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Results for “image and signal processing”

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DOE OSTI2020

Three-dimensional super line-localization in low signal-to-noise microscope images via prior-apprised unsupervised learning (PAUL)

Biological processes such as processive enzyme turnover and intracellular cargo tracking involve the dynamic motion of a small "article" along a curvilinear biopolymer track. To understand these processes that occur across multiple length and time scales, one must acquire both the trajectory of the particle and the position of the track along which it moves, possibly by combining high-resolution single-particle tracking with conventional microscopy. Yet, usually there is a significant resolution mismatch between these modalities: while the tracked particle is localized with a precision of 10 nm, the image of the surroundings is limited by optical difraction, with 200 nm lateral and 500 nm axial resolutions. Compared to the particle's trajectory, the surrounding curvilinear structure appears as a blurred and noisy image. This disparity in the spatial resolutions of the particle trajectory and the surrounding curvilinear structure image makes data reconstruction, as well as interpretation, particularly challenging. Analysis is further complicated when the curvilinear structures are oriented arbitrarily in 3D space. Here, we present a prior-apprised unsupervised learning (PAUL) approach to extract information from 3D images where the underlying features resemble a curved line such as a filament or microtubule. This three-stage framework starts with a Hessian-based feature enhancement, which is followed by feature registration, where local line segments are detected on repetitively sampled subimage tiles. In the final stage, statistical learning, segments are clustered based on their geometric relationships. Principal curves are then approximated from each segment group via statistical tools including principal component analysis, bootstrap and kernel transformation. This procedure is characterized on simulated images, where sub-voxel medium deviations from true curves have been achieved. The 3D PAUL approach has also been implemented for successful line localization in experimental 3D images of gold nanowires obtained using a multifocal microscope. Lastly, this work not only bridges the resolution gap between two microscopy modalities, but also allows us to conduct 3D super line-localization imaging experiments, without using super-resolution techniques.

42 ENGINEERING↗

DOE OSTI2023

Understanding Plant Signaling Via Innovations in Probe Delivery and Imaging

The goal of this project was to develop tools for studying plant processes in living tissues. We wanted a method for introducing probes for studying plant processes such that plants could remain intact and imaged iteratively. Towards this end, we successfully optimized carbon nanofibers that we showed could deliver non-permeable signaling probes/biomolecules to plant cells. These were created on a rigid backing and also successfully transferred to a flexible backing to use with curved plant structures. We also built fiber optic microscopes that permit iterative non-destructive fluorescence or light micrographs and created protocols and devices to stabilize plant organs during imaging. These tools were developed in conjunction with research aimed understanding receptor-mediated peptide trafficking and responses relevant to plant cell growth and defense tradeoff. During this project, we designed and built two fiberoptic fluorescence microscopes; (b) designed, fabricated and validated different nanospike designs for delivering probes to plants, including the feasibility of delivering DNA constructs for expression studies; (c) developed fluorescent peptide probes (active and inactive versions of a secreted receptor ligand called phytosulfokine or PSK) and performed mobility tests after application to plants using microscopy; (d) used appropriate genetic plant backgrounds to facilitate PSK trafficking and response mechanisms; (e) determined the transcriptional changes due to PSK-induced signaling related to growth/defense tradeoff; (f) performed experiments showing the growth/defense tradeoff involves repression of specific defense components in response to PSK. This project also involved the training of two PhD students and five Masters students.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Characterization of a 1D-imaging high-energy x-ray backlighter driven by the National Ignition Facility Advanced Radiographic Capability laser

