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Verticillium wilt (VW) is often referred to as the cancer of cotton and it has a detrimental effect on cotton yield and quality. Since the root system is the first to be infested, it is feasible to detect VW by root analysis in the early stages of the disease. In recent years, with the update of computing equipment and the emergence of large-scale high-quality data sets, deep learning has achieved remarkable results in computer vision tasks. However, in some specific areas, such as cotton root MRI image task processing, it will bring some challenges. For example, the data imbalance problem (there is a serious imbalance between the cotton root and the background in the segmentation task) makes it difficult for existing algorithms to segment the target. In this paper, we proposed two new methods to solve these problems. The effectiveness of the algorithms was verified by experimental results. The results showed that the new segmentation model improved the Dice and mIoU by 46% and 44% compared with the original model. And this model could segment MRI images of rapeseed root cross-sections well with good robustness and scalability. The new classification model improved the accuracy by 34.9% over the original model. The recall score and F1 score increased by 59% and 42%, respectively. The results of this paper indicate that MRI and deep learning have the potential for non-destructive early detection of VW diseases in cotton.

Background: Linking phenotypes and genotypes to identify genetic architectures that regulate important traits is crucial for plant breeding and the development of plant genomics. In recent years, genome-wide association studies (GWASs) have been applied extensively to interpret relationships between genes and traits. Successful GWAS application requires comprehensive genomic and phenotypic data from large populations. Although multiple high-throughput DNA sequencing approaches are available for the generation of genomics data, the capacity to generate high-quality phenotypic data is lagging far behind. Traditional methods for plant phenotyping mostly rely on manual measurements, which are laborious, inaccurate, and time-consuming, greatly impairing the acquisition of phenotypic data from large populations. In contrast, high-throughput phenotyping has unique advantages, facilitating rapid, non-destructive, and high-throughput detection, and, in turn, addressing the shortcomings of traditional methods.Aim of Review: This review summarizes the current status with regard to the integration of high-throughput phenotyping and GWAS in plants, in addition to discussing the inherent challenges and future prospects.Key Scientific Concepts of Review: High-throughput phenotyping, which facilitates non-contact and dynamic measurements, has the potential to offer high-quality trait data for GWAS and, in turn, to enhance the unraveling of genetic structures of complex plant traits. In conclusion, high-throughput phenotyping integration with GWAS could facilitate the revealing of coding information in plant genomes.

Deep learning and computer vision have become emerging tools for diseased plant phenotyping. Most previous studies focused on image-level disease classification. In this paper, pixel-level phenotypic feature (the distribution of spot) was analyzed by deep learning. Primarily, a diseased leaf dataset was collected and the corresponding pixel-level annotation was contributed. A dataset of apple leaves samples was used for training and optimization. Another set of grape and strawberry leaf samples was used as an extra testing dataset. Then, supervised convolutional neural networks were adopted for semantic segmentation. Moreover, the possibility of weakly supervised models for disease spot segmentation was also explored. Grad-CAM combined with ResNet-50 (ResNet-CAM), and that combined with a few-shot pretrained U-Net classifier for weakly supervised leaf spot segmentation (WSLSS), was designed. They were trained using image-level annotations (healthy versus diseased) to reduce the cost of annotation work. Results showed that the supervised DeepLab achieved the best performance (IoU = 0.829) on the apple leaf dataset. The weakly supervised WSLSS achieved an IoU of 0.434. When processing the extra testing dataset, WSLSS realized the best IoU of 0.511, which was even higher than fully supervised DeepLab (IoU = 0.458). Although there was a certain gap in IoU between the supervised models and weakly supervised ones, WSLSS showed stronger generalization ability than supervised models when processing the disease types not involved in the training procedure. Furthermore, the contributed dataset in this paper could help researchers get a quick start on designing their new segmentation methods in future studies.

