TrIncNet: a lightweight vision transformer network for identification of plant diseases.

In the agricultural sector, identifying plant diseases at their earliest possible stage of infestation still remains a huge challenge with respect to the maximization of crop production and farmers' income. In recent years, advanced computer vision techniques like Vision Transformers (ViTs) are being successfully applied to identify plant diseases automatically. However, the MLP module in existing ViTs is computationally expensive as well as inefficient in extracting promising features from diseased images. Therefore, this study proposes a comparatively lightweight and improved vision transformer network, also known as "TrIncNet" for plant disease identification. In the proposed network, we introduced a modified encoder architecture a.k.a. Trans-Inception block in which the MLP block of existing ViT was replaced by a custom inception block. Additionally, each Trans-Inception block is surrounded by a skip connection, making it much more resistant to the vanishing gradient problem. The applicability of the proposed network for identifying plant diseases was assessed using two plant disease image datasets viz: PlantVillage dataset and Maize disease dataset (contains in-field images of Maize diseases). The comparative performance analysis on both datasets reported that the proposed TrIncNet network outperformed the state-of-the-art CNN architectures viz: VGG-19, GoogLeNet, ResNet-50, Xception, InceptionV3, and MobileNet. Moreover, the experimental results also showed that the proposed network had achieved 5.38% and 2.87% higher testing accuracy than the existing ViT network on both datasets, respectively. Therefore, the lightweight nature and improved prediction performance make the proposed network suitable for being integrated with IoT devices to assist the stakeholders in identifying plant diseases at the field level.

Climate plays a dominant role over land management in governing soil carbon dynamics in North Western Himalayas.

The soil carbon (C) dynamics is strongly influenced by climate and land-use patterns in the Himalayas. Therefore, soils under five prominent land use [e.g., maize (Zea mays), horticulture, natural forest, grassland, and wasteland] were sampled down up to 30 cm depth under two climatic conditions viz., temperate and subtropical to assess the impacts of climate and landuse on soil C dynamics. Results demonstrated that irrespective of land use, temperate soil contains 30.66% higher C than subtropical soils. Temperate soils under natural forests had the higher total organic carbon (TOC, 21.90 g kg-1), Walkley-Black carbon (WBC, 16.42 g kg-1), contents, and stocks (TOC, 66.92 Mg ha-1 and WBC, 50.24 Mg ha-1), and total soil organic matter (TSOM, 3.78%) concentration as compared to other land uses like maize, horticulture, grassland, and wasteland. Under both climatic conditions, maize land use had the lowest TOC 9.63, 6.55 g kg-1 and WBC 7.22, 4.91 g kg-1 at 0-15 and 15-30 cm soil depth, respectively. Horticulture land use had 62.58 and 62.61% higher TOC and WBC over maize-based land use under subtropical and temperate climatic conditions at 0-30 cm soil depth, respectively. However, soils of maize land use under temperate conditions had ∼2 times more TOC than in subtropical conditions. The study inferred that the C-losses is more in the subtropical soil than in temperate soils. Hence, the subtropical region needs more rigorous adoption of C conservation farming practices than the temperate climatic setting. Although, the adoption of C storing and conserving practices is crucial under both climatic settings to arrest land degradation. Horticultural land uses along with conservation effective soil management practices may be encouraged to restore more soil C and to improve the livelihood security of the hill populace in the North Western Himalayas.

PDSE-Lite: lightweight framework for plant disease severity estimation based on Convolutional Autoencoder and Few-Shot Learning.

Plant disease diagnosis with estimation of disease severity at early stages still remains a significant research challenge in agriculture. It is helpful in diagnosing plant diseases at the earliest so that timely action can be taken for curing the disease. Existing studies often rely on labor-intensive manually annotated large datasets for disease severity estimation. In order to conquer this problem, a lightweight framework named "PDSE-Lite" based on Convolutional Autoencoder (CAE) and Few-Shot Learning (FSL) is proposed in this manuscript for plant disease severity estimation with few training instances. The PDSE-Lite framework is designed and developed in two stages. In first stage, a lightweight CAE model is built and trained to reconstruct leaf images from original leaf images with minimal reconstruction loss. In subsequent stage, pretrained layers of the CAE model built in the first stage are utilized to develop the image classification and segmentation models, which are then trained using FSL. By leveraging FSL, the proposed framework requires only a few annotated instances for training, which significantly reduces the human efforts required for data annotation. Disease severity is then calculated by determining the percentage of diseased leaf pixels obtained through segmentation out of the total leaf pixels. The PDSE-Lite framework's performance is evaluated on Apple-Tree-Leaf-Disease-Segmentation (ATLDS) dataset. However, the proposed framework can identify any plant disease and quantify the severity of identified diseases. Experimental results reveal that the PDSE-Lite framework can accurately detect healthy and four types of apple tree diseases as well as precisely segment the diseased area from leaf images by using only two training samples from each class of the ATLDS dataset. Furthermore, the PDSE-Lite framework's performance is compared with existing state-of-the-art techniques, and it is found that this framework outperformed these approaches. The proposed framework's applicability is further verified by statistical hypothesis testing using Student t-test. The results obtained from this test confirm that the proposed framework can precisely estimate the plant disease severity with a confidence interval of 99%. Hence, by reducing the reliance on large-scale manual data annotation, the proposed framework offers a promising solution for early-stage plant disease diagnosis and severity estimation.

