Classification of oat and groat kernels using NIR hyperspectral imaging

Hyperspectral imaging and its applications: A review

Hyperspectral imaging has emerged as an effective powerful tool in plentiful military, environmental, and civil applications over the last three decades. The modern remote sensing approaches are adequate for covering huge earth surfaces with phenomenal temporal, spectral, and spatial resolutions. These features make HSI more effective in various applications of remote sensing depending upon the physical estimation of identical material identification and manifold composite surfaces having accomplished spectral resolutions. Recently, HSI has attained immense significance in the research on safety and quality assessment of food, medical analysis, and agriculture applications. This review focuses on HSI fundamentals and its applications like safety and quality assessment of food, medical analysis, agriculture, water resources, plant stress identification, weed & crop discrimination, and flood management. Various investigators have promising solutions for automatic systems depending upon HSI. Future research may use this review as a baseline and future advancement analysis.

Quantification and classification of deoxynivalenol-contaminated oat samples by near-infrared hyperspectral imaging

Deoxynivalenol (DON) is the most occurring mycotoxin in oat and oat-based products. Near-infrared hyperspectral imaging (NIR-HSI) has been proposed as a promising methodology for analysing DON contamination in the food industry. The present study aims to apply NIR-HSI for DON detection in oat kernels and to quantify and classify naturally DON-contaminated oat samples. Unground and ground oat samples were scanned by NIR-HSI before their DON content was determined by HPLC. The data were pre-treated and analysed by PLS regression and four classification methods. The most efficient DON prediction model was for unground samples (R² = 0.75 and RMSEP = 403.18 μg/kg), using twelve characteristic wavelengths with a special interest in 1203 and 1388 nm. The random forest algorithm of unground samples according to the EU maximum limit for unprocessed oats (1750 μg/kg) achieved a classification accuracy of 77.8 %. These findings indicate that NIR-HSI is a promising tool for detecting DON in oats.

Single Seed Near-Infrared Hyperspectral Imaging for Classification of Perennial Ryegrass Seed

The detection of beneficial microbes living within perennial ryegrass seed causing no apparent defects is challenging, even with the most sensitive and conventional methods, such as DNA genotyping. Using a near-infrared hyperspectral imaging system (NIR-HSI), we were able to discriminate not only the presence of the commercial NEA12 fungal endophyte strain but perennial ryegrass cultivars of diverse seed age and batch. A total of 288 wavebands were extracted for individual seeds from hyperspectral images. The optimal pre-processing methods investigated yielded the best partial least squares discriminant analysis (PLS-DA) classification model to discriminate NEA12 and without endophyte (WE) perennial ryegrass seed with a classification accuracy of 89%. Effective wavelength (EW) selection based on GA-PLS-DA resulted in the selection of 75 wavebands yielding 88.3% discrimination accuracy using PLS-DA. For cultivar identification, the artificial neural network discriminant analysis (ANN-DA) was the best-performing classification model, resulting in >90% classification accuracy for Trojan, Alto, Rohan, Governor and Bronsyn. EW selection using GA-PLS-DA resulted in 87 wavebands, and the PLS-DA model performed the best, with no extensive compromise in performance, resulting in >89.1% accuracy. The study demonstrates the use of NIR-HSI reflectance data to discriminate, for the first time, an associated beneficial fungal endophyte and five cultivars of perennial ryegrass seed, irrespective of seed age and batch. Furthermore, the negligible effects on the classification errors using EW selection improve the capability and deployment of optimized methods for real-time analysis, such as the use of low-cost multispectral sensors for single seed analysis and automated seed sorting devices.

Deep Learning Combined with Hyperspectral Imaging Technology for Variety Discrimination of Fritillaria thunbergii

Traditional Chinese herbal medicine (TCHM) plays an essential role in the international pharmaceutical industry due to its rich resources and unique curative properties. The flowers, stems, and leaves of Fritillaria contain a wide range of phytochemical compounds, including flavonoids, essential oils, saponins, and alkaloids, which may be useful for medicinal purposes. Fritillaria thunbergii Miq. Bulbs are commonly used in traditional Chinese medicine as expectorants and antitussives. In this paper, a feasibility study is presented that examines the use of hyperspectral imaging integrated with convolutional neural networks (CNN) to distinguish twelve (12) Fritillaria varieties (n = 360). The performance of support vector machines (SVM) and partial least squares-discriminant analysis (PLS-DA) was compared with that of convolutional neural network (CNN). Principal component analysis (PCA) was used to assess the presence of cluster trends in the spectral data. To optimize the performance of the models, cross-validation was used. Among all the discriminant models, CNN was the most accurate with 98.88%, 88.89% in training and test sets, followed by PLS-DA and SVM with 92.59%, 81.94% and 99.65%, 79.17%, respectively. The results obtained in the present study revealed that application of HSI in conjunction with the deep learning technique can be used for classification of Fritillaria thunbergii varieties rapidly and non-destructively.

