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At least 235 records · Page 13

Segmentation Model Distillation [Poster]

The process of training object detection (OD) or image segmentation model requires both a substantial amount of data and technical knowledge, which often creates challenges in applying these types of models to their full potential. In order to streamline the process of developing these models, we propose a new pipeline where a foundation model assists in the dataset generation. Then this resulting dataset is used to fine-tune a fast light-weight model to perform the custom segmentation or OD. This resulting model is also fit for real-time image segmentation, such as in a video stream.

97 MATHEMATICS AND COMPUTING↗

Correlating energy density induced residual stress, porosity, and mechanical property variations in directed energy deposition using neutron diffraction and imaging techniques

In a directed energy deposition (DED) process, the energy density deposited into the materials drives the structure and properties. The energy density is influenced by several printing parameters, such as laser power, hatch spacing, scanning speed, etc. In this study, 316L stainless steels samples were fabricated with varying hatch spacing aiming to induce variations in sample microstructure and properties. A combination of techniques including engineering neutron diffraction, neutron computed tomography, and tensile testing, were employed to correlate the structure and macroscopic properties. Porosity was predominantly observed at the bottom of the deposited materials and was effectively reduced by decreased hatch spacing. Correlatively, compressive residual stress was observed at the bottom of the specimens, while internal stress is largely determined by the hatch spacing. The residual stress in general decreases as the hatch spacing decreases. The maximum ultimate tensile strength (UTS) was found to increase from 517.4 to 528.6 MPa with a strain increased from 0.847 to 0.897 as the hatch spacing decreased from 0.45 to 0.42 mm. However, further increase in energy density by reducing the hatch spacing resulted in a significant decrease in UTS (as low as 452 MPa). This work provides new insights from bulk non-destructive techniques into correlating energy density induced residual stress, porosity, and mechanical property variations in directed energy deposition.

316L stainless steel↗

Improving 3D reconstruction quality for root phenotyping: assessing the impact of camera calibration and imaging parameters

Arate 3D reconstruction is essential for high-throughput plant phenotyping, particularly for studying complex structures such as root systems. While photogrammetry and Structure from Motion (SfM) techniques have become widely used for 3D root imaging, the camera settings used are often underreported in studies, and the impact of camera calibration on model accuracyccu remains largely underexplored in plant science. In this study, we systematically evaluate the effects of focus, aperture, exposure time, and gain settings on the quality of 3D root models made with a multi-camera scanning system. We show through a series of experiments that calibration significantly improves model quality, with focus misalignment and shallow depth of field (DoF) being the most important factors affecting reconstruction accuracy. Our results further show that proper calibration has a greater effect on reducing noise than filtering it during post-processing, emphasizing the importance of optimizing image acquisition rather than relying solely on computational corrections. This work improves the repeatability and accuracy of 3D root imaging for phenotyping pipelines by giving useful calibration guidelines. This leads to better trait quantification for use in crop research and plant breeding in downstream analysis.

3D reconstruction↗

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↗

Grain2mesh: A Python and cubit mesh generator from unprocessed mesoscale images

Predicting bulk behavior from microscale features constitutes a key objective in multiscale modeling research, often involving numerical models composed of finite elements that capture the diversity of constituent phases, shapes, and orientations within the material. The Grain2mesh toolbox allows the user to input unprocessed mesoscopic images for automatic segmentation, pre-processing, quality control, and numerical mesh generation. The numerical mesh generation incorporates Cubit routines to generate robust multi-phase mesh structure for use in computational mechanics solvers. The python classes developed contain detailed documentation and examples to support standard usage and case-specific alternative options.

58 GEOSCIENCES↗

Imaging and Segmenting Grains and Subgrains Using Backscattered Electron Techniques

We present two new methods of processing data from backscattered electron signals in a scanning electron microscope to image grains and subgrains. The first combines data from multiple backscattered electron images acquired at different specimen geometries to (1) better reveal grain boundaries in recrystallized microstructures and (2) distinguish between recrystallized and unrecrystallized regions in partially recrystallized microstructures. The second utilizes spherical harmonic transform indexing of electron backscatter diffraction patterns to produce high angular resolution orientation data that enable the characterization of subgrains. Subgrains are produced during high-temperature plastic deformation and have boundary misorientation angles ranging from a few degrees down to a few hundredths of a degree. Here, we also present an algorithm to automatically segment grains from combined backscattered electron image data or grains and subgrains from high angular resolution electron backscatter diffraction data. Together, these new techniques enable rapid measurements of individual grains and subgrains from large populations.

