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A special issue of Remote Sensing (ISSN 2072-4292). This special issue belongs to the section "Environmental Remote Sensing".

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 62798

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Special Issue Editor

Dr. Mónica Pineda

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Guest Editor

Experimental Station of Zaidín, Spanish National Research Council, Granada, Spain
Interests: plant stress detection; plant phenotyping; chlorophyll fluorescence; multicolour fluorescence; thermography; hyperspectral reflectance

Special Issue Information

Plant pathogens are severe stress factors limiting the production yield of crops worldwide, and it is thought that they might be enhanced by the ongoing climate change. Thus, crop protection is essential for food production in a growing population world.

However, current agricultural policies are focused on minimizing the use of pesticides to reduce the negative impact of conventional farming on environmental and human health. The development of a precision agriculture based on nondestructive imaging techniques will allow the mapping of constraints in the crop fields, and eventually, their identification. Forecasting disease evolution will be decisive for decision making at the right time. Therefore, the scientific community has spent strong efforts towards the implementation of imaging techniques on proximal and remote sensing.

Combination of sensors such as RGB, multi- or hyperspectral reflectance, fluorescence, or thermal cameras can monitor physiological changes caused by pathogens in plants. The use of powerful mathematical tools is necessary to manage the complexity and large size of information thus obtained. Consequently, bid data algorithms learning from collected data and forecasting the potentially infected plants are required.

This Special Issue will welcome papers providing state-of-the-art applications of phenotyping for plant disease detection at different scales (greenhouses, field, ecosystems, etc.).

Dr. Mónica Pineda
Guest Editor

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Keywords

Imaging sensors
Plant disease
Fluorescence
Reflectance
Thermography
Remote sensing
Machine learning

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 188 KiB

Open AccessEditorial

An Overview of the Special Issue on Plant Phenotyping for Disease Detection

by Mónica Pineda

Remote Sens. 2021, 13(20), 4182; https://doi.org/10.3390/rs13204182 - 19 Oct 2021

Cited by 2 | Viewed by 2070

Abstract

According to the latest United Nations estimates in September 2021, the world’s population is now 7 [...] Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

Research

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16 pages, 9311 KiB

Open AccessEditor’s ChoiceArticle

Hyperspectral Imaging Combined with Machine Learning for the Detection of Fusiform Rust Disease Incidence in Loblolly Pine Seedlings

by Piyush Pandey, Kitt G. Payn, Yuzhen Lu, Austin J. Heine, Trevor D. Walker, Juan J. Acosta and Sierra Young

Remote Sens. 2021, 13(18), 3595; https://doi.org/10.3390/rs13183595 - 9 Sep 2021

Cited by 11 | Viewed by 4886

Abstract

Loblolly pine is an economically important timber species in the United States, with almost 1 billion seedlings produced annually. The most significant disease affecting this species is fusiform rust, caused by Cronartium quercuum f. sp. fusiforme. Testing for disease resistance in the greenhouse involves artificial inoculation of seedlings followed by visual inspection for disease incidence. An automated, high-throughput phenotyping method could improve both the efficiency and accuracy of the disease screening process. This study investigates the use of hyperspectral imaging for the detection of diseased seedlings. A nursery trial comprising families with known in-field rust resistance data was conducted, and the seedlings were artificially inoculated with fungal spores. Hyperspectral images in the visible and near-infrared region (400–1000 nm) were collected six months after inoculation. The disease incidence was scored with traditional methods based on the presence or absence of visible stem galls. The seedlings were segmented from the background by thresholding normalized difference vegetation index (NDVI) images, and the delineation of individual seedlings was achieved through object detection using the Faster RCNN model. Plant parts were subsequently segmented using the DeepLabv3+ model. The trained DeepLabv3+ model for semantic segmentation achieved a pixel accuracy of 0.76 and a mean Intersection over Union (mIoU) of 0.62. Crown pixels were segmented using geometric features. Support vector machine discrimination models were built for classifying the plants into diseased and non-diseased classes based on spectral data, and balanced accuracy values were calculated for the comparison of model performance. Averaged spectra from the whole plant (balanced accuracy = 61%), the crown (61%), the top half of the stem (77%), and the bottom half of the stem (62%) were used. A classification model built using the spectral data from the top half of the stem was found to be the most accurate, and resulted in an area under the receiver operating characteristic curve (AUC) of 0.83. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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18 pages, 2246 KiB

