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Original images, ground truth annotations, and precited masks from U-NET for a fungal species x nitrogen experiment

This document describes the “MicroVision-MV003” dataset. This folder contains three subfolders: “originals”, “predicted_masks”, and “gt_masks”. The “originals” folder contains 720 original images acquired using two imaging modalities: 360 images from overhead imaging and 360 images from transmission (raw) imaging. Naming scheme:YYYY-MM-dd__plate_strain_nitrogen-level_replication_experiment_imaging-modalityYYYY-MM-dd: 2024-12-20, 2024-12-21, 2024-12-22,2024-12-23,2024-12-24,2024-12-25,2024-12-26,2024-12-27,2024-12-28,2024-12-29,2024-12-30,2024-12-31.plate: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30.strain: FG, LE.nitrogen-level: N-1, N-10, N-100.replication: 1, 2, 3, 4, 5.experiment: MV.003.imaging-modality: overhead, transmission (raw). For example, the image2024-12-20__1_FG_N-10_3_MV.003_overheadwas taken on 2024-12-20. The plate number is 1, the fungal strain is FG, the nitrogen treatment is N-10, and the replication number is 3 for experiment MV.003, acquired using the overhead imaging modality. The “predicted_masks” folder contains masks generated by a trained U-Net model for the transmission imaging modality.The “gt_masks” folder contains 326 human hand-traced masks that serve as ground truth.

09 BIOMASS FUELS↗

Utah FORGE: Well 16A(78)-32 Perforation Images and Raw Data

This archive contains raw data of visual and acoustic mapping of perforations in Utah FORGE well 16A(78)-32 acquired during the August 2024 circulation program. The dataset includes downhole images captured by EV, a downhole visual analytics company, providing visual records of each perforation. Images are organized in two folders: one set with perforation visualization overlays and one without. An included Excel spreadsheet provides the organized raw data.

15 GEOTHERMAL ENERGY↗

Integrated photonic encoder for low power and high-speed image processing

Abstract Modern lens designs are capable of resolving greater than 10 gigapixels, while advances in camera frame-rate and hyperspectral imaging have made data acquisition rates of Terapixel/second a real possibility. The main bottlenecks preventing such high data-rate systems are power consumption and data storage. In this work, we show that analog photonic encoders could address this challenge, enabling high-speed image compression using orders-of-magnitude lower power than digital electronics. Our approach relies on a silicon-photonics front-end to compress raw image data, foregoing energy-intensive image conditioning and reducing data storage requirements. The compression scheme uses a passive disordered photonic structure to perform kernel-type random projections of the raw image data with minimal power consumption and low latency. A back-end neural network can then reconstruct the original images with structural similarity exceeding 90%. This scheme has the potential to process data streams exceeding Terapixel/second using less than 100 fJ/pixel, providing a path to ultra-high-resolution data and image acquisition systems.

47 OTHER INSTRUMENTATION↗

Integrated structural dynamics uncover new modes of B12 photoreceptor activation

**SACLA** A crystallographic pump-power titration was first carried-out with pump laser fluences of 12, 30, 60 and 120 uJ.cm-2 and a time delay of 3 us. Then, a time-series was performed with a pump-laser fluence of 30 uJ.cm-2 (~2.4 absorbed photon per chromophore) and time-delays of 10 ns, 300 ns, 3 µs, 100 us and 3 ms. Finally, two time-delays (10 ns and 3 us) were collected with a pump laser fluence of 12 uJ.cm-2. Raw images, crystFEL streams and merged mtzs are available for all collected dat **SwissFEL** A time series with a pump laser fluence of 30 mJ.cm-2 was performed at time delys of 3 µs and 10 ms. Raw images, crystFEL streams and merged mtzs are available for all collected datasets. Refined detector geometry for each experimental campaign is also provided (crystFEL format)

RIOS-SANTACRUZ, Ronald↗

Integrated structural dynamics uncover new modes of B12 photoreceptor activation

**SACLA** A crystallographic pump-power titration was first carried-out with pump laser fluences of 12, 30, 60 and 120 ??J.cm-2 and a time delay of 3 ??s. Then, a time-series was performed with a pump-laser fluence of 30 ??J.cm-2 (~2.4 absorbed photon per chromophore) and time-delays of 10 ns, 300 ns, 3 ??s, 100 ??s and 3 ms. Finally, two time-delays (10 ns and 3 ??s) were collected with a pump laser fluence of 12 ??J.cm-2. Raw images, crystFEL streams and merged mtzs are available for all collected dat **SwissFEL** A time series with a pump laser fluence of 30 mJ.cm-2 was performed at time delys of 3 ??s and 10 ms. Raw images, crystFEL streams and merged mtzs are available for all collected datasets. Refined detector geometry for each experimental campaign is also provided (crystFEL format)

