Hyperspectral images of grapevine leaves including healthy leaves and leaves with biotic and abiotic symptoms.

A hyperspectral imaging database was collected on two hundred and five grape plant leaves. Leaves were measured with a hyperspectral camera in the visible/near infrared spectral range under controlled conditions. This dataset contains hyperspectral acquisition of grape leaves of seven different varieties. For each variety, acquisitions were performed on healthy leaves and leaves with foliar symptoms caused by different grapevine diseases showing clear symptoms of biotic or abiotic stress on other organs. For each leaf, chemical measurements such as chlorophyll and flavonol contents were also performed.

Visible - Near infrared hyperspectral dataset of healthy and infected apple tree leaves images for the monitoring of apple fire blight.

This dataset consists of three groups of hyperspectral images of apple tree plants. The first group of images consists of a temporal monitoring of seven apple tree plants, infected with fire blight (Erwinia amylovora), and six control plants over a period of 15 days. The second group of images includes a temporal monitoring of three infected plants, seven plants subjected to water stress, and seven control plants. The third group of images corresponds to acquisitions made in the orchard on nine trees showing symptoms of fire blight and six control trees. The pixel locations of infected areas have been provided for all images featuring symptomatic plants.

Dataset containing spectral data from hyperspectral imaging and sugar content measurements of grapes berries in various maturity stage.

In the dataset presented in this article, two hundred and seventy four trays containing one hundred berries were measured by a hyperspectral camera in the visible/near-infrared spectral domain. This dataset was formed to study the use of hyperspectral imaging for maturity monitoring of grape berries [2]. This dataset contains reflectance spectra from hyperspectral camera of grape berries of three different varieties and chemical composition (sugar content).

Discriminating between Absorption and Scattering Effects in Complex Turbid Media by Coupling Polarized Light Spectroscopy with the Mueller Matrix Concept.

The separation of the combined effects of absorption and scattering in complex media is a major issue for better characterization and prediction of media properties. In this study, an approach coupling polarized light spectroscopy and the Mueller matrix concept were evaluated to address this issue. A set of 50 turbid liquid optical phantoms with different levels of scattering and absorption properties were made and measured at various orientations of polarizers and analyzers to obtain the 16 elements of the complete Mueller matrix in the VIS-NIR region. Partial least square (PLS) was performed to build calibration models from diffuse reflectance spectra in order to evaluate the potential of polarization spectroscopy through the elements of the Mueller matrix to predict physical and chemical parameters and hence, to discriminate scattering and absorption effects, respectively. In particular, it was demonstrated that absorption and scattering effects can be distinguished in the Rayleigh regime with linear and circular polarization from the M22 and M44 elements of the Mueller matrix, correspondingly.

Fast and robust NIRS-based characterization of raw organic waste: Using non-linear methods to handle water effects.

Fast characterization of organic waste using near infrared spectroscopy (NIRS) has been successfully developed in the last decade. However, up to now, an on-site use of this technology has been hindered by necessary sample preparation steps (freeze-drying and grinding) to avoid important water effects on NIRS. Recent research studies have shown that these effects are highly non-linear and relate both to the biochemical and physical properties of samples. To account for these complex effects, the current study compares the use of many different types of non-linear methods such as partial least squares regression (PLSR) based methods (global, clustered and local versions of PLSR), machine learning methods (support vector machines, regression trees and ensemble methods) and deep learning methods (artificial and convolutional neural networks). On an independent test data set, non-linear methods showed errors 28% lower than linear methods. The standard errors of prediction obtained for the prediction of total solids content (TS%), chemical oxygen demand (COD) and biochemical methane potential (BMP) were respectively 8%, 160 mg(O2).gTS-1 and 92 mL(CH4).gTS-1. These latter errors are similar to successful NIRS applications developed on freeze-dried samples. These findings hold great promises regarding the development of at-site and online NIRS solutions in anaerobic digestion plants.

Unsupervised analysis of NIRS spectra to assess complex plant traits: leaf senescence as a use case.

