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Dataset for Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

This repository hosts an AI-assisted image segmentation and analysis pipeline for Pantoea sp. YR343 cryo-electron microscopy (cryoEM) datasets. The workflow automates membrane thickness measurements, flagella detection, and field-of-view (FOV) screening from low-dose, high-resolution cryoEM micrographs eliminating the need for slow manual annotation. By integrating deep-learning based segmentation (YOLOv11) with quantitative post-processing, this toolkit provides a scalable and reproducible way to study bacterial morphology under hydrated, near-native conditions. The GitHub repository for AI-based tools for cryoEM bacteria ultrastructures can be found here: https://github.com/Sireesiru/Cryo-EM-Ultrastructures/tree/main

60 APPLIED LIFE SCIENCES

Thermal images collected during 3D printing with Cincinnati BAAM

This data set contains images produced to test the performance of anomaly and fault detection methods in the context of additive manufacturing. A total of 10 print jobs were executed using a Cincinnati BAAM (model 606) with a Cincinnati medium compression screw. The material used was compounded polylactic acid (PLA) with wood flour as a filler produced by Jabil (80% NatureWorks Ingeo 6060D amorphous PLA, % 100 mesh pine flour from American Wood Fiber). Print sheets were 1/4in polycarbonate.

36 MATERIALS SCIENCE

Dataset for Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM

Motivation Multiple deep learning model architectures can be used to segment bacterial membranes in cryoEM images. However, an AI-based tool advancement is often presented with only a single segmentation model for broad use, and this single model may show inconsistent results across datasets from different users. Here, we present the Top Model Decision Tree, a model screening framework to screen for the best model to generate bacterial inner and outer membrane masks based on user priorities. We use pre-trained segmentation models from YOLOv11, YOLO26, U-Net, Detectron2 and SAM3 fine-tuned on bacterial inner and outer membranes imaged with cryoEM. Run the Framework This notebook must be opened in Google Colab. Mount Google Drive and run with a GPU-based runtime. Open the notebook and follow steps to git clone in folders and files within this repository. There will be a repeating top_model_decision_tree.ipynb (notebook clone) that will not be used. Save your .png binary mask files and .csv table outputs within your Google Drive or download before closing the notebook. The models and all analysis/training scripts are available at [GitHub: https://github.com/Lynnicia/CryoEM_membranes_top_model_decision_tree and https://github.com/Sireesiru/Semantic-Segmentation-of-bacterial-cell-envelope-using-U-Nets.

59 BASIC BIOLOGICAL SCIENCES

From Chaos to Clarity: Autonomous Materials Discovery for Extreme Environments [Slides]

The pursuit of advanced functional materials for energy applications demands an understanding of their behavior under the most challenging conditions. Extreme environments, characterized by intense radiation, high temperatures, and corrosive chemistries, push materials to their limits, often revealing unexpected behaviors and degradation pathways. Traditional materials research approaches, relying on trial-and-error experimentation, are often slow and resource-intensive, ill-suited to the complexities of extreme environments. This talk will explore the transformative potential of autonomous materials science in revolutionizing our understanding of materials synthesis and degradation in extreme environments. By integrating advanced microscopy techniques, artificial intelligence, and robotic experimentation, we can accelerate the discovery and design of resilient materials for a sustainable future. The presentation will highlight recent breakthroughs in autonomous microscopy, computer vision, and machine learning, showcasing their ability to unravel complex material transformations at the atomic scale. The talk will also delve into the challenges and opportunities associated with deploying autonomous systems to probe extreme environments, emphasizing the importance of robust algorithms, real-time data analysis, and adaptive experimentation. The ultimate goal is to empower scientists with unprecedented capabilities to explore, understand, and engineer materials that can withstand the harshest conditions, paving the way for innovations in energy, aerospace, and beyond.

14 SOLAR ENERGY

Unveiling the Hidden Evolution of Crystal Defects and Disorder in Energy Materials

Control of point defects and disorder in functional thin films and 2D materials is critical to realizing their full potential in applications ranging from energy storage to advanced electronics. However, these phenomena are often poorly understood, difficult to characterize, and challenging to direct with precision. This presentation explores emerging multi-modal computer vision to decipher and predict order in materials across multiple length scales in the electron microscope, from the atomic to the nanoscale. By fusing data from diverse sources, these powerful models provide unprecedented insights into materials' lifecycles, enabling the control of defects and their associated properties at a fundamental level. This capability promises to transform materials design and accelerate the development of next-generation technologies.