TXRF spectral information enhanced by multivariate analysis: A new strategy for food fingerprint

The increased costumers' request of safe and high-quality food products makes food traceability a priority for frauds identification and quality certification. Elemental profiling is one of the strategies used for food traceability, and TXRF spectroscopy is widely used in food analysis even if its potentialities have not been fully investigated. In this work, a new method for food traceability using directly TXRF spectra coupled with multivariate analyses, was tested. Twenty-four different beans' genotypes (Phaseolus vulgaris L.) grown onto two different sites have been studied. After the development of the method for beans' analysis, TXRF spectra were collected and processed with PCA combined with SNV and GLSW filter obtaining a perfect clustering of the seeds according to their geographical origin. Finally, using PLS-DA, beans were correctly classified demonstrating that TXRF spectra can be successfully used as fingerprint for food/seed traceability and that elemental quantification procedure is not necessary to this aim.

Diagnosis and prognosis of COVID-19 employing analysis of patients' plasma and serum via LC-MS and machine learning

OBJECTIVE

To implement and evaluate machine learning (ML) algorithms for the prediction of COVID-19 diagnosis, severity, and fatality and to assess biomarkers potentially associated with these outcomes.

MATERIAL AND METHODS

Serum (n = 96) and plasma (n = 96) samples from patients with COVID-19 (acute, severe and fatal illness) from two independent hospitals in China were analyzed by LC-MS. Samples from healthy volunteers and from patients with pneumonia caused by other viruses (i.e. negative RT-PCR for COVID-19) were used as controls. Seven different ML-based models were built: PLS-DA, ANNDA, XGBoostDA, SIMCA, SVM, LREG and KNN.

RESULTS

The PLS-DA model presented the best performance for both datasets, with accuracy rates to predict the diagnosis, severity and fatality of COVID-19 of 93%, 94% and 97%, respectively. Low levels of the metabolites ribothymidine, 4-hydroxyphenylacetoylcarnitine and uridine were associated with COVID-19 positivity, whereas high levels of N-acetyl-glucosamine-1-phosphate, cysteinylglycine, methyl isobutyrate, l-ornithine and 5,6-dihydro-5-methyluracil were significantly related to greater severity and fatality from COVID-19.

CONCLUSION

The PLS-DA model can help to predict SARS-CoV-2 diagnosis, severity and fatality in daily practice. Some biomarkers typically increased in COVID-19 patients' serum or plasma (i.e. ribothymidine, N-acetyl-glucosamine-1-phosphate, l-ornithine, 5,6-dihydro-5-methyluracil) should be further evaluated as prognostic indicators of the disease.

Integrated spectral and textural features of hyperspectral imaging for prediction and visualization of stearic acid content in lamb meat

Stearic acid content is an important factor affecting mutton odor. To determine the distribution and content of stearic acid (C18:0) in lamb meat fast and nondestructively, a method integrating spectral and textural data of hyperspectral imaging (900-1700 nm) was proposed in this paper. Firstly, spectral information was obtained and preprocessed. Then, the spectral features were extracted by variable combination population analysis-genetic algorithm (VCPA-GA) and interval variable iterative space shrinking analysis (IVISSA). Subsequently, the prediction models of partial least squares regression (PLSR) and least-squares support vector machines (LSSVMs) were established and compared. The model constructed with SNVD-VCPA-GA-PLSR achieved better performance. To improve the prediction results of the models, the textural features were extracted using a gray-level co-occurrence matrix (GLCM) and fused with spectral features. The optimized model achieved good results, with R_c of 0.8716, RMSEC of 0.0793 g/100 g, RPD_c of 2.398, and R_p of 0.8121 with RMSEP of 0.1481 g/100 g and RPD_p of 1.756. Finally, the spatial distribution of the C18:0 content in lamb meat was visualized using an optimal model. The result indicated that it was feasible to predict and visualize the C18:0 content in lamb meat, providing a way for real-time detection of volatile fatty acid compounds in meat.

