Document Type : Review Article
Authors
1 School of Computer Science and Engineering, VIT-AP University, Andhra Pradesh, India.
2 School of computer science and Engineering, VIT-AP University, Andhra Pradesh, India.
Abstract
Plant phenotyping is one of the recent research areas that play an essential role to develop a better understanding of plant traits, genotypes, stresses, and other related features. It is regarded as essential concept as it facilitates development in several fields such as botany, agronomy, and genetics. Plant phenotype helps in acquiring relevant information about plant organs and whole features that allows the farmers to make informed plant cropping decisions. It includes the use of Deep Learning (DL) which is part of a machine learning technique that makes use of several processing layers to provide reliable outcomes from abstraction. DL-based approaches are highly useful in providing a sufficient amount of data related to plant strapping, stresses, and growth indices. Deep learning approaches are highly efficient in analysing plant phenotype and characterizing the phenotyping aspects by classifying the plant stress datasets into open, labelled, and broad-spectrum. In this paper, a review work makes an attempt to explore the efficiency of deep learning and filtering approaches in plant phenotyping. The recent works related to the DL principles have been utilized for digital image–based plant stress phenotyping. Then a comparative assessment of DL tools against other existing techniques, with respect to decision accuracy, data size requirement, and applicability in various scenarios. Therefore, it is strongly recommended in the study to use the imaging data process so that there is the attainment of accurate information from training datasets by using high-throughput systems like UAVs and other autonomous systems.
Keywords
- Chand, R. “Transforming Agriculture for Challenges of 21st Century”. Presidential Address at the 102nd Annual Conference of the Indian Economic Association, organised by Auro University, Surat; 2019.
- Hemantaranjan A. Advances in Plant Physiology. Scientific Publishers; 2016.
- Walter A, Liebisch F, Hund A. “Plant phenotyping: from bean weighing to image analysis”. Plant methods. 2015;11(1): 1-11.
- Das Choudhury S, Bashyam S, Qiu Y, Samal A, Awada T. “Holistic and component plant phenotyping using temporal image sequence”. Plant Methods 2018;14:35.
- Esgario JGM, Krohling RA, Ventura JA. “Deep learning for classification and severity estimation of coffee leaf biotic stress”. Electron. Agric. 2020; 169.
- Großkinsky DK, Svensgaard J, Christensen S, Roitsch T. “Plant phenomics and the need for physiological phenotyping across scales to narrow the genotype-to-phenotype knowledge gap”. J Experimental botany. 2015; 66(18):5429-5440.
- Das Choudhury S, Goswami S, Bashyam S, Samal A, Awada T. “Automated stem angle determination for temporal plant phenotyping analysis”, ICCV Workshop on Computer Vision Problems in Plant Phenotyping (Venice: ACM Press), 2017; 41–50.
- Najjar A, Zagrouba E. “Flower image segmentation based on color analysis and a supervised evaluation”. In: 2012 International Conference on Communications and Information Technology (ICCIT), 2012; 397–401.
- Nilsback ME, Zisserman A. “Automated Flower Classification over a Large Number of Classes," 2008 Sixth Indian Conference on Computer Vision, Graphics & Image Processing. 2008; 722-729.
- Flood PJ, Kruijer W, Schnabel SK, Schoor R, Jalink H, Snel JFH, Harbinson J, Aarts MGM. “Phenomics for photosynthesis, growth, and reflectance in Arabidopsis thaliana reveals circadian and long-term fluctuations inheritability”. Plant Methods, 2016; 12: 1–14.
- Pethybridge SJ, Nelson SC. “Leaf Doctor: a new portable application for quantifying plant disease severity”. Plant Dis. 2015; 99:1310–1316.
- Amara J. “A deep learning-based approach for banana leaf diseases classification”. In Lecture Notes in Informatics (LNI).Gesellschaft für Informatik. 2017;79–88.