SlypNet: Spikelet-based yield prediction of wheat using advanced plant phenotyping and computer vision techniques.

The application of computer vision in agriculture has already contributed immensely to restructuring the existing field practices starting from the sowing to the harvesting. Among the different plant parts, the economic part, the yield, has the highest importance and becomes the ultimate goal for the farming community. It depends on many genetic and environmental factors, so this curiosity about knowing the yield brought several precise pre-harvest prediction methods using different ways. Out of those techniques, non-invasive yield prediction techniques using computer vision have been proved to be the most efficient and trusted platform. This study developed a novel methodology, called SlypNet, using advanced deep learning networks, i.e., Mask R-CNN and U-Net, which can extract various plant morphological features like spike and spikelet from the visual image of the wheat plant and provide a high-throughput yield estimate with great precision. Mask R-CNN outperformed previous networks in spike detection by its precise detection performance with a mean average precision (mAP) of 97.57%, a F1 score of 0.67, and an MCC of 0.91 by overcoming several natural field constraints like overlapping and background interference, variable resolution, and high bushiness of plants. The spikelet detection module's accuracy and consistency were tested with about 99% validation accuracy of the model and the least error, i.e., a mean square error of 1.3 from a set of typical and complex views of wheat spikes. Spikelet yield cumulatively showed the probable production capability of each plant. Our method presents an integrated deep learning platform of spikelet-based yield prediction comprising spike and spikelet detection, leading to higher precision over the existing methods.

Deep learning-based approach for identification of diseases of maize crop.

In recent years, deep learning techniques have shown impressive performance in the field of identification of diseases of crops using digital images. In this work, a deep learning approach for identification of in-field diseased images of maize crop has been proposed. The images were captured from experimental fields of ICAR-IIMR, Ludhiana, India, targeted to three important diseases viz. Maydis Leaf Blight, Turcicum Leaf Blight and Banded Leaf and Sheath Blight in a non-destructive manner with varied backgrounds using digital cameras and smartphones. In order to solve the problem of class imbalance, artificial images were generated by rotation enhancement and brightness enhancement methods. In this study, three different architectures based on the framework of 'Inception-v3' network were trained with the collected diseased images of maize using baseline training approach. The best-performed model achieved an overall classification accuracy of 95.99% with average recall of 95.96% on the separate test dataset. Furthermore, we compared the performance of the best-performing model with some pre-trained state-of-the-art models and presented the comparative results in this manuscript. The results reported that best-performing model performed quite better than the pre-trained models. This demonstrates the applicability of baseline training approach of the proposed model for better feature extraction and learning. Overall performance analysis suggested that the best-performed model is efficient in recognizing diseases of maize from in-field images even with varied backgrounds.

A lightweight convolutional neural network for recognition of severity stages of maydis leaf blight disease of maize.

Maydis leaf blight (MLB) of maize (Zea Mays L.), a serious fungal disease, is capable of causing up to 70% damage to the crop under severe conditions. Severity of diseases is considered as one of the important factors for proper crop management and overall crop yield. Therefore, it is quite essential to identify the disease at the earliest possible stage to overcome the yield loss. In this study, we created an image database of maize crop, MDSD (Maydis leaf blight Disease Severity Dataset), containing 1,760 digital images of MLB disease, collected from different agricultural fields and categorized into four groups viz. healthy, low, medium and high severity stages. Next, we proposed a lightweight convolutional neural network (CNN) to identify the severity stages of MLB disease. The proposed network is a simple CNN framework augmented with two modified Inception modules, making it a lightweight and efficient multi-scale feature extractor. The proposed network reported approx. 99.13% classification accuracy with the f1-score of 98.97% on the test images of MDSD. Furthermore, the class-wise accuracy levels were 100% for healthy samples, 98% for low severity samples and 99% for the medium and high severity samples. In addition to that, our network significantly outperforms the popular pretrained models, viz. VGG16, VGG19, InceptionV3, ResNet50, Xception, MobileNetV2, DenseNet121 and NASNetMobile for the MDSD image database. The experimental findings revealed that our proposed lightweight network is excellent in identifying the images of severity stages of MLB disease despite complicated background conditions.