Rice Seed Purity Identification Technology Using Hyperspectral Image with LASSO Logistic Regression Model

Hyperspectral technology is used to obtain spectral and spatial information of samples simultaneously and demonstrates significant potential for use in seed purity identification. However, it has certain limitations, such as high acquisition cost and massive redundant information. This study integrates the advantages of the sparse feature of the least absolute shrinkage and selection operator (LASSO) algorithm and the classification feature of the logistic regression model (LRM). We propose a hyperspectral rice seed purity identification method based on the LASSO logistic regression model (LLRM). The feasibility of using LLRM for the selection of feature wavelength bands and seed purity identification are discussed using four types of rice seeds as research objects. The results of 13 different adulteration cases revealed that the value of the regularisation parameter was different in each case. The recognition accuracy of LLRM and average recognition accuracy were 91.67-100% and 98.47%, respectively. Furthermore, the recognition accuracy of full-band LRM was 71.60-100%. However, the average recognition accuracy was merely 89.63%. These results indicate that LLRM can select the feature wavelength bands stably and improve the recognition accuracy of rice seeds, demonstrating the feasibility of developing a hyperspectral technology with LLRM for seed purity identification.

Review on the photonic techniques suitable for automatic monitoring of the composition of multi-materials wastes in view of their posterior recycling

In the increasingly pressing context of improving recycling, optical technologies present a broad potential to support the adequate sorting of plastics. Nevertheless, the commercially available solutions (for example, employing near-infrared spectroscopy) generally focus on identifying mono-materials of a few selected types which currently have a market-interest as secondary materials. Current progress in photonic sciences together with advanced data analysis, such as artificial intelligence, enable bridging practical challenges previously not feasible, for example in terms of classifying more complex materials. In the present paper, the different techniques are initially reviewed based on their main characteristics. Then, based on academic literature, their suitability for monitoring the composition of multi-materials, such as different types of multi-layered packaging and fibre-reinforced polymer composites as well as black plastics used in the motor vehicle industry, is discussed. Finally, some commercial systems with applications in those sectors are also presented. This review mainly focuses on the materials identification step (taking place after waste collection and before sorting and reprocessing) but in outlook, further insights on sorting are given as well as future prospects which can contribute to increasing the circularity of the plastic composites' value chains.

A Review of the Discriminant Analysis Methods for Food Quality Based on Near-Infrared Spectroscopy and Pattern Recognition

Near-infrared spectroscopy (NIRS) combined with pattern recognition technique has become an important type of non-destructive discriminant method. This review first introduces the basic structure of the qualitative analysis process based on near-infrared spectroscopy. Then, the main pretreatment methods of NIRS data processing are investigated. Principles and recent developments of traditional pattern recognition methods based on NIRS are introduced, including some shallow learning machines and clustering analysis methods. Moreover, the newly developed deep learning methods and their applications of food quality analysis are surveyed, including convolutional neural network (CNN), one-dimensional CNN, and two-dimensional CNN. Finally, several applications of these pattern recognition techniques based on NIRS are compared. The deficiencies of the existing pattern recognition methods and future research directions are also reviewed.

Near-infrared Spectroscopy and Hyperspectral Imaging for Sugar Content Evaluation in Potatoes over Multiple Growing Seasons

Sugar content is one of the most important properties of potato tubers as it directly affects their processing and the final product quality, especially for fried products. In this study, data obtained from spectroscopic (interactance and reflectance) and hyperspectral imaging systems were used individually or fused to develop non-cultivar nor growing season-specific regression and classification models for potato tubers based on glucose and sucrose concentration. Data was acquired over three growing seasons for two potato cultivars. The most influential wavelengths were selected from the imaging systems using interval partial least squares for regression and sequential forward selection for classification. Hyperspectral imaging showed the highest regression performance for glucose with a correlation coefficient (ratio of performance to deviation) or r(RPD) of 91.8(2.41) which increased to 94%(2.91) when the data was fused with the interactance data. The sucrose regression results had the highest accuracy using data obtained from the interactance system with r(RPD) values of 74.5%(1.40) that increased to 84.4%(1.82) when the data was fused with the reflectance data. Classification was performed to identify tubers with either high or low sugar content. Classification performance showed accuracy values as high as 95% for glucose and 80.1% for sucrose using hyperspectral imaging, with no noticeable improvement when data was fused from the other spectroscopic systems. When testing the robustness of the developed models over different seasons, it was found that the regression models had r(RPD) values of 55(1.19)–90.3%(2.34) for glucose and 35.8(1.07)–82.2%(1.29) for sucrose. Results obtained in this study demonstrate the feasibility of developing a rapid monitoring system using multispectral imaging and data fusion methods for online evaluation of potato sugar content.