- Paproki A, Sirault X, Berry S, Furbank R, Fripp J. “A novel mesh processing based technique for 3D plant analysis”. BMC Plant Biology 2012; 12: 63.
- Costa JM, Grant OM, Chaves MM. “Thermography to explore plant-environment interactions”. J Experimental Botany. 2013; 64, 3937–3949.
- Li L, Zhang Q, Huang D. “A review of imaging techniques for plant phenotyping”. Sens. 2014; 14(11): 20078-20111.
- Rossini M, Fava F, Cogliati S. “Assessing canopy PRI from airborne imagery to map water stress in maize”. J. Photogrammetry Remote Sens. 2013; 86:168–177.
- Kingma DP, Ba J. Adam: A method for stochastic optimization. 2014.
- Guo Q, Liu J, Tao S, Xue B, Li L, Xu G, Pang S. “Perspectives and prospects of LiDAR in forest ecosystem monitoring and modelling”.Chinese Sci Bullet 2014; 59(6): 459-478.
- Jones HG, Vaughan RA. “Remote sensing of vegetation: principles, techniques, and applications” . Oxford: Oxford University Press; 2010.
- Pierna JF, Baeten V, Renier AM, Cogdill RP, Dardenne P. “Combination of support vector machines (SVM) and near‐infrared (NIR) imaging spectroscopy for the detection of meat and bone meal (MBM) in compound feeds”. Chemometrics: J. Chemometrics Soc. 2004; 18(7‐8): 341-349.
- Faragó D, Sass L, Valkai I, Andrási N, Szabados L. “PlantSize offers an affordable, non-destructive method to measure plant size and color in vitro”. plant sci.2018; 9: 219.
- Fahmi F, Trianda D, Andayani U, Siregar B. “Image processing analysis of geospatial uav orthophotos for palm oil plantation monitoring. In Journal of Physics”: Conference Series(Vol. 978, No. 1, p. 012064). IOP Publishing 2018.
- Mahmud MS, He L. “Measuring Tree Canopy Density Using A Lidar-Guided System for Precision Spraying. In 2020 ASABE Annual International Virtual Meeting(p. 1)”. American Society of Agricultural and Biological Engineers
- Zhang Q, Chen S, Yu T, Wang, Y. “Cherry recognition in natural environment based on the vision of picking robot”. In IOP Conference Series: Earth and Environmental Science(Vol. 61, No. 1, p. 012021). IOP Publishing 2017.
- Qi CR, Su H, Mo K, Guibas LJ. “Pointnet: Deep learning on point sets for 3d classification and segmentation”. In Proceedings of the IEEE conference on computer vision and pattern recognition(pp. 652-660) 2017.
- Taigman Y. DeepFace: “closing the gap to human-level performance in face verification”. In 2014 IEEE Conference on Computer Vision and Pattern Recognition, pp. 1701–1708, IEEE 2014.
- Hoyos‐Villegas V, Houx JH, Singh SK, Fritschi FB. “Ground‐based digital imaging as a tool to assess soybean growth and yield”. Crop Science, 2014; 54(4): 1756-1768.
- Moshou D, Bravo C, Oberti R, West J, Bodria L, McCartney A, Ramon H. “Plant disease detection based on data fusion of hyper-spectral and multi-spectral fluorescence imaging using Kohonen maps”. Real-Time Imaging2005; 11(2): 75-83.
- Arora A, Venkatesh K, Sharma RK, Saharan MS, Dilbaghi N, Sharma I, Tiwari R. “Evaluating vegetation indices for precision phenotyping of quantitative stripe rust reaction in wheat”. Wheat Res, 2014; 6,:74-80.
- Wu J, Cawse-Nicholson K, van Aardt J. “3D Tree reconstruction from simulated small footprint waveform lidar. Photogrammetric Eng”. Remote Sens.2013; 79(12): 1147-1157.
- Tao S, Guo Q, Xu S, Su Y, Li Y, Wu F. “A geometric method for wood-leaf separation using terrestrial and simulated lidar data. Photogrammetric Eng”. Remote Sens.2015; 81(10), 767-776.
