Relevant bibliographies by topics / Hyperspectral Phenotyping

Academic literature on the topic 'Hyperspectral Phenotyping'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Hyperspectral Phenotyping"

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Huang, Peikui, Xiwen Luo, Jian Jin, Liangju Wang, Libo Zhang, Jie Liu, and Zhigang Zhang. "Improving High-Throughput Phenotyping Using Fusion of Close-Range Hyperspectral Camera and Low-Cost Depth Sensor." Sensors 18, no. 8 (August 17, 2018): 2711. http://dx.doi.org/10.3390/s18082711.

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Hyperspectral sensors, especially the close-range hyperspectral camera, have been widely introduced to detect biological processes of plants in the high-throughput phenotyping platform, to support the identification of biotic and abiotic stress reactions at an early stage. However, the complex geometry of plants and their interaction with the illumination, severely affects the spectral information obtained. Furthermore, plant structure, leaf area, and leaf inclination distribution are critical indexes which have been widely used in multiple plant models. Therefore, the process of combination between hyperspectral images and 3D point clouds is a promising approach to solve these problems and improve the high-throughput phenotyping technique. We proposed a novel approach fusing a low-cost depth sensor and a close-range hyperspectral camera, which extended hyperspectral camera ability with 3D information as a potential tool for high-throughput phenotyping. An exemplary new calibration and analysis method was shown in soybean leaf experiments. The results showed that a 0.99 pixel resolution for the hyperspectral camera and a 3.3 millimeter accuracy for the depth sensor, could be achieved in a controlled environment using the method proposed in this paper. We also discussed the new capabilities gained using this new method, to quantify and model the effects of plant geometry and sensor configuration. The possibility of 3D reflectance models can be used to minimize the geometry-related effects in hyperspectral images, and to significantly improve high-throughput phenotyping. Overall results of this research, indicated that the proposed method provided more accurate spatial and spectral plant information, which helped to enhance the precision of biological processes in high-throughput phenotyping.
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Sarić, Rijad, Viet D. Nguyen, Timothy Burge, Oliver Berkowitz, Martin Trtílek, James Whelan, Mathew G. Lewsey, and Edhem Čustović. "Applications of hyperspectral imaging in plant phenotyping." Trends in Plant Science 27, no. 3 (March 2022): 301–15. http://dx.doi.org/10.1016/j.tplants.2021.12.003.

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Kuska, Matheus Thomas, Anna Brugger, Stefan Thomas, Mirwaes Wahabzada, Kristian Kersting, Erich-Christian Oerke, Ulrike Steiner, and Anne-Katrin Mahlein. "Spectral Patterns Reveal Early Resistance Reactions of Barley Against Blumeria graminis f. sp. hordei." Phytopathology® 107, no. 11 (November 2017): 1388–98. http://dx.doi.org/10.1094/phyto-04-17-0128-r.

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Differences in early plant–pathogen interactions are mainly characterized by using destructive methods. Optical sensors are advanced techniques for phenotyping host–pathogen interactions on different scales and for detecting subtle plant resistance responses against pathogens. A microscope with a hyperspectral camera was used to study interactions between Blumeria graminis f. sp. hordei and barley (Hordeum vulgare) genotypes with high susceptibility or resistance due to hypersensitive response (HR) and papilla formation. Qualitative and quantitative assessment of pathogen development was used to explain changes in hyperspectral signatures. Within 48 h after inoculation, genotype-specific changes in the green and red range (500 to 690 nm) and a blue shift of the red-edge inflection point were observed. Manual analysis indicated resistance-specific reflectance patterns from 1 to 3 days after inoculation. These changes could be linked to host plant modifications depending on individual host–pathogen interactions. Retrospective analysis of hyperspectral images revealed spectral characteristics of HR against B. graminis f. sp. hordei. For early HR detection, an advanced data mining approach localized HR spots before they became visible on the RGB images derived from hyperspectral imaging. The link among processes during pathogenesis and host resistance to changes in hyperspectral signatures provide evidence that sensor-based phenotyping is suitable to advance time-consuming and cost-expensive visual rating of plant disease resistances.
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Sadeghi-Tehran, Pouria, Nicolas Virlet, and Malcolm J. Hawkesford. "A Neural Network Method for Classification of Sunlit and Shaded Components of Wheat Canopies in the Field Using High-Resolution Hyperspectral Imagery." Remote Sensing 13, no. 5 (February 27, 2021): 898. http://dx.doi.org/10.3390/rs13050898.