Plastic deformation of samples compressed to Mbar pressures at high strain rates at the National Ignition Facility (NIF) forms the basis of ongoing material strength experiments in conditions relevant to meteor impacts, geophysics, armor development, and inertial confinement fusion. Hard x-ray radiography is the primary means of measuring the evolution of these samples, typically employing a slit-collimated high-Z microdot driven by the NIF laser to generate >40 keV x rays [E. Gumbrell et al., Rev. Sci. Instrum. 89, 10G118 (2018) and C. M. Huntington et al., Rev. Sci. Instrum. 89, 10G121 (2018)]. Alternatively, a dysprosium “micro-flag” target driven by the Advanced Radiographic Capability laser (~2 kJ, 10 ps) can deliver significantly higher spatiotemporal resolution [M. P. Hill et al., Rev. Sci. Instrum. 92, 033535 (2021)], especially in high-opacity samples. Here, initial experiments revealed problematic brightness and spectral gradients from this source, but by radiographing a set of diamond-turned, 105 µm-thick Pb test objects and supported by simulations using the 3D Monte Carlo code GEANT4, these geometry-dependent gradients across the field of view are quantified and mitigation strategies are assessed. In addition to significantly enhancing the modulation transfer function compared to the existing system, image stacking from multiple layers of image plate is shown to almost double the signal to noise ratio that will reduce uncertainties in future dynamic strength experiments.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Analysis and mitigation of an oscillating background on hybrid complementary metal-oxide semiconductor (hCMOS) imaging sensors at the National Ignition Facility

Nanosecond-gated hybrid complementary metal-oxide semiconductor imaging sensors are a powerful tool for temporally gated and spatially resolved measurements in high energy density science, including inertial confinement fusion, and in laser diagnostics. However, a significant oscillating background excited by photocurrent has been observed in image sequences during testing and in experiments at the National Ignition Facility (NIF). Characterization measurements and simulation results are used to explain the oscillations as the convolution of the pixel-level sensor response with a sensor-wide RLC circuit ringing. Finally, data correction techniques are discussed for NIF diagnostics, and for diagnostics where these techniques cannot be used, a proof-of-principle image correction algorithm is presented.

42 ENGINEERING↗

DOE OSTI2022

Spiking retina microscope

A spiking retina microscope comprising microscope optics and a neuromorphic imaging sensor. The microscope optics are configured to direct a magnified image of a specimen onto the neuromorphic imaging sensor. The neuromorphic imaging sensor comprises a plurality of sensor elements that are configured to generate spike signals in response to integrated light from the magnified image reaching a threshold. The spike signals may be processed by a processor unit to generate a result, such as tracking biological particles in a specimen comprising biological material.

Severa, William Mark↗

DOE OSTI2021

Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching

An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.

3D imaging↗

DOE OSTI2021

Removal of spurious data in Bragg coherent diffraction imaging: an algorithm for automated data preprocessing

Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution structural information from nanocrystalline materials. Here a BCDI sample consisting of a large number of randomly oriented nanoscale crystals is considered. Ideally, only one crystal is oriented to produce a Bragg peak on the detector. However, diffraction from other crystals often produces additional signals on the detector. Before the measured diffraction patterns can be processed into structural images, scientists routinely need to manually identify and remove the `alien' intensities from sources other than the intended crystal. With the development of modern high-coherence storage rings, such as the upgraded Advanced Photon Source (APS), the already slow process of manual preprocessing will be untenable for the large volumes of data that will be produced. An automated method of identifying and deleting alien intensities is proposed. This method exploits the fact that BCDI of a perfect crystal produces diffraction data with inversion symmetry around the Bragg peak. This approach uses the machine learning clustering method DBSCAN to distinguish between diffraction from multiple sources, and then calculates cluster size and inversion symmetry to assess whether clusters of intensity belong to desired data or alien signals. This approach can dramatically reduce the amount of time spent manually processing data, allowing BCDI data processing capabilities to keep pace with the technological advances of fourth-generation synchrotron light sources.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Deep learning-driven super-resolution in Raman hyperspectral imaging: Efficient high-resolution reconstruction from low-resolution data

Deep learning (DL) has become an indispensable tool in hyperspectral data analysis, automatically extracting valuable features from complex, high-dimensional datasets. Super-resolution reconstruction, an essential aspect of hyperspectral data, involves enhancing spatial resolution, particularly relevant to low-resolution hyperspectral data. Yet, the pursuit of super-resolution in hyperspectral analysis is fraught with challenges, including acquiring ground truth high-resolution data for training, generalization, and scalability. The pressing issue of extended spectral acquisition times, notably for high-resolution scans, is a significant roadblock in hyperspectral imaging. Super-resolution methods offer a promising solution by providing higher spatial resolution data to expedite data collection and yield more efficient outcomes. This paper delves into a practical application of these concepts using Raman imaging, where spectral acquisition times can be prohibitively long. In this context, DL-based super-resolution models demonstrate their efficacy by predicting and reconstructing high-resolution Raman data from low-resolution input, eliminating the need for resource-intensive high-resolution scans. While previous work often relied on substantial high-resolution datasets, this study showcases the ability to achieve similar outcomes even with limited data, presenting a more practical and cost-effective approach. In conclusion, the results offer a glimpse into the transformative potential of this technology to streamline hyperspectral imaging applications by saving valuable time and resources through the successful generation of high-resolution data from low-resolution inputs.