97 MATHEMATICS AND COMPUTING

AI-Driven Accelerated Inclusion Analysis for Energy Efficient Steelmaking (Final CRADA Report)

This was a collaborative effort between Lawrence Livermore National Security, LLC (LLNS) as manager and operator of Lawrence Livermore National Laboratory (LLNL) and ArcelorMittal USA Research LLC (“ArcelorMittal” as the Participant), to use scanning electron microscopy (SEM) images, computer vision and machine learning methods, and high-performance computing to accelerate the inclusion analysis process of liquid steel so that new methods can be used for near-real time process control on the shop floor.

36 MATERIALS SCIENCE

From Chaos to Clarity: Autonomous Materials Discovery for Extreme Environments

The pursuit of advanced functional materials for energy applications demands an understanding of their behavior under the most challenging conditions. Extreme environments, characterized by intense radiation, high temperatures, and corrosive chemistries, push materials to their limits, often revealing unexpected behaviors and degradation pathways. Traditional materials research approaches, relying on trial-and-error experimentation, are often slow and resource-intensive, ill-suited to the complexities of extreme environments. This talk will explore the transformative potential of autonomous materials science in revolutionizing our understanding of materials synthesis and degradation in extreme environments. By integrating advanced microscopy techniques, artificial intelligence, and robotic experimentation, we can accelerate the discovery and design of resilient materials for a sustainable future. The presentation will highlight recent breakthroughs in autonomous microscopy, computer vision, and machine learning, showcasing their ability to unravel complex material transformations at the atomic scale. The talk will also delve into the challenges and opportunities associated with deploying autonomous systems to probe extreme environments, emphasizing the importance of robust algorithms, real-time data analysis, and adaptive experimentation. Our ultimate goal is to empower scientists with unprecedented capabilities to explore, understand, and engineer materials that can withstand the harshest conditions, paving the way for innovations in energy, aerospace, and beyond.

artificial intelligence

Automated Waterbox Inspection for Nuclear Power Plants Using Computer Vision - Based Change Detection

Nuclear power plant waterboxes require regular inspection for leaks, missing components, and structural damage during maintenance outages. Traditional manual inspection is time-consuming and poses safety risks from confined space entry. We developed an automated computer vision system for drone-based waterbox inspection in partnership with Florida Light and Power. Our approach uses feature detection and matching to identify critical changes between baseline and current inspection images, automatically flagging additions (leaks/debris), removals (missing plugs), and translations (displaced components) while compensating for drone movement and environmental variations. We systematically evaluated six feature matching methods, from classical approaches (SIFT+BF) to state-of-the-art neural networks (SuperPoint+SuperGlue), using both standard benchmarks (HPatches) and waterbox-specific validation with real-world augmentations. SuperPoint+SuperGlue achieved superior performance with 7.82 pixels RMSE and 100% success rate—2.8x better accuracy than our baseline. While the pre-trained model has commercial licensing restrictions for nuclear deployment, our findings validate this architecture for custom training. We implemented a real-time GUI demonstrating the SIFT+BF approach for immediate deployment, processing drone feeds at 30 FPS with color-coded change visualization. Future work includes training a custom SuperPoint+SuperGlue model on waterbox data and integrating Vision-Language Models for automated reporting and maintenance guidance.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN

Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOViFT (adaptive optical vision Fourier transformer)—a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Alshaabi, Thayer [Howard Hughes Medical Institute,

Challenges and Vision for Standardization of Biopolymer Data Sets for Machine Learning

Machine learning (ML) is transforming materials research, yet potential for biopolymer discovery remains constrained by fragmented data and nonstandardized reporting. Biopolymers differ significantly from synthetic polymers, requiring specialized approaches to represent their biosynthetic origins, hierarchical structures, and application-specific metrics. In this Perspective, we identify three core challenges limiting biopolymer representation: information encoding, data quality, and data sharing. We describe the most pressing issues and propose commensurate approaches to address each key challenge. Recommendations include the design and adoption of biopolymer-specific fingerprinting and representation frameworks, development of hybrid human-large language model (LLM) data extraction strategies, and expanding Findable, Accessible, Interoperable, Reusable (FAIR)-compliant repositories. We propose a robust foundation to define interoperable, high-quality data sets that capture the full context of biopolymer materials. Standardized metadata, shared ontologies, and community-driven infrastructure would enable scalable, reproducible workflows and accelerate the ML-driven development of biopolymers.

