One-shot gas detection with transformer paired neural networks in Mako collected longwave infrared hyperspectral imagery
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Benham, Kevin Andrew↗
SEARCH · Engineering Papers
Results for “Hyperspectral”
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Unraveling plant phenotype to genotype associations with daily hyperspectral traits in Populus trichocarpa
Hyperspectral remote sensing is a powerful, high-throughput phenotyping tool that quantifies physiologically and structurally relevant wavelengths across diverse genotypes and over varying temporal scales. In this study, we combined tower-based continuous hyperspectral sensing with genome-wide association studies to analyze 1423 wavebands (400-900 nm) and derivative vegetation indices across 505 genotypes and the genetic architecture of hyperspectral phenotypes over time in Populus trichocarpa Torr. & Gray grown under field conditions. Wavelengths related to chlorophyll and carotenoid absorption spectra exhibited the strongest genetic variation resulting in 98 significant SNP associations. Notably, we found substantial overlap in genetic association between the blue and red spectral regions, indicative of carotenoids and chlorophyll, respectively, and identified more than 10 candidate genes associated with chloroplast function, underpinning photosynthetic activity. Furthermore, fluctuations in associations for vegetative indices, such as the chlorophyll:carotenoid index (CCI), across the growing season reveal a temporally dynamic genetic architecture of physiological traits associated with fall senescence of this temperate tree species. Finally, we also observed correlations (spearman rho = 0.3, p < 1x10 −8 ) between individual wavebands or vegetative indices and growth rate, assessed as the relative change of tree height over the growing season. The growth rate prediction was substantially improved by a regularization multivariate model (spearman rho>0.5, p < 1x10 −16 ), reinforcing the value of hyperspectral measurements for predicting traits linked to tree productivity. These findings highlight the potential of high-throughput, rapid, hyperspectral genome wide association studies GWAS to uncover physiologically meaningful genetic variation and offer promising insights for future acceleration for plant breeding.
09 BIOMASS FUELS↗
Deep learning-driven super-resolution in Raman hyperspectral imaging: Efficient high-resolution reconstruction from low-resolution data
Deep learning (DL) has become an indispensable tool in hyperspectral data analysis, automatically extracting valuable features from complex, high-dimensional datasets. Super-resolution reconstruction, an essential aspect of hyperspectral data, involves enhancing spatial resolution, particularly relevant to low-resolution hyperspectral data. Yet, the pursuit of super-resolution in hyperspectral analysis is fraught with challenges, including acquiring ground truth high-resolution data for training, generalization, and scalability. The pressing issue of extended spectral acquisition times, notably for high-resolution scans, is a significant roadblock in hyperspectral imaging. Super-resolution methods offer a promising solution by providing higher spatial resolution data to expedite data collection and yield more efficient outcomes. This paper delves into a practical application of these concepts using Raman imaging, where spectral acquisition times can be prohibitively long. In this context, DL-based super-resolution models demonstrate their efficacy by predicting and reconstructing high-resolution Raman data from low-resolution input, eliminating the need for resource-intensive high-resolution scans. While previous work often relied on substantial high-resolution datasets, this study showcases the ability to achieve similar outcomes even with limited data, presenting a more practical and cost-effective approach. In conclusion, the results offer a glimpse into the transformative potential of this technology to streamline hyperspectral imaging applications by saving valuable time and resources through the successful generation of high-resolution data from low-resolution inputs.
42 ENGINEERING↗
Fast Hyperspectral Neutron Tomography
Hyperspectral neutron computed tomography is a tomographic imaging technique in which thousands of wavelength-specific neutron radiographs are measured for each tomographic view. In conventional hyperspectral reconstruction, data from each neutron wavelength bin are reconstructed separately, which is extremely time-consuming. These reconstructions often suffer from poor quality due to low signal-to-noise ratios. Consequently, material decomposition based on these reconstructions tends to produce inaccurate estimates of the material spectra and erroneous volumetric material separation. In this paper, we present two novel algorithms for processing hyperspectral neutron data: fast hyperspectral reconstruction and fast material decomposition. Both algorithms rely on a subspace decomposition procedure that transforms hyperspectral views into low-dimensional projection views within an intermediate subspace, where tomographic reconstruction is performed. The use of subspace decomposition dramatically reduces reconstruction time while reducing both noise and reconstruction artifacts. We apply our algorithms to both simulated and measured neutron data and demonstrate that they reduce computation and improve the quality of the results relative to conventional methods.