Integration of spectroscopy and image for identifying fusarium damage in wheat kernels

Hyperspectral imaging (HSI) was studied for the detection of varying degrees of damage in wheat kernels caused by Fusarium head blight (Gibberella zeae), a major disease in wheat worldwide. A total of 810 wheat kernel samples were collected from a field trial with the three levels of Fusarium infection, healthy, moderate, and severe. Hyperspectral image of the wheat kernels was acquired over a wavelength range of 400-1000 nm. The raw spectral data were pre-processed, and then the optimal wavelengths were selected using principal component analysis (PCA), successive projection algorithm (SPA) and random forest (RF). The image features were extracted based on the optimal wavelengths, and then the spectral features and image features were combined as fusion features. Support vector machine (SVM), random forest (RF) and naive Bayes (NB) were employed to build the classification models to identify the degrees of Fuasrium damage based on spectral and fusion features. The best performance was obtained by using the SPA-RF method to select the optimal wavelengths and corresponding image features, with a classification accuracy of 96.44%. The method developed from this study can provide a more effective way to identify the degrees of Fusarium damage in wheat kernels.

Identification of Bacterial Blight Resistant Rice Seeds Using Terahertz Imaging and Hyperspectral Imaging Combined With Convolutional Neural Network

Because bacterial blight (BB) disease seriously affects the yield and quality of rice, breeding BB resistant rice is an important priority for plant breeders but the process is time-consuming. The feasibility of using terahertz imaging technology and near-infrared hyperspectral imaging technology to identify BB resistant seeds has therefore been studied. The two-dimensional (2D) spectral images and one-dimensional (1D) spectra provided by both imaging methods were used to build discriminant models based on a deep learning method, the convolutional neural network (CNN), and traditional machine learning methods, support vector machine (SVM), random forest (RF), and partial least squares discriminant analysis (PLS-DA). The highest classification accuracy was achieved by the discriminate model based on CNN using the terahertz absorption spectra. Confusion matrixes were pictured to show the identification details. The t-distributed stochastic neighbor embedding (t-SNE) method was used to visualize the process of CNN data processing. Terahertz imaging technology combined with CNN has great potential to quickly identify BB resistant rice seeds and is more accurate than using near-infrared hyperspectral imaging.

Rapid Classification of Wheat Grain Varieties Using Hyperspectral Imaging and Chemometrics

The classification of wheat grain varieties is of great value because its high purity is the yield and quality guarantee. In this study, hyperspectral imaging combined with the chemometric methods was applied to explore and implement the varieties classification of wheat seeds. The hyperspectral images of all the samples covering 874–1734 nm bands were collected. Exploratory analysis was first carried out while using principal component analysis (PCA) and linear discrimination analysis (LDA). Spectral preprocessing methods including standard normal variate (SNV), multiplicative scatter correction (MSC), and wavelet transform (WT) were introduced, and their effects on discriminant models were studied to eliminate the interference of instrumental and environmental factors. PCA loading, successive projections algorithm (SPA), and random frog (RF) were applied to extract feature wavelengths for redundancy elimination owing to the possibility of existing redundant spectral information. Classification models were developed based on full wavelengths and feature wavelengths using LDA, support vector machine (SVM), and extreme learning machine (ELM). This optimal model was finally utilized to generate visualization map to observe the classification performance intuitively. When comparing with other models, ELM based on full wavelengths achieved the best accuracy up to 91.3%. The overall results suggested that hyperspectral imaging was a potential tool for the rapid and accurate identification of wheat varieties, which could be conducted in large-scale seeds classification and quality detection in modern seed industry.