BACKGROUND: As a rapid and non-destructive method, Near Infrared Spectroscopy is classically proposed to assess plant traits in many scientific fields, to observe enlarged genotype panels and to document the temporal kinetic of some biological processes. Most often, supervised models are used. The signal is calibrated thanks to reference measurements, and dedicated models are generated to predict biological traits. An alternative unsupervised approach considers the whole spectra information in order to point out various matrix changes. Although more generic, and faster to implement, as it does not require a reference data set, this latter approach is rarely used to document biological processes, and does requires more information of the process. METHODS: In our work, an unsupervised model was used to document the flag leaf senescence of durum wheat (Triticum turgidum durum). Leaf spectra changes were observed using Moving Window Principal Component Analysis (MWPCA). The dates related to earlier and later spectra changes were compared to two key points on the senescence time course: senescence onset (T0) and the end of the leaf span (T1) derived from a supervised strategy. RESULTS: For almost all leaves and whatever the signal pre-treatments and window size considered, the MWPCA found significant spectral changes. The latter was highly correlated with T1 (0.59 ≤ r ≤ 0.86) whereas the correlations between the first significant spectrum changes and T0 were lower (0.09 ≤ r ≤ 0.56). These different relationships are discussed below since they define the potential as well as the limitations of MWPCA to model biological processes. CONCLUSION: Overall, our study demonstrates that the information contained in the spectra can be used when applying an unsupervised method, here the MWPCA, to characterize a complex biological phenomenon such leaf senescence. It also means that using whole spectra may be relevant in agriculture and plant biology.

Combination of multivariate curve resolution with factorial discriminant analysis for the detection of grapevine diseases using hyperspectral imaging. A case study: flavescence dorée.

Hyperspectral imaging is an emergent technique in viticulture that can potentially detect bacterial diseases in a non-destructive manner. However, the main problem is to handle the substantial amount of information obtained from this type of data, for which reliable data analysis tools are necessary. In this work, a combination of multivariate curve resolution-alternating least squares (MCR-ALS) and factorial discriminant analysis (FDA) is proposed to detect the flavescence dorée grapevine disease from hyperspectral imaging. The main purpose of MCR-ALS in this work was to provide chemically meaningful basic spectral signatures and distribution maps of the constituents needed to describe both healthy and infected leaf images by flavescence dorée. MCR scores (distribution maps) were used as the starting information for FDA to distinguish between healthy and infected pixels/images. Such an approach is presumably more powerful than the direct use of FDA on the raw imaging data, since MCR scores are compressed and noise-filtered information on pixel properties, which makes them more suitable for discrimination analysis. High levels of correct pixel discrimination rates (CR = 85.1%) for the MCR-ALS/FDA discrimination model were obtained. The model presents a lesser ability to determine infected leaves than healthy leaves. Nevertheless, only two images were misclassified. Therefore, the proposed strategy constitutes a good approach for the detection of flavescence dorée that could be potentially used to detect other phytopathologies.

On-site substrate characterization in the anaerobic digestion context: A dataset of near infrared spectra acquired with four different optical systems on freeze-dried and ground organic waste.

The near infrared spectra of thirty-three freeze-dried and ground organic waste samples of various biochemical composition were collected on four different optical systems, including a laboratory spectrometer, a transportable spectrometer with two measurement configurations (an immersed probe, and a polarized light system) and a micro-spectrometer. The provided data contains one file per spectroscopic system including the reflectance or absorbance spectra with the corresponding sample name and wavelengths. A reference data file containing carbohydrates, lipid and nitrogen content, biochemical methane potential (BMP) and chemical oxygen demand (COD) for each sample is also provided. This data enables the comparison of the optical systems for predictive model calibration based for example on Partial Least Squares Regression (PLS-R) [1], but could be used more broadly to test new chemometrics methods. For example, the data could be used to evaluate different transfer functions between spectroscopic systems [2]. This dataset enabled the research work reported by Mallet et al. 2021 [3].

Relating Near-Infrared Light Path-Length Modifications to the Water Content of Scattering Media in Near-Infrared Spectroscopy: Toward a New Bouguer-Beer-Lambert Law.

In near-infrared spectroscopy (NIRS), the linear relationship between absorbance and an absorbing compound concentration has been strictly defined by the Bouguer-Beer-Lambert law only for the case of transmission measurements of nonscattering media. However, various quantitative calibrations have been successfully built both on reflectance measurements and for scattering media. Although the lack of linearity for scattering media has been observed experimentally, the sound multivariate statistics and signal processing involved in chemometrics have allowed us to overcome this problem in most cases. However, in the case of samples with varying water content, important modifications of scattering levels still make calibrations difficult to build due to nonlinearities. Moreover, even when calibration procedures are successfully developed, many preprocessing methods used do not guarantee correct spectroscopic assignments (in the sense of a pure chemical absorbance). In particular, this may prevent correct modeling and interpretation of the structure of water. In this study, dynamic near-infrared spectra acquired during a drying process allow the study of the physical effects of water content variations, with a focus on the first overtone OH absorbance region. A model sample consisting of aluminum pellets mixed with water allowed us to study this specifically, without any other absorbing interaction terms related to the dry mass-absorbing constituents. A new formulation of the Bouguer-Beer-Lambert law is proposed, by expressing path length as a power function of water content. Through this new formulation, it is shown that a better and simpler prediction model of water content may be developed, with more precise and accurate identification of water absorbance bands.