Leaf nitrogen concentration (LNC) is a critical indicator of crop nutrient status. In this study, the feasibility of using visible and near-infrared spectroscopy combined with deep learning to estimate LNC in cotton leaves was explored. The samples were collected from cotton’s whole growth cycle, and the spectra were from different measurement environments. The random frog (RF), weighted partial least squares regression (WPLS), and saliency map were used for characteristic wavelength selection. Qualitative models (partial least squares discriminant analysis (PLS-DA), support vector machine for classification (SVC), convolutional neural network classification (CNNC) and quantitative models (partial least squares regression (PLSR), support vector machine for regression (SVR), convolutional neural network regression (CNNR)) were established based on the full spectra and characteristic wavelengths. Satisfactory results were obtained by models based on CNN. The classification accuracy of leaves in three different LNC ranges was up to 83.34%, and the root mean square error of prediction (RMSEP) of quantitative prediction models of cotton leaves was as low as 3.36. In addition, the identification of cotton leaves based on the predicted LNC also achieved good results. These results indicated that the nitrogen content of cotton leaves could be effectively detected by deep learning and visible and near-infrared spectroscopy, which has great potential for real-world application.

Herbicides and heavy metals are hazardous substances of environmental pollution, resulting in plant stress and harming humans and animals. Identification of stress types can help trace stress sources, manage plant growth, and improve stress-resistant breeding. In this research, hyperspectral imaging (HSI) and chlorophyll fluorescence imaging (Chl-FI) were adopted to identify the rice plants under two types of herbicide stresses (butachlor (DCA) and quinclorac (ELK)) and two types of heavy metal stresses (cadmium (Cd) and copper (Cu)). Visible/near-infrared spectra of leaves (L-VIS/NIR) and stems (S-VIS/NIR) extracted from HSI and chlorophyll fluorescence kinetic curves of leaves (L-Chl-FKC) and stems (S-Chl-FKC) extracted from Chl-FI were fused to establish the models to detect the stress of the hazardous substances. Novel end-to-end deep fusion models were proposed for low-level, middle-level, and high-level information fusion to improve identification accuracy. Results showed that the high-level fusion-based convolutional neural network (CNN) models reached the highest detection accuracy (97.7%), outperforming the models using a single data source (

Rapid determination of chlorophyll content is significant for evaluating cotton’s nutritional and physiological status. Hyperspectral technology equipped with multivariate analysis methods has been widely used for chlorophyll content detection. However, the model developed on one batch or variety cannot produce the same effect for another due to variations, such as samples and measurement conditions. Considering that it is costly to establish models for each batch or variety, the feasibility of using spectral preprocessing combined with deep transfer learning for model transfer was explored. Seven different spectral preprocessing methods were discussed, and a self-designed convolutional neural network (CNN) was developed to build models and conduct transfer tasks by fine-tuning. The approach combined first-derivative (FD) and standard normal variate transformation (SNV) was chosen as the best pretreatment. For the dataset of the target domain, fine-tuned CNN based on spectra processed by FD + SNV outperformed conventional partial least squares (PLS) and squares-support vector machine regression (SVR). Although the performance of fine-tuned CNN with a smaller dataset was slightly lower, it was still better than conventional models and achieved satisfactory results. Ensemble preprocessing combined with deep transfer learning could be an effective approach to estimate the chlorophyll content between different cotton varieties, offering a new possibility for evaluating the nutritional status of cotton in the field.

Radix Astragali is a prized traditional Chinese functional food that is used for both medicine and food purposes, with various benefits such as immunomodulation, anti-tumor, and anti-oxidation. The geographical origin of Radix Astragali has a significant impact on its quality attributes. Determining the geographical origins of Radix Astragali is essential for quality evaluation. Hyperspectral imaging covering the visible/short-wave near-infrared range (Vis-NIR, 380–1030 nm) and near-infrared range (NIR, 874–1734 nm) were applied to identify Radix Astragali from five different geographical origins. Principal component analysis (PCA) was utilized to form score images to achieve preliminary qualitative identification. PCA and convolutional neural network (CNN) were used for feature extraction. Measurement-level fusion and feature-level fusion were performed on the original spectra at different spectral ranges and the corresponding features. Support vector machine (SVM), logistic regression (LR), and CNN models based on full wavelengths, extracted features, and fusion datasets were established with excellent results; all the models obtained an accuracy of over 98% for different datasets. The results illustrate that hyperspectral imaging combined with CNN and fusion strategy could be an effective method for origin identification of Radix Astragali.

