Application of RGB-Imaging techniques for high-throughput plant phenotyping- A Review

Authors

DOI:

https://doi.org/10.24925/turjaf.v13is2.3678-3686.7951

Keywords:

High-throughput plant phenotyping, Image-based analysis, Plant breeding, RGB imaging, Sensor technologies

Abstract

High-throughput plant phenotyping plays an important role in plant breeding, identifying superior genotypes in a fast and accurate manner. Consequently, researchers are seeking new image-based plant phenotyping strategies to enhance phenotyping efficiency. RGB (red, green, blue) sensors and their applications offer a cost-effective and accessible approach while maintaining the advantageous characteristics of high-throughput phenotyping technologies. Various RGB image-based indices are now available to measure diverse phenotypic traits accurately. Despite a wide range of advantages, some limitations reduce the accuracy of the method. We systematically reviewed scientific articles published between 2000 and 2024 to ascertain the significance, available knowledge, and gaps in the domain of RGB image-based plant phenotyping. This review paper provides a comprehensive survey on the significance of current RGB imaging technologies and their applications in plant phenotyping, emphasizing their advantages and limitations. RGB image-based plant phenotyping demonstrates considerable accuracy in the estimation of morphological traits. However, this technique gives significantly lower accuracy for physiological traits compared with other sensors. Furthermore, variation of light conditions, varied backgrounds, and overlapping are major drawbacks of this technique. Future studies should focus on the development of precise image acquisition systems, advanced image processing techniques (including image segmentation), the identification of novel color parameters, the implementation of robust artificial intelligence and machine learning models, and the integration of complementary sensor technologies to address existing challenges.

References

Alaguero-Cordovilla, A., Gran-Gómez, F., Tormos-Moltó, S., & Pérez-Pérez, J. (2018). Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth. International Journal of Molecular Sciences, 19(12), 3888. https://doi.org/10.3390/ijms19123888

Araus, J. L., Kefauver, S. C., ZamanAllah, M., Olsen, M. S., & Cairns, J. E. (2018). Translating highthroughput phenotyping into genetic gain. Trends in Plant Science, 23(5), 451–466.

Brainard, S. H., Bustamante, J. A., Dawson, J. C., Spalding, E. P., & Goldman, I. L. (2021). A Digital Image-Based Phenotyping Platform for Analyzing Root Shape Attributes in Carrot. Frontiers in Plant Science, 12. https://doi.org/10.3389/fpls.2021.690031

Cabrera‐Bosquet, L., Crossa, J., Zitzewitz, von, Serret, M. D., & Araus, L. (2012). High‐throughput phenotyping and genomic selection: The frontiers of crop breeding converge F. Journal of Integrative Plant Biology, 54(5), 312–320.

Cen, H., Wan, L., Zhu, J., Li, Y., Li, X., Zhu, Y., Weng, H., Wu, W., Yin, W., & Xu, C. (2019). Dynamic monitoring of biomass of rice under different nitrogen treatments using a lightweight UAV with dual imageframe snapshot cameras. Plant Methods, 15, 1–16.

Chen, Y., Chao, K., & Kim, M. S. (2002). Machine vision technology for agricultural applications. Computers and Electronics in Agriculture, 36(23), 173–191.

Darrigues, A., Hall, J., van, Francis, D. M., Dujmovic, N., & Gray, S. (2008). Tomato analyzercolor test: a new tool for efficient digital phenotyping. Journal of the American Society for Horticultural Science, 133(4), 579–586.

Davies, E. R. (2012). Computer and machine vision: theory, algorithms, practicalities. Academic Press.

Deery, D., Jimenez-Berni, J., Jones, H., Sirault, X., & Furbank, R. (2014). Proximal Remote Sensing Buggies and Potential Applications for Field-Based Phenotyping. Agronomy, 4(3), 349–379. https://doi.org/10.3390/agronomy4030349

Dellen, B., Scharr, H., & Torras, C. (2015). Growth Signatures of Rosette Plants from Time-Lapse Video. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(6), 1470–1478. https://doi.org/10.1109/TCBB.2015.2404810

Diago, M.-P., Correa, C., Millán, B., Barreiro, P., Valero, C., & Tardaguila, J. (2012). Grapevine Yield and Leaf Area Estimation Using Supervised Classification Methodology on RGB Images Taken under Field Conditions. Sensors, 12(12), 16988–17006. https://doi.org/10.3390/s121216988

Fahlgren, N., Gehan, M. A., & Baxter, I. (2015). Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Current Opinion in Plant Biology, 24, 93–99. https://doi.org/10.1016/j.pbi.2015.02.006

FAO. (2024). Agricultural Production Statistics 2010–2023. FAOSTAT Analytical Briefs, No. 96.