36 MATERIALS SCIENCE↗

Chemical Imaging of Atmospheric Biomass Burning Particles from North American Wildfires

The effects of biomass burning aerosols (BBA) on radiative forcing and cloud formation depend on chemical composition and the internal structures of individual particles within smoke plumes. To improve our understanding of the chemical and physical properties of BBA emitted at different times of the day and their evolution during atmospheric aging, we conducted a study as a part of the Fire Influence on Regional to Global Environments and Air Quality field campaign. Particle samples were collected onboard a research aircraft from smoke plumes from a wildfire in eastern Oregon during late afternoon and nighttime flights on August 28, 2019. A time-resolved aerosol collector was used to collect samples on substrates for offline spectromicroscopic imaging to investigate the single-particle characteristics of BBA particles. Approximately 20,400 individual particles from 10 selected samples were analyzed using computer-controlled scanning electron microscopy coupled with energy-dispersive X-ray microanalysis, revealing their elemental composition, morphology, and viscosity. Elemental microanalysis indicated that aged potassium is likely found in the form of K 2 SO 4 , KNO 3 , and possible K-organic salts. Further chemical speciation and carbon bonding mapping within individual particles were conducted using synchrotron-based scanning transmission X-ray microscopy (STXM) coupled with near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Real-time, water-soluble light absorption measurements were acquired using a particle-into-liquid sampler instrument coupled to a liquid waveguide capillary cell and total organic analyzer. In the late afternoon samples, 65% of the total particle number population consisted entirely of organic components, compared to 46% in the nighttime particles. These differences were attributed to discrepancies in composition at the time of emission and to the daytime condensation and accumulation of photochemically formed secondary organic material on existing BBA particles, a process that halts at night. Microscopy images indicated that particle viscosity was lower in the nighttime particles (<10 1 Pa·s), likely due to increased relative humidity and a higher contribution from hygroscopic inorganic components. The chemical heterogeneity of individual particles was quantified using STXM-derived mixing state parameters. The nature of carbon bonding within individual particles was inferred from the extent of carbon sp 2 hybridization derived from NEXAFS spectra. Average percentages of sp 2 hybridization range between 40% and 60%, with no noticeable differences between late afternoon and nighttime flights. These findings were compared with the online optical properties of both late afternoon and nighttime smoke plumes, providing valuable insights into the complex relationship between chemical composition and optical properties of BBA particles at different times of the day.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Precipitation of gadolinium from magnetic resonance imaging contrast agents may be the Brass tacks of toxicity

The formation of gadolinium-rich nanoparticles in multiple tissues from intravenous magnetic resonance imaging contrast agents may be the initial step in rare earth metallosis. The mechanism of gadolinium-induced diseases is poorly understood, as is how these characteristic nanoparticles are formed. Gadolinium deposition has been observed with all magnetic resonance imaging contrast agent brands. Aside from endogenous metals and acidic conditions, little attention has been paid to the role of the biological milieu in the degradation of magnetic resonance imaging contrast agents into nanoparticles. Herein, we describe the decomposition of the commercial magnetic resonance imaging contrast agents Omniscan and Dotarem in the presence of oxalic acid, a well-known endogenous compound. Omniscan dechelated rapidly and preluded measurement by the means available, while Dotarem underwent a two-step decomposition process. The decomposition of both magnetic resonance imaging contrast agents by oxalic acid formed gadolinium oxalate (Gd 2 [C 2 O 4 ] 3 , Gd 2 Ox 3 ). Furthermore, both observed steps of the Dotarem reaction involved the associative addition of oxalic acid. Adding protein (bovine serum albumin) increased the rate of dechelation. Displacement reactions could occur at lysosomal pH. Through these studies, we have demonstrated that magnetic resonance imaging contrast agents can be dissociated by endogenous molecules, thus illustrating a metric by which gadolinium-based contrast agents (GBCAs) might be destabilized in vivo.

Gadodiamide↗

TomoPyUI : a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data ( i.e. organizing data/metadata, applying image filters etc. ) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI , a user interface for the well known tomography data processing package TomoPy . This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI , along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI , and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Rotational Millimeter-Wave Shoe Scanner Using the Discrete Fourier Transform for Backprojection-Based Image Reconstruction