Fast at-line characterization of solid organic waste: Comparing analytical performance of different compact near infrared spectroscopic systems with different measurement configurations.

Fast characterization of solid organic waste using near infrared spectroscopy has been successfully developed in the last decade. However, its adoption in biogas plants for monitoring the feeding substrates remains limited due to the lack of applicability and high costs. Recent evolutions in the technology have given rise to both more compact and more modular low-cost near infrared systems which could allow a larger scale deployment. The current study investigates the relevance of these new systems by evaluating four different Fourier transform near-infrared spectroscopic systems with different compactness (laboratory, portable, micro spectrometer) but also different measurement configurations (polarized light, at distance, in contact). Though the conventional laboratory spectrometer showed the best performance on the various biochemical parameters tested (carbohydrates, lipids, nitrogen, chemical oxygen demand, biochemical methane potential), the compact systems provided very close results. Prediction of the biochemical methane potential was possible using a low-cost micro spectrometer with an independent validation set error of only 91 NmL(CH4).gTS-1 compared to 60 NmL(CH4).gTS-1 for a laboratory spectrometer. The differences in performance were shown to result mainly from poorer spectral sampling; and not from instrument characteristics such as spectral resolution. Regarding the measurement configurations, none of the evaluated systems allowed a significant gain in robustness. In particular, the polarized light system provided better results when using its multi-scattered signal which brings further evidence of the importance of physical light-scattering properties in the success of models built on solid organic waste.

Unveiling non-linear water effects in near infrared spectroscopy: A study on organic wastes during drying using chemometrics.

In the context of organic waste management, near infrared spectroscopy (NIRS) is being used to offer a fast, non-destructive, and cost-effective characterization system. However, cumbersome freeze-drying steps of the samples are required to avoid water's interference on near infrared spectra. In order to better understand these effects, spectral variations induced by dry matter content variations were obtained for a wide variety of organic substrates. This was made possible by the development of a customized near infrared acquisition system with dynamic highly-resolved simultaneous scanning of near infrared spectra and estimation of dry matter content during a drying process at ambient temperature. Using principal components analysis, the complex water effects on near infrared spectra are detailed. Water effects are shown to be a combination of both physical and chemical effects, and depend on both the characteristics of the samples (biochemical type and physical structure) and the moisture content level. This results in a non-linear relationship between the measured signal and the analytical characteristic of interest. A typology of substrates with respect to these water effects is provided and could further be efficiently used as a basis for the development of local quantitative calibration models and correction methods accounting for these water effects.

Terahertz probing of sunflower leaf multilayer organization.

We analyze the multilayer structure of sunflower leaves from Terahertz data measured in the time-domain at a ps scale. Thin film reverse engineering techniques are applied to the Fourier amplitude of the reflected and transmitted signals in the frequency range f < 1.5 Terahertz (THz). Validation is first performed with success on etalon samples. The optimal structure of the leaf is found to be a 8-layer stack, in good agreement with microscopy investigations. Results may open the door to a complementary classification of leaves.

A New Optical Sensor Based on Laser Speckle and Chemometrics for Precision Agriculture: Application to Sunflower Plant-Breeding.

New instruments to characterize vegetation must meet cost constraints while providing accurate information. In this paper, we study the potential of a laser speckle system as a low-cost solution for non-destructive phenotyping. The objective is to assess an original approach combining laser speckle with chemometrics to describe scattering and absorption properties of sunflower leaves, related to their chemical composition or internal structure. A laser diode system at two wavelengths 660 nm and 785 nm combined with polarization has been set up to differentiate four sunflower genotypes. REP-ASCA was used as a method to analyze parameters extracted from speckle patterns by reducing sources of measurement error. First findings have shown that measurement errors are mostly due to unwilling residual specular reflections. Moreover, results outlined that the genotype significantly impacts measurements. The variables involved in genotype dissociation are mainly related to scattering properties within the leaf. Moreover, an example of genotype classification using REP-ASCA outcomes is given and classify genotypes with an average error of about 20%. These encouraging results indicate that a laser speckle system is a promising tool to compare sunflower genotypes. Furthermore, an autonomous low-cost sensor based on this approach could be used directly in the field.

