Full Text (PDF)
Review Article

Advances in Plant Phenotyping Tools for Agricultural Sustainability

Anjali Bhardwaj, Shikha Chaudhary

Author Information

Licence:

Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Indian Journal of Plant and Soil 13(1):p 53-70, January-June 2026. | DOI: https://doi.org/10.21088/ijps.2348.9677.13126.5

How Cite This Article:

Anjali Bhardwaj, Shikha Chaudhary. Advances in Plant Phenotyping Tools for Agricultural Sustainability. Ind J Plant Soil. 2026; 13(1): 53-70.

Timeline

Received : November 28, 2025         Accepted : January 10, 2026          Published : June 30, 2026

Abstract

The continuously rising population of the world and decreasing land for agriculture are highlighting the issue of sustainable agriculture and food security. The ancient methods of crop improvement require manual labour and time. The plant phenotyping techniques are providing a helping hand to plant breeders as they study plant phenotypes using imaging, aerial vehicles, sensors, robots, crop models etc. these tools accurately measure the visible traits of the plant such as plant height, physiology and response to stress in different conditions and thus speed up the crop breeding researches. The research is entering a new phase of development in which phenotyping is combined with machine learning, artificial intelligence, predictive crop models to support decision making in sustainable agriculture. The current review discusses the use of phenotyping tools in agriculture and the challenges that are still limiting the use of these novel techniques in agriculture and the possible solutions.


