additionally, implementation of a data generator using uproot allows the program to load input data into memory as needed while training or predicting, significantly reducing the amount of memory used. The data generator also allows for use of multiprocessing to speed up training and evaluating. This work illustrates that using machine learning methods for both classification and calibration has the potential to significantly improve particle reconstruction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

X-ray scattering based scanning tomography for imaging and structural characterization of cellulose in plants

X-ray and neutron scattering have long been used for structural characterization of cellulose in plants. Due to averaging over the illuminated sample volume, these measurements traditionally overlooked the compositional and morphological heterogeneity within the sample. Here, a scanning tomographic imaging method is described, using contrast derived from the X-ray scattering intensity, for virtually sectioning the sample to reveal its internal structure at a resolution of a few micrometres. This method provides a means for retrieving the local scattering signal that corresponds to any voxel within the virtual section, enabling characterization of the local structure using traditional data-analysis methods. This is accomplished through tomographic reconstruction of the spatial distribution of a handful of mathematical components identified by non-negative matrix factorization from the large dataset of X-ray scattering intensity. Joint analysis of multiple datasets, to find similarity between voxels by clustering of the decomposed data, could help elucidate systematic differences between samples, such as those expected from genetic modifications, chemical treatments or fungal decay. The spatial distribution of the microfibril angle can also be analyzed, based on the tomographically reconstructed scattering intensity as a function of the azimuthal angle.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Sequence2Self: Self-supervised image sequence denoising of pixel-level spray breakup morphology

Optical imaging of fast and transient phenomena such as the turbulent breakup of liquid sprays exhibit low signal-to-noise ratios due to the limited illumination intensity relative to the short exposure time. Image denoising is required to facilitate physical studies over these data but is challenging due to the absence of clean ground-truths and the stringency of the denoising task (e.g., strong and complex noise, limited resolution, preserving physical fidelity), preventing supervised and existing un-/self-supervised deep learning methods. To this end, Sequence2Self (Seq2S) is proposed, an extension of Self2Self (S2S) to image sequences that leverages both the signal’s spatial and temporal correlation. Seq2S is demonstrated on time-resolved x-ray phase contrast imaging of liquid jet fuel sprays in a gas turbine combustor, which possesses all of challenges detailed above. Experiments are conducted across four fuels with different breakup morphology using various state-of-the-art methods. Overall, many of the methods failed and Seq2S was most successful: (1) Accurate spray structures were reconstructed with consistent evolution across frames void of artifacts. (2) The performance was robust, invariant to the hyperparameter choice. (3) Computational time is short and can be made eligible for real-time denoising. In particular, the images denoised by Seq2S showed spray droplet diameter distributions with near-zero Kullback–Leibler divergence (0.01 ± 0.01) to a cleaner reference, whereas the second best method yielded 0.06 ± 0.03. In conclusion, this suggests that Seq2S can be reliably used prior to subsequent quantitative spray analyses as it retains (if not, improves) the statistical physical properties of the data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Multiscale spatial analysis of fracture arrangement and pattern reconstruction using Ripley's K-function

This work presents novel multiscale spatial data analytics using Ripley's K-function, as a measure of spatial interaction, to study one-dimensional arrangement of fractures. Fracture spatial arrangements are classified into clustered, anticlustered, or indistinguishable from random by testing statistical significance of the calculated Ripley's K-function. Characterizations of fracture arrangements are performed as a function of length scale and position. Analysis of the K-function along the study interval identifies where fracture clustering and anticlustering occur. Here, a simulation technique is also introduced here to statistically reconstruct spatial arrangements and to generate fracture realizations that are spatially similar to the fractures observed in the field. With this simulation technique, one can also fill spatial gaps in fracture measurements where data are absent, unreliable, or unused. Synthetic as well as field-measured 1D fracture datasets are used for testing and demonstration. Methods introduced in this work can be readily applied to fracture datasets observed in outcrops, borehole image logs, and cores.