Open AccessArticle

Identifying Optimal Wavelengths as Disease Signatures Using Hyperspectral Sensor and Machine Learning

by Xing Wei, Marcela A. Johnson, David B. Langston, Jr., Hillary L. Mehl and Song Li

Remote Sens. 2021, 13(14), 2833; https://doi.org/10.3390/rs13142833 - 19 Jul 2021

Cited by 28 | Viewed by 6374

Abstract

Hyperspectral sensors combined with machine learning are increasingly utilized in agricultural crop systems for diverse applications, including plant disease detection. This study was designed to identify the most important wavelengths to discriminate between healthy and diseased peanut (Arachis hypogaea L.) plants infected with Athelia rolfsii, the causal agent of peanut stem rot, using in-situ spectroscopy and machine learning. In greenhouse experiments, daily measurements were conducted to inspect disease symptoms visually and to collect spectral reflectance of peanut leaves on lateral stems of plants mock-inoculated and inoculated with A. rolfsii. Spectrum files were categorized into five classes based on foliar wilting symptoms. Five feature selection methods were compared to select the top 10 ranked wavelengths with and without a custom minimum distance of 20 nm. Recursive feature elimination methods outperformed the chi-square and SelectFromModel methods. Adding the minimum distance of 20 nm into the top selected wavelengths improved classification performance. Wavelengths of 501–505, 690–694, 763 and 884 nm were repeatedly selected by two or more feature selection methods. These selected wavelengths can be applied in designing optical sensors for automated stem rot detection in peanut fields. The machine-learning-based methodology can be adapted to identify spectral signatures of disease in other plant-pathogen systems. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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Graphical abstract

21 pages, 4033 KiB

Open AccessArticle

Detection of Root-Knot Nematode Meloidogyne luci Infestation of Potato Tubers Using Hyperspectral Remote Sensing and Real-Time PCR Molecular Methods

by Uroš Žibrat, Barbara Gerič Stare, Matej Knapič, Nik Susič, Janez Lapajne and Saša Širca

Remote Sens. 2021, 13(10), 1996; https://doi.org/10.3390/rs13101996 - 20 May 2021

Cited by 18 | Viewed by 4890

Abstract

Root-knot nematodes (Meloidogyne spp.) are considered the most aggressive, damaging, and economically important group of plant-parasitic nematodes and represent a significant limiting factor for potato (Solanum tuberosum) production and tuber quality. Meloidogyne luci has previously been shown to be a potato pest having significant reproductive potential on the potato. In this study we showed that M. luci may develop a latent infestation without visible symptoms on the tubers. This latent infestation may pose a high risk for uncontrolled spread of the pest, especially via seed potato. We developed efficient detection methods to prevent uncontrolled spread of M. luci via infested potato tubers. Using hyperspectral imaging and a molecular approach to detection of nematode DNA with real-time PCR, it was possible to detect M. luci in both heavily infested potato tubers and tubers without visible symptoms. Detection of infested tubers with hyperspectral imaging achieved a 100% success rate, regardless of tuber preparation. The real-time PCR approach detected M. luci with high sensitivity. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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20 pages, 8408 KiB

Open AccessArticle

Automatic Evaluation of Wheat Resistance to Fusarium Head Blight Using Dual Mask-RCNN Deep Learning Frameworks in Computer Vision

by Wen-Hao Su, Jiajing Zhang, Ce Yang, Rae Page, Tamas Szinyei, Cory D. Hirsch and Brian J. Steffenson