42 ENGINEERING↗

DOE OSTI2020

Above-threshold multiphoton photoemission from noble metal surfaces

Exciting solids with intense femtosecond laser pulses prompts electrons of the interrogated material to respond in a highly nonlinear manner, as is evident in the emission of high-order harmonic radiation and photoelectrons with kinetic energies well above that of the driving photons. Such high-field interactions can be resolved, for example, in above-threshold multiphoton photoemission (ATP) spectroscopy. In this work, we interrogate the nonlinear photoelectric responses of the pristine copper, silver, and gold noble metal surfaces in (111) and (100) crystal orientations in the perturbative regime. Using multiphoton photoemission spectroscopy (mPP) excited by finely tuned optical fields, we characterize enhancement of the mPP and ATP yields from (111) surfaces in selected k||-momentum ranges when the occupied Shockley surface (SS) states are (near-)resonantly coupled by multiphoton transitions to image potential (IP) intermediate states in the excitation process. The ATP signal from the IP states of (111) surfaces is largely defined by their formation through polarization of SS electrons; this observation is contrasted with ATP experiments from the Ag(100) surface, for which the SS becomes an unoccupied resonance and the IP states can only be excited from bands with significantly more bulk character. In addition, based on the optical power and nonlinear order-dependent mPP spectra, we provide evidence for ATP being a one-step, rather than a sequential process, as previously postulated.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Apparatus and method for visualization of particles suspended in a fluid and fluid flow patterns using ultrasound

An apparatus and method for real-time visualization of particulate matter suspended in a static or flowing fluid and fluid flow patterns in a pipe, tube, conduit, or other container, are described. Ultrasonic scanning and detection of scattered sound from the particles in the fluid create a real-time image of the particles, or of flow patterns in the liquid. A mechanical wobbler directs a piezoelectric transducer over a chosen angle in an oscillatory manner. The transducer is operated in a pulse-echo mode wherein the same transducer detects the return signal from the target region through which particles are passing and/or a flow is present. The pulse-echo measurements are made rapidly and continuously during a single sweep of the transducer over the chosen angle. Received signals are processed in the ultrasound scanner electronics module and displayed as an image in real-time.

42 ENGINEERING↗

DOE OSTI2025

FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images

The extracellular matrix (ECM) is a complex network of biomolecules that plays an integral role in the structure, processes, and signaling mechanisms of cells and tissues. Identifying and quantifying changes in these matrix components provides insight into the mechanisms behind specific tissue remodeling processes; however, quantifying these changes is challenging due to difficult imaging conditions, complexity of the ECM, and the subtlety of these changes. Current imaging techniques allow us to visualize these critical remodeling events and developments in image analysis have employed a combination of analysis software and machine learning techniques to improve the efficiency and accuracy with which features are measured. Although image analysis has seen much improvement in recent years, there has been no technique developed to address ambiguity in feature edges in electron microscopy images. Presented here is a new machine learning-based workflow for the analysis of microscopy images named FIRM (Feature Identification from Raw Microscopy) that uses a random forest classifier to identify ECM features of interest and generate binary segmentation masks for quantification with ImageJ-FIJI. FIRM performed with an F1 score of 0.794 and greater than 80% accuracy for number and size of features detected. FIRM had similar deviation from the ground truth in the number of identified fibrils, fibril size, and size distributions when compared to human analyses. The results suggest that FIRM performs as well as manual analysis and requires a fraction of the time. This analysis technique is more efficient, eliminates user bias, and can be easily optimized to identify a variety of features, making it useful for any discipline requiring image analysis.