References

  • 1.   Abdulridha J., Min A., Rouse M.N., Kianian S., Isler V., Yang C. Evaluation of stem rust disease in wheat fields by drone hyperspectral imaging. Sensors. 2023; 23 (8): 4154. doi: 10.3390/s23084154.
  • 2.   Abebe G., Tadesse T., Gessesse B. Assimilation of leaf area index from multisource earth observation data into the WOFOST model for sugarcane yield estimation. Int J Remote Sens. 2022; 43: 698–720. doi: 10.1080/01431161.2022.2027547.
  • 3.   Acosta M., Pena J., Sherafat A., Gonzalez C., Sherman T., Bhandari S., Raheja A. Investigating the potential of UAV-based hyperspectral sensor in detecting powdery mildew in grapes. In: Autonomous Air and Ground Sensing Systems for Agricultural Optimization and Phenotyping IX. SPIE; 2024. pp. 26–34.
  • 4.   An N., Welch S.M., Markelz R.C., Baker R.L., Palmer C.M., Ta J., Weinig C. Quantifying time-series of leaf morphology using 2D and 3D photogrammetry methods for highthroughput plant phenotyping. Computers Electron Agric. 2017; 135: 222–232.
  • 5.   Andreoli V., Cassardo C., Cavalletto S., Spanna F. Simulations on different grapevine cultivars with the IVINE crop growth model. Proc. 2019. doi: 10.6092/unibo/amsacta/6175.
  • 6.   Angidi S., Madankar K., Tehseen M.M., Bhatla A. Advanced high-throughput phenotyping techniques for managing abiotic stress in agricultural crops — a comprehensive review. Crops. 2025; 5(2): 8. doi: 10.3390/crops5020008.
  • 7.   Arya S., Sahoo R.N., Sehgal V.K, Bandyopadhyay K., Rejith R.G., Chinnusamy V., Manjaiah K.M. High-throughput chlorophyll fluorescence image-based phenotyping for water deficit stress tolerance in wheat. Plant Physiol Rep. 2024; 29: 1–16.
  • 8.   Asaari M.S.M., Mishra P., Mertens S., Dhondt S., Inzé D., Wuyts N, Scheunders P. Close-range hyperspectral image analysis for the early detection of stress responses in individual plants in a high-throughput phenotyping platform. ISPRS J Photogramm Remote Sens. 2018; 138: 121–138. doi: 10.1016/j. isprsjprs.2018.02.003.
  • 9.   Atkinson J.A., Pound M.P., Bennett M.J., Wells D.M. Uncovering the hidden half of plants using new advances in root phenotyping. Curr Opin Biotechnol. 2019; 55: 1–8. doi: 10.1016/j. copbio.2018.06.002.
  • 10.   Banerjee B.P., Joshi S., Thoday-Kennedy E, Pasam R.K., Tibbits J., Hayden M., Kant S. High-throughput phenotyping using digital and hyperspectral imaging-derived biomarkers for genotypic nitrogen response. J Exp Bot. 2020; 71(15): 4604–4615. doi: 10.1093/ jxb/eraa143.
  • 11.   Basso B., Ritchie J.T. Simulating crop growth and biogeochemical fluxes in response to land management using the SALUS model. In: Hamilton S, Doll JE, Robertson P, editors. The Ecology of Agricultural Landscapes: LongTerm Research on the Path to Sustainability. 1st ed. New York: Oxford University Press; 2015. p. 252–74.
  • 12.   Baye K.N. Advancements and emerging trends in crop phenomics. J. Smart Sustain. Farming. 2025; 1; 23-33.doi: 10.64026/JSSF/2025003
  • 13.   Behmann J., Acebron K., Emin D., Bennertz S., Matsubara S, Thomas S., Rascher U. Specim IQ: evaluation of a new, miniaturized handheld hyperspectral camera and its application for plant phenotyping and disease detection. Sensors. 2018; 18(2): 441. doi:10.3390/s18020441
  • 14.   Betegón-Putze I., Gonzalez A., Sevillano X., Blasco-Escámez D., Caño-Delgado A.I. MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings. Plant J. 2019; 98(6): 1145–56. doi:10.1111/tpj.14297
  • 15.   Bethge H., León A.M.T., Rüter P., Rath T, Heinemann D., Winkelmann T. Towards automated phenotyping in plant tissue culture: in situ fluorescence monitoring. In: Photonic Technologies in Plant and Agricultural Science. Vol. 12879. SPIE; 2024. p. 72–8.
  • 16.   Bock C.H., Nutter F.W. Jr. Detection and measurement of plant disease symptoms using visible-wavelength photography and image analysis. CABI Rev. 2011; 2011: 1–15.
  • 17.   Bodner G., Nakhforoosh A., Arnold T., Leitner D. Hyperspectral imaging: a novel approach for plant root phenotyping. Plant Methods. 2018;14:1–17. doi:10.1186/s13007-018-0352-1
  • 18.   Boote K..J, Jones J.W., Hoogenboom G. Simulation of crop growth: CROPGRO model. In: Peart RM, Shoup WD, editors. Agricultural Systems Modeling and Simulation. 1st ed. CRC Press; 2018. pp. 651–92.
  • 19.   Borianne P., Subsol G., Fallavier F., Dardou A, Audebert A. GT-RootS: an integrated software for automated root system measurement from high-throughput phenotyping platform images. Comput Electron Agric. 2018; 150: 328–42. doi:10.1016/j.compag.2018.05.003
  • 20.   Brewer M.T., Lang L., Fujimura K., Dujmovic N., Gray S., van der Knaap E. Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. Plant Physiol. 2006; 141: 15–25. doi:10.1104/pp.105.074344
  • 21.   Brown T.B., Cheng R., Sirault X.R., Rungrat T., Murray K.D., Trtilek M., Borevitz J.O. TraitCapture: genomic and environment modelling of plant phenomic data. Curr Opin Plant Biol. 2014; 18: 73-9. doi:10.1016/j. pbi.2013.11.002
  • 22.   Burton A.L., Williams M., Lynch J.P., Brown K.M. RootScan: software for high-throughput analysis of root anatomical traits. Plant Soil. 2012; 357: 189-203. doi:10.1007/s11104-012- 1127-3
  • 23.   Cai J., Zeng Z., Connor J.N., Huang C.Y., Melino V., Kumar P., Miklavcic S.J. RootGraph: a graphic optimization tool for automated image analysis of plant roots. J Exp Bot. 2015; 66: 6551–62. doi:10.1093/jxb/erv361
  • 24.   Cai P., Chen G., Yang H., Li X., Zhu K., Wang T., Zhang X. Detecting individual plants infected with pine wilt disease using drones and satellite imagery: a case study in Xianning, China. Remote Sens. 2023; 15(1): 1–17. doi:10.3390/rs15010257
  • 25.   Camargo Rodriguez A.V., Ober E.S. AquaCropR: Crop growth model for R. Agronomy. 2019; 9(378): 1–10. doi:10.3390/ agronomy9070378
  • 26.   Carpenter A.E., Jones T.R., Lamprecht M.R., Clarke C., Kang I.H., Friman O., Sabatini D.M. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006; 7(10): R100. doi:10.1186/ gb-2006-7-10-r100
  • 27.   Chizk T.M., Lee J.A., Clark J.R., Worthington ML. ShinyFruit: interactive fruit phenotyping software and its application in blackberry. Front Plant Sci. 2023; 14: 1155851. doi:10.3389/ fpls.2023.1155851