Fawzy, E., Harb, A., Allam, D. G., & Abdelraouf, E. (2022). Thermal and RGB imaging as potential tools for assessing chlorophyll and nutritional performance of pepper (Capsicum annum). Journal of Agricultural and Environmental Sciences, 21(3), 80–100.

Feldmann, M. J., Hardigan, M. A., Famula, R. A., López, C. M., Tabb, A., Cole, G. S., & Knapp, S. J. (2020). Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry. GigaScience, 9(5). https://doi.org/10.1093/gigascience/giaa030

Feng, H., Tao, H., Li, Z., Yang, G., & Zhao, C. (2022). Comparison of UAV RGB imagery and hyperspectral remote sensing data for monitoring winter wheat growth. Remote Sensing, 14(15), 3811.

Fiorani, F., & Schurr, U. (2013). Future scenarios for plant phenotyping. Annual Review of Plant Biology, 64(1), 267–291.

Fu, X., Bai, Y., Zhou, J., Zhang, H., & Xian, J. (2021). A method for obtaining field wheat freezing injury phenotype based on RGB camera and software control. Plant Methods, 17(1). https://doi.org/10.1186/s13007-021-00821-7

Gang, M.-S., Kim, H.-J., & Kim, D.-W. (2022). Estimation of Greenhouse Lettuce Growth Indices Based on a Two-Stage CNN Using RGB-D Images. Sensors, 22(15), 5499. https://doi.org/10.3390/s22155499

Ge, Y., Bai, G., Stoerger, V., & Schnable, J. C. (2016). Temporal dynamics of maize plant growth, water use, and leaf water content using automated high throughput RGB and hyperspectral imaging. Computers and Electronics in Agriculture, 127, 625–632. https://doi.org/10.1016/j.compag.2016.07.028

Gill, T., Gill, S. K., Saini, D. K., Chopra, Y., de Koff, J. P., & Sandhu, K. S. (2022). A Comprehensive Review of High Throughput Phenotyping and Machine Learning for Plant Stress Phenotyping. Phenomics. https://doi.org/10.1007/s43657-022-00048-z

Granier, C., L. Aguirrezabal, Chenu, K., Sarah Jane Cookson, Dauzat, M., Philippe Hamard, Thioux, J. J., Rolland, G., Sandrine Bouchier-Combaud, Lebaudy, A., Muller, B., Thierry Simonneau, & François Tardieu. (2006). PHENOPSIS, an automated platform for reproducible phenotyping of plant responses to soil water deficit in arabidopsis thaliana permitted the identification of an accession with low sensitivity to soil water deficit. New Phytologist, 169(3), 623–635. https://doi.org/10.1111/j.1469-8137.2005.01609.x

Guo, Y., Chen, S., Wu, Z., Wang, S., Robin Bryant, C., Senthilnath, J., Cunha, M., & Fu, Y. H. (2021). Integrating Spectral and Textural Information for Monitoring the Growth of Pear Trees Using Optical Images from the UAV Platform. Remote Sensing, 13(9), 1795. https://doi.org/10.3390/rs13091795

Hobart, M., Pflanz, M., Weltzien, C., & Schirrmann, M. (2020). Growth Height Determination of Tree Walls for Precise Monitoring in Apple Fruit Production Using UAV Photogrammetry. Remote Sensing, 12(10), 1656. https://doi.org/10.3390/rs12101656

Holland, K. H., Lamb, D. W., & Schepers, J. S. (2012). Radiometry of proximal active optical sensors (AOS) for agricultural sensing. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(6), 1793–1802.

