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DOE OSTI2023

Data associated with “Different methods of estimating riverbed sediment grain size diverge at the basin scale ” (v2)

This data package is associated with the publication “Different methods of estimating riverbed sediment grain size diverge at the basin scale” published in Frontiers in Earth Science (Regier et al., 2025). The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (d50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual methods to measure d50 are time-consuming and ignore larger grains, while model-based methods to estimate d50 often over-generalize basin characteristics, and therefore cannot accurately represent site-scale heterogeneity. Here, we apply a machine learning-enabled photogrammetry methodology (You Only Look Once, or YOLO) for estimating d50 for grains > 2 mm based on images collected from streams and rivers throughout the Yakima River Basin (YRB). To understand how such methods may help bridge the gaps in resolution and accuracy between manual and catchment characteristics model-based d50 estimates, we compared YOLO d50 values to manual and model-based estimates across the YRB. We found distinct differences among methods for d50 averages and variability, and relationships between d50 estimates and basin characteristics. Source images can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052. This data package was originally published in May 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. In addition to the readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; (4) and subfolders containing data, figures, and scripts. The data folder contains datasets used for the analyses in the manuscript in image, text-delimited or geospatially-referenced formats. The figures folder contains the figures from the manuscript in different formats. The scripts folder contains all of the scripts used to complete the analyses in the manuscript. All files are .csv, .rds, .dbf, .prj, .shp, .shx, .jpg, .png, .R, .Rproj, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Remote sensing images, DEM, and point clouds associated with “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds”

This data package is associated with the publication “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds” published in Frontiers in Environmental Science, Environmental Informatics and Remote Sensing (Bao et al., 2026; doi: 10.3389/fenvs.2026.1725258). This data package includes the drone photos for a section of Umtanum Creek in Washington, Unted States. The photos were used to reconstruct the 3-dimensional (3D) digital elevation model (DEM) of the riverbed for the investigated stream section. The reconstruction results from four approaches are provided: (1) unoccupied aerial vehicle (UAV, colloquially known as drone) imagery-based Structure-from-Motion (SfM), (2) a machine learning-based 3D reconstruction model, Visual Geometry Grounded Deep Structure from Motion (VGGSfM), (3) Visual Geometry Grounded Transformer for long sequence of images (VGGT-Long), and (4) handheld smartphone LiDAR scanning. The ground truth measurements by tripod-mounted optical level kit and ground control points GPS locations for evaluating the accuracy of the four reconstruction approaches are also provided in this data package. A preliminary version of this data package was published in October 2025 at the time of manuscript submission. It was updated in March 2026, at the time of manuscript acceptance, to include additional metadata (this readme, data dictionary, and file level metadata). The data did not change. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) 8 folders; (2) the detailed flight configuration html files; (3) field metadata; (4) a readme; (5) a data dictionary; and (6) file-level metadata. The folders “2024_10_18_d01” and “2024_10_18_d02” contain the original drone photos for the two drone flights (d01 and d02) on October 18, 2024. The reconstruction results from each of the approaches are in the folders called “ODM_SfM”, “VGGSfM”, “VGGTLong”, and “LiDAR”. The ground truth measurements are in the folder called “optical_level_kit”. Lastly, results comparing the different approaches are in the folder called “comparisons”. All files are .csv, .html, .jpg, .obj, .txt, and .npy. For information on using the .obj and .npy files, see the readme files within the same folder as the files.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

WHONDRS Surface Water and Sediment Geochemistry and Organic Matter Characterization Data from Streams across HJ Andrews Experimental Forest, Oregon (v2)