Chowdhury, Mohammad Samin Nur [Purdue University]↗
APPL Hyperspectral_Imaging_Dataset_for_Heritability_Analysis_in_Populus_trichocarpa
This dataset contains hyperspectral imaging data collected at the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory. Natural variants of Populus trichocarpa were imaged using a high-throughput hyperspectral phenotyping pipeline to quantify spectral reflectance traits for downstream quantitative genetics analyses. The dataset includes hyperspectral image files and derived reflectance data products suitable for extracting spectral features across the measured wavelength range (e.g., VNIR and/or SWIR, depending on instrument configuration), along with associated sample metadata (e.g., genotype identifiers, experimental design factors, and imaging run identifiers). These data were generated to support analyses of broad-sense heritability of hyperspectral traits and their relationships with biochemical phenotypes (including lignin traits from Py-MBMS).
APPL↗
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↗
Precision Plant Biomass Characterization in Agriculture: Harnessing Machine Learning and Hyperspectral Imaging [Slides]
Efficient Biomass Separation Object detection of anatomical parts (Cob, Stalk, Husk) in IR images enables precise separation, improving preprocessing (e.g., drying, grinding) for biofuel production. Detailed Biomass Characterization with Hyperspectral Data Hyperspectral imaging captures spectral signatures of biomass, allowing for the identification of specific traits like moisture content, lignin levels, and nutrient composition, leading to optimized treatments for each biomass part. Enhanced Feedstock Quality By leveraging hyperspectral data, feedstock can be processed based on its chemical composition, improving conversion efficiency and biofuel yield. Automation for Large-Scale Operations Automated object detection and hyperspectral data analysis reduce manual labor, ensuring accurate sorting and faster processing, making large-scale biofuel production more efficient. Maximized Biomass Utilization Accurate identification of biomass properties minimizes waste and ensures that each part is processed according to its highest biofuel potential.
09 BIOMASS FUELS↗
Hyperspectral radiance mapping and chromatic correction for temperature measurement in laser-heated diamond anvil cells
In laser-heated diamond anvil cell (DAC) experiments, the effective heated region typically decreases in size with increasing pressure, leading to steeper thermal gradients. Under these conditions, chromatic aberration in the optical path from sample to detector can significantly create bias in spectro-radiometric temperature measurement. We present a radiance-mapping approach using a hyperspectral camera that records 25 spectral channels spanning 605–875 nm at each pixel in a single exposure, providing spatially and spectrally resolved radiance in each frame. This enables chromatic effects to be recorded and corrected in data processing. We developed a procedure for hyperspectral mapping, involving per-camera calibration, crosstalk removal, measured spectral throughput functions, and optional sub-pixel co-registration to minimize chromatic distortion. The calibrated radiance maps are then used to derive temperature maps of the laser-heated hotspots. For smaller heating spots, the radiance mapping approach reveals chromatic shifts that conventional spectro-radiometric methods cannot quantify. Ambient-pressure heating experiments confirm accurate temperature retrieval. At high pressure, application of the hyperspectral system to a platinum-heating experiment at 12 GPa demonstrates stable temperature reconstruction under steep thermal gradients. Beyond mitigating chromatic aberrations, the ability to diagnose optical artifacts separately from emissivity variations during controlled test experiments or in situ suggests a path toward more rigorous spectral emissivity analysis and improved modeling of thermal transport in laser-heated DAC experiments.