Science & Technology - Other Topics↗

DOE OSTI2025

Distinguishing isotropic and anisotropic signals for X-ray total scattering using machine learning

Understanding structure–property relationships is essential for advancing technologies based on thin films. X-ray pair distribution function (PDF) analysis can access relevant atomic structure details spanning local-, mid- and long-range structure. While X-ray PDF has been adapted for thin films on amorphous substrates, measurements on single-crystal substrates are necessary to accurately determine structure origins for some thin film materials, especially those for which the substrate changes the accessible structure and properties. However, when measuring films on single-crystal substrates, high-intensity anisotropic Bragg spots saturate 2D detector images, overshadowing the thin films' isotropic scattering signal. This renders previous data processing methods for films on amorphous substrates unsuitable for films on single-crystal substrates. To address this measurement need, we developed IsoDAT2D, an innovative data processing approach using unsupervised machine learning algorithms. The program combines dimensionality reduction and clustering algorithms to separate thin film and single-crystal substrate X-ray scattering signals. We use SimDAT2D , a program we developed to generate simulated thin film data, to validate IsoDAT2D . Here we also use IsoDAT2D to isolate X-ray total scattering signal from a thin film on a single-crystal substrate. The resulting PDF data are compared with similar data processed using previous methods, especially substrate subtraction for single-crystal and amorphous substrates. PDF data from IsoDAT2D -identified X-ray total scattering data are significantly better than from single-crystal substrate subtraction, but not as reliable as PDF data from amorphous substrate subtraction. With IsoDAT2D , there are new opportunities to expand PDF to a wider variety of thin films, including those on single-crystal substrates, with which new structure–property relationships can be elucidated to enable fundamental understanding and technological advances.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Using cloud radar to investigate the effect of rainfall on migratory insect flight

The fate of migrating insects that encounter rainfall in flight is a critical consideration when modelling insect movement, but few field observations of this common phenomenon have ever been collected due to the logistical challenges of witnessing these encounters. Operational cloud radars have been deployed around the world by meteorological agencies to study precipitation physics, and as a byproduct, provide a rich database of insect observations that is freely available to researchers. Although considered unwanted ‘clutter’ by the meteorologists who collect the data, the analysis method presented here enables ecologists to delineate co-occurring signals from insects and raindrops. We present a method that uses image processing techniques on cloud radar velocity spectra to examine the fate of migrating insects when they encounter precipitation. By analysing velocity spectra, we can distinguish flying insects from falling rain and compare the relative density of insects in flight before, during and after the rainfall. We demonstrate the method on a case of insect migration in Oklahoma, USA. Using this method, we show the first reconstructed images of migrating insect layers in flight during rainfall. Our analysis shows that mild to moderate rainfall diminishes the number of insects aloft but does not cause full termination of migratory flight, as has previously been suggested. We hope this technique will spur further investigations of how changing weather conditions impact insect migration, and enable some of the first of such studies in regions of the world that are underrepresented in the literature.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Mitigating Shear-dependent Object Detection Biases with Metacalibration

M ETACALIBRATION is a new technique for measuring weak gravitational lensing shear that is unbiased for isolated galaxy images. Here we test M ETACALIBRATION with overlapping, or "blended" galaxy images. Using standard M ETACALIBRATION , we find a few percent shear measurement bias for galaxy densities relevant for current surveys, and that this bias increases with increasing galaxy number density. We show that this bias is not due to blending itself, but rather to shear-dependent object detection. If object detection is shear-independent, no deblending of images is needed, in principle. We demonstrate that detection biases are accurately removed when including object detection in the M ETACALIBRATION process, a technique we call M ETADETECTION . This process involves applying an artificial shear to images of small regions of sky and performing detection on the sheared images, as well as measurements that are used to calculate a shear response. We demonstrate that the method can accurately recover weak shear signals even in highly blended scenes. In the M ETACALIBRATION process, the space between objects is sheared coherently, which does not perfectly match the real universe in which some, but not all, galaxy images are sheared coherently. We find that even for the worst case scenario, in which the space between objects is completely unsheared, the resulting shear bias is at most a few tenths of a percent for future surveys. We discuss additional technical challenges that must be met in order to implement M ETADETECTION for real surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Particle velocity measurement within a free-falling particle curtain using microscopic shadow velocimetry