  • 28.   Cho S., Kim T., Jung D.H., Park S.H., Na Y., Ihn Y.S., Kim K. Plant growth information measurement based on object detection and image fusion using a smart farm robot. Comput Electron Agric. 2023; 207: 107738. doi:10.1016/j.compag.2023.107738
  • 29.   Chopin J., Laga H., Huang C.Y., Heuer S., Miklavcic S.J. RootAnalyzer: a crosssection image analysis tool for automated characterization of root cells and tissues. PLoS One. 2015; 10(9): e0137655. doi:10.1371/ journal.pone.0137655
  • 30.   Clark R.T., Famoso A.N., Zhao K., Shaff J.E., Craft E.J., Bustamante C.D., Kochian L.V. Highthroughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ. 2013; 36: 454–66. doi:10.1111/ j.1365-3040.2012.02587.x
  • 31.   Cobb J.N., Declerck G., Greenberg A., Clark R., McCouch S. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement. Theor Appl Genet. 2013; 126(4): 867–87. doi:10.1007/s00122-013-2066-0
  • 32.   Colmer J., O’Neill C.M., Wells R., Bostrom A., Reynolds D., Websdale D., Zhou J. SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine learning–based phenotypic analysis of crop seed germination. New Phytol. 2020; 228(3): 778–93. doi:10.1111/nph.16765
  • 33.   Corbeels M., Chirat G., Messad S., Thierfelder C. Performance and sensitivity of the DSSAT crop growth model in simulating maize yield under conservation agriculture. Eur J Agron. 2016; 76: 41–53. doi:10.1016/j.eja.2016.02.002
  • 34.   Cozzolino D. Advantages and limitations of using near infrared spectroscopy in plant phenomics applications. Comput Electron Agric. 2023; 212: 108078. doi:10.1016/j. compag.2023.108078
  • 35.   da Silva J.M. Monitoring photosynthesis by in vivo chlorophyll fluorescence: application to high-throughput plant phenotyping. In: Najafpour M, editor. Applied Photosynthesis— New Progress. 1st ed. IntechOpen; 2016. p. 4–20. doi:10.5772/65238
  • 36.   Deery D., Jimenez-Berni J., Jones H., Sirault X., Furbank R. Proximal remote sensing buggies and potential applications for field-based phenotyping. Agronomy. 2014; 4(3): 349–79. doi:10.3390/agronomy4030349
  • 37.   Demidchik V.V., Shashko A.Y., Bandarenka U.Y., Smolikova G.N., Przhevalskaya D.A., Charnysh MA, Medvedev S.S. Plant phenomics: fundamental bases, software and hardware platforms, and machine learning. Russ J Plant Physiol. 2020; 67: 397–412. doi:10.1134/S1021443720030068
  • 38.   Dhakal K. Application of Machine Learning and Hyperspectral Imaging in Plant Phenomics Research [dissertation]. Knoxville (TN): University of Tennessee; 2023. doi:10.7290/ df9n-2m61
  • 39.   Dong X., Peng B., Sieckenius S., Raman R., Conley M.M., Leskovar D.I. Leaf water potential of field crops estimated using NDVI in ground-based remote sensing: opportunities to increase prediction precision. PeerJ. 2021; 9: e12447. doi:10.7717/peerj.12447
  • 40.   Dong X., Zhao K., Wang Q., Wu X., Huang Y., Wu X., Hao G. PlantPAD: a platform for largescale image phenomics analysis of disease in plant science. Nucleic Acids Res. 2024; 52(4): gkae108. doi:10.1093/nar/gkae108
  • 41.   ElManawy A.I., Sun D., Abdalla A., Zhu Y., Cen H. HSI-PP: A flexible open-source software for hyperspectral imaging-based plant phenotyping. Comput Electron Agric. 2022; 200: 107208. doi:10.1016/j.compag.2022.107208
  • 42.   Feng X., Zhan Y., Wang Q., Yang X., Yu C., Wang H., He Y. Hyperspectral imaging combined with machine learning as a tool to obtain high-throughput plant salt-stress phenotyping. Plant J. 2020; 101: 1448–61. doi:10.1111/tpj.14594
  • 43.   Galkovskyi T., Mileyko Y., Bucksch A., Moore B., Symonova O., Price C.A., Weitz J.S. GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol. 2012; 12: 116. doi:10.1186/1471- 2229-12-116.
  • 44.   Gano B., Bhadra S., Vilbig J.M., Ahmed N., Sagan V., Shakoor N. Drone-based imaging sensors, techniques, and applications in plant phenotyping for crop breeding: a comprehensive review. Plant Phenome J. 2024; 7(1): e20092. doi:10.1002/ppj2.20092
  • 45.   Gilbert R.A., Boote K.J., Bennett J.M. Onfarm testing of the PNUTGRO crop growth model in Florida. Peanut Sci. 2002; 29: 58–65. doi:10.3146/0095-3679(2002)029
  • 46.   Gong Y., Yang K., Lin Z., Fang S., Wu X., Zhu R., Peng Y. Remote estimation of leaf area index (LAI) with unmanned aerial vehicle (UAV) imaging for different rice cultivars throughout the entire growing season. Plant Methods. 2021; 17: 88. doi:10.1186/s13007-021-00787-8
  • 47.   González A., Sevillano X., Betegón-Putze I., Blasco-Escámez D., Ferrer M., Caño-Delgado A.I. MyROOT 2.0: an automatic tool for highthroughput and accurate primary root length measurement. Comput Electron Agric. 2020; 168: 105106. doi:10.1016/j.compag.2019.105106
  • 48.   Hale G., Yuan N., Mendu L., Ritchie G., Mendu V. Canopeo app as image-based phenotyping tool in controlled environment utilizing Arabidopsis mutants. PLoS One. 2024; 19(2): e0296675. doi:10.1371/journal.pone.0296675
  • 49.   Hastings A., Clifton-Brown J., Wattenbach M., Mitchell C.P., Smith P. The development of MISCANFOR, a new Miscanthus crop growth model: towards more robust yield predictions under different climatic and soil conditions. GCB Bioenergy. 2009;1:154–70. doi:10.1111/ j.1757-1707.2009.01011.x
  • 50.   Haverkort A.J., Franke A.C., Steyn J.M., Pronk A.A., Caldiz D.O., Kooman P.L. A robust potato model: LINTUL-Potato-DSS. Potato Res. 2015; 58: 313–27. doi:10.1007/s11540-015- 9303-5
  • 51.   Herrero-Huerta M., Raumonen P., GonzalezAguilera D. 4DRoot: root phenotyping software for temporal 3D scans by X-ray computed tomography. Front Plant Sci. 2022; 13: 1056807. doi:10.3389/fpls.2022.1056807
  • 52.   Hosoi F., Omasa K. Estimation of vertical plant area density profiles in a rice canopy at different growth stages by high-resolution portable scanning lidar with a lightweight mirror. ISPRS J Photogramm Remote Sens. 2012; 74: 11–9. doi:10.1016/j.isprsjprs.2012.06.002
  • 53.   Hu G., Ren Z., Chen J., Ren N., Mao X. Using the MSFNet Model to Explore the Temporal and Spatial Evolution of Crop Planting Area and Increase Its Contribution to the Application of UAV Remote Sensing. Drones. 2024; 8(1): 1–28. doi:10.3390/drones8090432
  • 54.   Hu W., Zhang C., Jiang Y., Huang C., Liu Q., Xiong L., Chen F. Nondestructive 3D image analysis pipeline to extract rice grain traits using X-ray computed tomography. Plant Phenomics. 2020;2020:1–14. doi:10.34133/2020/3414926