Computational insights into RNAi-based therapeutics for foot and mouth disease of Bos taurus.

Foot-and-mouth disease (FMD) endangers a large number of livestock populations across the globe being a highly contagious viral infection in wild and domestic cloven-hoofed animals. It adversely affects the socioeconomic status of millions of households. Vaccination has been used to protect animals against FMD virus (FMDV) to some extent but the effectiveness of available vaccines has been decreased due to high genetic variability in the FMDV genome. Another key aspect that the current vaccines are not favored is they do not provide the ability to differentiate between infected and vaccinated animals. Thus, RNA interference (RNAi) being a potential strategy to control virus replication, has opened up a new avenue for controlling the viral transmission. Hence, an attempt has been made here to establish the role of RNAi in therapeutic developments for FMD by computationally identifying (i) microRNA (miRNA) targets in FMDV using target prediction algorithms, (ii) targetable genomic regions in FMDV based on their dissimilarity with the host genome and, (iii) plausible anti-FMDV miRNA-like simulated nucleotide sequences (SNSs). The results revealed 12 mature host miRNAs that have 284 targets in 98 distinct FMDV genomic sequences. Wet-lab validation for anti-FMDV properties of 8 host miRNAs was carried out and all were observed to confer variable magnitude of antiviral effect. In addition, 14 miRBase miRNAs were found with better target accessibility in FMDV than that of Bos taurus. Further, 8 putative targetable regions having sense strand properties of siRNAs were identified on FMDV genes that are highly dissimilar with the host genome. A total of 16 SNSs having > 90% identity with mature miRNAs were also identified that have targets in FMDV genes. The information generated from this study is populated at http://bioinformatics.iasri.res.in/fmdisc/ to cater the needs of biologists, veterinarians and animal scientists working on FMD.

SpikeSegNet-a deep learning approach utilizing encoder-decoder network with hourglass for spike segmentation and counting in wheat plant from visual imaging.

BACKGROUND: High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set of germplasm and breeding lines in controlled and field conditions. It is also required for precision agriculture where the application of nitrogen, water, and other inputs at this critical stage is necessary. Further, counting of spikes is an important measure to determine yield. Digital image analysis and machine learning techniques play an essential role in non-destructive plant phenotyping analysis. RESULTS: In this study, an approach based on computer vision, particularly object detection, to recognize and count the number of spikes of the wheat plant from the digital images is proposed. For spike identification, a novel deep-learning network, SpikeSegNet, has been developed by combining two proposed feature networks: Local Patch extraction Network (LPNet) and Global Mask refinement Network (GMRNet). In LPNet, the contextual and spatial features are learned at the local patch level. The output of LPNet is a segmented mask image, which is further refined at the global level using GMRNet. Visual (RGB) images of 200 wheat plants were captured using LemnaTec imaging system installed at Nanaji Deshmukh Plant Phenomics Centre, ICAR-IARI, New Delhi. The precision, accuracy, and robustness (F1 score) of the proposed approach for spike segmentation are found to be 99.93%, 99.91%, and 99.91%, respectively. For counting the number of spikes, "analyse particles"-function of imageJ was applied on the output image of the proposed SpikeSegNet model. For spike counting, the average precision, accuracy, and robustness are 99%, 95%, and 97%, respectively. SpikeSegNet approach is tested for robustness with illuminated image dataset, and no significant difference is observed in the segmentation performance. CONCLUSION: In this study, a new approach called as SpikeSegNet has been proposed based on combined digital image analysis and deep learning techniques. A dedicated deep learning approach has been developed to identify and count spikes in the wheat plants. The performance of the approach demonstrates that SpikeSegNet is an effective and robust approach for spike detection and counting. As detection and counting of wheat spikes are closely related to the crop yield, and the proposed approach is also non-destructive, it is a significant step forward in the area of non-destructive and high-throughput phenotyping of wheat.