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(1) Background: Information rich hyperspectral sensing, together with robust image analysis, is providing new research pathways in plant phenotyping. This combination facilitates the acquisition of spectral signatures of individual plant organs as well as providing detailed information about the physiological status of plants. Despite the advances in hyperspectral technology in field-based plant phenotyping, little is known about the characteristic spectral signatures of shaded and sunlit components in wheat canopies. Non-imaging hyperspectral sensors cannot provide spatial information; thus, they are not able to distinguish the spectral reflectance differences between canopy components. On the other hand, the rapid development of high-resolution imaging spectroscopy sensors opens new opportunities to investigate the reflectance spectra of individual plant organs which lead to the understanding of canopy biophysical and chemical characteristics. (2) Method: This study reports the development of a computer vision pipeline to analyze ground-acquired imaging spectrometry with high spatial and spectral resolutions for plant phenotyping. The work focuses on the critical steps in the image analysis pipeline from pre-processing to the classification of hyperspectral images. In this paper, two convolutional neural networks (CNN) are employed to automatically map wheat canopy components in shaded and sunlit regions and to determine their specific spectral signatures. The first method uses pixel vectors of the full spectral features as inputs to the CNN model and the second method integrates the dimension reduction technique known as linear discriminate analysis (LDA) along with the CNN to increase the feature discrimination and improves computational efficiency. (3) Results: The proposed technique alleviates the limitations and lack of separability inherent in existing pre-defined hyperspectral classification methods. It optimizes the use of hyperspectral imaging and ensures that the data provide information about the spectral characteristics of the targeted plant organs, rather than the background. We demonstrated that high-resolution hyperspectral imagery along with the proposed CNN model can be powerful tools for characterizing sunlit and shaded components of wheat canopies in the field. The presented method will provide significant advances in the determination and relevance of spectral properties of shaded and sunlit canopy components under natural light conditions.
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Brugger, Anna, Jan Behmann, Stefan Paulus, Hans-Georg Luigs, Matheus Thomas Kuska, Patrick Schramowski, Kristian Kersting, Ulrike Steiner, and Anne-Katrin Mahlein. "Extending Hyperspectral Imaging for Plant Phenotyping to the UV-Range." Remote Sensing 11, no. 12 (June 12, 2019): 1401. http://dx.doi.org/10.3390/rs11121401.

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Previous plant phenotyping studies have focused on the visible (VIS, 400–700 nm), near-infrared (NIR, 700–1000 nm) and short-wave infrared (SWIR, 1000–2500 nm) range. The ultraviolet range (UV, 200–380 nm) has not yet been used in plant phenotyping even though a number of plant molecules like flavones and phenol feature absorption maxima in this range. In this study an imaging UV line scanner in the range of 250–430 nm is introduced to investigate crop plants for plant phenotyping. Observing plants in the UV-range can provide information about important changes of plant substances. To record reliable and reproducible time series results, measurement conditions were defined that exclude phototoxic effects of UV-illumination in the plant tissue. The measurement quality of the UV-camera has been assessed by comparing it to a non-imaging UV-spectrometer by measuring six different plant-based substances. Given the findings of these preliminary studies, an experiment has been defined and performed monitoring the stress response of barley leaves to salt stress. The aim was to visualize the effects of abiotic stress within the UV-range to provide new insights into the stress response of plants. Our study demonstrated the first use of a hyperspectral sensor in the UV-range for stress detection in plant phenotyping.
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Banerjee, Bikram P., Sameer Joshi, Emily Thoday-Kennedy, Raj K. Pasam, Josquin Tibbits, Matthew Hayden, German Spangenberg, and Surya Kant. "High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response." Journal of Experimental Botany 71, no. 15 (March 18, 2020): 4604–15. http://dx.doi.org/10.1093/jxb/eraa143.

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Abstract The development of crop varieties with higher nitrogen use efficiency is crucial for sustainable crop production. Combining high-throughput genotyping and phenotyping will expedite the discovery of novel alleles for breeding crop varieties with higher nitrogen use efficiency. Digital and hyperspectral imaging techniques can efficiently evaluate the growth, biophysical, and biochemical performance of plant populations by quantifying canopy reflectance response. Here, these techniques were used to derive automated phenotyping of indicator biomarkers, biomass and chlorophyll levels, corresponding to different nitrogen levels. A detailed description of digital and hyperspectral imaging and the associated challenges and required considerations are provided, with application to delineate the nitrogen response in wheat. Computational approaches for spectrum calibration and rectification, plant area detection, and derivation of vegetation index analysis are presented. We developed a novel vegetation index with higher precision to estimate chlorophyll levels, underpinned by an image-processing algorithm that effectively removed background spectra. Digital shoot biomass and growth parameters were derived, enabling the efficient phenotyping of wheat plants at the vegetative stage, obviating the need for phenotyping until maturity. Overall, our results suggest value in the integration of high-throughput digital and spectral phenomics for rapid screening of large wheat populations for nitrogen response.
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Behmann, Jan, Anne-Katrin Mahlein, Stefan Paulus, Heiner Kuhlmann, Erich-Christian Oerke, and Lutz Plümer. "Calibration of hyperspectral close-range pushbroom cameras for plant phenotyping." ISPRS Journal of Photogrammetry and Remote Sensing 106 (August 2015): 172–82. http://dx.doi.org/10.1016/j.isprsjprs.2015.05.010.

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Oerke, Erich-Christian, Katja Herzog, and Reinhard Toepfer. "Hyperspectral phenotyping of the reaction of grapevine genotypes toPlasmopara viticola." Journal of Experimental Botany 67, no. 18 (August 27, 2016): 5529–43. http://dx.doi.org/10.1093/jxb/erw318.

