Hyperspectral Image Target Detection Using Deep Ensembles for Robust Uncertainty Quantification.
Abstract not provided.
Sahay, Rajeev↗
SEARCH · Engineering Papers
Results for “hyperspectral”
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HyperKube: A Kubernetes Based System for the Automation of Processing and Analysis of Hyperspectral Data Obtained from Multiple Hyperspectral Imaging Systems
Hyperspectral imagery is an emerging field of technology that has enormous potential for remote and proximal sensing in numerous areas of research. The plant phenotyping community is applying this technology to advance the throughput and accuracy of plant phenotypes based on airborne and lab-based hyperspectral imaging technology. Here we report an automated processing and analysis pipeline for four different hyperspectral imaging platforms, discuss the data issues involved, and present a strategy for computing and data architecture to handle hyperspectral data.
47 OTHER INSTRUMENTATION↗
One-shot gas detection with transformer paired neural networks in Mako collected longwave infrared hyperspectral imagery
Explore the source record for details and available documents.
Benham, Kevin Andrew↗
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↗
An Unmanned Aerial System (UAS) for concurrent measurements of solar-induced chlorophyll fluorescence and hyperspectral reflectance toward improving crop monitoring
Unmanned aerial system (UAS)-based remote sensing can provide high spatial- and temporal-resolution crop monitoring for precision management. Existing crop monitoring UAS primarily use conventional techniques such as multi-spectral broadband vegetation indices (VIs) to track canopy structure/biomass. Recently developed lightweight hyperspectral sensors can track crop physiology and performance via complementary signals such as solar-induced chlorophyll fluorescence (SIF) and photochemical reflectance index (PRI) that can be derived from hyperspectral reflectance. However, few existing UAS can acquire high-quality SIF and hyperspectral reflectance. Here, we designed a novel UAS that simultaneously captures far-red SIF and hyperspectral reflectance, using a single bifurcated fiber and motorized arm to measure downwelling and upwelling irradiance. The UAS was tested over (1) a heterogeneous corn field with spatially varying crop yield potential and (2) a set of soybean and corn plots under differing nutrient treatments. Our UAS can maintain stability under low-to-moderate winds (2–3 m/s) with <0.4 m geolocation accuracy, <0.1 m altitude drift, and <1.5° error of the fiber optic from nadir position during scanning. Weekly seasonal campaigns reveal that SIF outperforms conventional VIs such as the normalized difference vegetation index (NDVI) for distinguishing plots with different crop yield potential, especially after canopy closure when NDVI tends to saturate. The UAS can capture the diurnal dynamics of SIF and PRI for both corn and soybean. At the seasonal scale, SIF acquired from the UAS correlates well with that from a fixed SIF tower system ( R 2 = 0.81), which measured the same target albeit with different footprints, demonstrating the capability of UAS in characterizing the seasonal progression of crop activity. In conclusion, our newly developed UAS provides high-quality SIF and hyperspectral reflectance, facilitating mechanistic understanding of the physiological control on photosynthesis dynamics. Our findings also imply that this UAS could enable extension of fixed tower-based systems to monitor multiple targets from diurnal to seasonal scales and improve monitoring of heterogeneous fields.
59 BASIC BIOLOGICAL SCIENCES↗
Cross-scale sensing of field-level crop residue cover: Integrating field photos, airborne hyperspectral imaging, and satellite data
Conservation tillage practices can bring benefits to agricultural sustainability. Accurate spatial and temporal resolved information of field-scale crop residue cover, which reflects tillage intensity, is highly valuable for evaluating the outcomes of government conservation programs and voluntary ecosystem service markets, as well as facilitating agroecosystem modeling to quantify cropland biogeochemical processes. Remote sensing has the potential to cost-effectively detect crop residue cover, however, existing regional-scale studies were limited by insufficient ground truth data, scale mismatch between coarse satellite pixels and ground data, and the lack of key spectral data for detecting crop residues. Therefore, this study developed an innovative cross-sensing framework to integrate proximal sensing, airborne hyperspectral imaging, and satellite Earth Observation through deep learning to quantify field-level crop residue cover fractions at the regional scale. Specifically, we have collected intensive ground orthographic photos and conducted airborne hyperspectral surveys at corn and soybean fields of Champaign and nearby counties in Illinois, the heartland of the U.S. Corn Belt. Through semi-automatic labeling aided by ResNet-50 and superpixel image segmentation, we obtained 6719 records of ground residue fractions. With these ground data, we developed the 1-dimensional convolution neural network (CNN) model using airborne hyperspectral reflectance, which has 0.5m spatial resolution and 3–5 nm spectral resolution from 400 to 2400 nm, to predict residue fractions. By applying the CNN model to airborne pixels, we augmented “ground truth” data of crop residues and further combined them with Harmonized Landsat and Sentinel-2 (HLS) satellite data to quantify regional residue fractions at 30 m resolution. Results show that airborne hyperspectral imagery with CNN can accurately detect residue fractions (R 2 = 0.82, relative RMSE = 11.73%) to effectively generate quasi “ground truth” data to support satellite upscaling to all fields. With independent ground data for testing, we found that the ground-airborne-satellite integrative framework achieved better predictions in estimating crop residue cover (R 2 = 0.67, relative RMSE = 17.53%) than the conventional ground-satellite upscaling (R 2 = 0.22, relative RMSE = 32.09%). Here we also found that the shortwave infrared wavelengths, particularly 2100–2300 nm, are vital for predicting crop residue cover. Sentinel-2 and Landsat-8 data have a comparable capability to track residue fractions due to similar shortwave infrared wavelengths. This study highlights the high accuracy of hyperspectral imaging to detect agroecosystem tillage management practices and the advantages of cross-scale sensing to cost-effectively integrate multi-source data to quantify field-level agroecosystem variables across scales.