A Hyperspectral Imaging Approach for Classifying Geographical Origins of Rhizoma Atractylodis Macrocephalae Using the Fusion of Spectrum-Image in VNIR and SWIR Ranges (VNIR-SWIR-FuSI)

Hyperspectral data processing technique has gained increasing interests in the field of chemical and biomedical analysis. However, appropriate approaches to fusing features of hyperspectral data-cube are still lacking. In this paper, a new data fusion approach was proposed and applied to discriminate Rhizoma Atractylodis Macrocephalae (RAM) slices from different geographical origins using hyperspectral imaging. Spectral and image features were extracted from hyperspectral data in visible and near-infrared (VNIR, 435-1042 nm) and short-wave infrared (SWIR, 898-1751 nm) ranges, respectively. Effective wavelengths were extracted from pre-processed spectral data by successive projection algorithm (SPA). Meanwhile, gray-level co-occurrence matrix (GLCM) and gray-level run-length matrix (GLRLM) were employed to extract textural variables. The fusion of spectrum-image in VNIR and SWIR ranges (VNIR-SWIR-FuSI) was implemented to integrate those features on three fusion dimensions, i.e., VNIR and SWIR fusion, spectrum and image fusion, and all data fusion. Based on data fusion, partial least squares-discriminant analysis (PLS-DA) and support vector machine (SVM) were utilized to establish calibration models. The results demonstrated that VNIR-SWIR-FuSI could achieve the best accuracies on both full bands (97.3%) and SPA bands (93.2%). In particular, VNIR-SWIR-FuSI on SPA bands achieved a classification accuracy of 93.2% with only 23 bands, which was significantly better than those based on spectra (80.9%) or images (79.7%). Thus it is more rapid and possible for industry applications. The current study demonstrated that hyperspectral imaging technique with data fusion holds the potential for rapid and nondestructive sorting of traditional Chinese medicines (TCMs).

Rapid Measurement of Soybean Seed Viability Using Kernel-Based Multispectral Image Analysis

Viability is an important quality factor influencing seed germination and crop yield. Current seed-viability testing methods rely on conventional manual inspections, which use destructive, labor-intensive and time-consuming measurements. The aim of this study is to distinguish between viable and nonviable soybean seeds, using a near-infrared (NIR) hyperspectral imaging (HSI) technique in a rapid and nondestructive manner. The data extracted from the NIR⁻HSI of viable and nonviable soybean seeds were analyzed using a partial least-squares discrimination analysis (PLS-DA) technique for classifying the viable and nonviable soybean seeds. Variable importance in projection (VIP) was used as a waveband selection method to develop a multispectral imaging model. Initially, the spectral profile of each pixel in the soybean seed images was subjected to PLS-DA analysis, which yielded a reasonable classification accuracy; however, the pixel-based classification method was not successful for high accuracy detection for nonviable seeds. Another viability detection method was then investigated: a kernel image threshold method with an optimum-detection-rate strategy. The kernel-based classification of seeds showed over 95% accuracy even when using only seven optimal wavebands selected through VIP. The results show that the proposed multispectral NIR imaging method is an effective and accurate nondestructive technique for the discrimination of soybean seed viability.

Variety identification of oat seeds using hyperspectral imaging: investigating the representation ability of deep convolutional neural network

Variety identification of seeds is critical for assessing variety purity and ensuring crop yield. In this paper, a novel method based on hyperspectral imaging (HSI) and deep convolutional neural network (DCNN) was proposed to discriminate the varieties of oat seeds. The representation ability of DCNN was also investigated. The hyperspectral images with a spectral range of 874–1734 nm were primarily processed by principal component analysis (PCA) for exploratory visual distinguishing. Then a DCNN trained in an end-to-end manner was developed. The deep spectral features automatically learnt by DCNN were extracted and combined with traditional classifiers (logistic regression (LR), support vector machine with RBF kernel (RBF_SVM) and linear kernel (LINEAR_SVM)) to construct discriminant models. Contrast models were built based on the traditional classifiers using full wavelengths and optimal wavelengths selected by the second derivative (2nd derivative) method. The comparison results showed that all DCNN-based models outperformed the contrast models. DCNN trained in an end-to-end manner achieved the highest accuracy of 99.19% on the testing set, which was finally employed to visualize the variety classification. The results demonstrated that the deep spectral features with outstanding representation ability enabled HSI together with DCNN to be a reliable tool for rapid and accurate variety identification, which would help to develop an on-line system for quality detection of oat seeds as well as other grain seeds.

The excellent representation ability of deep spectral features enables hyperspectral imaging combined with deep convolutional neural network to be a powerful tool for large-scale seeds detection in modern seed industry.

