Wheat stripe rust grading by deep learning with attention mechanism and images from mobile devices

Wheat stripe rust is one of the main wheat diseases worldwide, which has significantly adverse effects on wheat yield and quality, posing serious threats on food security. Disease severity grading plays a paramount role in stripe rust disease management including breeding disease-resistant wheat varieties. Manual inspection is time-consuming, labor-intensive and prone to human errors, therefore, there is a clearly urgent need to develop more effective and efficient disease grading strategy by using automated approaches. However, the differences between wheat leaves of different levels of stripe rust infection are usually tiny and subtle, and, as a result, ordinary deep learning networks fail to achieve satisfying performance. By formulating this challenge as a fine-grained image classification problem, this study proposes a novel deep learning network C-DenseNet which embeds Convolutional Block Attention Module (CBAM) in the densely connected convolutional network (DenseNet). The performance of C-DenseNet and its variants is demonstrated via a newly collected wheat stripe rust grading dataset (WSRgrading dataset) at Northwest A&F University, Shaanxi Province, China, which contains a total of 5,242 wheat leaf images with 6 levels of stripe rust infection. The dataset was collected by using various mobile devices in the natural field condition. Comparative experiments show that C-DenseNet with a test accuracy of 97.99% outperforms the classical DenseNet (92.53%) and ResNet (73.43%). GradCAM++ network visualization also shows that C-DenseNet is able to pay more attention to the key areas in making the decision. It is concluded that C-DenseNet with an attention mechanism is suitable for wheat stripe rust disease grading in field conditions

Significant Remote Sensing Vegetation Indices: A Review of Developments and Applications

Vegetation Indices (VIs) obtained from remote sensing based canopies are quite simple and effective algorithms for quantitative and qualitative evaluations of vegetation cover, vigor, and growth dynamics, among other applications. These indices have been widely implemented within RS applications using different airborne and satellite platforms with recent advances using Unmanned Aerial Vehicles (UAV). Up to date, there is no unified mathematical expression that defines all VIs due to the complexity of different light spectra combinations, instrumentation, platforms, and resolutions used. Therefore, customized algorithms have been developed and tested against a variety of applications according to specific mathematical expressions that combine visible light radiation, mainly green spectra region, from vegetation, and nonvisible spectra to obtain proxy quantifications of the vegetation surface. In the real-world applications, optimization VIs are usually tailored to the specific application requirements coupled with appropriate validation tools and methodologies in the ground. The present study introduces the spectral characteristics of vegetation and summarizes the development of VIs and the advantages and disadvantages from different indices developed. This paper reviews more than 100 VIs, discussing their specific applicability and representativeness according to the vegetation of interest, environment, and implementation precision. Predictably, research, and development of VIs, which are based on hyperspectral and UAV platforms, would have a wide applicability in different areas

Segmentation of field grape bunches via an improved pyramid scene parsing network

With the continuous expansion of wine grape planting areas, the mechanization and intelligence of grape harvesting have gradually become the future development trend. In order to guide the picking robot to pick grapes more efficiently in the vineyard, this study proposed a grape bunches segmentation method based on Pyramid Scene Parsing Network (PSPNet) deep semantic segmentation network for different varieties of grapes in the natural field environments. To this end, the Convolutional Block Attention Module (CBAM) attention mechanism and the atrous convolution were first embedded in the backbone feature extraction network of the PSPNet model to improve the feature extraction capability. Meanwhile, the proposed model also improved the PSPNet semantic segmentation model by fusing multiple feature layers (with more contextual information) extracted by the backbone network. The improved PSPNet was compared against the original PSPNet on a newly collected grape image dataset, and it was shown that the improved PSPNet model had an Intersection-over-Union (IoU) and Pixel Accuracy (PA) of 87.42% and 95.73%, respectively, implying an improvement of 4.36% and 9.95% over the original PSPNet model. The improved PSPNet was also compared against the state-of-the-art DeepLab-V3+ and U-Net in terms of IoU, PA, computation efficiency and robustness, and showed promising performance. It is concluded that the improved PSPNet can quickly and accurately segment grape bunches of different varieties in the natural field environments, which provides a certain technical basis for intelligent harvesting by grape picking robots

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology

The Application of Genetic and Genomic Biotechnology in Aquaculture

This Special Issue, “The Application of Genetic and Genomic Biotechnology in Aquaculture,” collates 14 published manuscripts covering different aspects of implementing advanced molecular genetics and genomic science in aquaculture [...

Traffic Safety Improvement via Optimizing Light Environment in Highway Tunnels

Driving in tunnel areas depends more heavily on light conditions than that on open roadways. Traditional lighting systems in highway tunnels adjust lighting parameters only caring about outside light luminance, and focus is usually on energy conservation; however, little concern is about drivers’ actual physical and psychological needs. How to leverage the enormous research progress of traffic safety, light environment, human factors engineering, and modern lighting sources to create an ideal tunnel light environment that aids with ensuring driving safety and lower interference effects caused by the change of light environment will greatly improve safety level and reduce adverse influence on drivers’ visual health in a tunnel area. An intelligent lighting control system designed with multiple influence factors are systematically considered. Based on sensor data from outside natural light conditions, target lighting parameters are determined per each lighting zone requires; then, lighting commands will be transferred and parsed by adaptive lighting controllers and modules, eventually LED lighting properties are altered step by step. This system helps a lot with optimizing tunnel lighting quality and improving drivers’ visual performance; as a result, it contributes to lower the fluctuation of drivers’ workload and get a smooth traffic flow, and ultimately this technically ensures physical and mental health of drivers in a tunnel area

The Application of Genetic and Genomic Biotechnology in Aquaculture

This Special Issue, “The Application of Genetic and Genomic Biotechnology in Aquaculture,” collates 14 published manuscripts covering different aspects of implementing advanced molecular genetics and genomic science in aquaculture [...

Wheat Stripe Rust Grading by Deep Learning With Attention Mechanism and Images From Mobile Devices

Author Contributions ZM designed and performed the experiment, selected algorithm, analyzed data, and wrote the manuscript. XZ trained algorithms and analyzed data. JS analyzed data and wrote the manuscript. DH collected data and monitored data analysis. BS conceived the study and participated in its design. All authors contributed to the article and approved the submitted version. Funding This work was funded by the Fundamental Research Funds for the Central Universities (No.2452019028).Peer reviewedPublisher PD

Agricultural Environmental Information Collection Device Based on Raspberry Pi

International audienceIntegrated agricultural environmental information real-time collection, transmission and management is extremely critical for precision agriculture (PA). This paper describes the basic knowledge and primary principles used in an agricultural environmental information collection device. The device is based on Raspberry Pi, combining with GPS module, some digital sensors and analog sensors to measure environmental temperature and humidity, barometric pressure, light intensity, soil moisture and other environmental information accurate collection. All collected data was real-time transmitted to a remote server specified database for management. In the experiment process, the device has been proved to have the ability to catch the distributed information and also can get different centralized data management. The results show the integration of operational information collection, transmission and management, as well as the use of open source software to make it easy to collect multiple types of data parallelism, which provides an important solution for the rapid transformation of agricultural production