Horgan, G. W., Song, Y., Glasbey, C. A., van der Heijden, G. W. A. M., Polder, G., Dieleman, J. A., Bink, M. C. A. M., & van Eeuwijk, F. A. (2015). Automated estimation of leaf area development in sweet pepper plants from image analysis. Functional Plant Biology, 42(5), 486. https://doi.org/10.1071/fp14070

Houle, D., Govindaraju, Diddahally R, & Omholt, S. (2010). Phenomics: the next challenge. Nature Reviews Genetics, 11(12), 855–866.

Jia, L., Buerkert, A., Chen, X., Roemheld, V., & Zhang, F. (2004). Low-altitude aerial photography for optimum N fertilization of winter wheat on the North China Plain. Field Crops Research, 89(2-3), 389–395. https://doi.org/10.1016/j.fcr.2004.02.014

Jiang, S., Wu, X., Wang, Q., Pei, Z., Wang, Y., Jin, J., Guo, Y., Song, R., Zang, L., Liu, Y.-J., & Hao, G. (2024). Auto-LIA: The Automated Vision-Based Leaf Inclination Angle Measurement System Improves Monitoring of Plant Physiology. Plant Phenomics, 6, 0245. https://doi.org/10.34133/plantphenomics.0245

Jiang, Y., & Yang, Y. (2022). High-throughput phenotyping for plant growth and biomass yield of switch grass under a controlled environment. Grass Research, 2(1), 1–7. https://doi.org/10.48130/gr-2022-0004

Johansen, K., Morton, M. J. L., Malbeteau, Y., Aragon, B., Al-Mashharawi, S., Ziliani, M. G., Angel, Y., Fiene, G., Negrão, S., Mousa, M. A. A., Tester, M. A., & McCabe, M. F. (2020). Predicting Biomass and Yield in a Tomato Phenotyping Experiment Using UAV Imagery and Random Forest. Frontiers in Artificial Intelligence, 3(28). https://doi.org/10.3389/frai.2020.00028

Jollet, D., Junker-Frohn, L. V., Steier, A., Meyer-Lüpken, T., & Müller-Linow, M. (2023). A new computer vision workflow to assess yield quality traits in bush bean (Phaseolus vulgaris L.). Smart Agricultural Technology, 5, 100306–100306. https://doi.org/10.1016/j.atech.2023.100306

Kim, D.-W., Yun, H. S., Jeong, S.-J., Kwon, Y.-S., Kim, S.-G., Lee, W. S., & Kim, H.-J. (2018). Modeling and Testing of Growth Status for Chinese Cabbage and White Radish with UAV-Based RGB Imagery. Remote Sensing, 10(4), 563. https://doi.org/10.3390/rs10040563

Kim, J., & Chung, Y. S. (2021). A short review of RGB sensor applications for accessible high-throughput phenotyping. Journal of Crop Science and Biotechnology, 24(5), 495–499. https://doi.org/10.1007/s12892-021-00104-6

Kior, A., Yudina, L., Zolin, Y., Sukhov, V., & Sukhova, E. (2024). RGB imaging as a tool for remote sensing of characteristics of terrestrial plants: A review. Plants, 13(9), 1262.

Kolhar, S., & Jagtap, J. (2021). Plant trait estimation and classification studies in plant phenotyping using machine vision – A review. Information Processing in Agriculture, 10(1). https://doi.org/10.1016/j.inpa.2021.02.006

Li, L., Zhang, Q., & Huang, D. (2014). A Review of Imaging Techniques for Plant Phenotyping. Sensors, 14(11), 20078–20111. https://doi.org/10.3390/s141120078

Liming, X., & Yanchao, Z. (2010). Automated strawberry grading system based on image processing. Computers and Electronics in Agriculture, 71, S32–S39.

Liu, Y., Chen, Y., Wen, M., Lu, Y., & Ma, F. (2023). Accuracy comparison of estimation on cotton leaf and plant nitrogen content based on UAV digital image under different nutrition treatments. Agronomy, 13(7), 1686.

Liu, Y., Hatou, K., Aihara, T., Kurose, S., Akiyama, T., Kohno, Y., Lu, S., & Omasa, K. (2021). A robust vegetation index based on different UAV RGB images to estimate SPAD values of naked barley leaves. Remote Sensing, 13(4), 686.

Luana, S., de, Valentim, D. A., Andrade, M. T., Conti, L., & Rossi, G. (2020). Determining the leaf area index and percentage of area covered by coffee crops using UAV RGB images. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 13, 6401–6409.