36 MATERIALS SCIENCE

A Smart Vision-Aided RICH (Robotic Interface Control and Handling) System for VULCAN

High-flux neutron beams and high-efficiency detectors enable rapid neutron diffraction measurements at the Engineering Materials Diffractometer (VULCAN) at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory (ORNL). To optimize beam time utilization, efficient sample exchange, alignment, and automated measurements are essential. Recent advances in artificial intelligence (AI) have expanded the capabilities of robotic systems. Here, we report the development of a Robotic Interactive Control and Handling (RICH) system for sample handling at VULCAN, designed to support high-throughput experiments and reduce overhead time. The RICH system employs a six-axis desktop robot integrated with AI-based computer vision models capable of recognizing and localizing samples in real time from instrument and depth-resolving cameras. Vision algorithms combine these detections to align samples with designated measurement positions or place them within complex sample environments such as furnaces. This integration of machine learning-assisted vision with robotic handling demonstrates the feasibility of autonomous sample detection and preparation, offering a pathway toward fully unmanned neutron scattering experiments.

automation

WEBAT (Wind Energy with Bat AI-based Tracker) [SWR-24-121]

The WEBAT (Wind Energy with Bat AI-based Tracker) is a Python-based bat tracking software, integrating machine learning and computer vision with infrared thermal sensors to enhance the monitoring and protection of bats in proximity to wind turbines.

Ryu, Sora [National Renewable Energy Laboratory (N

Discovering Strong Gravitational Lenses in the Dark Energy Survey with Interactive Machine Learning and Crowd-sourced Inspection with Space Warps

We conduct a search for strong gravitational lenses in the Dark Energy Survey (DES) Year 6 imaging data. We implement a pre-trained Vision Transformer (ViT) for our machine learning (ML) architecture and adopt interactive machine learning to construct a training sample with multiple classes to address common types of false positives. Our ML model reduces ∼236 million DES cutout images to 22,564 targets of interest, including ∼85% of previously reported galaxy–galaxy lens candidates discovered in DES. These targets were visually inspected by citizen scientists, who ruled out ∼90% as false positives. Of the remaining 2618 candidates, 149 were expert-classified as “definite” lenses and 516 as “probable” lenses, for a total of 665 systems, with 147 of these candidates being newly identified. Additionally, we trained a second ViT to find double-source plane lens systems, finding at least one double-source system. Our main ViT excels at identifying galaxy–galaxy lenses, consistently assigning high scores to candidates with high expert assessments. The top 800 ViT-scored images include ∼100 of our “definite” lens candidates. This selection is an order of magnitude higher in purity than previous convolutional neural-network-based lens searches and demonstrates the feasibility of applying our methodology for discovering large samples of lenses in future surveys.

79 ASTRONOMY AND ASTROPHYSICS

3D reconstruction and neural rendering for adversarial machine learning

While evasion attacks on computer vision systems have been widely studied, creating attacks that remain effective under significant changes in viewpoint continues to be challenging. Traditional approaches often rely on affine transformations of images, but these approaches degrade at larger perspective shifts and often produce unrealistic or ineffective perturbations. Recent methods use differentiable renderers to improve viewpoint robustness, but they typically depend on manually constructed 3D models. We introduce a semi-automated pipeline that generates physically printable and perspective-invariant adversarial patches using only a small set of 2D images. Our method integrates 3D reconstruction, neural rendering, adversarial patch optimization, and an object detection victim model into a unified workflow. We use 2D Gaussian Splatting for high fidelity mesh reconstruction and FlexPara for surface parameterization that produces texture maps suitable for patch editing. Together, these components form a fully differentiable pipeline in PyTorch3D that links texture modification to model outputs, enabling efficient optimization of patches that remain effective across many viewpoints. The complete process, from image capture to patch printing and physical evaluation, can be completed within a few hours. We demonstrate the effectiveness of the resulting patches through attacks on the YOLOv8 object detection model and discuss remaining challenges and opportunities for improving robustness and scalability.