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Ribes, Mathieu, Gaspard Russias, Denis Tregoat, and Antoine Fournier. "Towards Low-Cost Hyperspectral Single-Pixel Imaging for Plant Phenotyping." Sensors 20, no. 4 (February 19, 2020): 1132. http://dx.doi.org/10.3390/s20041132.

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Hyperspectral imaging techniques have been expanding considerably in recent years. The cost of current solutions is decreasing, but these high-end technologies are not yet available for moderate to low-cost outdoor and indoor applications. We have used some of the latest compressive sensing methods with a single-pixel imaging setup. Projected patterns were generated on Fourier basis, which is well-known for its properties and reduction of acquisition and calculation times. A low-cost, moderate-flow prototype was developed and studied in the laboratory, which has made it possible to obtain metrologically validated reflectance measurements using a minimal computational workload. From these measurements, it was possible to discriminate plant species from the rest of a scene and to identify biologically contrasted areas within a leaf. This prototype gives access to easy-to-use phenotyping and teaching tools at very low-cost.
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Ma, Dongdong, Tanzeel U. Rehman, Libo Zhang, Hideki Maki, Mitchell R. Tuinstra, and Jian Jin. "Modeling of Environmental Impacts on Aerial Hyperspectral Images for Corn Plant Phenotyping." Remote Sensing 13, no. 13 (June 28, 2021): 2520. http://dx.doi.org/10.3390/rs13132520.

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Aerial imaging technologies have been widely applied in agricultural plant remote sensing. However, an as yet unexplored challenge with field imaging is that the environmental conditions, such as sun angle, cloud coverage, temperature, and so on, can significantly alter plant appearance and thus affect the imaging sensor’s accuracy toward extracting plant feature measurements. These image alterations result from the complicated interaction between the real-time environments and plants. Analysis of these impacts requires continuous monitoring of the changes through various environmental conditions, which has been difficult with current aerial remote sensing systems. This paper aimed to propose a modeling method to comprehensively understand and model the environmental influences on hyperspectral imaging data. In 2019, a fixed hyperspectral imaging gantry was constructed in Purdue University’s research farm, and over 8000 repetitive images of the same corn field were taken with a 2.5 min interval for 31 days. Time-tagged local environment data, including solar zenith angle, solar irradiation, temperature, wind speed, and so on, were also recorded during the imaging time. The images were processed for phenotyping data, and the time series decomposition method was applied to extract the phenotyping data variation caused by the changing environments. An artificial neural network (ANN) was then built to model the relationship between the phenotyping data variation and environmental changes. The ANN model was able to accurately predict the environmental effects in remote sensing results, and thus could be used to effectively eliminate the environment-induced variation in the phenotyping features. The test of the normalized difference vegetation index (NDVI) calculated from the hyperspectral images showed that variance in NDVI was reduced by 79%. A similar performance was confirmed with the relative water content (RWC) predictions. Therefore, this modeling method shows great potential for application in aerial remote sensing applications in agriculture, to significantly improve the imaging quality by effectively eliminating the effects from the changing environmental conditions.
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Dissertations / Theses on the topic "Hyperspectral Phenotyping"

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Alisaac, Elias [Verfasser]. "Phenotyping of wheat resistance to Fusarium head blight using hyperspectral imaging / Elias Alisaac." Bonn : Universitäts- und Landesbibliothek Bonn, 2021. http://d-nb.info/1228978948/34.

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Leucker, Marlene [Verfasser]. "Phenotyping of Cercospora beticola resistance of sugar beet genotypes by hyperspectral imaging / Marlene Leucker." Bonn : Universitäts- und Landesbibliothek Bonn, 2018. http://d-nb.info/1163013196/34.

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Makdessi, Nathalie Al. "Couplage entre modélisation opto-physique des scènes de végétation complexes et chimiométrie : application au phénotypage par imagerie hyperspectrale de proximité." Thesis, Montpellier, 2017. http://www.theses.fr/2017MONTS017.