RIOS-SANTACRUZ, Ronald↗

CHESS 2025: Orthorectified airborne RGB imagery from NEON AOP surveys

This dataset provides Level 1 (L1) and Level 3 (L3) orthorectified Red-Green-Blue (RGB) imagery collected for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). This high-resolution imagery is a photographic record of red, green, and blue visible light from sunlight reflected off of the Earth’s surface. The data comprise full-color images of the ground surface and are primarily intended to provide context to imaging spectroscopy and light detection and ranging (LiDAR) data. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. RGB images were acquired using the PhaseOne IXM-RS150F high-resolution digital camera onboard the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP). The package data include both an L1 product comprising one camera frame per file and an L3 mosaic aligned to the Universal Transverse Mercator (UTM) Zone 13N grid and the World Geodetic System (WGS) 84 projection. Both products are provided in geotif (.tif) format at 0.1 m ground resolution. The bulk of the imagery was collected during the main CHESS field campaign from June 13 to July 15, 2025. Additional images of a portion of the Upper Taylor (UPTA) domain were collected on September 18, 2025, to fill gaps in imagery identified after the main campaign was complete. RGB camera imagery is not radiometrically calibrated, and therefore pixel values should not be exploited for scientific analysis. Pixel values have undergone a manual adjustment to enhance feature identification. The imagery is rigorously geolocated which does allow for reliable geometric information to be retrieved. To generate the orthorectified imagery, the NEON AOP camera captured visible spectrum in red, green, and blue bands. The raw images were then processed using NEON’s camera orthorectification workflow. A boresight calibration flight was made to build a complete camera, distortion, and alignment model. Color balance/white balance and exposure correction were applied to the raw RGB images. The corrected images were orthorectified by ray-tracing image pixels to a lidar-derived digital surface model (DSM) mesh using the refined camera model, outputting orthorectified raster pixels on a regular grid. Flightline-level data were mosaicked by selecting per-pixel contributions from overlapping orthorectified images using line-of-sight (LOS) zenith angle minimization to reduce edge distortions. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

Self-calibration strategies for reducing systematic slope measurement errors of autocollimators in deflectometric profilometry

Deflectometric profilometers are used to precisely measure the form of beam shaping optics of synchrotrons and X-ray free-electron lasers. They often utilize autocollimators which measure slope by evaluating the displacement of a reticle image on a detector. Based on our privileged access to the raw image data of an autocollimator, novel strategies to reduce the systematic measurement errors by using a set of overlapping images of the reticle obtained at different positions on the detector are discussed. It is demonstrated that imaging properties such as, for example, geometrical distortions and vignetting, can be extracted from this redundant set of images without recourse to external calibration facilities. This approach is based on the fact that the properties of the reticle itself do not change – all changes in the reticle image are due to the imaging process. Firstly, by combining interpolation and correlation, it is possible to determine the shift of a reticle image relative to a reference image with minimal error propagation. Secondly, the intensity of the reticle image is analysed as a function of its position on the CCD and a vignetting correction is calculated. Thirdly, the size of the reticle image is analysed as a function of its position and an imaging distortion correction is derived. It is demonstrated that, for different measurement ranges and aperture diameters of the autocollimator, reductions in the systematic errors of up to a factor of four to five can be achieved without recourse to external measurements.

47 OTHER INSTRUMENTATION↗

AGR-2 TRISO Layer Thickness Imaging Archive

As a part of fuel quality control characterization, optical microscopy images of particle cross sections near midplane were acquired at Oak Ridge National Laboratory (ORNL). These particles were produced by the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program’s AGR-2 irradiation campaign. These images may be of use for the development of image processing algorithms with the benchmark values measured at ORNL. This report provides those benchmark values, along with the raw images and data generated by the ORNL particle layer thickness analysis process.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

AGR-2 TRISO Shadow Imaging Archive

As a part of fuel quality control characterization, backlit shadow images of particles produced by the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program’s AGR-2 irradiation campaign were acquired at Oak Ridge National Laboratory (ORNL). These images may be of use for the development of image processing algorithms with the benchmark values measured at ORNL. This report provides those benchmark values, along with the raw images and data generated by the ORNL shadow imaging process.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Raw electron microscopy images for "The Importance of Nano-edges in Atomic Stencilling and Chiroptically Active Assembly of Patchy Gold Tetrahedra"