- Haug S, Ostermann J. “A crop/weed field image dataset for the evaluation of computer vision based precision agriculture tasks”. In European Conference on Computer Vision(pp. 105-116). Springer, Cham 2014.
- Goodfellow IJ, Pouget-Abadie J, Mirza M, Xu B, Warde-Farley D, Ozair S, Bengio Y. “Generative adversarial networks” arXiv preprint arXiv:1406.2661.
- Bengio Y. Learning deep architectures for AI. Now Publishers Inc; 2009.
- Gharde Y, Singh PK, Dubey RP, Gupta PK. “Assessment of yield and economic losses in agriculture due to weeds in India”. Crop Protection, 2018; 107, 12-18.
- Nkemelu DK, Omeiza D, Lubalo N. “Deep convolutional neural network for plant seedlings classification” arXiv preprint arXiv:1811.08404.
- Girshick R. “Rich feature hierarchies for accurate object detection and semantic segmentation”. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2014; 580–587, IEEE.
- Tai AP, Martin MV, Heald CL. (). “Threat to future global food security from climate change and ozone air pollution”. Nature Climate Change, 2014; 4(9): 817-821.
- Singh D, Jain N, Jain P, Kayal P, Kumawat S, Batra N. “PlantDoc: a dataset for visual plant disease detection”. In Proceedings of the 7th ACM IKDD CoDS and 25th COMAD 2020; 249-253.
- Hughes D, Salathé M. “An open access repository of images on plant health to enable the development of mobile disease diagnostics”,arXiv preprint arXiv:1511.08060.
- Campos J, Llop J, Gallart M, García-Ruiz F, Gras A, Salcedo R, Gil E. “Development of canopy vigour maps using UAV for site-specific management during vineyard spraying process”.Precision Agriculture, 2019; 20(6): 1136-1156.
- Rhoads F, Yonts C. “Irrigation Scheduling for Corn–Why and How. National Corn Handbook”.Water Management (Irrigation). US Department of Agriculture (USDA)
- Calderón R, Navas-Cortés JA, Lucena C, Zarco-Tejada PJ. “High-resolution airborne hyperspectral and thermal imagery for early detection of Verticillium wilt of olive using fluorescence, temperature and narrow-band spectral indices”.Remote Sens. Environ. 2013; 139: 231-245.
- Sullivan DG, Shaw JN, Mask PL, Rickman D, Guertal EA, Luvall J, Wersinger JM. (). “Evaluation of multispectral data for rapid assessment of wheat straw residue cover”.Soil Sci. Soc. America 2004; 68(6): 2007-2013.
- Ghazali MF, Wikantika K, Harto AB, Kondoh, A. “Generating soil salinity, soil moisture, soil pH from satellite imagery and its analysis”. Process Agric 2020; 7(2), 294-306.
- Kumar NS, Anouncia SM, Prabu M. “Application of Satellite Remote Sensing to find Soil Fertilization by using Soil Colour”. J. Online Eng. 2013; 9(2).
- Chandra A L, Desai S V, Guo W, Balasubramanian VN. “Computer vision with deep learning for plant phenotyping in agriculture: A survey,”arXiv preprint arXiv:2006.11391.
- Murray N J, Phinn SR, DeWitt M, Ferrari R, Johnston R, Lyons MB, Fuller R A. “The global distribution and trajectory of tidal flats”.Nat. 2019; 565(7738), 222-225.
- Barbedo JGA. “Factors influencing the use of deep learning for plant disease recognition”. Biosyst Eng 2018;172:84–91.
- Brahimi M, Arsenovic M, Laraba S, Sladojevic S, Boukhalfa KMA. “Deep learning for plant diseases: detection and saliency map visualisation”. Springer International Publishing; 2018.