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L'imagerie hyperspectrale de proximité est un outil prometteur pour le phénotypage ou la surveillance de la végétation. En association avec la régression des moindres carrés partiels ou PLS-R, elle permet de construire des cartographies de haute résolution spatiale du contenu chimique à l’échelle de la canopée. Cependant, plusieurs phénomènes optiques doivent être pris en compte lors de l'application de cette approche aux scènes de végétation dans des conditions naturelles. Notamment, les facteurs additifs et multiplicatifs liés respectivement à la réflexion spéculaire et à l'inclinaison des feuilles qui peuvent être surmontés par prétraitement. Mais le phénomène qui pose le plus de défis est la réflexion multiple. Il se produit lorsqu'une feuille est éclairée en partie par la lumière directe, et en partie par la réflexion ou la transmission de la lumière des feuilles voisines, induisant de forts effets non linéaires sur son spectre de réflectance. Bien que cet effet puisse être pris en compte dans certains modèles de télédétection à l’échelle de la canopée, aucune étude n’a été proposée à ce jour sur la façon dont un tel phénomène affecte les évaluations spectrales de la biochimie végétale par imagerie de proximité. L'objectif de la présente étude était d'analyser ces effets dans le contexte de l'imagerie hyperspectrale à des fins de phénotypage végétal et de proposer des méthodes chimiométriques pour les surmonter. Le développement méthodologique a été basé sur des outils de simulation inclus dans la plate-forme open source OpenAlea (http://openalea.gforge.inria.fr/dokuwiki/doku.php). Une scène typique de canopée de blé a été modélisée à l'aide du modèle Adel-Wheat et combinée au modèle de propagation de la lumière Caribu. L'outil proposé simule la réflectance apparente de chaque feuille visible dans la canopée pour une réflectance et une transmittance réelles données, permettant de synthétiser des images hyperspectrales réalistes. Cette approche par simulation nous a permis, dans un premier temps, d’analyser la distribution dans l’espace spectral des perturbations engendrées par les réflexions multiples, puis d’en déduire une méthode de correction applicable dans le cas d’une régression PLS. La méthode est basée sur la construction de deux sous-espaces W et B générés respectivement par la formulation analytique des réflexions multiples et la variable d'intérêt. Ceci nous permet alors de définir une matrice de projection sur B selon la direction W (projection oblique), qui permet de supprimer l’effet des réflexions multiples tout en conservant l’information utile. Il suffit ensuite d’appliquer cette projection à chaque spectre lors de l’apprentissage et de la mise en œuvre du modèle PLS. La méthode a d’abord été développée et paramétrée sur les données simulées, dans le contexte de l’évaluation de la teneur en azote (LNC) de feuilles de blé. Pour cela, les spectres de réflectance (450-1100 nm) de 57 feuilles de blé ont été collectés à l'aide d'un spectromètre ASD (FieldSpec®, Analytical Spectral Devices, Inc., Boulder, Colorado, USA), tandis que leur LNC a été mesuré à l'aide d'analyses chimiques. Des modèles de régression avec et sans projection oblique ont alors été construits à partir des spectres ASD et appliqués sur l’ensemble des données simulées. Le modèle avec projection oblique a donné d’excellents résultats (R² = 0.931; RMSEP = 0.29% DM) en comparaison du modèle classique (R² = 0.915; RMSEP = 0.42% DM).La même méthode a ensuite été appliquée en conditions réelles, sur des feuilles de blé cultivées en pot et au champ. Pour cela, des feuilles ont été collectées et imagées à plat sur fond noir pour la construction des modèles PLS, qui ont ensuite été appliqués aux plantes sur pied. Ces expérimentations ont confirmé d’une part que la PLS-R classique entraînait une forte surestimation du LNC sur les feuilles entourées d’autres feuilles, d’autre part que la projection oblique évitait cette surestimation
Short range hyperspectral imagery is a promising tool for phenotyping and vegetation survey. When associated with partial least square regression (PLS-R), it allows high spatial resolution mapping of the plant chemical content at the canopy scale. However, several optical phenomena have to be taken into account when applying this approach to vegetation scenes in natural conditions. For instance, additive and multiplicative factors due respectively to specular reflection and leaf inclination can be overcome by spectral preprocessing. But the most challenging phenomenon is multiple scattering. It appears when a leaf is partly lightened by the reflected or transmitted light from surrounding leaves, resulting in strong non linear effects in its apparent reflectance spectrum. Though this effect can be taken into account in some remote sensing models at the canopy scale, no study has been proposed until now concerning its impact on spectral prediction of vegetation chemical content by short range imagery.The objective of this project, associated with a PhD work, was to analyze these effects in the context of hyperspectral imagery for vegetation phenotyping purpose, and to propose spectral processing methods to overcome them.The methodological development has been based on simulation tools included in the open source platform OpenAlea (http://openalea.gforge.inria.fr/dokuwiki/doku.php). A typical wheat canopy scene has been modelled using Adel-Wheat and combined with the light propagation model Caribu. The proposed tool simulates the apparent reflectance of every visible leaf in the canopy for a given actual reflectance and transmittance, allowing to synthetize realistic hyperspectral images.This simulation approach has allowed us, in a first step, to analyze the distribution of deviations due to multiple scattering in the spectral space, and then to infer a correction method in the frame of PLS regression. This method relies on the building of two subspaces EW and EB respectively generated by the analytic formulation of multiple scattering and by the variable of interest. It allows us to define a projection operation on EB subspace along EW direction (oblique projection), in order to remove multiple scattering effects while preserving useful information. This projection operation is then applied on every spectra during learning phase and using phase of the PLS model.The method has first been developed and tuned using simulated data, in the frame of leaf nitrogen content (LNC) prediction of wheat leaves. For this purpose, reflectance spectra (450-1100 nm) of 57 wheat leaves have been collected using a ASD filed spectrometer (FieldSpec®, Analytical Spectral Devices, Inc., Boulder, Colorado, USA), while their LNC was measured through reference chemical analyses. Regression models with and without oblique projection have then been built from the ASD spectra and applied to simulated data. The model with oblique projection provided excellent results (R² = 0.931; RMSEP = 0.29% DM), compared to the classical one (R² = 0.915; RMSEP = 0.42% DM).The same method has then been applied in real conditions on wheat pot plants and field plants. For this purpose, some leaves have been collected and laid on a black paper background to be imaged, in order to build PLS models that have then been applied on in-situ plants. These experimentations have confirmed that the classical PLS-R induces a strong overestimation of LNC on leaves surrounded by other leaves, and that oblique projection corrects this overestimation (same prediction on surrounded then isolated leaf)
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(9224231), Dongdong Ma. "Ameliorating Environmental Effects on Hyperspectral Images for Improved Phenotyping in Greenhouse and Field Conditions." Thesis, 2020.