47 OTHER INSTRUMENTATION↗
Applications Of Machine Learning to Gas Plume Analysis In Longwave Infrared Hyperspectral Images
Longwave infrared hyperspectral images can be used for gas plume analysis, as many gases exhibit distinct absorption features in this portion of the electromagnetic spectrum. In practice, accurately identifying weak gas signatures is difficult because the observed radiance is dominated by background radiance, which varies with material, temperature, and viewing conditions. Many gas plume analysis pipelines operate on single images, limiting the ability to leverage spatial and multi-view information that could enhance the analysis. The goal of this dissertation is to explore how machine learning and deep learning methods can complement classical approaches to improve gas plume identification in longwave infrared hyperspectral imagery, and to investigate the use of neural radiance fields for hyperspectral scene reconstruction.
3D Scene Reconstruction↗
Hyperspectral leaf reflectance of grasses varies with evolutionary lineage more than with site
Abstract To predict ecological responses at broad environmental scales, grass species are commonly grouped into two broad functional types based on photosynthetic pathway. However, closely related species may have distinctive anatomical and physiological attributes that influence ecological responses, beyond those related to photosynthetic pathway alone. Hyperspectral leaf reflectance can provide an integrated measure of covarying leaf traits that may result from phylogenetic trait conservatism and/or environmental conditions. Understanding whether spectra‐trait relationships are lineage specific or reflect environmental variation across sites is necessary for using hyperspectral reflectance to predict plant responses to environmental changes across spatial scales. We measured hyperspectral leaf reflectance (400–2400 nm) and 12 structural, biochemical, and physiological leaf traits from five grass‐dominated sites spanning the Great Plains of North America. We assessed if variation in leaf reflectance spectra among grass species is explained more by evolutionary lineage (as captured by tribes or subfamilies), photosynthetic pathway (C 3 or C 4 ), or site differences. We then determined whether leaf spectra can be used to predict leaf traits within and across lineages. Our results using redundancy analysis ordination (RDA) show that grass tribe identity explained more variation in leaf spectra (adjusted R 2 = 0.12) than photosynthetic pathway, which explained little variation in leaf spectra (adjusted R 2 = 0.00). Furthermore, leaf reflectance from the same tribe across multiple sites was more similar than leaf reflectance from the same site across tribes (adjusted R 2 = 0.12 and 0.08, respectively). Across all sites and species, trait predictions based on spectra ranged considerably in predictive accuracies ( R 2 = 0.65 to <0.01), but R 2 was >0.80 for certain lineages and sites. The relationship between Vc max , a measure of photosynthetic capacity, and spectra was particularly promising. Chloridoideae, a lineage more common at drier sites, appears to have distinct spectra‐trait relationships compared with other lineages. Overall, our results show that evolutionary relatedness explains more variation in grass leaf spectra than photosynthetic pathway or site, but consideration of lineage‐ and site‐specific trait relationships is needed to interpret spectral variation across large environmental gradients.
Pau, Stephanie [Department of Geography University↗
Reagent-free Hyperspectral Diagnosis of SARS-CoV-2 Infection in Saliva Samples
Rapid, reagent-free pathogen-agnostic diagnostics that can be performed at the point of need are vital for preparedness against future outbreaks. Yet, many current strategies are pathogen-specific and require several reagents. We present hyperspectral sensing, using light to non-invasively measure the composition of several molecules to form a spectral signature, to overcome these barriers. To generate these spectral signatures, we present the ProSpectral TM V1, a novel, miniaturized hyperspectral platform with high spectral resolution with two mini-spectrometers. Furthermore, we developed state-of-the-art ML pipelines for near real-time analysis of spectral signatures in saliva samples. We found that we could accurately identify SARS-CoV-2 infection status in double-blinded saliva samples and demonstrate 100% accuracy on a hold out test dataset. To our knowledge, this establishes the fastest hyperspectral diagnostic platform and in a small form factor, and executable with liquid samples, without ligands or reagents, all while maintaining PCR level specificity and sensitivity.