- Johannes A, Picon A, Alvarez-Gila A, Echazarra J, RodriguezVaamonde S, Navajas AD, et al. “Automatic plant disease diagnosis using mobile capture devices, applied on a wheat use case”. Comput Electron Agric 2017;138:200–209.
- Yu K, Anderegg J, Mikaberidze A, Karisto P, Mascher F, McDonald BA, et al. “Hyperspectral canopy sensing of wheat septoria tritici blotch disease”. Front Plant Sci 2018.
- Azadbakht M, Ashourloo D, Aghighi H, Radiom S, Alimohammadi A. “Wheat leaf rust detection at canopy scale under different LAI levels using machine learning techniques”. Comput Electron Agric
- Lu J, Hu J, Zhao G, Mei F, Zhang C. “An in-field automatic wheat disease diagnosis system”. Comput Electron Agric 2017;142: 369–79.
- Singh V, Varsha, Misra AK. “Detection of unhealthy region of plant leaves using image processing and genetic algorithm”. In: Conf Proceeding - 2015 Int Conf Adv Comput Eng Appl ICACEA 2015 2015:1028–32.
- Lu Y, Yi S, Zeng N, Liu Y, Zhang Y. “Identification of rice diseases using deep convolutional neural networks.” Neurocomputing 2017; 267:378–84.
- Jensen T, Apan A, Zeller L. “Crop maturity mapping using a low-cost low-altitude remote sensing system”. In Proceedings of the 2009 Surveying and Spatial Sciences Institute Biennial International Conference (SSC 2009)(pp. 1231-1243). Surveying and Spatial Sciences Institute 2009.
- Not cited
- Castelao Tetila E, Brandoli Machado B, Menezes GK, Oliveira A da S, Alvarez M, Amorim WP, et al. “Automatic recognition of soybean leaf diseases using UAV images and deep convolutional neural networks”. IEEE Geosci Remote Sens Lett 2019:1–5.
- Ramesh S, Vydeki D. “Recognition and classification of paddy leaf diseases using Optimized Deep Neural network with Jaya algorithm”. Inf Process Agric
- DeChant C, Wiesner-Hanks T, Chen S, Stewart EL, Yosinski J, Gore MA, et al. “Automated identification of northern leaf blight-infected maize plants from field imagery using deep learning”. Phytopathology 2017;107:1426–1432.
- Pramod Prasad, Siddanna Savadi, S.C. Bhardwaj & P.K. Gupta. “The progress of leaf rust research in wheat”. Fungal Biology. 2020; 124: 537-550.
- Anupama Gidhi, Manish Kumar & Kunal Mukhopadhyay . “The auxin response factor gene family in wheat (Triticum aestivum L.): Genome-wide identification, characterization and expression analyses in response to leaf rust”.South African Journal of Botany 2020; 1 -14
- Hasanzader, N. Safaie, M. R. Eslahi, S. T. Dadrezaei, S. N. Tabatabaei. “Economic returns from the foliar fungicide application to control leaf rust in winter wheat cultivars in southwest Iran (Khuzestan Province)”. J. Saudi Soc. Agricultural Sci. 2020; 19:199–206.
- Peng Chen, Hong-Mei Zhan , Bao-Min Yao, Song-Can Chen, Guo-Xin Sun, Yong-Guan Zhu. “Bioavailable arsenic and amorphous iron oxides provide reliable predictions for arsenic transfer in soil-wheat systems”. J. Hazard. Mater. 2020; 383.
- Dong yan zhang, Gao Chen, Xun Yin , Rong-Jie Hu, Chun-Yan Gu, Zheng-Gao Pan, Xin-Gen Zhou, Yu Chen. “Integrating spectral and image data to detect Fusarium head blight of wheat”. Electron. Agric. 2020; 175.
- Tao Liu, Wen Chen, Wei Wu &Xinkai Zhu. “Detection of aphids in wheat fields using a computer vision technique”. Biosystem Eng. 2016; 141:82-93.