Discrimination of Chrysanthemum Varieties Using Hyperspectral Imaging Combined with a Deep Convolutional Neural Network

Rapid and accurate discrimination of Chrysanthemum varieties is very important for producers, consumers and market regulators. The feasibility of using hyperspectral imaging combined with deep convolutional neural network (DCNN) algorithm to identify Chrysanthemum varieties was studied in this paper. Hyperspectral images in the spectral range of 874–1734 nm were collected for 11,038 samples of seven varieties. Principal component analysis (PCA) was introduced for qualitative analysis. Score images of the first five PCs were used to explore the differences between different varieties. Second derivative (2nd derivative) method was employed to select optimal wavelengths. Support vector machine (SVM), logistic regression (LR), and DCNN were used to construct discriminant models using full wavelengths and optimal wavelengths. The results showed that all models based on full wavelengths achieved better performance than those based on optimal wavelengths. DCNN based on full wavelengths obtained the best results with an accuracy close to 100% on both training set and testing set. This optimal model was utilized to visualize the classification results. The overall results indicated that hyperspectral imaging combined with DCNN was a very powerful tool for rapid and accurate discrimination of Chrysanthemum varieties. The proposed method exhibited important potential for developing an online Chrysanthemum evaluation system.

Identification of Hybrid Okra Seeds Based on Near-Infrared Hyperspectral Imaging Technology

Near-infrared (874–1734 nm) hyperspectral imaging technology combined with chemometrics was used to identify parental and hybrid okra seeds. A total of 1740 okra seeds of three different varieties, which contained the male parent xiaolusi, the female parent xianzhi, and the hybrid seed penzai, were collected, and all of the samples were randomly divided into the calibration set and the prediction set in a ratio of 2:1. Principal component analysis (PCA) was applied to explore the separability of different seeds based on the spectral characteristics of okra seeds. Fourteen and 86 characteristic wavelengths were extracted by using the successive projection algorithm (SPA) and competitive adaptive reweighted sampling (CARS), respectively. Another 14 characteristic wavelengths were extracted by using CARS combined with SPA. Partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM) were developed based on the characteristic wavelength and full-band spectroscopy. The experimental results showed that the SVM discriminant model worked well and that the correct recognition rate was over 93.62% based on full-band spectroscopy. As for the discriminative model that was based on characteristic wavelength, the SVM model based on the CARS algorithm was better than the other two models. Combining the CARS+SVM calibration model and image processing technology, a pseudo-color map of sample prediction was generated, which could intuitively identify the species of okra seeds. The whole process provided a new idea for agricultural breeding in the rapid screening and identification of hybrid okra seeds.

Production of an innovative biowaste-derived fertilizer: Rapid monitoring of physical-chemical parameters by hyperspectral imaging

In this work the possibility to apply hyperspectral imaging as a fast and non-destructive technique for the monitoring of the production process at pilot plant scale of an innovative biowaste-derived fertilizer was explored. Different mixtures of urban organic waste, farm organic residues, biochar and vegetable active principles were selected and utilized in two different European countries, Italy and Spain, for the production of the innovative fertilizer. The biowaste-derived fertilizer samples were collected from the pilot plant piles at different curing time and acquired by the hyperspectral imaging device. Spectra have been collected in the near infrared wavelength range (1000-1700 nm). Conventional analyses were carried out on the same samples in order to find correlations between the physical-chemical parameters detected at laboratory scale, and the acquired reflectance spectra. The investigated parameters were: pH, electrical conductivity, soluble total organic carbon and soluble total nitrogen. Hyperspectral data were processed adopting chemometric strategies through the application of principal component analysis, for exploratory purposes, and partial least squares analysis to establish correlations between spectral features and measured physical-chemical parameters. Good correlations, with R² ranging between 0.85 and 0.96, were obtained for all the investigated parameters. Results showed as the proposed approach, based on hyperspectral imaging, is suitable to be adopted for a rapid and non-destructive monitoring of waste-derived fertilizer production.