  • 55.   Hu Y., Zhang Z. GridFree: A python package of image analysis for interactive grain counting and measuring. Plant Physiol. 2021; 186(4): 2239–52. doi:10.1093/plphys/kiab226
  • 56.   Hudson O., Hudson D., Brahmstedt C., Brawner J. The ear unwrapper: a maize ear image acquisition pipeline for disease severity phenotyping. AgriEngineering. 2023; 5(2): 1216–25.
  • 57.   Itoh A., Njane S.N., Hirafuji M., Guo W. PREPs: An Open-Source Software for HighThroughput Field Plant Phenotyping. Plant Phenomics. 2024; 6: 1–10.
  • 58.   Jadhav Y., Thakur N.R., Ingle K.P., Ceasar S.A. The role of phenomics and genomics in delineating the genetic basis of complex traits in millets. Physiol Plant. 2024; 176(3): e14349. doi:10.1111/ppl.14349.
  • 59.   Jahnke S., Menzel M.I., Van Dusschoten D., Roeb G.W., Bühler J., Minwuyelet S., Schurr U. Combined MRI–PET dissects dynamic changes in plant structures and functions. Plant J. 2009; 59: 634–44. doi:10.1111/j.1365- 313X.2009.03888.x
  • 60.   Jakusch P., Kocsis T., Székely I.K., Hatvani I.G. The application of magnetic resonance imaging (MRI) to the examination of plant tissues and water barriers. Acta Biol Hung. 2018; 69: 423–36.
  • 61.   Jayanthy S., Kiruthika G., Lakshana G., Pragatheshwaran M. Early Cotton Plant Disease Detection using Drone Monitoring and Deep Learning. In: 2024 IEEE International Conference for Women in Innovation, Technology & Entrepreneurship (ICWITE); 2024 Feb. p. 625-30.
  • 62.   Jégo G., Pattey E., Liu J. Using Leaf Area Index, retrieved from optical imagery, in the STICS crop model for predicting yield and biomass of field crops. Field Crops Res. 2012; 131: 63-74.
  • 63.   Jiang N., Zhu X.G. Modern phenomics to empower holistic crop science, agronomy, and breeding research. J Genet Genomics. 2024; 51: 1-11.
  • 64.   Jimenez-Berni J.A., Deery D.M., RozasLarraondo P, Condon A.T.G., Rebetzke G.J., James R.A., Sirault X.R. High throughput determination of plant height, ground cover, and above-ground biomass in wheat with LiDAR. Front Plant Sci. 2018; 9: 1-18.
  • 65.   Kumar J., Pratap A., Kumar S. Phenomics of Crop Plants: Trends, Options and Limitations. New Delhi: ICAR; 2015. doi:10.1007/978-81- 322-2226-2
  • 66.   Krishnan P., Sharma R.K., Dass A., Kukreja A., Srivastav R., Gill S.C.. Web-based crop model: Web InfoCrop–Wheat to simulate the growth and yield of wheat. Comput Electron Agric. 2016; 127: 324-35. doi:10.1016/j. compag.2016.06.008
  • 67.   Kulig B., Skowera B., Klimek-Kopyra A., Kołodziej S., Grygierzec W. The use of the WOFOST model to simulate water-limited yield of early potato cultivars. Agronomy. 2020; 10(1): 81. doi:10.3390/agronomy10010081
  • 68.   Kumar A., Prasad M.N.V. Lead-induced toxicity and interference in chlorophyll fluorescence in Talinum triangulare grown hydroponically. Photosynthetica. 2015; 53(1): 66-71.
  • 69.   Kwon T.R., Kim K.H., Yoon H.J., Lee S.K., Kim B.K., Siddiqui Z.S. Phenotyping of plants for drought and salt tolerance using infra-red thermography. Plant Breed Biotechnol. 2015; 3: 299-307. doi:10.9787/PBB.2015.3.4.299
  • 70.   Leiva F., Vallenback P., Ekblad T., Johansson E, Chawade A. Phenocave: an automated, standalone, and affordable phenotyping system for controlled growth conditions. Plants. 2021; 10(9): 1817. doi:10.3390/plants10091817
  • 71.   Li L, Zhang Q, Huang D. A review of imaging techniques for plant phenotyping. Sensors. 2014; 14(11): 20078-20111. doi:10.3390/ s141120078
  • 72.   Li M., Shamshiri R.R., Weltzien C., Schirrmann M. Crop monitoring using Sentinel-2 and UAV multispectral imagery: a comparison case study in Northeastern Germany. Remote Sens. 2022; 14(20): 1-21.
  • 73.   Li X, Liang Z., Yang G., Lin T., Liu B. Assessing the severity of Verticillium wilt in cotton fields and constructing pesticide application prescription maps using unmanned aerial vehicle (UAV) multispectral images. Drones. 2024; 8(5): 176
  • 74.   Lin Y. LiDAR: An important tool for nextgeneration phenotyping technology of high potential for plant phenomics? Comput Electron Agric. 2015; 119: 61-73.
  • 75.   Lisbinski F.C., Mühl D.D., Oliveira L.D., Coronel D.A. Perspectivas e desafios da agricultura 4.0 para o setor agrícola. In: VIII Simpósio da Ciência do Agronegócio; 2020. p. 422-31.
  • 76.   Liu X., Chen F., Barlage M., Zhou G., Niyogi D. Noah-MP-Crop: Introducing dynamic crop growth in the Noah-MP land-surface model. J Geophys Res Atmos. 2016; 121: 13, 953–13,972. doi:10.1002/2016JD025597
  • 77.   Liu Y., Feng H., Yue J., Li Z., Yang G., Song X., Yang X., Zhao Y. Remote-sensing estimation of potato above-ground biomass based on spectral and spatial features extracted from high-definition digital camera images. Comput Electron Agric. 2022; 198: 1–13. doi:10.1016/j. compag.2022.107089
  • 78.   Liu Y., Liu G., Sun H., An L., Zhao R., Liu M, Tang W, Li M., Yan X., Ma Y., Zhao F. Exploring multi-features in UAV-based optical and thermal infrared images to estimate disease severity of wheat powdery mildew. Comput Electron Agric. 2024;225:1–17.
  • 79.   Lu Y., Jin J., Kueppers L.M. Crop growth and irrigation interact to influence surface fluxes in a regional climate-cropland model (WRF3.3- CLM4 crop). Clim Dyn. 2015; 45: 3347–63.
  • 80.   Lv Z., Meng R., Man J., Zeng L., Wang M., Xu B., Gao R., Sun R., Zhao F. Modeling of winter wheat fAPAR by integrating unmanned aircraft vehicle-based optical, structural, and thermal measurement. Int J Appl Earth Obs Geoinf. 2021; 102: 1–13.
  • 81.   Ma C., Liu M., Ding F., Li C., Cui Y., Chen W., Wang Y. Wheat growth monitoring and yield estimation based on remote sensing data assimilation into the SAFY crop growth model. Sci Rep. 2022; 12(1): 1–16.
  • 82.   Maki M., Sekiguchi K., Homma K., Hirooka Y, Oki K. Estimation of rice yield by SIMRIW-RS, a model that integrates remote sensing data into a crop growth model. J Agric Meteorol. 2017; 73: 2-8.
  • 83.   Mansoor S., Karunathilake E.M.B.M., Tuan T.T., Chung Y.S. Genomics, Phenomics, and Machine Learning in Shaping the Future of Plant Research: Advancements and Challenges. Hortic Plant J. 2024.
  • 84.   Marzougui A., McGee R.J., Van Vleet S., Sankaran S. Remote sensing for field pea yield estimation: A study of multi-scale data fusion approaches in phenomics. Front Plant Sci. 2023; 14: 1–18.