58 GEOSCIENCES↗

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 OSTI2020

Interpreting nanovoids in atom probe tomography data for accurate local compositional measurements

Quantifying chemical compositions around nanovoids is a fundamental task for research and development of various materials. Atom probe tomography (APT) and scanning transmission electron microscopy (STEM) are currently the most suitable tools because of their ability to probe materials at the nanoscale. Both techniques have limitations, particularly APT, because of insufficient understanding of void imaging. Here, we employ a correlative APT and STEM approach to investigate the APT imaging process and reveal that voids can lead to either an increase or a decrease in local atomic densities in the APT reconstruction. Simulated APT experiments demonstrate the local density variations near voids are controlled by the unique ring structures as voids open and the different evaporation fields of the surrounding atoms. We provide a general approach for quantifying chemical segregations near voids within an APT dataset, in which the composition can be directly determined with a higher accuracy than STEM-based techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Seeing in with X-rays: 4D Strain and Thermometry Measurements for Thermal-Mechanical Testing

Understanding temperature-dependent material decomposition and structural deformation induced by combined thermal-mechanical environments is critical for safety qualification of hardware under accident scenarios. Seeing in with X-rays elucidated the physics necessary to develop X-ray strain and thermometry diagnostics for use in optically opaque environments. Two parallel thermometry schemes were explored: X-ray fluorescence and X-ray diffraction of inorganic doped ceramics– colloquially known as thermographic phosphors. Two parallel surface strain techniques–Path-Integrated Digital Image Correlation and Frequency Multiplexed Digital Image Correlation–were demonstrated. Finally, preliminary demonstration of time-resolved digital volume correlation was performed by taking advantage of limited view reconstruction techniques. Additionally, research into blended ceramic-metal coatings was critical to generating intrinsic thermographic patterns for the future combination of X-ray strain and thermometry measurements.

36 MATERIALS SCIENCE↗

DOE OSTI2026

ODIN: Confirmation and 3D Reconstruction of Six Massive Protoclusters at Cosmic Noon

Protoclusters represent sites of accelerated galaxy formation and extreme astrophysical activity characteristic of dense environments. Identifying massive protoclusters and mapping their spatial structures are therefore crucial for understanding how large-scale environment influences galaxy evolution. We combine wide-field Lyα imaging from the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey with extensive Dark Energy Spectroscopic Instrument and ancillary spectroscopy across the extended COSMOS and XMM Large Scale Structure (LSS) fields (≈14 deg$^{2}$) to search for massive protoclusters. We confirm six systems at z ≈ 2.4 and ≈ 3.1, including three newly identified structures and three which overlap with previously known structures and/or systems detected using other tracers. We reconstruct their three-dimensional structures, estimate descendant halo masses, and for one structure at z ≈ 3.12, demonstrate that overlapping narrowband filters (NB497 and N501) provide accurate redshift tomography for emission-line galaxies. One protocluster at z ≈ 2.45 overlaps with one of the LATIS tomographic fields, enabling direct comparison between galaxy and H i overdensities traced by Lyα forest absorption. Another at z ≈ 3.12 hosts a massive quiescent galaxy (M$_{*}$ ≈ 1.2 × 10$^{11}$M$_{⊙}$), suggesting that overdense environments may play a role in accelerating galaxy assembly and quenching. Comparing Lyα emission properties across environments, we find that protocluster galaxies exhibit higher median line fluxes and a deficit of faint emitters relative to the field. The effect is strongest when combining 2D and 3D density information, indicating that galaxies in the densest protocluster cores are most affected by environmental processes. This effect is stronger at z ≈ 3.1 than at z ≈ 2.4, suggesting possible redshift evolution.

Ortiz, Ashley [Purdue U.] (ORCID:000900083184304X)↗

DOE OSTI2023

Multislice Electron Tomography Using Four-Dimensional Scanning Transmission Electron Microscopy

Electron tomography offers useful three-dimensional (3D) structural information, which cannot be observed by two-dimensional imaging. By combining annular dark-field scanning transmission electron microscopy (ADF STEM) with aberration correction, the resolution of electron tomography has reached atomic resolution. However, tomography based on ADF STEM inherently suffers from several issues, including a high electron-dose requirement, poor contrast for light elements, and artifacts from image-contrast nonlinearity. Here, we develop an alternative method called multislice electron tomography (MSET) based on four-dimensional STEM tilt series. In this study, our simulations show that multislice-based 3D reconstruction can effectively reduce undesirable reconstruction artifacts from the nonlinear contrast, allowing precise determination of atomic structures with improved sensitivity for low-Z elements, at considerably low electron-dose conditions. We expect that the MSET method can be applied to a wide variety of materials, including radiation-sensitive samples and materials containing light elements whose 3D atomic structures have never been fully elucidated due to electron-dose limitations or nonlinear imaging contrast.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Uncovering the three-dimensional structure of upconverting core–shell nanoparticles with multislice electron ptychography