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Hyperspectral imaging has become one of the most popular technologies in plant phenotyping because it can efficiently and accurately predict numerous plant physiological features such as plant biomass, leaf moisture content, and chlorophyll content. Various hyperspectral imaging systems have been deployed in both greenhouse and field phenotyping activities. However, the hyperspectral imaging quality is severely affected by the continuously changing environmental conditions such as cloud cover, temperature and wind speed that induce noise in plant spectral data. Eliminating these environmental effects to improve imaging quality is critically important. In this thesis, two approaches were taken to address the imaging noise issue in greenhouse and field separately. First, a computational simulation model was built to simulate the greenhouse microclimate changes (such as the temperature and radiation distributions) through a 24-hour cycle in a research greenhouse. The simulated results were used to optimize the movement of an automated conveyor in the greenhouse: the plants were shuffled with the conveyor system with optimized frequency and distance to provide uniform growing conditions such as temperature and lighting intensity for each individual plant. The results showed the variance of the plants’ phenotyping feature measurements decreased significantly (i.e., by up to 83% in plant canopy size) in this conveyor greenhouse. Secondly, the environmental effects (i.e., sun radiation) on aerial hyperspectral images in field plant phenotyping were investigated and modeled. An artificial neural network (ANN) method was proposed to model the relationship between the image variation and environmental changes. Before the 2019 field test, a gantry system was designed and constructed to repeatedly collect time-series hyperspectral images with 2.5 minutes intervals of the corn plants under varying environmental conditions, which included sun radiation, solar zenith angle, diurnal time, humidity, temperature and wind speed. Over 8,000 hyperspectral images of corn (Zea mays L.) were collected with synchronized environmental data throughout the 2019 growing season. The models trained with the proposed ANN method were able to accurately predict the variations in imaging results (i.e., 82.3% for NDVI) caused by the changing environments. Thus, the ANN method can be used by remote sensing professionals to adjust or correct raw imaging data for changing environments to improve plant characterization.
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Angel, Yoseline. "Monitoring crop development and health using UAV-based hyperspectral imagery and machine learning." Diss., 2021. http://hdl.handle.net/10754/670149.

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Agriculture faces many challenges related to the increasing food demands of a growing global population and the sustainable use of resources in a changing environment. To address them, we need reliable information sources, like exploiting hyperspectral satellite, airborne, and ground-based remote sensing data to observe phenological traits through a crops growth cycle and gather information to precisely diagnose when, why, and where a crop is suffering negative impacts. By combining hyperspectral capabilities with unmanned aerial vehicles (UAVs), there is an increased capacity for providing time-critical monitoring and new insights into patterns of crop development. However, considerable effort is required to effectively utilize UAV-integrated hyperspectral systems in crop-modeling and crop-breeding tasks. Here, a UAV-based hyperspectral solution for mapping crop physiological parameters was explored within a machine learning framework. To do this, a range of complementary measurements were collected from a field-based phenotyping experiment, based on a diversity panel of wild tomato (Solanum pimpinellifolium) that were grown under fresh and saline conditions. From the UAV data, positionally accurate reflectance retrievals were produced using a computationally robust automated georectification and mosaicking methodology. The resulting multitemporal UAV data were then employed to retrieve leaf-chlorophyll (Chl) dynamics via a machine learning framework. Several approaches were evaluated to identify the best-performing regression supervised methods. An investigation of two learning strategies (i.e., sequential and retraining) and the value of using spectral bands and vegetation indices (VIs) as prediction features was also performed. Finally, the utility of UAVbased hyperspectral phenotyping was demonstrated by detecting the effects of salt-stress on the different tomato accessions by estimating the salt-induced senescence index from the retrieved Chl dynamics, facilitating the identification of salt-tolerant candidates for future investigations. This research illustrates the potential of UAV-based hyperspectral imaging for plant phenotyping and precision agriculture. In particular, a) developing systematic imaging calibration and pre-processing workflows; b) exploring machine learning-driven tools for retrieving plant phenological dynamics; c) establishing a plant stress detection approach from hyperspectral-derived metrics; and d) providing new insights into using computer vision, big-data analytics, and modeling strategies to deal effectively with the complexity of the UAV-based hyperspectral data in mapping plant physiological indicators.
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Makdessi, Nathalie al. "Couplage entre modélisation opto-physique des scènes de végétation complexes et chimiométrie : application au phénotypage par imagerie hyperspectrale de proximité." Thesis, 2017. http://www.theses.fr/2017MONTS017/document.