  • 85.   Mathieu L., Reder M., Siah A., Ducasse A., Langlands-Perry C., Marcel T.C., Morel JB, Saintenac C., Ballini E. SeptoSympto: a precise image analysis of Septoria tritici blotch disease symptoms using deep learning methods on scanned images. Plant Methods.2024; 20(1): 1–14.
  • 86.   Meixner M., Tomasella M., Foerst P., Windt C.W. A small-scale MRI scanner and complementary imaging method to visualize and quantify xylem embolism formation. New Phytol. 2020; 226: 1517-29.
  • 87.   Miart F., Fontaine J.X., Pineau C., Demailly H., Thomasset B., Van Wuytswinkel O., Pageau K., Mesnard F. MuSeeQ, a novel supervised image analysis tool for the simultaneous phenotyping of the soluble mucilage and seed morphometric parameters. Plant Methods. 2018; 14(1): 112. doi:10.1186/s13007-018-0377-5 70.
  • 88.   Mishra P., Asaari M.S.M., Herrero-Langreo A., Lohumi S., Diezma B, Scheunders P. Close range hyperspectral imaging of plants: A review. Biosyst Eng. 2017; 164: 49-67.
  • 89.   Miyoshi Y., Nagao Y., Yamaguchi M., Suzui N., Yin Y.G., Kawachi N., Yoshida E., Takyu S, Tashima H., Uga Y. Plant root PET: visualization of photosynthate translocation to roots in rice plant. J Instrum. 2021; 16(10): 101101.
  • 90.   Mo X., Liu S., Lin Z., Xu Y., Xiang Y., McVicar T.R. Prediction of crop yield, water consumption and water use efficiency with a SVAT-crop growth model using remotely sensed data on the North China Plain. Ecol Model. 2005; 183: 301-22.
  • 91.   Moustaka J., Moustakas M. Early-stage detection of biotic and abiotic stress on plants by chlorophyll fluorescence imaging analysis. Biosensors. 2023; 13(4).
  • 92.   Munns R., James R.A., Sirault X.R., Furbank R.T., Jones H.G. New phenotyping methods for screening wheat and barley for beneficial responses to water deficit. J Exp Bot. 2010; 61(13): 3499–507.doi:10.1093/jxb/erq224
  • 93.   Nendel C., Berg M., Kersebaum K.C., Mirschel W., Specka X., Wegehenkel M., Wenkel K.O., Wieland R. The MONICA model: Testing predictability for crop growth, soil moisture and nitrogen dynamics. Ecol Model. 2011; 222: 1614-25.
  • 94.   Ntakos G. Prikaziuk E., ten Den T., Reidsma P., Vilfan N., van der Wal T., van der Tol C. Coupled WOFOST-SCOPE model for remotesensing-based crop growth simulations. Comput Electron Agric. 2024; 225: 1-15.
  • 95.   Omari R.A., Addo E.S., Matey D.M., Fujii Y., Okazaki S., Oikawa Y., Bellingrath-Kimura SD. Influence of organic inputs with mineral fertilizer on maize yield and soil microbial biomass dynamics in different seasons in a tropical acrisol. Environ Sustain. 2020; 3: 45-57.
  • 96.   Pace J., Gardner C., Romay C., Ganapathysubramanian B., Lübberstedt T. Genome-wide association analysis of seedling root development in maize (Zea mays L.). BMC Genomics. 2015; 16(1): 78. doi:10.1186/ s12864-015-1391-6
  • 97.   Padilla FLM, Maas S.J., González-Dugo M.P., Mansilla F., Rajan N., Gavilán P., Domínguez J. Monitoring regional wheat yield in Southern Spain using the GRAMI model and satellite imagery. Field Crops Res. 2012; 130: 145-54. doi:10.1016/j.fcr.2012.02.025
  • 98.   Paproki A., Sirault X, Berry S., Furbank R., Fripp J. A novel mesh processing-based technique for 3D plant analysis. BMC Plant Biol. 2012; 12: 63. doi:10.1186/1471-2229-12-63
  • 99.   Pascuzzi I.A., Symonova O., Mileyko Y., Hao Y., Belcher H., Harer J., Weitz J.S., Benfey P.N. Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol. 2010; 152: 1148-57.
  • 100.   Patil S.M., Choudhary S., Kholova J., Chandramouli M., Jagarlapudi A. Applications of UAVs: Image-Based Plant Phenotyping. In: Priyadarshan P., Jain S., Penna S., Al-Khayri J., editors. Digital Agriculture: A Solution for Sustainable Food and Nutritional Security. Cham: Springer International Publishing; 2024. p. 341-67.
  • 101.   Pereyra-Irujo G.A., Gasco E.D., Peirone L.S., Aguirrezábal L.A. GlyPh: a low-cost platform for phenotyping plant growth and water use. Funct Plant Biol. 2012; 39: 905-13.
  • 102.   Pérez-Bueno M.L., Pineda M., Cabeza F.M., Barón M. Multicolor fluorescence imaging as a candidate for disease detection in plant phenotyping. Front Plant Sci. 2016; 7: 1-11.
  • 103.   Pflugfelder D., Metzner R., van Dusschoten D., Reichel R., Jahnke S., Koller R. Non-invasive imaging of plant roots in different soils using magnetic resonance imaging (MRI). Plant Methods. 2017; 13(1): 1-9.
  • 104.   Porter J.R., Jamieson P.D., Wilson D.R. Comparison of the wheat simulation models AFRCWHEAT2, CERES-Wheat and SWHEAT for non-limiting conditions of crop growth. Field Crops Res. 1993; 33: 131-57.
  • 105.   Pound M.P., Fozard S., Torres Torres M., Forde BG, French AP. AutoRoot: open-source software employing a novel image analysis approach to support fully-automated plant phenotyping. Plant Methods. 2017; 13(1): 1-10.
  • 106.   Pound M.P., French A.P., Atkinson J.A., Wells D.M., Bennett M.J., Pridmore T. RootNav: navigating images of complex root architectures. Plant Physiol. 2013; 162: 1802-14.
  • 107.   Prashar A., Jones H.G. Infra-red thermography as a high-throughput tool for field phenotyping. Agronomy. 2014; 4(3): 397-417.
  • 108.   Prasomphan S. Rice bacterial infection detection using ensemble technique on unmanned aerial vehicles images. Comput Syst Sci Eng. 2023; 44(2): 1121–34. doi:10.32604/csse.2023.025452
  • 109.   Pratap A., Gupta S., Nair R.M., Gupta S.K., Schafleitner R., Basu P.S., Singh C.M., Prajapati U., Gupta A.K., Nayyar H., et al. Using plant phenomics to exploit the gains of genomics. Agronomy. 2019; 9(3): 126. doi:10.3390/ agronomy9030126
  • 110.   Rahman H., Ramanathan V., Jagadeeshselvam N., Ramasamy S., Rajendran S., Ramachandran M, Sudheer P.D.V.N., Chauhan S., Natesan S., Muthurajan R. Phenomics: Technologies and applications in plant and agriculture. In: Barh D., Khan M.S., Davies E., editors. PlantOmics: The Omics of Plant Science. 1st ed. Springer India; 2015. p. 385–411. doi:10.1007/978-81- 322-2172-2_13
  • 111.   Rellán-Álvarez R., Lobet G., Lindner H., Pradier P.L., Sebastian J., Yee M.C., Geng Y., Trontin C., LaRue T., Schrager-Lavelle A, Haney C.H., Nieu R., Maloof J., Dinneny J.R. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife. 2015; 4: e07597. doi:10.7554/eLife.07597
