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DOE OSTI2026

Data for Spatial Analysis of Cell Patterning to Aid Genetic and Phenotypic Understanding of Grass Stomatal Density: A Case Study in Maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

AI/ML↗

DOE OSTI2025

Rapid spatial analysis of surrogate TRISO fuel particles using laser-induced breakdown spectroscopy image analysis

Laser-induced breakdown spectroscopy (LIBS) mapping enables rapid elemental and spatial analysis of solid samples. In this work, surrogate TRi-structural ISOtropic (TRISO) particles with various layers consisting of Zr, W, C, and Si were used to demonstrate the use of a new thickness measurement tool developed to analyze elemental images generated from LIBS maps. Zr particles with varying outer-layer thicknesses ranging from 16 to 32 μm were measured with scanning electron microscopy with energy dispersive spectroscopy (SEM-EDS) and LIBS with both a complementary metal-oxide-semiconductor (CMOS) detector and an intensified charged coupled device (ICCD) detector. LIBS maps of particles were completed using CMOS and ICCD spectrometers with effective spatial resolutions of 4 and 2 μm, respectively. The novel thickness measurement tool identified layer regions within a LIBS map and then identified the locations of the boundaries between these layers. The tool then generated up to 1000 random profiles stemming radially from the center region, which were used to measure the layer thickness/radius. This image analysis tool demonstrated LIBS's ability to provide values comparable with SEM-EDS (3.7% relative difference) along with a 95% reduction in measurement time. Furthermore, the precision of these measurements was on par with the SEM-EDS measurements at <15% relative standard deviation. Following the analysis of the Zr particles, W particles with increased complexity (e.g., five versus three layers) were analyzed using both the CMOS and ICCD spectrometers simultaneously. The spatial dimensions were extracted with an average relative difference of 2.7% and an average relative standard deviation of 9%.

Andrews, Hunter B. [Oak Ridge National Laboratory ↗

DOE OSTI2023

Multiscale spatial analysis of fracture nodes in two dimensions

Spatial arrangement of fractures as a function of scale is an important component of fracture quantification for inferential and predictive modeling. Available methods that analyze fracture spatial arrangement are based on one-dimensional spacing data; therefore, they are limited to semi-parallel fractures. Such methods cannot be applied to fracture networks in higher dimensions, particularly when fractures have different orientations. Here to characterize fracture arrangements in two dimensions, we propose using Ripley’s K-function, as a method of point pattern analysis, to quantify spatial arrangement of fracture nodes. Fracture nodes, such as barycenters, intersection points, and tips, are point-based representations of fracture locations and connectivity within the fracture network. We introduce formulations for isotropic as well as directional analyses of spatial arrangement. In addition, we derive formulations for edge correction in circular and rectangular study domains. Finally, we demonstrate applications of Ripley’s K-function on two natural fracture datasets. Our proposed method supports quantification and characterization of fracture spatial arrangements that allow practitioners to build representative models of fractures in the subsurface.

02 PETROLEUM↗

DOE OSTI2026

Spatial analysis of cell patterning to aid genetic and phenotypic understanding of grass stomatal density: A case study in maize

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Multiscale spatial analysis of fracture arrangement and pattern reconstruction using Ripley's K-function

This work presents novel multiscale spatial data analytics using Ripley's K-function, as a measure of spatial interaction, to study one-dimensional arrangement of fractures. Fracture spatial arrangements are classified into clustered, anticlustered, or indistinguishable from random by testing statistical significance of the calculated Ripley's K-function. Characterizations of fracture arrangements are performed as a function of length scale and position. Analysis of the K-function along the study interval identifies where fracture clustering and anticlustering occur. Here, a simulation technique is also introduced here to statistically reconstruct spatial arrangements and to generate fracture realizations that are spatially similar to the fractures observed in the field. With this simulation technique, one can also fill spatial gaps in fracture measurements where data are absent, unreliable, or unused. Synthetic as well as field-measured 1D fracture datasets are used for testing and demonstration. Methods introduced in this work can be readily applied to fracture datasets observed in outcrops, borehole image logs, and cores.

58 GEOSCIENCES↗

DOE OSTI2020

Non-destructive spatial analysis of phosphatase activity and total protein distribution in the rhizosphere using a root blotting method