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L'imagerie hyperspectrale de proximité est un outil prometteur pour le phénotypage ou la surveillance de la végétation. En association avec la régression des moindres carrés partiels ou PLS-R, elle permet de construire des cartographies de haute résolution spatiale du contenu chimique à l’échelle de la canopée. Cependant, plusieurs phénomènes optiques doivent être pris en compte lors de l'application de cette approche aux scènes de végétation dans des conditions naturelles. Notamment, les facteurs additifs et multiplicatifs liés respectivement à la réflexion spéculaire et à l'inclinaison des feuilles qui peuvent être surmontés par prétraitement. Mais le phénomène qui pose le plus de défis est la réflexion multiple. Il se produit lorsqu'une feuille est éclairée en partie par la lumière directe, et en partie par la réflexion ou la transmission de la lumière des feuilles voisines, induisant de forts effets non linéaires sur son spectre de réflectance. Bien que cet effet puisse être pris en compte dans certains modèles de télédétection à l’échelle de la canopée, aucune étude n’a été proposée à ce jour sur la façon dont un tel phénomène affecte les évaluations spectrales de la biochimie végétale par imagerie de proximité. L'objectif de la présente étude était d'analyser ces effets dans le contexte de l'imagerie hyperspectrale à des fins de phénotypage végétal et de proposer des méthodes chimiométriques pour les surmonter. Le développement méthodologique a été basé sur des outils de simulation inclus dans la plate-forme open source OpenAlea (http://openalea.gforge.inria.fr/dokuwiki/doku.php). Une scène typique de canopée de blé a été modélisée à l'aide du modèle Adel-Wheat et combinée au modèle de propagation de la lumière Caribu. L'outil proposé simule la réflectance apparente de chaque feuille visible dans la canopée pour une réflectance et une transmittance réelles données, permettant de synthétiser des images hyperspectrales réalistes. Cette approche par simulation nous a permis, dans un premier temps, d’analyser la distribution dans l’espace spectral des perturbations engendrées par les réflexions multiples, puis d’en déduire une méthode de correction applicable dans le cas d’une régression PLS. La méthode est basée sur la construction de deux sous-espaces W et B générés respectivement par la formulation analytique des réflexions multiples et la variable d'intérêt. Ceci nous permet alors de définir une matrice de projection sur B selon la direction W (projection oblique), qui permet de supprimer l’effet des réflexions multiples tout en conservant l’information utile. Il suffit ensuite d’appliquer cette projection à chaque spectre lors de l’apprentissage et de la mise en œuvre du modèle PLS. La méthode a d’abord été développée et paramétrée sur les données simulées, dans le contexte de l’évaluation de la teneur en azote (LNC) de feuilles de blé. Pour cela, les spectres de réflectance (450-1100 nm) de 57 feuilles de blé ont été collectés à l'aide d'un spectromètre ASD (FieldSpec®, Analytical Spectral Devices, Inc., Boulder, Colorado, USA), tandis que leur LNC a été mesuré à l'aide d'analyses chimiques. Des modèles de régression avec et sans projection oblique ont alors été construits à partir des spectres ASD et appliqués sur l’ensemble des données simulées. Le modèle avec projection oblique a donné d’excellents résultats (R² = 0.931; RMSEP = 0.29% DM) en comparaison du modèle classique (R² = 0.915; RMSEP = 0.42% DM).La même méthode a ensuite été appliquée en conditions réelles, sur des feuilles de blé cultivées en pot et au champ. Pour cela, des feuilles ont été collectées et imagées à plat sur fond noir pour la construction des modèles PLS, qui ont ensuite été appliqués aux plantes sur pied. Ces expérimentations ont confirmé d’une part que la PLS-R classique entraînait une forte surestimation du LNC sur les feuilles entourées d’autres feuilles, d’autre part que la projection oblique évitait cette surestimation
Short range hyperspectral imagery is a promising tool for phenotyping and vegetation survey. When associated with partial least square regression (PLS-R), it allows high spatial resolution mapping of the plant chemical content at the canopy scale. However, several optical phenomena have to be taken into account when applying this approach to vegetation scenes in natural conditions. For instance, additive and multiplicative factors due respectively to specular reflection and leaf inclination can be overcome by spectral preprocessing. But the most challenging phenomenon is multiple scattering. It appears when a leaf is partly lightened by the reflected or transmitted light from surrounding leaves, resulting in strong non linear effects in its apparent reflectance spectrum. Though this effect can be taken into account in some remote sensing models at the canopy scale, no study has been proposed until now concerning its impact on spectral prediction of vegetation chemical content by short range imagery.The objective of this project, associated with a PhD work, was to analyze these effects in the context of hyperspectral imagery for vegetation phenotyping purpose, and to propose spectral processing methods to overcome them.The methodological development has been based on simulation tools included in the open source platform OpenAlea (http://openalea.gforge.inria.fr/dokuwiki/doku.php). A typical wheat canopy scene has been modelled using Adel-Wheat and combined with the light propagation model Caribu. The proposed tool simulates the apparent reflectance of every visible leaf in the canopy for a given actual reflectance and transmittance, allowing to synthetize realistic hyperspectral images.This simulation approach has allowed us, in a first step, to analyze the distribution of deviations due to multiple scattering in the spectral space, and then to infer a correction method in the frame of PLS regression. This method relies on the building of two subspaces EW and EB respectively generated by the analytic formulation of multiple scattering and by the variable of interest. It allows us to define a projection operation on EB subspace along EW direction (oblique projection), in order to remove multiple scattering effects while preserving useful information. This projection operation is then applied on every spectra during learning phase and using phase of the PLS model.The method has first been developed and tuned using simulated data, in the frame of leaf nitrogen content (LNC) prediction of wheat leaves. For this purpose, reflectance spectra (450-1100 nm) of 57 wheat leaves have been collected using a ASD filed spectrometer (FieldSpec®, Analytical Spectral Devices, Inc., Boulder, Colorado, USA), while their LNC was measured through reference chemical analyses. Regression models with and without oblique projection have then been built from the ASD spectra and applied to simulated data. The model with oblique projection provided excellent results (R² = 0.931; RMSEP = 0.29% DM), compared to the classical one (R² = 0.915; RMSEP = 0.42% DM).The same method has then been applied in real conditions on wheat pot plants and field plants. For this purpose, some leaves have been collected and laid on a black paper background to be imaged, in order to build PLS models that have then been applied on in-situ plants. These experimentations have confirmed that the classical PLS-R induces a strong overestimation of LNC on leaves surrounded by other leaves, and that oblique projection corrects this overestimation (same prediction on surrounded then isolated leaf)
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(8789954), Ali Masjedi. "MULTI-TEMPORAL MULTI-MODAL PREDICTIVE MODELLING OF PLANT PHENOTYPES." Thesis, 2020.