  • 112.   Ren S., Chen H., Hou J., Zhao P., Dong Q.G., Feng H. Based on historical weather data to predict summer field-scale maize yield: Assimilation of remote sensing data to WOFOST model by ensemble Kalman filter algorithm. Comput Electron Agric. 2024; 219: 108822. doi:10.1016/j.compag.2024.108822
  • 113.   Rigoulot S.B., Schimel T.M., Lee J.H., Sears R.G., Brabazon H., Layton J.S., Stewart C.N. Jr. Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants. Plant Biotechnol J. 2021; 19(4): 830–43. doi:10.1111/pbi.13510
  • 114.   Ristova D., Rosas U., Krouk G., Ruffel S., Birnbaum K.D., Coruzzi G.M. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. Plant Physiol. 2013; 161(3): 1086–96. doi:10.1104/ pp.112.210872
  • 115.   Robil J.M., Gao K., Neighbors C.M., Boeding M., Carland F.M., Bunyak F., McSteen P. GrasVIQ: an image analysis framework for automatically quantifying vein number and morphology in grass leaves. Plant J. 2021; 107(2): 629–48. doi:10.1111/tpj.15299
  • 116.   Roshni P., Prajwala K.A. Phenomics: approaches and application in crop improvement. Curr J Appl Sci Technol. 2019; 33(3): 1–10. doi:10.9734/cjast/2019/v33i330080
  • 117.   Roth L., Camenzind M., Aasen H., Kronenberg L., Barendregt C., Camp K.H., Hund A. Repeated multiview imaging for estimating seedling tiller counts of wheat genotypes using drones. Plant Phenomics. 2020; 2020: 3729715. doi:10.34133/2020/3729715
  • 118.   Sakamoto T., Gitelson A.A., Arkebauer T.J. MODIS-based corn grain yield estimation model incorporating crop phenology information. Remote Sens Environ. 2013; 131: 215–31. doi:10.1016/j.rse.2012.12.017
  • 119.   Santiago G., Magalhaes Cisdeli P.H., Carcedo A.J.P., Marziotte L., Mayor L., Ciampitti IA. Deep learning methods using imagery from a smartphone for recognizing sorghum panicles and counting grains at a plant level. Plant Phenomics. 2024; 6: 1-11. doi:10.34133/ plantphenomics.0234
  • 120.   Sarić R., Nguyen V.D., Burge T., Berkowitz O., Trtílek M., Whelan J., Čustović E. Applications of hyperspectral imaging in plant phenotyping. Trends Plant Sci. 2022; 27(3): 301- 15. doi:10.1016/j.tplants.2021.12.003
  • 121.   Seethepalli A., Dhakal K., Griffiths M., Guo H., Freschet G.T., York L.M. RhizoVision Explorer: Open-source software for root image analysis and measurement standardization. AoB Plants. 2021; 13(4): 1-15. doi:10.3389/fpls.2023.1214801
  • 122.   Setiyono T.D., Quicho E.D., Holecz F.H., Khan N.I., Romuga G., Maunahan A., Garcia C., Rala A., Raviz J., Mabalay M.R. Rice yield estimation using synthetic aperture radar (SAR) and the ORYZA crop growth model: development and application of the system in South and Southeast Asian countries. Int J Remote Sens. 2019; 40: 8093-124. doi:10.1080/01431161.2018.1547457
  • 123.   Singh B., Kumar S., Elangovan A., Vasht D., Arya S., Duc N.T., Swami P., Pawar G.S., Raju D., Krishna H., Sathee L., Dalal M., Sahoo R.N., Chinnusamy V. Phenomics-based prediction of plant biomass and leaf area in wheat using machine learning approaches. Front Plant Sci. 2023; 14: 1-16. doi:10.3389/fpls.2023.1214801
  • 124.   Singh S., Bajpai R., Rashid M.M., Teli B., Kumar G. Plant disease detection with the help of advanced imaging sensors. In: Artificial Intelligence and Smart Agriculture Applications. Auerbach Publications; 2022. p.163-84. doi:10.1201/9781003311782-8
  • 125.   Song C.Y., Zhang F., Li J.S., Xie J.Y., Chen Y.G., Hang Zhou, Zhang J.X. Detection of maize tassels for UAV remote sensing image with an improved YOLOX model. J Integr Agric. 2023; 22: 1671-83. doi:10.1016/j.jia.2022.09.021
  • 126.   Tang R., Supit I., Hutjes R., Zhang F., Wang X., Chen X., Zhang F., Chen X. Modelling growth of chili pepper (Capsicum annuum L.) with the WOFOST model. Agric Syst. 2023; 209: 1-13. doi:10.1016/j.agsy.2023.103688
  • 127.   Tao H., Xu S., Tian Y., Li Z., Ge Y., Zhang J., Wang Y., Zhou G., Deng X., Zhang Z., Ding Y., Jiang D., Jin S. Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives. Plant Commun. 2022; 3: 1-39. doi:10.1016/j.xplc.2022.100344
  • 128.   Tardieu F., Cabrera-Bosquet L., Pridmore T., Bennett M. Plant phenomics, from sensors to knowledge. Curr Biol. 2017; 27: R770-83. doi:10.1016/j.cub.2017.05.055
  • 129.   Thakur S., Sharma S., Barela A., Nagre S.P. Plant phenomics through proximal remote sensing: A review for improved crop yield. Pharma Innov J. 2023; 12(5): 2432-42. doi:10.22271/ tpi.2023.v12.i5ai.20057
  • 130.   Tian Y., Xie L., Wu M., Yang B., Ishimwe C., Ye D., Weng H. Multicolor fluorescence imaging for the early detection of salt stress in Arabidopsis. Agronomy. 2021; 11(3): 1-12. doi:10.3390/agronomy11030497
  • 131.   Togninalli M., Wang X., Kucera T., Shrestha S., Juliana P., Mondal S., Pinto F., Govindan V., Crespo-herrera L., Poland J. Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics. Bioinformatics. 2023; 39(1): 1-11. doi:10.1093/bioinformatics/btac784
  • 132.   Tomé F., Jansseune K., Saey B., Grundy J., Vandenbroucke K., Hannah M.A., Redestig H. rosettR: protocol and software for seedling area and growth analysis. Plant Methods. 2017; 13(1): 1-10. doi:10.1186/s13007-017-0176-0
  • 133.   Ubbens J.R., Stavness I. Deep plant phenomics: a deep learning platform for complex plant phenotyping tasks. Front Plant Sci. 2017; 8: 1190. doi:10.3389/fpls.2017.01190
  • 134.   Van Diepen C.V., Wolf J., Van Keulen H., Rappoldt C. WOFOST: a simulation model of crop production. Soil Use Manage. 1989; 5(1): 16-24. doi:10.1111/j.1475-2743.1989.tb00755.x
  • 135.   Van Harsselaar J.K., Claußen J., Lübeck J., Wörlein N., Uhlmann N, Sonnewald U, Gerth S. X-ray CT phenotyping reveals bi-phasic growth phases of potato tubers exposed to combined abiotic stress. Front Plant Sci. 2021; 12: 1-15. doi:10.3389/fpls.2021.661227
  • 136.   Vasseur F., Cornet D., Beurier G., Messier J., Rouan L., Bresson J., Violle C. A perspective on plant phenomics: coupling deep learning and near-infrared spectroscopy. Front Plant Sci. 2022; 13: 836488. doi:10.3389/fpls.2022.836488
  • 137.   Villalobos F.J., Hall A.J., Ritchie J.T., Orgaz F. OILCROP‐SUN: A development, growth, and yield model of the sunflower crop. Agron J. 1996; 88(3): 403-15. doi:10.2134/ agronj1996.00021962008800030017x