60 APPLIED LIFE SCIENCES↗
Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems
Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.
59 BASIC BIOLOGICAL SCIENCES↗
Fast Data Processing for Hyperspectral Sensors on Small Platforms
Hyperspectral imaging is a very promising technology for nuclear proliferation detection. However, due to size and weight restrictions, small hyperspectral platforms such as satellites and small drones lack the on-board computing resources for accurate, real-time analysis of the enormous flow of data that a continuously operating hyperspectral sensor generates. This severely limits satellite systems, which can collect far more data than what they can telemeter, and hinders the ability of all platforms to adapt their missions on the fly in response to observations. This program addresses the hyperspectral data processing challenge through development of new, fast and accurate algorithms that produce data products in real time. The algorithms circumvent the major computational bottlenecks in existing processing streams, and would be incorporated in lightweight, power-efficient single-board computer systems. The toolkit of fast algorithms will be immediately useful in current and future hyperspectral systems being built by the Government and by private industry, including drone-based systems and satellite constellations that acquire timely global imagery.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Airborne hyperspectral imaging of cover crops through radiative transfer process-guided machine learning
Cover cropping between cash crop growing seasons is a multifunctional conservation practice. Timely and accurate monitoring of cover crop traits, notably aboveground biomass and nutrient content, is beneficial to agricultural stakeholders to improve management and understand outcomes. Currently, there is a scarcity of spatially and temporally resolved information for assessing cover crop growth. Remote sensing has a high potential to fill this need, but conventional empirical regression operated with coarse-resolution multispectral data has large uncertainties. Therefore, this study utilized airborne hyperspectral imaging techniques and developed new process-guided machine learning approaches (PGML) for cover crop monitoring. Specifically, we deployed an airborne hyperspectral system covering visible to shortwave-infrared wavelengths (400–2400 nm) to acquire high spatial (0.5 m) and spectral (3–5 nm) resolution reflectance over 23 cover crop fields across Central Illinois in March and April of 2021. Airborne hyperspectral surface reflectance with high spectral and spatial resolution can be well matched with field data to quantify cover crop traits. Furthermore, the PGML models were pre-trained by synthetic data from soil-vegetation radiative transfer modeling (one million records), and then fine-tuned with field data of cover crop biomass and nutrient content. Results show that airborne hyperspectral data with PGML can achieve high accuracy to predict cover crop aboveground biomass (R 2 = 0.72, relative RMSE = 15.16%) and nitrogen content (R 2 = 0.69, relative RMSE = 16.59%) through leave-one-field-out cross-validation. Unlike the pure data-driven approach (e.g., partial least-squares regression), PGML incorporated radiative transfer knowledge and obtained higher predictive performance with fewer field data. Meanwhile, with field data for model fine-tuning, PGML predicted biomass more accurately than the inversion of radiative transfer models. Here we also found that the red edge has a high contribution in quantifying aboveground biomass and nitrogen content, followed by green and shortwave spectra. This study demonstrated the first attempt of utilizing hyperspectral remote sensing to accurately quantify cover crop traits. We highlight the strength of PGML in exploiting sensing data to quantify ecosystem variables to advance agroecosystem monitoring for sustainable agricultural management.