Singhvi, Vivaan [ORNL] (ORCID:0009000586288221)

Out-of-distribution detection with non-parametric density estimation for models predicting processing history of uranium ore concentrates

The rapid advancement in machine learning (ML) and computer vision (CV) coincides with the growth of interest in deploying these ML/CV models in numerous fields from medicine to social science. Similar to those areas, we have witnessed a great number of works in materials science employing ML/CV models – neural networks in particular – in their studies in recent years. These models have proven to obtain accurate performance in various tasks. However, these models struggle to attain a similar performance when encountering test samples coming from a distribution that is different from the training set. More importantly, they fail without providing any warning to the users. Therefore, we propose a framework for detecting out-of-distribution (OOD) samples to alert users when a human intervention might be necessary in this work. Specifically, we explore the use of a non-parametric density estimation method to detect OOD samples. Here, we assess OOD detection capability of the proposed framework on ML models developed for categorizing precipitation routes of U 3 O 8 when encountering OOD datasets that contain samples (1) undergone different imaging acquisition process, (2) undergone different material synthesis process, and (3) different materials than ID set. Through those experiments, we achieve an average area under the receiver operating characteristic (AUROC) of at least 91% on average in detecting OOD samples. With minimal overhead cost and superior performance, the proposed framework enables a reliable and safe system when deploying in real-world scenarios.

Convolutional neural networks

Effective Defect Detection Using Instance Segmentation for NDI

Ultrasonic testing is a common Non-Destructive Inspection (NDI) method used in aerospace manufacturing. However, the complexity and size of the ultrasonic scans make it challenging to identify defects through visual inspection or machine learning models. Using computer vision techniques to identify defects from ultrasonic scans is an evolving research area. In this study, we used instance segmentation to identify the presence of defects in the ultrasonic scan images of composite panels that are representative of real components manufactured in aerospace. We used two models based on Mask- RCNN (Detectron 2) and YOLO 11 respectively. Additionally, we implemented a simple statistical pre-processing technique that reduces the burden of requiring custom-tailored pre-processing techniques. Our study demonstrates the feasibility and effectiveness of using instance segmentation in the NDI pipeline by significantly reducing data pre-processing time, inspection time, and overall costs.

computer vision techniques

Machine learning materials properties with accurate predictions, uncertainty estimates, domain guidance, and persistent online accessibility

One compelling vision of the future of materials discovery and design involves the use of machine learning (ML) models to predict materials properties and then rapidly find materials tailored for specific applications. However, realizing this vision requires both providing detailed uncertainty quantification (model prediction errors and domain of applicability) and making models readily usable. At present, it is common practice in the community to assess ML model performance only in terms of prediction accuracy (e.g. mean absolute error), while neglecting detailed uncertainty quantification and robust model accessibility and usability. Here, we demonstrate a practical method for realizing both uncertainty and accessibility features with a large set of models. We develop random forest ML models for 33 materials properties spanning an array of data sources (computational and experimental) and property types (electrical, mechanical, thermodynamic, etc). All models have calibrated ensemble error bars to quantify prediction uncertainty and domain of applicability guidance enabled by kernel-density-estimate-based feature distance measures. All data and models are publicly hosted on the Garden-AI infrastructure, which provides an easy-to-use, persistent interface for model dissemination that permits models to be invoked with only a few lines of Python code. We demonstrate the power of this approach by using our models to conduct a fully ML-based materials discovery exercise to search for new stable, highly active perovskite oxide catalyst materials.

domain of applicability

Advancing 3D surface imaging: single-axis structured light illumination plenoptic camera with machine learning integration

Structured light illumination (SLI) is a configurable 3D surface imaging modality that can function largely independently of surface texture. At the same time, machine learning (ML) approaches are providing new ways to capture relevant information from SLI patterns, avoiding the need to develop advanced computer vision algorithms. By projecting an optical pattern onto a surface and measuring the apparent distortion of that pattern, one can determine surface topography from a single image. Common realizations of SLI 3D imaging use off-axis SLI to allow for parallax-based determination of depth; however, in constrained geometries, the ability to make single-axis measurements can be of major benefit. While plenoptic imaging (PI) cameras have long been developed for the purpose of single-axis 3D imaging, they are generally reliant on the surface texture of the measured object, thus making them unreliable in certain experimental conditions. Therefore, we present a single-axis 3D SLI plenoptic camera, which combines the single-axis benefits of PI technology while using coaxial SLI to maintain indifference to surface conditions. We also present a study of the camera capabilities paired with the development of several algorithms, including traditional feature tracking methods as well as ML methods, which are found to enhance resolution and range. We report depth sensitivity down to 0.2% $\frac{dz}{z_0}$. The single-axis SLI 3D plenoptic camera demonstrates potential applicability for in-situ topographical measurements under a wide range of conditions including, but not limited to, objects without trackable surface texture, high temperatures, and constrained geometry environments.

Imaging systems