  • 138.   Wan L., Zhang J., Dong X., Du X., Zhu J., Sun D., Liu Y., He Y., Cen H. Unmanned aerial vehiclebased field phenotyping of crop biomass using growth traits retrieved from PROSAIL model. Comput Electron Agric. 2021; 187: 1-12. doi:10.1016/j.compag.2021.106297
  • 139.   Wang D., Chen H., Wang Z., Ma Y. Inversion of soil salinity according to different salinization grades using multi-source remote sensing. Geocarto Int. 2020; 37(4): 1274–93. doi:10.1080 /10106049.2020.1762766
  • 140.   Wedeking R., Maucourt M., Deborde C., Moing A., Gibon Y., Goldbach H.E., Wimmer M.A. 1H-NMR metabolomic profiling reveals a distinct metabolic recovery response in shoots and roots of temporarily drought-stressed sugar beets. PLoS One. 2018; 13(5): e0196102. doi:10.1371/journal.pone.0196102
  • 141.   Wegehenkel M., Mirschel W. Crop growth, soil water and nitrogen balance simulation on three experimental field plots using the OPUS model—a case study. Ecol Model. 2006; 190: 116-32. doi:10.1016/j.ecolmodel.2005.04.025
  • 142.   Williams J.R., Jones C.A., Kiniry J.R., Spanel D.A. The EPIC crop growth model. Trans Am Soc Agric Eng. 1989; 32(2): 497-511. doi:10.13031/2013.31032
  • 143.   Wu J., Wu Q., Pagès L., Yuan Y., Zhang X., Du M., Tian X., Li Z. RhizoChamber-Monitor: a robotic platform and software enabling characterization of root growth. Plant Methods. 2018; 14(1): 1-15. doi:10.1186/s13007-018-0307-7
  • 144.   Wu S., Yang P., Ren J., Chen Z., Li H. Regional winter wheat yield estimation based on the WOFOST model and a novel VW-4DEnSRF assimilation algorithm. Remote Sensing Environ. 2021; 255: 1-22. doi:10.1016/j. rse.2020.112289
  • 145.   Wu T., Dai J., Shen P., Liu H., Wei Y. Seedscreener: A novel integrated wheat germplasm phenotyping platform based on NIR-feature detection and 3D-reconstruction. Comput Electron Agric. 2023; 215: 1-15. doi:10.1016/j.compag.2023.108468
  • 146.   Xu Z., Valdes C., Clarke J. Existing and potential statistical and computational approaches for the analysis of 3D CT images of plant roots. Agronomy. 2018; 8(9): 1-20. doi:10.3390/ agronomy8090182
  • 147.   Yang W., Duan L., Chen G., Xiong L., Liu Q. Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies. Curr Opin Plant Biol. 2013; 16(2): 180-7. doi:10.1016/j. pbi.2013.03.005
  • 148.   Yang W., Feng H., Zhang X., Zhang J., Doonan J.H., Batchelor W.D., Yan J. Crop phenomics and high-throughput phenotyping: past decades, current challenges, and future perspectives. Mol Plant. 2020; 13(2): 187–214. doi:10.1016/j.molp.2020.01.008
  • 149.   Yang W., Liu T., Tang X., Xu G., Ma Z., Yang H., Wu W. Research Progress on Plant Phenomics in the Context of Smart Agriculture. J Henan Agric Sci. 2022; 51(7): 1-12.
  • 150.   Yang X., Wang J., Li F., Zhou C., Wu M., Zheng C., Yang L., Li Z., Li Y., Guo S., Song C. RotatedStomataNet: a deep rotated object detection network for directional stomata phenotype analysis. Plant Cell Rep. 2024; 43(1): 1-18.
  • 151.   Yang X., Yang Y.N., Xue L.J., Zou M.J., Liu J.Y., Chen F., Xue H.W. Rice ABI5-Like1 regulates abscisic acid and auxin responses by affecting the expression of ABRE-containing genes. Plant Physiol. 2011; 156: 1397-409. doi:10.1104/ pp.111.179730
  • 152.   Yasrab R., Pound M.P., French A.P., Pridmore T.P. Rootnet: A convolutional neural networks for complex plant root phenotyping from highdefinition datasets. BioRxiv. 2020; 5: 1-11.
  • 153.   Yépez-Ponce D.F., Salcedo J.V., RoseroMontalvo P.D., Sanchis J. Mobile robotics in smart farming: current trends and applications. Front Artif Intell. 2023; 6: 1-13. doi:10.3389/ frai.2023.1061328
  • 154.   Ying W. Phenomic studies on diseases: potential and challenges. Phenomics. 2023; 3(3): 285-99. doi:10.1002/phen.202300029
  • 155.   Zhai Y., Zhou L., Qi H., Gao P., Zhang C. Application of visible/near-infrared spectroscopy and hyperspectral imaging with machine learning for high-throughput plant heavy metal stress phenotyping: a review. Plant Phenomics. 2023; 5: 1-16. doi:10.34133/ plantphenomics.0050
  • 156.   Zhang C., Zhou L., Xiao Q., Bai X., Wu B., Wu N., Feng L. End-to-end fusion of hyperspectral and chlorophyll fluorescence imaging to identify rice stresses. Plant Phenomics. 2022; 2022: 1-14. doi:10.34133/2022/9862910
  • 157.   Zhang H., Ge Y., Xie X., Atefi A., Wijewardane N.K., Thapa S. High throughput analysis of leaf chlorophyll content in sorghum using RGB, hyperspectral, and fluorescence imaging and sensor fusion. Plant Methods. 2022; 18(1): 1-17. doi:10.1186/s13007-022-00926-w
  • 158.   Zhang L.Z., Werf W.V., Cao W.X., Li B., Pan X., Spiertz J.H.J. Development and validation of SUCROS-Cotton: a potential crop growth simulation model for cotton. NJAS Wagening J Life Sci. 2008; 56(1-2): 59-83.
  • 159.   Zhang M., Zhou J., Sudduth K.A., Kitchen N.R. Estimating maize yield and effects of variablerate nitrogen application using UAV-based RGB imagery. Biosyst Eng. 2020; 189: 24-35. doi:10.1016/j.biosystemseng.2019.12.003
  • 160.   Zhao C., Liu B., Xiao L., Hoogenboom G., Boote K.J., Kassie B.T., Pavan W., Shelia V., Kim K.S., Hernandez-Ochoa I.M., Asseng S. A SIMPLE crop model. Eur J Agron. 2019; 104: 97-106. doi:10.1016/j.eja.2018.11.007
  • 161.   Zhao H., Wang N, Sun H., Zhu L., Zhang K., Zhang Y, Zhu J., Li A., Bai Z., Liu X., Dong H., Liu L., Li C. RhizoPot platform: a highthroughput in situ root phenotyping platform with integrated hardware and software. Front Plant Sci. 2022; 13: 889234. doi:10.3389/ fpls.2022.889234
  • 162.   Zhou J., Applegate C., Alonso A.D., Reynolds D, Orford S, Mackiewicz M, Pullen N. Leaf-GP: an open and automated software application for measuring growth phenotypes for Arabidopsis and wheat. Plant Methods. 2017; 13(1): 81. doi:10.1186/s13007-017-0211-0
  • 163.   Zhou Y., Kamruzzaman M., Schnable P., Krishnamoorthy B., Kalyanaraman A., Wang B. Pheno-Mapper: an interactive toolbox for the visual exploration of phenomics data. In: Proceedings of the 12th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics; 2021 Aug. p. 1-10.
  • 164.   Zia H, Harris NR, Merrett GV, Rivers M, Coles N. The impact of agricultural activities on water quality: A case for collaborative catchmentscale management using integrated wireless sensor networks. Comput Electron Agric. 2013; 96: 126-38. doi:10.1016/j.compag.2013.04.013