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High-throughput phenotyping using high spatial, spectral, and temporal resolution remote sensing (RS) data has become a critical part of the plant breeding chain focused on reducing the time and cost of the selection process for the “best” genotypes with respect to the trait(s) of interest. In this study, the potential of accurate and reliable sorghum biomass prediction using hyperspectral and LiDAR data acquired by sensors mounted on UAV platforms is investigated. Experiments comprised multiple varieties of grain and forage sorghum, including some photoperiod sensitive varieties, providing an opportunity to evaluate a wide range of genotypes and phenotypes.

Feature extraction is investigated, where various novel features, as well as traditional features, are extracted directly from the hyperspectral imagery and LiDAR point cloud data and input to classical machine learning (ML) regression based models. Predictive models are developed for multiple experiments conducted during the 2017, 2018, and 2019 growing seasons at the Agronomy Center for Research and Education (ACRE) at Purdue University. The impact of the regression method, data source, timing of RS and field-based biomass reference data acquisition, and number of samples on the prediction results are investigated. R2 values for end-of-season biomass ranged from 0.64 to 0.89 for different experiments when features from all the data sources were included. Using geometric based features derived from the LiDAR point cloud and the chemistry-based features extracted from hyperspectral data provided the most accurate predictions. The analysis of variance (ANOVA) of the accuracies of the predictive models showed that both the data source and regression method are important factors for a reliable prediction; however, the data source was more important with 69% significance, versus 28% significance for the regression method. The characteristics of the experiments, including the number of samples and the type of sorghum genotypes in the experiment also impacted prediction accuracy.

Including the genomic information and weather data in the “multi-year” predictive models is also investigated for prediction of the end of season biomass. Models based on one and two years of data are used to predict the biomass yield for the future years. The results show the high potential of the models for biomass and biomass rank predictions. While models developed using one year of data are able to predict biomass rank, using two years of data resulted in more accurate models, especially when RS data, which encode the environmental variation, are included. Also, the possibility of developing predictive models using the RS data collected until mid-season, rather than the full season, is investigated. The results show that using the RS data until 60 days after sowing (DAS) in the models can predict the rank of biomass with R2 values of around 0.65-0.70. This not only reduces the time required for phenotyping by avoiding the manual sampling process, but also decreases the time and the cost of the RS data collections and the associated challenges of time-consuming processing and analysis of large data sets, and particularly for hyperspectral imaging data.

In addition to extracting features from the hyperspectral and LiDAR data and developing classical ML based predictive models, supervised and unsupervised feature learning based on fully connected, convolutional, and recurrent neural networks is also investigated. For hyperspectral data, supervised feature extraction provides more accurate predictions, while the features extracted from LiDAR data in an unsupervised training yield more accurate prediction.

Predictive models based on Recurrent Neural Networks (RNNs) are designed and implemented to accommodate high dimensional, multi-modal, multi-temporal data. RS data and weather data are incorporated in the RNN models. Results from multiple experiments focused on high throughput phenotyping of sorghum for biomass predictions are provided and evaluated. Using proposed RNNs for training on one experiment and predicting biomass for other experiments with different types of sorghum varieties illustrates the potential of the network for biomass prediction, and the challenges relative to small sample sizes, including weather and sensitivity to the associated ground reference information.