This dataset contains the raw transmission electron microscopy (TEM) and scanning electron microscopy (SEM) images used in the main figures of the paper “The Importance of Nano-edges in Atomic Stencilling and Chiroptically Active Assembly of Patchy Gold Tetrahedra (2026).” All the images were acquired at the Materials Research Laboratory, University of Illinois at Urbana-Champaign, by Qian Chen group. 1. We provide five subfolders, each named according to the corresponding figure numbers in the paper. 2. All files in the subfolders for Figures 1–3 and 5 are named as "Panel [letter]_*", where [letter] (e.g., a, b, c) represents the raw images used for the corresponding panels. 3. All files in the subfolder for Figure 4 correspond to panel f and show the configurations of patchy tetrahedra synthesized at varying concentrations of iodide and 2-naphthalenethiol. They are named "Experiment_[number]", where [number] represents the corresponding data points in the phase diagram. 4. In TEM images, the bright and dark regions indicate the polymer patches and nanoparticle cores, respectively. 5. In SEM images, the bright and dark regions indicate the nanoparticle cores and polymer patches, respectively. 6. Abbreviations in file names: HAADF-STEM (high-angle annular dark-field scanning transmission electron microscopy), PINEM (photon-induced near-field electron microscopy), and RCP/LCP (left-/right-handed circularly polarized).

chirality↗

Detailed Characterization of CZT Detector Response for Improved Coded-Aperture Imaging Performance

Gamma-ray imaging is a powerful method for locating and quantifying sources of radiation. The coded-aperture technique demonstrates superior angular resolution in comparison to other methods (e.g., Compton reconstruction). In this method, a mask constructed of highly attenuating material encodes the scene as a shadow pattern on a position-sensitive detector; this pattern can then be used to recreate the origin(s) of incident radiation. This is typically done through convolution of the mask and shadow patterns. Iterative methods which attempt to reconstruct the observed shadow pattern using a weighted combination of simulated patterns may also be employed. In either case, errors in event position reconstruction due to detector imperfections alter the shadow pattern and will therefore degrade system performance and may introduce imaging artifacts. These effects can be mitigated with a detailed understanding of such errors – allowing for the generation of representative simulations that include the errors and/or correction of raw imager data to remove the errors. We present a calibration process for a commercially available cadmium zinc telluride (CZT) gamma imager which provides a comprehensive characterization of the spatial and energy dependence of event reconstruction. By illuminating a mask featuring a regular grid of pinholes with a calibration source, the localized response of the detector can be measured with fine granularity. These local responses are combined to generate a full detector response map which can be used to distort simulations in a manner that is representative of the observed detector data. Details of the calibration procedure and an assessment of the impact of its end products on the performance of iterative imaging methods will be presented.

Ziock, Klaus-Peter↗

Data supporting the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure"

This dataset contains atomic force microscopy images associated with the manuscript "Nanometer Scale Imaging to Develop Quantitative Descriptors of Bipolar Membrane Junction Structure" by Maria Kelly, Emily R. Dunn, Ellis A. Spickermann, Josephine N. Gruber, César A. Lasalde-Ramírez, P. N. Romero Zavala, Éowyn Lucas, Ankur Gupta, Harry A. Atwater, and Wilson A. Smith. The dataset contains both raw images as well as segmented images produced by the image processing workflow described in the manuscript. A readme file and meta data file are included to provide additional details regarding the sample identity, image acquisition parameters, and file naming scheme.

36 MATERIALS SCIENCE↗

AGR-1 UCO Kernel Phase Analysis Imaging Archive

UCO kernels in tri-structural isotropic (TRISO) particles consist of a heterogeneous mixture of uranium oxide and uranium carbide. During the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program, mean kernel composition was specified based on bulk measurements of uranium, oxygen, and carbon content, as well as the resulting O/U, C/U, and O+C/U ratios. Further development of quality control characterization methods has resulted in a method for more direct measurement of phase fractions on a per-kernel basis using optical microscopy of polished kernel cross sections. This report provides benchmark values for this analysis method when applied to kernels from the AGR-1 campaign and to the raw images used.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Towards AI Based Data Classification for Decision Making During Testing

During the development of high-consequence items, test systems should be capable of differentiating between test failures resulting from narrowly missing requirements versus those indicating potentially catastrophic faults. In many instances, classifying the data corresponds to simply identifying whether measured waveforms have approximately the anticipated shape. Cast in this light, the problem reduces to converting raw data into a form optimal for use with neural network classifiers. This manuscript investigates different means of representing raw data for image classification. Raw data plots and Short Time Fourier Transform (STFT) spectrograms are classified by both custom built, small-scale, Convolution Neural Networks (CNN) and open-source, multi-million parameter, pre-trained deep CNNs. In the case of time varying frequency content, the STFTs provide images with greater detail and can be accurately classified with simpler networks. This requires less memory and runs faster than classifying the raw data using the more sophisticated options—making STFTs optimal for applications with memory constraints. STFTs are not a panacea. In some cases the time-domain signal contains useful information that should not be discarded. Rather than using raw data or STFTs, the images can be constructed from both by using red and green channels of an RGB image to visualize the real and imaginary components of the transform, with the raw data occupying the blue channel.