Data Sharing Statement

There are no additional data available. All raw data and code are available upon request.

Funding

This research received no funding.

Author Contributions

All authors contributed significantly to the work and approve its publication.

Ethics Declaration

This article does not involve any human or animal subjects, and therefore does not require ethics approval.

Acknowledgements

We would like to express our gratitude to the patients, their families, and all those who have contributed to this study.

Conflicts of Interest

No conflicts of interest in this work.


About this article


Cite this article

Anjali Bhardwaj, Shikha Chaudhary. Advances in Plant Phenotyping Tools for Agricultural Sustainability. Ind J Plant Soil. 2026; 13(1): 53-70.


Licence:

Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Received Accepted Published
November 28, 2025 January 10, 2026 June 30, 2026

DOI: https://doi.org/10.21088/ijps.2348.9677.13126.5

Keywords

PhenomicsAgricultural sustainabilityFood securityImaging toolsMachine learningRemote sensing

Article Level Metrics

Last Updated

Sunday 16 August 2026, 16:27:59 (IST)


766

Accesses

14
202
00

Citations


NA
NA
NA

Download citation


Article Keywords


Keyword Highlighting

Highlight selected keywords in the article text.


Timeline


Received November 28, 2025
Accepted January 10, 2026
Published June 30, 2026

licence


Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Access this article



Share