A Reliable Methodology for Determining Seed Viability by Using Hyperspectral Data from Two Sides of Wheat Seeds

This study investigated the possibility of using visible and near-infrared (VIS/NIR) hyperspectral imaging techniques to discriminate viable and non-viable wheat seeds. Both sides of individual seeds were subjected to hyperspectral imaging (400-1000 nm) to acquire reflectance spectral data. Four spectral datasets, including the ventral groove side, reverse side, mean (the mean of two sides' spectra of every seed), and mixture datasets (two sides' spectra of every seed), were used to construct the models. Classification models, partial least squares discriminant analysis (PLS-DA), and support vector machines (SVM), coupled with some pre-processing methods and successive projections algorithm (SPA), were built for the identification of viable and non-viable seeds. Our results showed that the standard normal variate (SNV)-SPA-PLS-DA model had high classification accuracy for whole seeds (>85.2%) and for viable seeds (>89.5%), and that the prediction set was based on a mixed spectral dataset by only using 16 wavebands. After screening with this model, the final germination of the seed lot could be higher than 89.5%. Here, we develop a reliable methodology for predicting the viability of wheat seeds, showing that the VIS/NIR hyperspectral imaging is an accurate technique for the classification of viable and non-viable wheat seeds in a non-destructive manner.

Discrimination of CRISPR/Cas9-induced mutants of rice seeds using near-infrared hyperspectral imaging

Identifying individuals with target mutant phenotypes is a significant procedure in mutant exploitation for implementing genome editing technology in a crop breeding programme. In the present study, a rapid and non-invasive method was proposed to identify CRISPR/Cas9-induced rice mutants from their acceptor lines (huaidao-1 and nanjing46) using hyperspectral imaging in the near-infrared (NIR) range (874.41–1733.91 nm) combined with chemometric analysis. The hyperspectral imaging data were analysed using principal component analysis (PCA) for exploratory purposes, and a support vector machine (SVM) and an extreme learning machine (ELM) were applied to build discrimination models for classification. Meanwhile, PCA loadings and a successive projections algorithm (SPA) were used for extracting optimal spectral wavelengths. The SVM-SPA model achieved best performance, with classification accuracies of 93% and 92.75% being observed for calibration and prediction sets for huaidao-1 and 91.25% and 89.50% for nanjing46, respectively. Furthermore, the classification of mutant seeds was visualized on prediction maps by predicting the features of each pixel on individual hyperspectral images based on the SPA-SVM model. The above results indicated that NIR hyperspectral imaging together with chemometric data analysis could be a reliable tool for identifying CRISPR/Cas9-induced rice mutants, which would help to accelerate selection and crop breeding processes.

Hyperspectral image analysis for rapid and accurate discrimination of bacterial infections: A benchmark study

With the rapid diffusion of Full Laboratory Automation systems, Clinical Microbiology is currently experiencing a new digital revolution. The ability to capture and process large amounts of visual data from microbiological specimen processing enables the definition of completely new objectives. These include the direct identification of pathogens growing on culturing plates, with expected improvements in rapid definition of the right treatment for patients affected by bacterial infections. In this framework, the synergies between light spectroscopy and image analysis, offered by hyperspectral imaging, are of prominent interest. This leads us to assess the feasibility of a reliable and rapid discrimination of pathogens through the classification of their spectral signatures extracted from hyperspectral image acquisitions of bacteria colonies growing on blood agar plates. We designed and implemented the whole data acquisition and processing pipeline and performed a comprehensive comparison among 40 combinations of different data preprocessing and classification techniques. High discrimination performance has been achieved also thanks to improved colony segmentation and spectral signature extraction. Experimental results reveal the high accuracy and suitability of the proposed approach, driving the selection of most suitable and scalable classification pipelines and stimulating clinical validations.

Segmentation in dermatological hyperspectral images: dedicated methods

Background

Segmentation of hyperspectral medical images is one of many image segmentation methods which require profiling. This profiling involves either the adjustment of existing, known image segmentation methods or a proposal of new dedicated methods of hyperspectral image segmentation. Taking into consideration the size of analysed data, the time of analysis is of major importance. Therefore, the authors proposed three new dedicated methods of hyperspectral image segmentation with special reference to the time of analysis.

Methods

The segmentation methods presented in this paper were tested and profiled to the images acquired from different hyperspectral cameras including SOC710 Hyperspectral Imaging System, Specim sCMOS-50-V10E. Correct functioning of the method was tested for over 10,000 2D images constituting the sequence of over 700 registrations of the areas of the left and right hand and the forearm.