An active 3D microwave / millimeter-wave shoe scanner was previously developed at the Pacific Northwest National Laboratory (PNNL) using two linear arrays scanned over a rectilinear aperture. The radar system chirps a frequency sweep from 10-40 GHz. These frequencies allow imaging through optically opaque material such as leather, rubber, plastics, and other dielectrics. The system was designed to detect concealed items in the soles of shoes while allowing people to leave their shoes on through a security checkpoint. To shrink the footprint of the system, a new iteration of the design has been developed that scans the two linear arrays over a circular aperture. This new footprint opens the possibility of it being installed in the floor of a cylindrical millimeter-wave body scanner. The backprojection-based multilayer dielectric image reconstruction developed at PNNL can easily handle arbitrary spatial sampling, accommodating the new rotational shoe scanner design. Commonly, the fast Fourier transform (FFT) is used to efficiently compute the range response from the data collected by the system as a preprocessing step to the backprojection algorithm. It was found that converting to range using the discrete Fourier transform (DFT) directly has some advantages over the FFT. For example, nonlinear and non-uniform frequency sweeps can easily be compensated for during the computation of the DFT and only the range bins of interest need to be computed and their spacing can be chosen arbitrarily. Because the range conversion step of the image reconstruction is the fastest part of the process there is very little speed penalty for using the DFT over the FFT and it can even increase the speed of image reconstruction when the ranges of interest are fewer than the total span that is calculated in the FFT.

Millimeter-wave imaging, microwave imaging, shoe s↗

Broadband unidirectional visible imaging using wafer-scale nano-fabrication of multi-layer diffractive optical processors

We present a broadband and polarization-insensitive unidirectional imager that operates at the visible part of the spectrum, where image formation occurs in one direction, while in the opposite direction, it is blocked. This approach is enabled by deep learning-driven diffractive optical design with wafer-scale nano-fabrication using high-purity fused silica to ensure optical transparency and thermal stability. Our design achieves unidirectional imaging across three visible wavelengths (covering red, green, and blue parts of the spectrum), and we experimentally validated this broadband unidirectional imager by creating high-fidelity images in the forward direction and generating weak, distorted output patterns in the backward direction, in alignment with our numerical simulations. This work demonstrates wafer-scale production of diffractive optical processors, featuring 16 levels of nanoscale phase features distributed across two axially aligned diffractive layers for visible unidirectional imaging. This approach facilitates mass-scale production of ~0.5 billion nanoscale phase features per wafer, supporting high-throughput manufacturing of hundreds to thousands of multi-layer diffractive processors suitable for large apertures and parallel processing of multiple tasks. Beyond broadband unidirectional imaging in the visible spectrum, this study establishes a pathway for artificial-intelligence-enabled diffractive optics with versatile applications, signaling a new era in optical device functionality with industrial-level, massively scalable fabrication.

36 MATERIALS SCIENCE↗

Concept Lens: Visual Comparison and Evaluation of Generative Model Manipulations

Generative models are becoming a transformative technology for the creation and editing of images. However, it remains challenging to harness these models for precise image manipulation. These challenges often manifest as inconsistency in the editing process, where both the type and amount of semantic change, depend on the image being manipulated. Moreover, there exist many methods for computing image manipulations, whose development is hindered by the matter of inconsistency. This paper aims to address these challenges by improving how we evaluate, compare, and explore the space of manipulations offered by a generative model. We present Concept Lens, a visual interface that is designed to aid users in understanding semantic concepts carried in image manipulations, and how these manipulations vary over generated images. Given the large space of possible images produced by a generative model, Concept Lens is designed to support the exploration of both generated images, and their manipulations, at multiple levels of detail. To this end, the layout of Concept Lens is informed by two hierarchies: a hierarchical organization of (1) original images, grouped by their similarities, and (2) image manipulations, where manipulations that induce similar changes are grouped together. This layout allows one to discover the types of images that consistently respond to a group of manipulations, and vice versa, manipulations that consistently respond to a group of codes. We show the benefits of this design across multiple use cases, specifically, studying the quality of manipulations for a single method, and offering a means of comparing different methods.

clustering↗

Shelf-life of ball-milled catalyst inks for the fabrication of fuel cell electrodes

A major factor driving fuel cell costs is the quantity of precious metal required. Therefore, it is important to understand a timeframe where inks can be reused. Here, in this work, we explore differences between a freshly prepared catalyst ink and one that has been stored for over a year – comparing ink properties, cathode catalyst layer microstructure, and their respective fuel cell performance. Ink studies revealed smaller agglomerate sizes and a decrease in shear viscosity for the aged ink. Longer storage time also results in fewer cracks and a more uniform ionomer distribution, as evidenced by microscopy characterization of rod-coated electrodes. Lastly, polarization curves show improved performance at higher current densities for the electrode prepared from the aged ink. We rationalize such effect in terms of enhanced ionomer adsorption onto the catalyst over time.