59 BASIC BIOLOGICAL SCIENCES↗
Hyperspectral segmentation of plants in fabricated ecosystems
Hyperspectral imaging provides a powerful tool for analyzing above-ground plant characteristics in fabricated ecosystems, offering rich spectral information across diverse wavelengths. This study presents an efficient workflow for hyperspectral data segmentation and subsequent data analytics, minimizing the need for user annotation through the use of ensembles of sparse mixed scale convolution neural networks. The segmentation process leverages the diversity of ensembles to achieve high accuracy with minimal labeled data, reducing labor-intensive annotation efforts. To further enhance robustness, we incorporate image alignment techniques to address spatial variability in the dataset. Downstream analysis focuses on using the segmented data for processing spectral data, enabling monitoring of plant health. This approach provides a scalable solution for spectral segmentation, and facilitates actionable insights into plant conditions in complex, controlled environments. Our results demonstrate the utility of combining advanced machine learning techniques with hyperspectral analytics for high-throughput plant monitoring.
Zwart, Petrus H.↗
Hyperspectral traits (TSWIFT) UC Davis Populus trichocarpa Common Garden
This dataset provides tower-based hyperspectral remote sensing measurements of individualPopulustrees collected with the TSWIFT system to support genetic analyses of canopy photosynthetic traits over time under drought. From 2022-08-18 to 2022-10-18, spectra were repeatedly acquired from the same targeted canopy area of each tree using fixed pointing coordinates. The dataset includes hyperspectral measurements from 400–900 nm and ultraspectral measurements from 730–780 nm. These spectra enable calculation of reflectance-based vegetation indices and other spectral traits, including solar-induced fluorescence (SIF) retrievals from the ultraspectral region. Because measurements were collected exclusively over a drought treatment plot, derived phenotypes are intended for drought-context genetic association and prediction analyses.
09 BIOMASS FUELS↗
Leveraging hyperspectral phenotyping for accurate, non-destructive prediction of metabolite profiles in poplar under drought stress
Accurately predicting drought tolerance in woody perennial bioenergy crops is critical for sustainable biomass production under fluctuating precipitation. Hyperspectral imaging (HSI) in the visible-near-infrared (VNIR) and shortwave-infrared (SWIR) ranges offers a promising approach for predicting plant biochemical traits, yet its application in metabolite profiling remains underexplored. We integrated VNIR+SWIR HSI with untargeted metabolomics to investigate drought-induced metabolic shifts in Populus leaves from eight Populus genotypes. Metabolite profiling identified 127 compounds, with 73 showing significant drought responses spanning amino acids (AA), carbohydrates (CHO), phenolic glycosides (PG), organic acids (OA), fatty acids and alcohols (FA), terpenes (T), phenolic metabolites (P), and unclassified metabolites. Spectral analysis revealed consistently higher reflectance across VNIR and SWIR wavelengths in drought-stressed plants, corresponding with increased accumulation of AA and reduced CHO and PG levels. Least absolute shrinkage and selection operator (LASSO) regression modeling identified robust spectral predictors of metabolite concentrations, associating VNIR wavelengths (500–700 nm) predominantly with AA and P, whereas SWIR wavelengths (1680–1700 nm) reliably predicted CHO, OA, and T. Several stable spectral-metabolite associations persisted across the two watering regimes (drought vs. well-watered), highlighting their potential as spectral biomarkers for non-destructive stress monitoring. Minimal genotype-specific variation suggests that observed spectral and metabolic responses were driven primarily by environmental factors, likely reflecting limited genetic diversity among the commercial Populus genotypes examined. This work establishes VNIR+SWIR hyperspectral imaging as a powerful, non-destructive phenotyping tool for precision monitoring and targeted improvement of drought resilience in bioenergy crops.
Biochemical trait prediction↗
Influence of Atmospheric Slant Path on Geostationary Hyperspectral Infrared Sounder Radiance Simulations
Accurately simulating a geostationary hyperspectral infrared sounder is critical for quantitative applications. Traditional radiation simulations of such instruments often overlook the influence of slant observation geometry by using vertical profile assumption, leading to inadequate simulation accuracy. By using global atmospheric profiles with 1 km spatial resolution, the slant-path effects on brightness temperature simulations are quantified. Experiments indicate that the slant geometry has less impact on longwave brightness temperature simulations and has a substantial impact on middle-wave brightness temperature simulations. It may introduce 0.5 K (or more) uncertainty to brightness temperatures of water vapor absorption channels when the satellite zenith angle is greater than 45°. Considering the slant profile is recommended for quantitative applications of geostationary hyperspectral sounder data, such as sounding retrieval and data assimilation.