Phosphorus (P) is an essential macronutrient for plant growth, but bioavailable P in soils is often limited due to immobilization resulting from pH and geochemical interactions. Understanding the dynamics of P in soils and elucidating the mechanisms by which plants access P from their environment are critical to evaluating productivity, particularly in nutrient poor environments. Phosphorus from organic matter can act as a major source of P for organisms in soil systems. Phosphatases, enzymes that liberate inorganic P from organic sources, are produced by both plants and microbes and are considered one of the most active classes of enzymes in soil. In this work we developed a root blotting method to spatially image phosphatase activity in the rhizosphere. Proteins from the rhizosphere are transferred to a nitrocellulose membrane while retaining their enzymatic activity and two-dimensional spatial distribution. Subsequent application of a fluorogenic phosphatase indicator, DDAO phosphate, enables visualization of the distribution of phosphatase activity in the sample. The proteins can then be fixed to the membrane and treated with a SYPRO® Ruby gel stain, a fluorescent total protein stain, allowing for visualization of total protein distribution. Taken together, the images of phosphatase activity and total protein localization can be mapped back to the root architecture and provide insight into factors affecting the spatial distribution of enzymatic activity and protein accumulation in the rhizosphere. Notably, this method can be applied to plants growing in rhizoboxes containing soil or soilless growth mixtures (e.g., sand or various potting mixes) and, because of the non-destructive nature of this approach, be performed over time to track changes. We anticipate that this fluorescent indicator imaging technique on root blots can be used in diverse plant-microbe-soil systems to better understand the role of phosphatases in P acquisition and soil P cycling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Spatial analysis of social capital and community heterogeneity at the United States county level

Not Available

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2022

Short-term temporal and spatial analysis for post-fire vegetation regrowth characterization and mapping in a Mediterranean ecosystem using optical and SAR image time-series

Not Available

De Luca, Giandomenico↗

DOE OSTI2021

Effects of raster terrain representation on GIS shortest path analysis

Spatial analysis extracts meaning and insights from spatially referenced data, where the results are highly dependent on the quality of the data used and the manipulations on the data when preparing it for analysis. Users should understand the impacts that data representations may have on their results in order to prevent distortions in their outcomes. We study the consequences of two common data preparations when locating a linear feature performing shortest path analysis on raster terrain data: 1) the connectivity of the network generated by connecting raster cells to their neighbors, and 2) the range of the attribute scale for assigning costs. Such analysis is commonly used to locate transmission lines, where the results could have major implications on project cost and its environmental impact. Experiments in solving biobjective shortest paths show that results are highly dependent on the parameters of the data representations, with exceedingly variable results based on the choices made in reclassifying attributes and generating networks from the raster. Based on these outcomes, we outline recommendations for ensuring geographic information system (GIS) data representations maintain analysis results that are accurate and unbiased.

Medrano, F. Antonio (ORCID:000000025913632X)↗

DOE OSTI2021

Multimodal Analysis of Spatially Heterogeneous Microstructural Refinement and Softening Mechanisms in Three-Pass Friction Stir Processed Al4Si Alloy

Multiple thermally and thermomechanically induced microstructural refinement mechanisms can be activated in metallic alloys when subjected to solid phase processing methods such as friction stir processing (FSP). In this work, we provide detailed descriptions of the relationship between region-specific microstructural refinement mechanisms and the variation in microhardness, through a systematic and multimodal microstructural characterization of an FSP-processed 75% cold-rolled Al-4 at.% Si model binary alloy. Spatially resolved high-energy synchrotron X-ray diffraction, electron backscattered diffraction, and scanning transmission electron microscopy were used to understand the spatially heterogeneous microstructural evolution due to FSP. Results provide insights into how mechanisms such as static recovery, static recrystallization, dynamic recovery and recrystallization, geometric and continuous dynamic recrystallization, and particle-stimulated static or dynamic grain nucleation may occur heterogeneously in the microstructure as a function of the distance from the stir zone in processed alloys, directly influencing the degree of softening. The systematic analysis of microstructures and hardness in the FSP-processed model binary alloy given in this work highlights the rich microstructural domains that can be uniquely harnessed through solid phase processing of metallic alloys.

Al4Si, Friction Stir Processing, Geometric Dynamic↗

DOE OSTI2022

spopt: a python package for solving spatial optimization problems in PySAL

Spatial optimization is a major spatial analytical tool in management and planning, the significance of which cannot be overstated. Spatial optimization models play an important role in designing and managing effective and efficient service systems such as transportation, education, public health, environmental protection, and commercial investment among others. To this end, spopt (spatial optimization) is under active development for the inclusion of newly proposed models and methods for regionalization, facility location, and transportation-oriented solutions (Feng et al., 2021). Spopt is a submodule in the open-source spatial analysis library PySAL (Python Spatial Analysis Library) founded by Dr. Sergio J. Rey and Dr. Luc Anselin in 2005 (Rey et al., 2015, 2021; Rey & Anselin, 2007). The goal of developing spopt is to provide management and decision-making support to all relevant practitioners and to further promote the appropriate and meaningful application of spatial optimization models in practice.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Automated Registration of Vector Data to Overhead Imagery

The availability of open source, remote sensing-derived vector data has increased exponentially in recent years. Unfortunately, these vector data are rarely made available with the corresponding source images from which objects were extracted. As such, these derived datasets are commonly used in combination with target images which differ from the source. Satellite viewing geometry can cause objects, extracted from a source image, to appear shifted when overlaid with a target image. Whether for purely cartographic purposes, reusability of preexisting training labels, or any spatial analysis where spatial correspondence between vector and image are required, the following paragraphs outline a method to address this challenge through the automated registration of vector data to overhead imagery, including existing literature regarding this challenge, followed by a case study of Sioux Falls, South Dakota.