Remote Sens. 2021, 13(1), 26; https://doi.org/10.3390/rs13010026 - 23 Dec 2020

Cited by 92 | Viewed by 7950

Abstract

In many regions of the world, wheat is vulnerable to severe yield and quality losses from the fungus disease of Fusarium head blight (FHB). The development of resistant cultivars is one means of ameliorating the devastating effects of this disease, but the breeding process requires the evaluation of hundreds of lines each year for reaction to the disease. These field evaluations are laborious, expensive, time-consuming, and are prone to rater error. A phenotyping cart that can quickly capture images of the spikes of wheat lines and their level of FHB infection would greatly benefit wheat breeding programs. In this study, mask region convolutional neural network (Mask-RCNN) allowed for reliable identification of the symptom location and the disease severity of wheat spikes. Within a wheat line planted in the field, color images of individual wheat spikes and their corresponding diseased areas were labeled and segmented into sub-images. Images with annotated spikes and sub-images of individual spikes with labeled diseased areas were used as ground truth data to train Mask-RCNN models for automatic image segmentation of wheat spikes and FHB diseased areas, respectively. The feature pyramid network (FPN) based on ResNet-101 network was used as the backbone of Mask-RCNN for constructing the feature pyramid and extracting features. After generating mask images of wheat spikes from full-size images, Mask-RCNN was performed to predict diseased areas on each individual spike. This protocol enabled the rapid recognition of wheat spikes and diseased areas with the detection rates of 77.76% and 98.81%, respectively. The prediction accuracy of 77.19% was achieved by calculating the ratio of the wheat FHB severity value of prediction over ground truth. This study demonstrates the feasibility of rapidly determining levels of FHB in wheat spikes, which will greatly facilitate the breeding of resistant cultivars. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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20 pages, 3232 KiB

Open AccessArticle

Detection of Two Different Grapevine Yellows in Vitis vinifera Using Hyperspectral Imaging

by Nele Bendel, Andreas Backhaus, Anna Kicherer, Janine Köckerling, Michael Maixner, Barbara Jarausch, Sandra Biancu, Hans-Christian Klück, Udo Seiffert, Ralf T. Voegele and Reinhard Töpfer

Remote Sens. 2020, 12(24), 4151; https://doi.org/10.3390/rs12244151 - 18 Dec 2020

Cited by 31 | Viewed by 4403

Abstract

Grapevine yellows (GY) are serious phytoplasma-caused diseases affecting viticultural areas worldwide. At present, two principal agents of GY are known to infest grapevines in Germany: Bois noir (BN) and Palatinate grapevine yellows (PGY). Disease management is mostly based on prophylactic measures as there are no curative in-field treatments available. In this context, sensor-based disease detection could be a useful tool for winegrowers. Therefore, hyperspectral imaging (400–2500 nm) was applied to identify phytoplasma-infected greenhouse plants and shoots collected in the field. Disease detection models (Radial-Basis Function Network) have successfully been developed for greenhouse plants of two white grapevine varieties infected with BN and PGY. Differentiation of symptomatic and healthy plants was possible reaching satisfying classification accuracies of up to 96%. However, identification of BN-infected but symptomless vines was difficult and needs further investigation. Regarding shoots collected in the field from different red and white varieties, correct classifications of up to 100% could be reached using a Multi-Layer Perceptron Network for analysis. Thus, hyperspectral imaging seems to be a promising approach for the detection of different GY. Moreover, the 10 most important wavelengths were identified for each disease detection approach, many of which could be found between 400 and 700 nm and in the short-wave infrared region (1585, 2135, and 2300 nm). These wavelengths could be used further to develop multispectral systems. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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17 pages, 2393 KiB

Open AccessArticle

Laboratory and UAV-Based Identification and Classification of Tomato Yellow Leaf Curl, Bacterial Spot, and Target Spot Diseases in Tomato Utilizing Hyperspectral Imaging and Machine Learning

by Jaafar Abdulridha, Yiannis Ampatzidis, Jawwad Qureshi and Pamela Roberts

Remote Sens. 2020, 12(17), 2732; https://doi.org/10.3390/rs12172732 - 24 Aug 2020

Cited by 73 | Viewed by 7657

Abstract

Tomato crops are susceptible to multiple diseases, several of which may be present during the same season. Therefore, rapid disease identification could enhance crop management consequently increasing the yield. In this study, nondestructive methods were developed to detect diseases that affect tomato crops, such as bacterial spot (BS), target spot (TS), and tomato yellow leaf curl (TYLC) for two varieties of tomato (susceptible and tolerant to TYLC only) by using hyperspectral sensing in two conditions: a) laboratory (benchtop scanning), and b) in field using an unmanned aerial vehicle (UAV-based). The stepwise discriminant analysis (STDA) and the radial basis function were applied to classify the infected plants and distinguish them from noninfected or healthy (H) plants. Multiple vegetation indices (VIs) and the M statistic method were utilized to distinguish and classify the diseased plants. In general, the classification results between healthy and diseased plants were highly accurate for all diseases; for instance, when comparing H vs. BS, TS, and TYLC in the asymptomatic stage and laboratory conditions, the classification rates were 94%, 95%, and 100%, respectively. Similarly, in the symptomatic stage, the classification rates between healthy and infected plants were 98% for BS, and 99–100% for TS and TYLC diseases. The classification results in the field conditions also showed high values of 98%, 96%, and 100%, for BS, TS, and TYLC, respectively. The VIs that could best identify these diseases were the renormalized difference vegetation index (RDVI), and the modified triangular vegetation index 1 (MTVI 1) in both laboratory and field. The results were promising and suggest the possibility to identify these diseases using remote sensing. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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17 pages, 2589 KiB