Dataset of visible-near infrared handheld and micro-spectrometers - comparison of the prediction accuracy of sugarcane properties.

In the dataset presented in this article, sixty sugarcane samples were analyzed by eight visible / near infrared spectrometers including seven micro-spectrometers. There is one file per spectrometer with sample name, wavelength, absorbance data [calculated as log10 (1/Reflectance)], and another file for reference data, in order to assess the potential of the micro-spectrometers to predict chemical properties of sugarcane samples and to compare their performance with a LabSpec spectrometer. The Partial Least Square Regression (PLS-R) algorithm was used to build calibration models. This open access dataset could also be used to test new chemometric methods, for training, etc.

Combining light polarization and speckle measurements with multivariate analysis to predict bulk optical properties of turbid media.

This study aims to investigate the combination of speckle pattern analysis, polarization parameters, and chemometric tools to predict the optical absorption and scattering properties of materials. For this purpose, an optical setup based on light polarization and speckle measurements was developed, and turbid samples were measured at 405 and 660 nm. First, a backscattered polarized speckle acquisition was performed on a set of 41 samples with various scattering (${\mu}_s$µs) and absorbing (${{\mu}_a}$µa) coefficients. Then, several parameters were computed from the polarized speckle images, and prediction models were built using stepwise multiple linear regression. For scattering media, ${{\mu}_s}$µs was predicted with ${R^{2} = 0.9}$R2=0.9 using two parameters. In the case of scattering and absorbing media, prediction results using two parameters were ${R^{2} = 0.62}$R2=0.62 for ${{\mu}_s}$µs and ${R^{2} = 0.8}$R2=0.8 for ${{\mu}_a}$µa. The overall results obtained in this research showed that the combination of speckle pattern analysis, polarization parameters, and chemometric tools to predict the optical bulk properties of materials show interesting promise.

Coupling Waveguide-Based Micro-Sensors and Spectral Multivariate Analysis to Improve Spray Deposit Characterization in Agriculture.

The leaf coverage surface is a key measurement of the spraying process to maximize spray efficiency. To determine leaf coverage surface, the development of optical micro-sensors that, coupled with a multivariate spectral analysis, will be able to measure the volume of the droplets deposited on their surface is proposed. Rib optical waveguides based on Ge-Se-Te chalcogenide films were manufactured and their light transmission was studied as a response to the deposition of demineralized water droplets on their surface. The measurements were performed using a dedicated spectrophotometric bench to record the transmission spectra at the output of the waveguides, before (reference) and after drop deposition, in the wavelength range between 1200 and 2000 nm. The presence of a hollow at 1450 nm in the relative transmission spectra has been recorded. This corresponds to the first overtone of the O-H stretching vibration in water. This result tends to show that the optical intensity decrease observed after droplet deposition is partly due to absorption by water of the light energy carried by the guided mode evanescent field. The probe based on Ge-Se-Te rib optical waveguides is thus sensitive throughout the whole range of volumes studied, i.e., from 0.1 to 2.5 µL. Principal Component Analysis and Partial Least Square as multivariate techniques then allowed the analysis of the statistics of the measurements and the predictive character of the transmission spectra. It confirmed the sensitivity of the measurement system to the water absorption, and the predictive model allowed the prediction of droplet volumes on an independent set of measurements, with a correlation of 66.5% and a precision of 0.39 µL.

Effect of the Architecture of Fiber-Optic Probes Designed for Soluble Solid Content Prediction in Intact Sugar Beet Slices.

Sugar beet is the second biggest world contributor to sugar production and the only one grown in Europe. One of the main limitations for its competitiveness is the lack of effective tools for assessing sugar content in unprocessed sugar beet roots, especially in breeding programs. In this context, a dedicated near infrared (NIR) fiber-optic probe based approach is proposed. NIR technology is widely used for the estimation of sugar content in vegetable products, while optic fibers allow a wide choice of technical properties and configurations. The objective of this research was to study the best architecture through different technical choices for the estimation of sugar content in intact sugar beet roots. NIR spectral measurements were taken on unprocessed sugar beet samples using two types of geometries, single and multiple fiber-probes. Sugar content estimates were more accurate when using multiple fiber-probes (up to R2 = 0.93) due to a lesser disruption of light specular reflection. In turn, on this configuration, the best estimations were observed for the smallest distances between emitting and collecting fibers, reducing the proportion of multiply scattered light in the spectra. Error of prediction (RPD) values of 3.95, 3.27 and 3.09 were obtained for distances between emitting and collecting fibers of 0.6, 1.2 and 1.8 µm respectively. These high RPD values highlight the good predictions capacities of the multi-fiber probes. Finally, this study contributes to a better understanding of the effects of the technical properties of optical fiber-probes on the quality of spectral models. In addition, and beyond this specificity related to sugar beet, these findings could be extended to other turbid media for quantitative optical spectroscopy and eventually to validate considered fiber-optic probe design obtained in this experimental study.