McKee, Jacob↗

DOE OSTI2024

Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the tissue, rather than local gene expression changes driven by cell-cell interactions. We propose a new statistical procedure called niche-differential expression (niche-DE) analysis that identifies cell-type-specific niche-associated genes, which are differentially expressed within a specific cell type in the context of specific spatial niches. We further develop niche-LR, a method to reveal ligand-receptor signaling mechanisms that underlie niche-differential gene expression patterns. Niche-DE and niche-LR are applicable to low-resolution spot-based spatial transcriptomics data and data that is single-cell or subcellular in resolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

DARHT Radiographic Analysis of Spatially Modulated Objects

This document describes some analysis methods that can be performed using the Kaleidoscope test object (KTO) in order to assess DARHT radiography performance. The goal of these methods is to provide a simple metric of radiographic performance to compare different system configurations at DARHT. Specifically, these methods can be used to assess the Tiffany configurations to determine relative radiographic performance. To demonstrate the methods, we show results analysis performed on the ‘Tiffany A’ shot conducted in July 2021.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility

Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. In this study, we sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at –80 °C, vacuumed sealed and stored at –80 °C, with matrix preapplied before storage at –80 °C, under a nitrogen atmosphere and stored at –80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at –80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Development of a Neutron List Mode Collar (LMCL) and a List Mode Response Matrix Analysis Concept

This report was prepared for the Safeguards Program of the US Department of Energy’s (DOE’s) National Nuclear Security Administration (NNSA), Office of Defense Nuclear Nonproliferation Research and Development (DNN R&D). The report presents the development of the neutron nondestructive assay system, the List Mode Collar (LMCL) for the project OR16-List Mode for Collar-PD1La “List Mode Response Matrix for Advanced Correlated Neutron Analysis for Nuclear Safeguards.” The new list mode electronics developed under this project, and a spatial analysis concept called the List Mode Response Matrix are also described in this report. Analysis algorithms based on classification methods are published in a separate report. This research addresses the need to expand the capabilities of current nondestructive assay systems used for nuclear safeguards applications and considers the sustainability of safeguards technologies by the development of a “retrofit” concept using electronics based on modern standards. Furthermore, employing list mode data acquisition enabled the development of a spatial analysis concept and empirical measurement of a spatial response not previously used for safeguards neutron counting applications or measured in a traditional neutron collar detector and, therefore, provides new capability.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Large-scale spatially explicit analysis of carbon capture at cellulosic biorefineries

The large-scale production of cellulosic biofuels would involve spatially distributed systems including biomass fields, logistics networks and biorefineries. Better understanding of the interactions between landscape-related decisions and the design of biorefineries with carbon capture and storage (CCS) in a supply chain context is needed to enable efficient systems. Here we analyse the cost and greenhouse gas mitigation potential for cellulosic biofuel supply chains in the US Midwest using realistic spatially explicit land availability and crop productivity data and consider fuel conversion technologies with detailed CCS design for their associated CO 2 streams. Optimization methods identify trade-offs and design strategies leading to systems with attractive environmental and economic performance. Strategic and operational decisions depend on underlying spatial features and are sensitive to biofuel demand and CCS incentives. US CCS incentives neglect to motivate greenhouse gas mitigation from all supply chain emission sources, which leverage spatial interactions between CCS, electricity prices and the biomass landscape.

09 BIOMASS FUELS↗

DOE OSTI2021

A spatial evaluation of Arctic sea ice and regional limitations in CMIP6 historical simulations

The Arctic sea ice response to a warming climate is assessed in a subset of models participating in Phase 6 of the Coupled Model Intercomparison Project (CMIP6), using several metrics in comparison with satellite observations and results from the Pan-Arctic Ice Ocean Modeling and Assimilation System and the Regional Arctic System Model. Our study examines the historical representation of sea ice extent, volume, and thickness using spatial analysis metrics, such as the integrated ice-edge error, Brier score, and Spatial Probability Score. We find that the CMIP6 multi-model mean captures the mean annual cycle and 1979-2014 sea ice trends remarkably well. However, individual models experience a wide range of uncertainty in the spatial distribution of sea ice when compared against satellite measurements and reanalysis data. Our metrics expose common and individual regional model biases, which sea ice temporal analyses alone do not capture. We identify large ice edge and ice thickness errors in Arctic sub-regions, implying possible model specific limitations in or lack of representation of some key physical processes. We postulate that many of them could be related to the oceanic forcing, especially in the marginal and shelf seas, where seasonal sea ice changes are not adequately simulated. We therefore conclude that an individual model’s ability to represent the observed/reanalysis spatial distribution still remains a challenge. We propose the spatial analysis metrics as useful tools to diagnose model limitations, narrow down possible processes affecting them, and guide future model improvements critical to the representation and projections of Arctic climate change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