08 HYDROGEN↗

Gain characterization of LGAD sensors with beta particles and 28-MeV protons

Low Gain Avalanche Diodes, also known as LGADs, are widely considered for fast-timing applications in high energy physics, nuclear physics, space science, medical imaging, and precision measurements of rare processes. Such devices are silicon-based and feature an intrinsic gain due to a p + -doped layer that allows the production of a controlled avalanche of carriers, with multiplication on the order of 10–100. This technology can provide time resolution on the order of 20–30 ps, and variants of this technology can provide precision tracking too. The characterization of LGAD performance has so far primarily been focused on the interaction of minimum ionizing particles for high energy and nuclear physics applications. This article expands the study of LGAD performance to highly-ionizing particles, such as 28-MeV protons, which are relevant for several future scientific applications, e.g. in biology and medical physics, among others. These studies were performed with a beam of 28-MeV protons from a tandem Van de Graaff accelerator at Brookhaven National Laboratory and beta particles from a ^90Sr source; these were used to characterize the response and the gain of an LGAD as a function of bias voltage and collected charge. Here, the experimental results are also compared to TCAD simulations.

47 OTHER INSTRUMENTATION↗

Jupyter notebooks for analyzing transmission SAXS/WAXS from beamline 7.3.3 during operando membrane fouling experiments v1.0

This software consists of python-based Jupyter Notebooks for processing transmission x-ray scattering images collected at beamline 7.3.3 at the Advanced Light Source. The measurements considered in these analyses are collected during membrane fouling experiments, where contaminants in the water deposit on/attach to the membrane surface. This software is used to elucidate the mechanisms of membrane fouling that occur during these operando membrane fouling experiments, but the analyses provided in these scripts can be extended to other scientific cases.

Landsman, Matthew [Lawrence Berkeley National Labo↗

PRISMA: PARALLEL REFINEMENT AND INTEGRATION SYSTEM FOR MULTI-AZIMUTHAL ANALYSIS

The Parallel Refinement and Integration System for Multi-azimuthal Analysis (PRISMA, version 1.1.0) is a Python application for processing X-ray diffraction (XRD) image data. PRISMA wraps GSAS-II to perform azimuthally-binned peak refinement, computes per-frame strain and d-spacing from those fits, and provides three PyQt5 graphical interfaces: (1) a Recipe Builder for selecting GSAS-II control (.imctrl) files, optional mask (.immask) files or threshold-ased masking, reference and experiment image sets, peaks, zimuthal range and bin size, and an optional ceria-based auto-calibration; (2) a Batch Processor that uses Dask on local workstations and pure MPI (mpi4py.futures.MPICommExecutor) on HPC to distribute GSAS-II refinement across cores or compute nodes and write results to a 4-dimensional (peaks x frames x azimuths x measurements) Zarr dataset; and (3) a Data Analyzer that renders heatmaps of fit parameters, strain, frame-to-frame deltas, and percent-change-vs-reference, and exports user-defined subsections to CSV or Excel. The peak-refinement algorithm is deterministic. Benchmark on ALCF Crux: a 20,000-image set, single-peak fit in frame mode with 44 azimuthal bins on 128 nodes x 128 workers, 48 seconds total wall time.

Lorenzo Martin, Maria De La Cinta [Argonne Nationa↗

The Measurement of Grain Size by Electron Beam Backscattered Diffraction

The method of electron back-scatter diffraction provides an analytic means to identify crystalline phase and the grain size of structural materials. The need to utilize imaging parameters consistent with revealing the contributing microstructural scale is often overlooked through packaged imaging scripts. It is shown that imaging parameters consistent with a post processing assessment of low misorientation angles between boundaries are achievable as using pixel sizes on the order of 10 1 nm.

36 MATERIALS SCIENCE↗

EcoBOT: an AI/ML enabled automated phenotyping capability for model plants

Introduction: Advances in automation and AI/ML offer new opportunities for plant science, including design, modeling, and analysis. This study aimed to develop an automated platform for researching small model plants under axenic conditions and integrate it with AI/ML tools. Methods: The EcoBOT platform was developed, which consists of sterile containers (EcoFABs) for growing plants and imaging for monitoring plant growth and health. Brachypodium distachyon was grown on the EcoBOT, and its response to nutrient limitation and copper stress was evaluated. Results: The results showed that Brachypodium distachyon grown in the EcoBOT maintained sterility and responded to nutrient limitation and copper stress. Analysis of over 6,500 root and shoot images revealed varying sensitivity and response rates to copper. Bayesian Optimization was used to improve model accuracies relating copper concentrations to plant biomass via sequential experiments, resulting in a >30% improvement. Discussion: The findings of this study demonstrate the potential of the EcoBOT platform for researching plant responses to environmental factors. Future experiments could focus on relating other chemical stresses and microbial interactions to create generalized models of plant responses.

AI image analysis↗