Open AccessArticle

Identification of Wheat Yellow Rust Using Spectral and Texture Features of Hyperspectral Images

by Anting Guo, Wenjiang Huang, Huichun Ye, Yingying Dong, Huiqin Ma, Yu Ren and Chao Ruan

Remote Sens. 2020, 12(9), 1419; https://doi.org/10.3390/rs12091419 - 30 Apr 2020

Cited by 89 | Viewed by 6707

Abstract

Wheat yellow rust is one of the most destructive diseases in wheat production and significantly affects wheat quality and yield. Accurate and non-destructive identification of yellow rust is critical to wheat production management. Hyperspectral imaging technology has proven to be effective in identifying plant diseases. We investigated the feasibility of identifying yellow rust on wheat leaves using spectral features and textural features (TFs) of hyperspectral images. First, the hyperspectral images were preprocessed, and healthy and yellow rust-infected samples were obtained by creating regions of interest. Second, the extraction of spectral reflectance characteristics and vegetation indices (VIs) were performed from the preprocessed hyperspectral images, and the TFs were extracted using the grey-level co-occurrence matrix from the images transformed by principal component analysis. Third, the successive projections algorithm was employed to choose the optimum wavebands (OWs), and correlation-based feature selection was employed to select the optimal VIs and TFs (those most sensitive to yellow rust and having minimal redundancy between features). Finally, identification models of wheat yellow rust were established using a support vector machine and different features. Six OWs (538, 598, 689, 702, 751, and 895 nm), four VIs (nitrogen reflectance index, photochemical reflectance index, greenness index, and anthocyanin reflectance index), and four TFs (correlation 1, correlation 2, entropy 2, and second moment 3) were selected. The identification models based on the OWs, VIs, and TFs provided overall accuracies of 83.3%, 89.5%, and 86.5%, respectively. The TF results were especially encouraging. The models with the combination of spectral features and TFs exhibited better performance than those using the spectral features or TFs alone. The accuracies of the models with the combined features (OWs and TFs, Vis, and TFs) were 90.6% and 95.8%, respectively. These values were 7.3% and 6.3% higher, respectively, than those of the models using only the OWs or VIs. The model with the combined feature (VIs and TFs) had the highest accuracy (95.8%) and was used to map the yellow rust lesions on wheat leaves with different damage levels. The results showed that the yellow rust lesions on the leaves could be identified accurately. Overall, the combination of spectral features and TFs of hyperspectral images significantly improved the identification accuracy of wheat yellow rust. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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Review

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21 pages, 546 KiB

Open AccessReview

Thermal Imaging for Plant Stress Detection and Phenotyping

by Mónica Pineda, Matilde Barón and María-Luisa Pérez-Bueno

Remote Sens. 2021, 13(1), 68; https://doi.org/10.3390/rs13010068 - 27 Dec 2020

Cited by 114 | Viewed by 15530

Abstract

In the last few years, large efforts have been made to develop new methods to optimize stress detection in crop fields. Thus, plant phenotyping based on imaging techniques has become an essential tool in agriculture. In particular, leaf temperature is a valuable indicator of the physiological status of plants, responding to both biotic and abiotic stressors. Often combined with other imaging sensors and data-mining techniques, thermography is crucial in the implementation of a more automatized, precise and sustainable agriculture. However, thermal data need some corrections related to the environmental and measuring conditions in order to achieve a correct interpretation of the data. This review focuses on the state of the art of thermography applied to the detection of biotic stress. The work will also revise the most important abiotic stress factors affecting the measurements as well as practical issues that need to be considered in order to implement this technique, particularly at the field scale. Full article

(This article belongs to the Special Issue Plant Phenotyping for Disease Detection)

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