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Book chapters on the topic "Hyperspectral Phenotyping"

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Gampa, Suraj, and Rubi Quiñones. "Data-Driven Techniques for Plant Phenotyping Using Hyperspectral Imagery." In Intelligent Image Analysis for Plant Phenotyping, 175–94. First edition. | Boca Raton, FL : CRC Press, 2021.: CRC Press, 2020. http://dx.doi.org/10.1201/9781315177304-11.

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Bhugra, Swati, Nitish Agarwal, Shubham Yadav, Soham Banerjee, Santanu Chaudhury, and Brejesh Lall. "Extraction of Phenotypic Traits for Drought Stress Study Using Hyperspectral Images." In Lecture Notes in Computer Science, 608–14. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-69900-4_77.

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Potgieter, Andries B., James Watson, Barbara George-Jaeggli, Gregory McLean, Mark Eldridge, Scott C. Chapman, Kenneth Laws, et al. "The Use of Hyperspectral Proximal Sensing for Phenotyping of Plant Breeding Trials." In Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, 127–47. CRC Press, 2018. http://dx.doi.org/10.1201/9781315164151-5.

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Conference papers on the topic "Hyperspectral Phenotyping"

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Arnold, Thomas, Raimund Leitner, and Gernot Bodner. "Near infrared hyperspectral imaging system for root phenotyping." In Sensing for Agriculture and Food Quality and Safety IX, edited by Moon S. Kim, Byoung-Kwan Cho, Bryan A. Chin, and Kuanglin Chao. SPIE, 2017. http://dx.doi.org/10.1117/12.2262441.

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Accettura, Margot, Carl Salvaggio, Timothy Bauch, Joe Mallia, and Nina Raqueno. "Hyperspectral detection of methane stressed vegetation." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping III, edited by J. Alex Thomasson, Mac McKee, and Robert J. Moorhead. SPIE, 2018. http://dx.doi.org/10.1117/12.2304045.

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Hurley, Sean, Marc Horney, and Aaron Drake. "Using hyperspectral imagery to detect water stress in vineyards." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping IV, edited by J. Alex Thomasson, Mac McKee, and Robert J. Moorhead. SPIE, 2019. http://dx.doi.org/10.1117/12.2518660.

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Zhu, Feiyu, Yu Pan, Tian Gao, Harkamal Walia, and Hongfeng Yu. "Interactive Visualization of Time-Varying Hyperspectral Plant Images for High-Throughput Phenotyping." In 2019 IEEE International Conference on Big Data (Big Data). IEEE, 2019. http://dx.doi.org/10.1109/bigdata47090.2019.9006003.

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Luculescu, Marius Cristian, Luciana Cristea, Sorin Constantin Zamfira, and Attila Laszlo Boer. "Using hyperspectral sensors for crop vegetation status monitoring in precision agriculture." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping III, edited by J. Alex Thomasson, Mac McKee, and Robert J. Moorhead. SPIE, 2018. http://dx.doi.org/10.1117/12.2305156.

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Bhandari, Subodh, Amar Raheja, Mohammad R. Chaichi, Frank H. Pham, Tristan M. Sherman, Matthew B. Dohlen, and Sharafat U. Khan. "Lettuce plant health assessment using UAV-based hyperspectral sensor and proximal sensors." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping V, edited by J. Alex Thomasson and Alfonso F. Torres-Rua. SPIE, 2020. http://dx.doi.org/10.1117/12.2557686.

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Bagherian, Kamand, Rafael Bidese Puhl, Yin Bao, Qiong Zhang, Alvaro Sanz-Saez, Charles Chen, and Phat Dang. "Phenotyping Agronomic Traits of Peanuts using UAV-based Hyperspectral Imaging and Deep Learning." In 2022 Houston, Texas July 17-20, 2022. St. Joseph, MI: American Society of Agricultural and Biological Engineers, 2022. http://dx.doi.org/10.13031/aim.202200814.

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Xie, Chuanqi, Ce Yang, and Ali Moghimi. "Detection of cold stressed maize seedlings for high throughput phenotyping using hyperspectral imagery." In SPIE Commercial + Scientific Sensing and Imaging, edited by David P. Bannon. SPIE, 2017. http://dx.doi.org/10.1117/12.2262781.

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Hamidisepehr, Ali, and Michael Sama. "A low-cost method for collecting hyperspectral measurements from a small unmanned aircraft system." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping III, edited by J. Alex Thomasson, Mac McKee, and Robert J. Moorhead. SPIE, 2018. http://dx.doi.org/10.1117/12.2305934.

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Bhandari, Subodh, Amar Raheja, Mohammad R. Chaichi, Frank Pham, Tristan Sherman, Matt Dohlen, and Sharafat Khan. "Comparing the effectiveness of hyperspectral and multispectral data in detecting citrus nitrogen and water stresses." In Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping IV, edited by J. Alex Thomasson, Mac McKee, and Robert J. Moorhead. SPIE, 2019. http://dx.doi.org/10.1117/12.2518822.

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