Ma, Z., Rayhana, R., Feng, K., Liu, Z., Xiao, G., Ruan, Y., & Sangha, J. S. (2022). A review on sensing technologies for high throughput plant phenotyping. IEEE Open Journal of Instrumentation and Measurement, 1, 1–21.

Mahlein, A. (2016). Plant disease detection by imaging sensors–parallels and specific demands for precision agriculture and plant phenotyping. Plant Disease, 100(2), 241–251.

Mahlein, A.-K., Steiner, U., Hillnhütter, C., Dehne, H.-W., & Oerke, E.-C. (2012). Hyperspectral imaging for small-scale analysis of symptoms caused by different sugar beet diseases. Plant Methods, 8(1), 3. https://doi.org/10.1186/1746-4811-8-3

Mansoor, S., Karunathilake, E. M. B. M., Tuan, T. T., & Chung, Y. S. (2024). Genomics, Phenomics, and Machine Learning in Transforming Plant Research: Advancements and Challenges. Horticultural Plant Journal. https://doi.org/10.1016/j.hpj.2023.09.005

Minaee, S., Boykov, Y., Porikli, F., Plaza, A., Kehtarnavaz, N., & Terzopoulos, D. (2021). Image segmentation using deep learning: A survey. IEEE Transactions on Pattern Analysis and Machine Intelligence, 44(7), 3523–3542.

Mir, R. R., Reynolds, M., Pinto, F., Khan, M. A., & Bhat, M. A. (2019). High throughput phenotyping for crop improvement in the genomics era. Plant Science, 282, 60–72.

Montes, J. M., Melchinger, Albrecht E, & Reif, J. C. (2007). Novel throughput phenotyping platforms in plant genetic studies. Trends in Plant Science, 12(10), 433–436.

Musse, M., Hajjar, G., Ali, N., Billiot, B., Joly, G., Jérémy Pépin, Stéphane Quellec, Sylvain Challois, Mariette, F., Cambert, M., Fontaine, C., Ngo-Dinh, C., Jamois, F., Barbary, A., Leconte, P., Deleu, C., & Leport, L. (2021). A global non-invasive methodology for the phenotyping of potato under water deficit conditions using imaging, physiological and molecular tools. Plant Methods, 17(1). https://doi.org/10.1186/s13007-021-00771-0

Omari, M. K., Lee, J., Faqeerzada, M. A., Joshi, R., Park, E., & Cho, B. (2020). Digital image based plant phenotyping: a review. Korean Journal of Agricultural Science, 47(1), 119–130.

Qiu, R., Wei, S., Zhang, M., Li, H., Sun, H., Liu, G., & Li, M. (2018). Sensors for measuring plant phenotyping: A review. Int J Agric & Biol Eng, 11(2), 1–17.

Rasmussen, J., Ntakos, G., Nielsen, J., Svensgaard, J., Poulsen, R. N., & Christensen, S. (2016). Are vegetation indices derived from consumer grade cameras mounted on UAVs sufficiently reliable for assessing experimental plots? European Journal of Agronomy, 74, 75–92.

Rehman, T. U., Ma, D., Wang, L., Zhang, L., & Jin, J. (2020). Predictive spectral analysis using an end-to-end deep model from hyperspectral images for high-throughput plant phenotyping. Computers and Electronics in Agriculture, 177, 105713. https://doi.org/10.1016/j.compag.2020.105713

Rezzouk, F. Z., Gracia Romero, A., Kefauver, S. C., Gutiérrez, N. A., Aranjuelo, I., Serret, M. D., & Luis, A. J. (2020). Remote sensing techniques and stable isotopes as phenotyping tools to assess wheat yield performance: Effects of growing temperature and vernalization. Plant Science, 295, 110281.

Rocha, R., Fernando, D., Bandeira, M., Alves, L., & Jorge. (2022). Image-based phenotyping of cassava roots for diversity studies and carotenoids prediction. PLOS ONE, 17(1), e0263326–e0263326. https://doi.org/10.1371/journal.pone.0263326

Sie, E. K., Oteng-Frimpong, R., Kassim, Y. B., Puozaa, D. K., Adjebeng-Danquah, J., Masawudu, A. R., ... & Balota, M. (2022). RGB-image method enables indirect selection for leaf spot resistance and yield estimation in a groundnut breeding program in Western Africa. Frontiers in Plant Science, 13, 957061.