Results

As a result, three new methods of hyperspectral image segmentation have been proposed: fast analysis of emissivity curves (SKE), 3D segmentation (S3D) and hierarchical segmentation (SH). They have the following features: are fully automatic; allow for implementation of fast segmentation methods; are profiled to hyperspectral image segmentation; use emissivity curves in the model form, can be applied in any type of objects not necessarily biological ones, are faster (SKE—2.3 ms, S3D—1949 ms, SH—844 ms for the computer with Intel^® Core i7 4960X CPU 3.6 GHz) and more accurate (SKE—accuracy 79 %, S3D—90 %, SH—92 %) in comparison with typical methods known from the literature.

Conclusions

Profiling and/or proposing new methods of hyperspectral image segmentation is an indispensable element of developing software. This ensures speed, repeatability and low sensitivity of the algorithm to changing parameters.

Recent developments and applications of hyperspectral imaging for quality evaluation of agricultural products: a review

Food quality and safety is the foremost issue for consumers, retailers as well as regulatory authorities. Most quality parameters are assessed by traditional methods, which are time consuming, laborious, and associated with inconsistency and variability. Non-destructive methods have been developed to objectively measure quality attributes for various kinds of food. In recent years, hyperspectral imaging (HSI) has matured into one of the most powerful tools for quality evaluation of agricultural and food products. HSI allows characterization of a sample's chemical composition (spectroscopic component) and external features (imaging component) in each point of the image with full spectral information. In order to track the latest research developments of this technology, this paper gives a detailed overview of the theory and fundamentals behind this technology and discusses its applications in the field of quality evaluation of agricultural products. Additionally, future potentials of HSI are also reported.

Hyperspectral imaging in medicine: image pre-processing problems and solutions in Matlab

The paper presents problems and solutions related to hyperspectral image pre-processing. New methods of preliminary image analysis are proposed. The paper shows problems occurring in Matlab when trying to analyse this type of images. Moreover, new methods are discussed which provide the source code in Matlab that can be used in practice without any licensing restrictions. The proposed application and sample result of hyperspectral image analysis.

NIR spectroscopy as a tool for discriminating between lichens exposed to air pollution

Lichens are used as biomonitors of air pollution because they are extremely sensitive to the presence of substances that alter atmospheric composition. Fifty-one thalli of two different varieties of Pseudevernia furfuracea (var. furfuracea and var. ceratea) were collected far from local sources of air pollution. Twenty-six of these thalli were then exposed to the air for one month in the industrial port of Genoa, which has high levels of environmental pollution. The possibility of using Near-infrared spectroscopy (NIRS) for generating a 'fingerprint' of lichens was investigated. Chemometric methods were successfully applied to discriminate between samples from polluted and non-polluted areas. In particular, Principal Component Analysis (PCA) was applied as a multivariate display method on the NIR spectra to visualise the data structure. This showed that the difference between samples of different varieties was not significant in comparison to the difference between samples exposed to different levels of environmental pollution. Then Linear Discriminant Analysis (LDA) was carried out to discriminate between lichens based on their exposure to pollutants. The distinction between control samples (not exposed) and samples exposed to the air in the industrial port of Genoa was evaluated. On average, 95.2% of samples were correctly classified, 93.0% of total internal prediction (5 cross-validation groups) and 100.0% of external prediction (on the test set) was achieved.

Spectral and Image Integrated Analysis of Hyperspectral Data for Waxy Corn Seed Variety Classification

The purity of waxy corn seed is a very important index of seed quality. A novel procedure for the classification of corn seed varieties was developed based on the combined spectral, morphological, and texture features extracted from visible and near-infrared (VIS/NIR) hyperspectral images. For the purpose of exploration and comparison, images of both sides of corn kernels (150 kernels of each variety) were captured and analyzed. The raw spectra were preprocessed with Savitzky-Golay (SG) smoothing and derivation. To reduce the dimension of spectral data, the spectral feature vectors were constructed using the successive projections algorithm (SPA). Five morphological features (area, circularity, aspect ratio, roundness, and solidity) and eight texture features (energy, contrast, correlation, entropy, and their standard deviations) were extracted as appearance character from every corn kernel. Support vector machines (SVM) and a partial least squares–discriminant analysis (PLS-DA) model were employed to build the classification models for seed varieties classification based on different groups of features. The results demonstrate that combining spectral and appearance characteristic could obtain better classification results. The recognition accuracy achieved in the SVM model (98.2% and 96.3% for germ side and endosperm side, respectively) was more satisfactory than in the PLS-DA model. This procedure has the potential for use as a new method for seed purity testing.