We report an optical method for particle velocity measurement that is suitable for the measurement of particle velocities within dense particle-laden flows with high spatial resolution. The technique is based on particle shadow velocimetry with the use of a long-distance microscopic lens for images collection. The narrow depth of field of the lens allows particles within the focal plane to have much higher pattern intensities than those outside it on the collected images. Data processing was then employed to remove particles from outside the focal plane based on the gradient of the signal and a threshold. Following this, particle velocity was calculated from two successive images in the usual way. The technique was successfully demonstrated in a free-falling particle curtain with volume fractions in the four-way coupling regime of near-spherical micro-particles falling under gravity. The method was successfully employed to measure the transverse velocity profile through the curtain, which is the first time that such a measurement has been performed. Other highly-fidelity experimental data, which is also well suited to model development and validation, include the particle mass flow rate, curtain thickness and opacity.

Han, Shipu (ORCID:0000000278545882)↗

DOE OSTI2022

Detecting the Presence of Intrusive Drilling in Secure Transport Containers Using Non-Contact Millimeter-Wave Radar

We employ a 77–81 GHz frequency-modulated continuous-wave (FMCW) millimeter-wave radar to sense anomalous vibrations during vehicle transport at highway speeds for the first time. Secure metallic containers can be breached during transport by means of drilling into their sidewalls but detecting a drilling signature is difficult because the large vibrations of transport drown out the small vibrations of drilling. For the first time, we demonstrate that it is possible to use a non-contact millimeter-wave radar sensor to detect this micron-scale intrusive drilling while highway-speed vehicle movement shakes the container. With the millimeter-wave radar monitoring the microdoppler signature of the container’s vibrating walls, we create a novel signal-processing pipeline consisting of range–angle tracking, time–frequency analysis, horizontal stripe image convolution, and principal component analysis to create a robust and powerful detection statistic to alarm if drilling is present. To support this pipeline, we develop a statistical model combining the vibrating container and the random vibrations induced by vehicle movement to explore the robustness of the sensor’s detection capabilities. The presented results strongly support the inclusion of a millimeter-wave radar vibration sensor into a transport security system.

Wagner, Samuel↗

DOE OSTI2024

Direct mechanistic connection between acoustic signals and melt pool morphology during laser powder bed fusion

Various nondestructive diagnostic techniques have been proposed for in situ process monitoring of laser powder bed fusion (LPBF), including melt pool pyrometry, whole-layer optical imaging, acoustic emission, atomic emission spectroscopy, high speed melt pool imaging, and thermionic emission. Correlations between these in situ monitoring signals and defect formation have been demonstrated with acoustic signals having been shown to predict pore formation with especially high confidence in recent machine learning studies. Here, in this work, time-resolved acoustic data are collected in both the conduction and keyhole welding regimes of LPBF-processed Ti-6Al-4V alloy. A non-dimensionalized Strouhal number analysis, used in whistle aeroacoustics, is applied to demonstrate that the acoustic signals recorded in the keyhole regimes can be directly associated with the vapor depression morphology. This mechanistic understanding developed from whistle aeroacoustics shows that acoustic monitoring during the LPBF process can provide a direct probe into the vapor depression dynamics and defect occurrence, especially in the keyhole regimes relevant to printing and defect formation.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A three-point velocity estimation method for two-dimensional coarse-grained imaging data

Time delay and velocity estimation methods have been widely studied subjects in the context of signal processing, with applications in many different fields of physics. The velocity of waves or coherent fluctuation structures is commonly estimated as the distance between two measurement points divided by the time lag that maximizes the cross correlation function between the measured signals, but this is demonstrated to result in erroneous estimates for two spatial dimensions. We present an improved method to accurately estimate both components of the velocity vector, relying on three non-aligned measurement points. We introduce a stochastic process describing the fluctuations as a superposition of uncorrelated pulses moving in two dimensions. Using this model, we show that the three-point velocity estimation method, using time delays calculated through cross correlations, yields the exact velocity components when all pulses have the same velocity. The two- and three-point methods are tested on synthetic data generated from realizations of such processes for which the underlying velocity components are known. The results reveal the superiority of the three-point technique. Finally, we demonstrate the applicability of the velocity estimation on gas puff imaging data of strongly intermittent plasma fluctuations due to the radial motion of coherent, blob-like structures at the boundary of the Alcator C-Mod tokamak.

Materials Science↗