Singh, H., Kumar, N., & Kumar, A. (2024). Enhancing Resource Use Efficiency in Crops Through Plant Functional Traits. Plant Functional Traits for Improving Productivity. Springer, Singapore, 97–117. https://doi.org/10.1007/978-981-97-1510-7_6

Tan, G. D., Chaudhuri, U., Varela, S., Ahuja, N., & Leakey, A. D. B. (2024). Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and case study on stomatal patterning. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erae395

Tharuka, M. V. T., & Wijerathne, H. P. B. (2024). Development of an image-based alternative method for soil plant analysis development (SPAD) reading. Young Scientists’ Conference on Multidisciplinary Research-2024, 1.

Van Dusschoten, D., Metzner, R., Kochs, J., Postma, J. A., Pflugfelder, D., Bühler, J., Schurr, U., & Jahnke, S. (2016). Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging. Plant Physiology, 170(3), 1176–1188. https://doi.org/10.1104/pp.15.01388

Van, Burchfield, D. R., Witt, T. D., Price, K. P., & Sharda, A. (2020). Drones in agriculture. Advances in Agronomy, 162, 1–30.

Walter, A., Finger, R., Huber, R., & Buchmann, N. (2017). Opinion: Smart farming is key to developing sustainable agriculture. Proceedings of the National Academy of Sciences, 114(24), 6148–6150. https://doi.org/10.1073/pnas.1707462114

Walter, A., Liebisch, F., & Hund, A. (2015). Plant phenotyping: from bean weighing to image analysis. Plant Methods, 11(1), 14. https://doi.org/10.1186/s13007-015-0056-8

Walter, J., Edwards, J., Cai, J., McDonald, G., Miklavcic, S. J., & Kuchel, H. (2019). High-throughput field imaging and basic image analysis in a wheat breeding programme. Frontiers in plant science, 10, 449.

Wasonga, D. O., Yaw, A., Kleemola, J., Alakukku, L., & Mäkelä, P. S. A. (2021). Red-Green-Blue and Multispectral Imaging as Potential Tools for Estimating Growth and Nutritional Performance of Cassava under Deficit Irrigation and Potassium Fertigation. Remote Sensing, 13(4), 598. https://doi.org/10.3390/rs13040598

Widjaja Putra, B. T., & Soni, P. (2017). Enhanced broadband greenness in assessing Chlorophyll a and b, Carotenoid, and Nitrogen in Robusta coffee plantations using a digital camera. Precision Agriculture, 19(2), 238–256. https://doi.org/10.1007/s11119-017-9513-x

Xiao, Q., Bai, X., Zhang, C., & He, Y. (2021). Advanced high-throughput plant phenotyping techniques for genome-wide association studies: A review. Journal of Advanced Research, 35, 215–230. https://doi.org/10.1016/j.jare.2021.05.002

Yadav, S. P., Ibaraki, Y., & Dutta Gupta, S. (2009). Estimation of the chlorophyll content of micropropagated potato plants using RGB based image analysis. Plant Cell, Tissue and Organ Culture (PCTOC), 100(2), 183–188. https://doi.org/10.1007/s11240-009-9635-6

Yonis, B. O., Pino del Carpio, D., Wolfe, M., Jannink, J.-L., Kulakow, P., & Rabbi, I. (2020). Improving root characterisation for genomic prediction in cassava. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-64963-9

Yu, L., Shi, J., Huang, C., Duan, L., Wu, D., Fu, D., Wu, C., Xiong, L., Yang, W., & Liu, Q. (2020). An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning. The Crop Journal, 9(1), 42–56. https://doi.org/10.1016/j.cj.2020.06.009

Zhu, Y., Gu, Q., Zhao, Y., Wan, H., Wang, R., Zhang, X., & Cheng, Y. (2022). Quantitative Extraction and Evaluation of Tomato Fruit Phenotypes Based on Image Recognition. Frontiers in Plant Science, 13, 859290. https://doi.org/10.3389/fpls.2022.859290

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23.11.2025