60 APPLIED LIFE SCIENCES↗
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]↗
Using soil library hyperspectral reflectance and machine learning to predict soil organic carbon: Assessing potential of airborne and spaceborne optical soil sensing
Soil organic carbon (SOC) is a key variable to determine soil functioning, ecosystem services, and global carbon cycles. Spectroscopy, particularly optical hyperspectral reflectance coupled with machine learning, can provide rapid, efficient, and cost-effective quantification of SOC. However, how to exploit soil hyperspectral reflectance to predict SOC concentration, and the potential performance of airborne and satellite data for predicting surface SOC at large scales remain relatively underknown. Here, this study utilized a continental-scale soil laboratory spectral library (37,540 full-pedon 350–2500 nm reflectance spectra with SOC concentration of 0–780 g·kg –1 across the US) to thoroughly evaluate seven machine learning algorithms including Partial-Least Squares Regression (PLSR), Random Forest (RF), K-Nearest Neighbors (KNN), Ridge, Artificial Neural Networks (ANN), Convolutional Neural Networks (CNN), and Long Short-Term Memory (LSTM) along with four preprocessed spectra, i.e. original, vector normalization, continuum removal, and first-order derivative, to quantify SOC concentration. Furthermore, by using the coupled soil-vegetation-atmosphere radiative transfer model, we simulated twelve airborne and spaceborne hyper/multi-spectral remote sensing data from surface bare soil laboratory spectra to evaluate their potential for estimating SOC concentration of surface bare soils. Results show that LSTM achieved best predictive performance of quantifying SOC concentration for the whole data sets (R 2 = 0.96, RMSE = 30.81 g·kg –1 ), mineral soils (SOC ≤ 120 g·kg –1 , R 2 = 0.71, RMSE = 10.60 g·kg –1 ), and organic soils (SOC > 120 g·kg –1 , R 2 = 0.78, RMSE = 62.31 g·kg –1 ). Spectral data preprocessing, particularly the first-order derivative, improved the performance of PLSR, RF, Ridge, KNN, and ANN, but not LSTM or CNN. We found that the SOC models of mineral and organic soils should be distinguished given their distinct spectral signatures. Finally, we identified that the shortwave infrared is vital for airborne and spaceborne hyperspectral sensors to monitor surface SOC. This study highlights the high accuracy of LSTM with hyperspectral/multispectral data to mitigate a certain level of noise (soil moisture <0.4 m 3 ·m –3 , green leaf area < 0.3 m 2 ·m –2 , plant residue <0.4 m 2 ·m –2 ) for quantifying surface SOC concentration. Forthcoming satellite hyperspectral missions like Surface Biology and Geology (SBG) have a high potential for future global soil carbon monitoring, while high-resolution satellite multispectral fusion data can be an alternative.
54 ENVIRONMENTAL SCIENCES↗
Wildfires Temperature Estimation by Complementary Use of Hyperspectral PRISMA and Thermal (ECOSTRESS & L8)
This paper deals with detection and temperature analysis and of wildfires using PRISMA imagery. Precursore IperSpettrale della Missione Applicativa (Hyperspectral Precursor of the Application Mission, PRISMA) is a new hyperspectral mission by ASI (Agenzia Spaziale Italiana, Italian Space Agency) launched in 2019. This mission provides hyperspectral images with a spectral range of 400–2,500 nm and an average spectral resolution less than 12 nm and a spatial resolution of 30 m/pixel. This study focuses on the wildfire temperature estimation over the Bootleg Fire, US 2021. The analysis starts by considering the Hyperspectral Fire Detection Index (HFDI) which is used to analyze the informative content of the images, along with the analysis of some specific visible, near-infrared and shortwave-infrared bands. This first analysis is used as input to perform a temperature estimation of the areas with active wildfire. Surface temperature is retrieved using PRISMA radiance and a linear mixing model based on two background components (vegetation and burn scar) and two active fire components. PRISMA temperatures are compared with LST (Land Surface Temperature) products from NASA's ECOSTRESS and Landsat 8 which imaged the Bootleg Fire before and after PRISMA. A critical discussion of the results obtained with PRISMA is presented, followed by the advantages and limitation of the proposed approach.
54 ENVIRONMENTAL SCIENCES↗
More chemical detection through less sampling: amplifying chemical signals in hyperspectral data cubes through compressive sensing
Compressive sensing (CS) is a method of sampling which permits some classes of signals to be reconstructed with high accuracy even when they were sampled at sub-Nyquist rates. In this paper we explore a phenomenon in which bandwise CS sampling of a hyperspectral data cube followed by reconstruction can actually result in amplification of chemical signals contained in the cube. Perhaps most surprisingly, chemical signal amplification generally seems to increase as the level of sampling decreases. In some examples, the chemical signal is significantly stronger in a data cube reconstructed from 10% CS sampling than it is in the raw, 100% sampled data cube. We explore this phenomenon in two real-world datasets including the Physical Sciences Inc. Fabry-Perot interferometer sensor multispectral dataset and the Johns Hopkins Applied Physics Lab FTIR-based longwave infrared sensor hyperspectral dataset. Each of these datasets contains the release of a chemical simulant, such as glacial acetic acid, triethyl phospate, and sulfur hexafluoride, and in all cases we use the adaptive coherence estimator (ACE) to detect a target signal in the hyperspectral data cube. We end the paper by suggesting some theoretical justifications for why chemical signals would be amplified in CS sampled and reconstructed hyperspectral data cubes and discuss some practical implications.
Hyperspectral imagery, Compressive Sensing, single↗
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↗
Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel
Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize ( Zea mays ) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.
Tross, Michael C.↗
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↗