- Yue Shi, Wenjiang Huang,& Xianfeng Zhou.”Detection and discrimination of pests and diseases in winter wheat based on spectral indices and kernel discriminant analysis”. Electron. Agric. 2017;141: 171–180
- Yanjun Zhu, Zhiguo Cao, Hao Lu & Yanan Li. “In-field automatic observation of wheat heading stage using computer vision”. Biosystems eng. 2016;143: 28-41.
- Dimitrios Moshou, Xanthoula-Eirini Pantazi, Dimitrios Kateris, Ioannis Gravalos. “Water stress detection based on optical multisensor fusion with a least squares support vector machine classifier”. Image Analysis in Agriculture. 2014; 117:15-22.
- Qiu Xia Hu, Ji Tian, Dong jian He.” Wheat leaf lesion color image segmentation with improved multi- channel selection based on the Chan–Vese model”. Electron Agriculture. 2017; 135: 260–268.
- Michael Schirrmann, Andre Hamdorf, Andreas Garz , Anton Ustyuzhanin & Karl-Heinz Dammer. “Estimating wheat biomass by combining image clustering with crop height”. Computers and Electronics in Agriculture. 2016;121:374–384
- Matusinsky P, Frei P, Mikolasova R, Svacinova, L. Tvaruzek & T. Spitzer. “Species-specific detection of Bipolaris sorokiniana from wheat and barley tissues”. Crop Protection. 2010; 29: 1325-1330.
- Noureddine Bouras, Stephen E. Strelkov. “The anthraquinone catenarin is phytotoxic and produced in leaves and kernels of wheat infected by Pyrenophora tritici-repentis”. Physiological and Molecular Plant Pathology. 2008; 72:87–95.
- Christoph Romer, Kathrin Bürling, Mauricio Hunsche, Till Rumpf, Georg Noga, & Lutz Plümer. “Robust fitting of fluorescence spectra for pre-symptomatic wheat leaf rust detection with Support Vector Machines”. Electron. Agriculture. 2011; 79:180–188.
- Karl-Heinz Dammer, Bernd Möller, Bernd Rodemann &, Dirk Heppner. “Detection of head blight (Fusarium ssp.) in winter wheat by color and multispectral image analyses”. Crop Protect. 2011; 30:420-428.
- Xun Zhang, Guanghe Zhou & Xifeng Wang. “Detection of wheat dwarf virus (WDV) in wheat and vector leafhopper (Psammotettix alienus Dahlb.) by real-time PCR”. Virological Methods. 2010;169:416–419.
- Zhang Jing Cheng, Yuan Lin, Wang Ji-hua, Huang Wen-jiang, Chen Li-ping, & Dong-yan. “Detection of wheat dwarf virus (WDV) in wheat and vector leafhopper (Psammotettix alienus Dahlb.) by real-time PCR”, J of Integrative Agriculture. 2012; 11(9): 1474-1484.
- Zhao Hui, Zhang ZhengBin, Shao HongBo, Xu Ping & M.J. Foulkes . “Genetic correlation and path analysis of transpiration efficiency for wheat flag leaves”. Experimental Botany. 2008; 64:128–134.
- Wang N, Zhang N, Wei J, Peterson DE. “A real-time, embedded, weed-detection system for use in wheat fields”. Precision Agriculture. 2007; 98:276 – 285.
- Berdugo CA, Steiner U, Dehne H-W , Oerke E-C. “Effect of bixafen on senescence and yield formation of wheat. Pesticide Biochemistry and Physiol”. 2012; 104:171–177.
- Wang N, Zhang N, Wei J, Stoll Q, Peterson DE. “A real-time, embedded, weed-detection system for use in wheat fields”. Eng. 2012; 98:276 – 285.
- Yang Z, Rao MN, Elliott NC, Kindler SD, Popham TW. “Differentiating stress induced by greenbugs and Russian wheat aphids in wheat using remote sensing”. Electron. Agriculture. 2009; 67: 64–70.