Sodium pyrosulfite is a browning inhibitor used for the storage of fresh-cut potato slices. Excessive use of sodium pyrosulfite can lead to sulfur dioxide residue, which is harmful for the human body. The sulfur dioxide residue on the surface of fresh-cut potato slices immersed in different concentrations of sodium pyrosulfite solution was classified by near-infrared hyperspectral imaging (NIR-HSI) system and portable near-infrared (NIR) spectrometer. Principal component analysis was used to analyze the object-wise spectra, and support vector machine (SVM) model was established. The classification accuracy of calibration set and prediction set were 98.75% and 95%, respectively. Savitzky–Golay algorithm was used to recognize the important wavelengths, and SVM model was established based on the recognized important wavelengths. The final classification accuracy was slightly less than that based on the full spectra. In addition, the pixel-wise spectra extracted from NIR-HSI system could realize the visualization of different samples, and intuitively reflect the differences among the samples. The results showed that it was feasible to classify the sulfur dioxide residue on the surface of fresh-cut potato slices immersed in different concentration of sodium pyrosulfite solution by NIR spectra. It provided an alternative method for the detection of sulfur dioxide residue on the surface of fresh-cut potato slices.

Color index and water content are important indicators for evaluating the quality of fresh-cut potato tuber slices. In this study, hyperspectral imaging combined with multivariate analysis was used to detect the color parameters (L*, a*, b*, Browning index (BI), L*/b*) and water content of fresh-cut potato tuber slices. The successive projections algorithm (SPA) and competitive adaptive reweighted sampling (CARS) were used to extract characteristic wavelengths, partial least squares (PLS) and least squares support vector machine (LS-SVM) were utilized to establish regression models. For color prediction, R2c, R2p and RPD of all the LSSVM models established for the five color indicators L*, a*, b*, BI, L*/b* were exceeding 0.90, 0.84 and 2.1, respectively. For water content prediction, R2c, R2p, and RPD of the LSSVM models were over 0.80, 0.77 and 1.9, respectively. LS-SVM model based on full spectra was used to reappear the spatial distribution of color and water content in fresh-cut potato tuber slices by pseudo-color imaging since it performed best in most cases. The results illustrated that hyperspectral imaging could be an effective method for color and water content prediction, which could provide solid theoretical basis for subsequent grading and processing of fresh-cut potato tuber slices.

Rapid and nondestructive determination of quality attributes in fresh and dry Chrysanthemum morifolium is of great importance for quality sorting and monitoring during harvest and trade. Near-infrared hyperspectral imaging covering the spectral range of 874–1734 nm was used to detect chlorogenic acid, luteolin-7-O-glucoside, and 3,5-O-dicaffeoylquinic acid content in Chrysanthemum morifolium. Fresh and dry Chrysanthemum morifolium flowers were studied for harvest and trade. Pixelwise spectra were preprocessed by wavelet transform (WT) and area normalization, and calculated as average spectrum. Successive projections algorithm (SPA) was used to select optimal wavelengths. Partial least squares (PLS), extreme learning machine (ELM), and least-squares support vector machine (LS-SVM) were used to build calibration models based on full spectra and optimal wavelengths. Calibration models of fresh and dry flowers obtained good results. Calibration models for chlorogenic acid in fresh flowers obtained best performances, with coefficient of determination (R2) over 0.85 and residual predictive deviation (RPD) over 2.50. Visualization maps of chlorogenic acid, luteolin-7-O-glucoside, and 3,5-O-dicaffeoylquinic acid in single fresh and dry flowers were obtained. The overall results showed that hyperspectral imaging was feasible to determine chlorogenic acid, luteolin-7-O-glucoside, and 3,5-O-dicaffeoylquinic acid. Much more work should be done in the future to improve the prediction performance.