54 ENVIRONMENTAL SCIENCES↗
Chlorophyll- a dynamics in the lower Amazon River: insights from in situ and hyperspectral remote sensing using OCI-PACE
Chlorophyll-a concentration (Chla) is a key indicator of phytoplankton biomass and aquatic trophic status. However, satellite-derived Chla in sediment-rich waters, such as those found in the Lower Amazon River, remains challenging. The present study characterizes in situ Chla levels and their relationships with geographic, physical, and biogeochemical parameters in the Lower Amazon. Data collected between 2014 and 2017 across four hydrological seasons included measurements of Chla, remote sensing reflectance, and water quality parameters such as total suspended sediment, conductivity, water surface temperature, dissolved oxygen, pH, dissolved organic carbon and coloured dissolved organic matter. An empirical model was developed to estimate Chla using simulated hyperspectral bands from NASA’s PACE mission, achieving high performance (R 2 = 0.76; RMSE = 0.11 μg·L −1 ). Red bands proved particularly effective for Chla retrieval, while the addition of ultraviolet bands further enhanced model accuracy. The application of the developed model to satellite imagery yielded results consistent with in situ observations for the same hydrologic season. Seasonal variation and geographic location were major factors influencing Chla dynamics. This study provides a novel contribution to Chla estimation in optically complex, highly turbid waters and highlights the potential of the PACE mission to enhance global aquatic ecosystem monitoring. In conclusion, by offering freely available hyperspectral data with high radiometric resolution, PACE represents a significant advancement in the realm of remote sensing of aquatic environments.
Amazon River↗
Leveraging hyperspectral imaging to identify drought tolerant Populus species and genotypes within species
The aim of this study was to identity variation in drought tolerance across genotypes of Populus deltoides, Populus trichocarpa, and hybrids of the two species. A panel of 102 Populus genotypes, comprising 37 genotypes of P. trichocarpa, 37 of P. deltoides and 28 unique hybrid genotypes (P. trichocarpa x P. deltoides and P. deltoides x P. trichocarpa) were evaluated in the greenhouse under two treatments, well-watered (WW) and drought (DS). Plant physiological data were collected throughout the experiment once the drought treatment began. Throughout the experiment, we tracked soil volumetric water content, pot weight, stomatal conductance, quantum yield of photosystem II, and electron transport rate. In addition to those measurements, upon completion of the experiment, we assessed above and belowground plant biomass, plant height and stem diameter, leaf number, specific leaf area, relative water content, total protein, and total chlorophyll. We obtained hyperspectral signatures of one leaf from each plant at the end of the experiment. Columns BC – LL are hyperspectral averages for one leaf from each plant at each wavelength as described in the column header.
Hyper-spectral imaging, Populus, plant stress tole↗
HAMscope: a snapshot Hyperspectral Autofluorescence Miniscope for real-time molecular imaging
We introduce HAMscope, a compact, snapshot hyperspectral autofluorescence miniscope that enables real-time, label-free molecular imaging in a wide range of biological systems. By integrating a thin polymer diffuser into a widefield miniscope, HAMscope spectrally encodes each frame and employs a probabilistic deep learning framework to reconstruct 30-channel hyperspectral stacks (452-703 nm) or directly infer molecular composition maps from single images. A scalable multi-pass U-Net architecture with transformer-based attention and per pixel uncertainty estimation enables high spatio-spectral fidelity (mean absolute error ∼0.0048) at video rates. While initially demonstrated in plant systems, including lignin, chlorophyll, and suberin imaging in intact poplar and cork tissues, the platform is readily adaptable to other applications such as neural activity mapping, metabolic profiling, and histopathology. We show that the system generalizes to out-of-distribution tissue types and supports direct molecular mapping without the need for spectral unmixing. HAMscope establishes a general framework for compact, uncertainty-aware spectral imaging that combines minimal optics with advanced deep learning, offering broad utility for real-time biochemical imaging across neuroscience, environmental monitoring, and biomedicine.
59 BASIC BIOLOGICAL SCIENCES↗