In photon upconverting core–shell nanoparticles, structure strongly dictates performance. Typical imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional methods insufficient for fully characterizing these structures. Phase retrieval techniques provide a promising alternative imaging mode, and, in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core–shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle, we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Enabling dynamic 3D coherent diffraction imaging via adaptive latent space tuning of generative autoencoders

Abstract Coherent diffraction imaging (CDI) is an advanced non-destructive 3D X-ray imaging technique for measuring a sample’s electron density. The main challenge of CDI is loss of phase information in diffraction intensity measurements, resulting in lengthy iterative reconstruction processes that can return non-unique solutions, which pose challenges for experiments attempting to track dynamic sample evolution through multiple states. As the increased brightness of fourth-generation light sources enables faster sample measurements and drives operando experiments with Bragg CDI, there is a growing need for faster reconstruction techniques that can keep pace. We have developed an adaptive generative autoencoder approach for uniquely tracking a sample’s electron density as it dynamically evolves. Our approach adaptively tunes the low-dimensional latent embedding of a generative autoencoder, enabling a computationally efficient manner to account for time-varying shifting distributions in real-time. Analytic proof of convergence is provided as well as numerical demonstration of sample tracking with noisy measurements.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Three-dimensional nanoscale reduced-angle ptycho-tomographic imaging with deep learning (RAPID)

X-ray ptychographic tomography is a nondestructive method for three dimensional (3D) imaging with nanometer-sized resolvable features. The size of the volume that can be imaged is almost arbitrary, limited only by the penetration depth and the available scanning time. Here we present a method that rapidly accelerates the imaging operation over a given volume through acquiring a limited set of data via large angular reduction and compensating for the resulting ill-posedness through deeply learned priors. The proposed 3D reconstruction method “RAPID” relies initially on a subset of the object measured with the nominal number of required illumination angles and treats the reconstructions from the conventional two-step approach as ground truth. It is then trained to reproduce equal fidelity from much fewer angles. After training, it performs with similar fidelity on the hitherto unexamined portions of the object, previously not shown during training, with a limited set of acquisitions. In our experimental demonstration, the nominal number of angles was 349 and the reduced number of angles was 21, resulting in a x140 aggregate speedup over a volume of 4.48 x 93.18 x 3.92 μm 3 and with (14nm) 3 feature size, i.e. ~ 10 8 voxels. RAPID’s key distinguishing feature over earlier attempts is the incorporation of atrous spatial pyramid pooling modules into the deep neural network framework in an anisotropic way. We found that adjusting the atrous rate improves reconstruction fidelity because it expands the convolutional kernels’ range to match the physics of multi-slice ptychography without significantly increasing the number of parameters.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Automatic 3D image registration for nano-resolution chemical mapping using synchrotron spectro-tomography

Nano-resolution synchrotron X-ray spectro-tomography has been demonstrated as a powerful tool for probing the three-dimensional (3D) structural and chemical heterogeneity of a sample. By reconstructing a number of tomographic data sets recorded at different X-ray energy levels, the energy-dependent intensity variation in every given voxel fingerprints the corresponding local chemistry. The resolution and accuracy of this method, however, could be jeopardized by non-ideal experimental conditions, e.g. instability in the hardware system and/or in the sample itself. Herein is presented one such case, in which unanticipated sample deformation severely degrades the data quality. Here, to address this issue, an automatic 3D image registration method is implemented to evaluate and correct this effect. The method allows the redox heterogeneity in partially delithiated Li x Ta 0.3 Mn 0.4 O 2 battery cathode particles to be revealed with significantly improved fidelity.

3D image registration↗

DOE OSTI2020

Reconstruction of the interatomic forces from dynamic scanning transmission electron microscopy data

We explore the possibility for reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy data. In this work, scanning transmission electron microscopy (STEM) is used to observe the dynamic motion of Si atoms at the edge of monolayer graphene under continuous electron beam illumination. The resulting time-lapsed STEM images represent the snapshots of observed chemical states of the system. We use two approaches: potential of mean force calculation using a radial distribution function and a direct fitting of the graphene–Si interatomic pairwise potentials with force matching, to reconstruct the force fields in the materials. These studies lay the foundation for quantitative analysis of materials energetics from STEM data through the sampling of the metastable states in the chemical space of the system.

42 ENGINEERING↗