This dataset supports a broader study developing conceptual models for river corridor critical zone processes across spatial scales and was generated in collaboration with the HJ Andrews River Corridor Critical Zone Workshop in 2025. The dataset provides surface water geochemistry (dissolved organic carbon, total dissolved nitrogen) from 48 sites across the HJ Andrews Experimental Forest, Oregon (https://andrewsforest.oregonstate.edu). Some of the sites have been impacted by the Holiday Farm Fire and the Lookout Fire in 2020 and 2023, respectively. Related data were collected as part of the workshop and will be published separately in collaboration with other workshop attendees and available at http://www.hydroshare.org/resource/b274c4a234bf4b12b7cb8a54a696c629. Related genomic data can be found on the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1503030 (see critical details section below for more information). Additional related data collected in 2016 from a similar effort can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3377027 and http://www.hydroshare.org/resource/ea6c0832885a46c3939e7bb22e48e754 and are described within https://doi.org/10.5194/essd-11-1-2019 (Ward et al., 2019). This data package was originally published in March 2026. It was updated in August 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of field photos, (2) a folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data, (3) a data checks report, (4) a folder of sample data, (5) file-level metadata, (6) data dictionary, (7) field metadata, (8) readme, (9) international generic sample number (IGSN) mapping file; and (10) field protocol. The sample data subfolder contains surface water and sediment (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages, (2) total dissolved nitrogen data and averages, (3) methods codes, (4) FTICR-MS methods; and (5) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains the CoreMS processed data and seven subfolders, thee containing .xml files for each sample type (sediment, surface water and blank samples), three containing the sediment CoreMS output files for each sample type (sediment, surface water and blank samples), and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .Rmd, .py, .cal, .json, .jpg, or .jpeg.

Biogeochemistry↗

DOE OSTI2024

Laboratory time series moisture manipulative experiment from sediment across the contiguous US: time series aerobic respiration and geochemistry (v2)

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration across the contiguous United States (CONUS). The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS CONUS-Scale Model-Sample Study (CM). This study was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. The data package associated with the CM study is available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689. CM sampling began in April 2022 and ended in October 2023. This study uses subsamples from a subset of CM samples collected between June 2022 and June 2023. The original field samples were labeled as CM_###. Subsequent subsamples for this study were labeled as EC_###. The labels from the field samples and the EC subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EC_001 is a subsample from CM_001). See the critical details section below for more details on sample naming. This data package was originally published in August 2024. It was updated in February 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate this data package, see this infographic from the River Corridor SFA https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) adenosine triphosphate (ATP); (4) percent carbon and nitrogen; (5) effect size; (6) iron (II); (7) gravimetric moisture; (8) respiration rates and raw dissolved oxygen values; (9) specific conductance; (10) pH; (11) temperature; (12) a summary containing median values of each data type for each treatment (wet and dry); (13) methods codes; (14) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla FTICR-MS data. This folder contains three subfolders, one containing the sediment .xml data files, one containing the sediment CoreMS output files, the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Spatial Study 2022: Surface Water Samples, Cotton Strip Degradation, and Hydrologic Sensor Data across the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides data and photos generated from sample collection during the same one-week period at 48 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. The contents include surface water geochemistry data; river substrate grain size photos; stream depth data; manual chamber open channel respiration data; and field metadata (including qualitative information on instream and river corridor characteristics). Grain size photos can be used to improve estimates of channel substrate D50 data. The dataset also includes tensile strength and photos from cotton strip field degradation experiments; five-week sensor time series temperature, dissolved oxygen, pressure, pH, specific conductance, chlorophyll A, and turbidity data; plots of the sensor data; and R scripts used to generate the plots. Samples collected during this study were labeled as “Second Spatial Study” or “SSS.” A subset of data from the SSS samples were published in the contiguous United States (CONUS)-Scale Model-Sample (CM) study data package available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689 that presents data from across the CONUS. SSS data published in the CM data package were not included in this data package. They include dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), total nitrogen (TN), grain size, aerobic sediment respiration, dissolved oxygen (DO), and temperature. Parent IDs and Site IDs are consistent between the SSS and CM data packages, and they can be mapped directly so data across packages can be used together. Additionally, sensor data from a similar 2021 spatial study can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052 and 2021 sample data can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1898914. The 2021 spatial study had some sites in common with this 2022 spatial study. This dataset is comprised of three photo folders and one main data folder with six subfolders. The photo folders contain photographs and videos of cotton strip retrieval and sediment quadrats. The main data folder consists of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) total suspended solids (TSS) data and cotton strip tensile strength data and averages; (5) field protocol; (6) readme; (7) methods codes; (8) international generic sample number (IGSN) mapping file; (9) sensor installation methods summary; (10) stream depth and averages; and (11) Ultrameter data and averages. The Sonar subfolder consists of Sonar time-series depth data and a processing script. The BarotrollAtm, DepthHOBO, MantaRiver, miniDOT, and miniDOTManualChamber subfolders contain time-series data, plots, and summary files. All files are .csv, .pdf, .txt, .R, .Rmd, .jpg, .jpeg, .AVI, .mp4, or .mov. The data package was originally published in April 2023. It was updated in August 2023 (v2; modified files) and September 2024 (v3; modified files). See the change history section in the readme for details. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