Exploring the potential of PROCOSINE and close-range hyperspectral imaging to study the effects of fungal diseases on leaf physiology.

The detection of plant diseases, including fungi, is a major challenge for reducing yield gaps of crops across the world. We explored the potential of the PROCOSINE radiative transfer model to assess the effect of the fungus Pseudocercospora fijiensis on leaf tissues using laboratory-acquired submillimetre-scale hyperspectral images in the visible and near-infrared spectral range. The objectives were (i) to assess the dynamics of leaf biochemical and biophysical parameters estimated using PROCOSINE inversion as a function of the disease stages, and (ii) to discriminate the disease stages by using a Linear Discriminant Analysis model built from the inversion results. The inversion results show that most of the parameter dynamics are consistent with expectations: for example, the chlorophyll content progressively decreased as the disease spreads, and the brown pigments content increased. An overall accuracy of 78.7% was obtained for the discrimination of the six disease stages, with errors mainly occurring between asymptomatic samples and first visible disease stages. PROCOSINE inversion provides relevant ecophysiological information to better understand how P. fijiensis affects the leaf at each disease stage. More particularly, the results suggest that monitoring anthocyanins may be critical for the early detection of this disease.

Potential of vis-NIR spectroscopy to monitor the silica precipitation reaction.

Controlling production online is an important issue for chemical companies. Visible and near-infrared (NIR) spectroscopy offers a number of important advantages for process monitoring, and has been used since the 1980s. For complex media such as silica precipitation samples, it is interesting to be able to study independently the scattering and absorption effects. From the scattering coefficient it is possible to extract information on the physical structure of the medium. In this work, the physical changes were monitored during a silica precipitation reaction by simple measurement of collimated transmittance NIR spectra. It is shown that it is possible to differentiate samples before and after the gel point, which is a key parameter for monitoring the process. From these NIR spectra the scattering coefficients were simply extracted, allowing a global vision of the physical changes in the medium. Then principal component analysis of the spectra allowed refinement of the understanding of the scattering effects, in combination with particle size monitoring.

Simulation Method Linking Dense Microalgal Culture Spectral Properties in the 400-750 nm Range to the Physiology of the Cells.

This work describes a method to model the optical properties over the (400-750 nm) spectral range of a dense microalgal culture using the chemical and physical properties of the algal cells. The method was based on a specific program called AlgaSim coupled with the adding-doubling method: at the individual cell scale, AlgaSim simulates the spectral properties of one model, three-layer spherical algal cell from its size and chemical composition. As a second step, the adding-doubling method makes it possible to retrieve the total transmittance of the algal medium from the optical properties of the individual algal cells. The method was tested by comparing the simulated total transmittance spectra for dense marine microalgal cultures of Isochrysis galbana (small flagellates) and Phaeodactylum tricornutum (diatoms) to spectra measured using an experimental spectrophotometric setup. Our study revealed that the total transmittance spectra simulated for the quasi-spherical cells of Isochrysis galbana were in good agreement with the measured spectra over the whole spectral range. For Phaeodactylum tricornutum, large differences between simulated and measured spectra were observed over the blue part of the transmittance spectra, probably due to non-spherical shape of the algal cells. Prediction of the algal cell density, mean size and pigment composition from the total transmittance spectra measured on algal samples was also investigated using the reversal of the method. Mean cell size was successfully predicted for both species. The cell density was also successfully predicted for spherical Isochrysis galbana, with a relative error below 7%, but not for elongated Phaeodactylum tricornutum with a relative error up to 26%. The pigments total quantity and composition, the carotenoids:chlorophyll ratio in particular, were also successfully predicted for Isochrysis galbana with a relative error below 8%. However, the pigment predictions and measurements for Phaeodactylum tricornutum showed large discrepancies, with a relative error up to 88%. These results give strong support for the development of a promising tool providing rapid and accurate estimations of biomass and physiological status of a dense microalgal culture based on only light transmittance properties.