- Kawcher Ahmed, Tasmia Rahman Shahidi, Syed Md. Irfanul Alam &Sifat Momen. “Rice Leaf Disease Detection Using Machine Learning Techniques”. 2019 International Conference on Sustainable Technologies for Industry0. 2019.
- Ramesh S, D.vydeki. “Rice Blast Disease Detection and Classification using Machine Learning Algorithm”. 2nd International Conference on Micro-Electronics and Telecommunication Engineering, 2018.
- Puskara Sharma, Pankaj Hans & Subhash Chand Gupta. “Classification Of Plant Leaf Diseases Using Machine Learning And Image Preprocessing Techniques”. 10th International Conference on Cloud Computing, Data Science & Engineering (Confluence)
- Paula Ramos-Giraldo, Steven Mirsky,Chris Reberg-Horton, Edgar Lobaton & Anna M. Locke. “Drought Stress Detection Using Low-Cost Computer Vision Systems and Machine Learning Techniques”. IEEE IT professional. 2020; 22(3).
- Wenhao Zhang, Mark F. Hansen, Timothy N. Volonakis, Melvyn Smith, Lyndon Smith & Jim Wilson. “Broad-Leaf Weed Detection in Pasture”. 3rd IEEE International Conference on Image, Vision and Computing
- Asif Iqbal and Kamrul Hasan Talukder, “Detection of Potato Disease Using Image Segmentation and Machine Learning”. International Conference on Wireless Communications Signal Processing and Networking (WiSPNET)
- Gayathri S, Joy Winnie Wise DC, Baby Shamini P, Muthukumaran, N. “Image Analysis and Detection of Tea Leaf Disease using Deep Learning”. Proceedings of the International Conference on Electronics and Sustainable Communication Systems (ICESC 2020).
- Karim Laabassi, Mohammed Amin Belarbi, Saÿd Mahmoudi, Sidi Ahmed Mahmoudi & Kaci Ferhat, “Wheat varieties identification based on a deep learning approach”, J. Saudi Soc. Agricultural Sci. 2021;20: 281–289.
- Koh JC, Spangenberg G, Kant S. “Automated Machine Learning for High-Throughput Image-Based Plant Phenotyping”.Remote Sens. 2021; 13(5): 858.
- Sagan V, Maimaitijiang M, Sidike P, Eblimit K, Peterson KT, Hartling S, Mockler T. “UAV-based high-resolution thermal imaging for vegetation monitoring, and plant phenotyping using ICI 8640 P, FLIR Vue Pro R 640, and thermomap cameras”.Remote Sens. 2019; 11(3): 330.
- Liu B. “Identification of apple leaf diseases based on deep convolutional neural networks”. Symmetry 2018; 10: 11.
- Ramcharan A. “Deep learning for image-based cassava disease detection”. Plant Sci. 2017; 8:1852.
- Ferentinos KP. “Deep learning models for plant disease detection and diagnosis”. Electron. Agric. 2018;145: 311–318
- Mohanty SP. “Using deep learning for image-based plant disease detection”. Plant Sci. 2016; 7, 1419.
- Cruz AC. “X-FIDO: an effective application for detecting olive quick decline syndrome with deep learning and data fusion. Front”. Plant Sci. 2017; 8: 1741.
- Fujita E. “Basic investigation on a robust and practical plant diagnostic system”. In 2016 15th IEEE International Conference on Machine Learning and Applications (ICMLA), pp. 989–992, IEEE 2016.
- Sladojevic S. “Deep neural networks based recognition of plant diseases by leaf image classification”. Intell. Neurosci. 2016; 328980189.
- Ha J.G. “Deep convolutional neural network for classifying Fusarium wilt of radish from unmanned aerial vehicles”. Appl. Remote Sens. 2017; 11:042621.
- Ghosal S. “An explainable deep machine vision framework for plant stress phenotyping”. Natl. Acad. Sci. U. S. A. 2018; 115, 4613–4618.