97 MATHEMATICS AND COMPUTING↗

Image processing pipeline for AI-driven nanoparticle megalibrary characterization

Recent innovations have made it possible to produce megalibraries, millions of structurally and compositionally distinct nanoparticles on a chip. These megalibraries yield vast volumes of data that are impossible to analyze manually, necessitating the development of automated tools. In previous work, we created a binary classification machine learning model to select quality nanoparticle images for downstream analysis. In this work, we show that adding a custom image processing step before training can produce significantly higher-performing models in a fraction of the time and make them more robust to different image noise levels and microscope acquisition settings. The image processing pipeline proposed here effectively cleans raw nanoparticle images, enhances key features, and allows us to use much lower resolution images and simpler neural network model architectures. These features result in higher performance and significant cost savings. Experiments demonstrate superior performance relative to baseline, including an 18.2% improvement in recall and a 13.1% increase in accuracy. Given the high cost of downstream analysis, it is critical to minimize false positives, and our best-performing model reaches a precision of 95.9% and a weighted F-score of 95.1% on an unseen test set. Additionally, model training time is reduced from hours to less than a minute. We also show that, using this custom image processing pipeline, model performance is significantly improved at lower pixel resolutions compared to downsizing alone. We expect that adopting this pipeline for AI-driven automated nanoparticle characterization will allow researchers to rapidly and accurately analyze much greater volumes of data, thereby accelerating materials discovery.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Hyperspectral acquisition with ScanImage at the single pixel level: application to time domain coherent Raman imaging

We present a comprehensive strategy and its practical implementation using the commercial ScanImage software platform to perform hyperspectral point scanning microscopy when a fast time-dependent signal varies at each pixel level. In the proposed acquisition scheme, the scan along the X-axis is slowed down while the data acquisition is maintained at a high pace to enable the rapid acquisition of the time-dependent signal at each pixel level. The ScanImage generated raw 2D images have a very asymmetric aspect ratio between X and Y, the X axis encoding both for space and time acquisition. The results are X-axis macro-pixel where the associated time-dependent signal is sampled to provide hyperspectral information. We exemplified the proposed hyperspectral scheme in the context of time-domain coherent Raman imaging, where a pump pulse impulsively excites molecular vibrations that are subsequently probed by a time-delayed probe pulse. In this case, the time-dependent signal is a fast acousto-optics delay line that can scan a delay of 4.5ps in 25 μ s at each pixel level. With this acquisition scheme, we demonstrate ultra-fast hyperspectral vibrational imaging in the low frequency range [10 cm −1 , 150 cm −1 ] over a 500 μm field of view (64 x 64 pixels) in 130ms (∼ 7.5 frames/s). The proposed acquisition scheme can be readily extended to other applications requiring the acquisition of a fast-evolving signal at each pixel level.

Metais, Samuel↗

NDVI and Multispectral Images, UAS Flights, Council Road Site, Seward Peninsula, Alaska, June 2022

The dataset contains Normalized Difference Vegetation Index (NDVI) and multispectral images collected on June 18, 2022 using an UAS (Unmanned Aerial System) Yuneec H520, Mapir Survey 3, and Parrot Sequoia cameras. This data was created to accompany the following datasets:- NGEE Arctic CO2, CH4 and Energy Eddy-Covariance (EC) Flux Tower Auxiliary Measurements, Council Road Mile Marker 71, Seward Peninsula, Alaska (https://doi.org/10.5440/1526749)- Sun-induced chlorophyll fluorescence/eddy covariance measurements at NGEE Arctic Council site, Seward Peninsula, Alaska, 2022 (https://doi.org/10.15485/2466175)- NGEE Arctic Meteorological Data from Instrumented PCDC Stations, Council Site, Seward Peninsula, Alaska, 2018 - 2023 (https://doi.org/10.5440/1529604)Survey 3 is RGN (Red, Greeen, Near Infra Red) camera with 87° Horizontal Field of View (HFOV) (19mm) f/2.8 Aperture, 550nm/660nm/850nm (Red+Green+NIR) filter transmission and produced geo referenced jpg and raw format images. Parrot Sequoia is a camera with 16 megapixel RGB (Red, Green, Blue) sensor and 1.2 megapixel monochrome sensors in discrete spectral bands: Green (550nm - 40Nm Bandwidth), Red (660nm - 40nm Bandwidth), Red Edge (735nm - 10nm Bandwidth) and Near Infrared (790nm - 40nm Bandwidth).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

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↗