Creation and Research of 3D Models for Digital Plant Phenotyping
- Authors: Ivaschuk O.A.1, Berezhnoy V.A.2, Maslakov Y.N.1, Fedorov V.I.1
-
Affiliations:
- Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
- Belgorod State National Research University
- Issue: No 4 (2022)
- Pages: 78-87
- Section: Analysis of Textual and Graphical Information
- URL: https://journal-vniispk.ru/2071-8594/article/view/270492
- DOI: https://doi.org/10.14357/20718594220408
- ID: 270492
Cite item
Full Text
Abstract
In the article, the authors present the results of the development and research of methods for creating 3D models of plants grown in vitro, which provide the ability to accurately record the morphometric indicators of the growth of individual parts, organs of plants and plants as a whole, cultivated on different nutrient media. The presented methods and algorithms in a complex solve the problems arising in the process of studying plants in a test tube, related to the complexity of the plant structure, the occurrence of distortions at the borders of the test tube, its possible fogging, as well as the influence of the human factor. A bank of 792 3D models for plants of 6 species has been created, which allows conducting simulation experiments to identify cause-and-effect relationships, forecasting and gaining new knowledge. The developed methods were checked for adequacy, an example of use for a specific plant was presented. The presented methods and algorithms can become the basis for the implementation of the process of digital phenotyping of plants.
About the authors
Olga A. Ivaschuk
Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
Author for correspondence.
Email: o.ivashchuk@rgau-msha.ru
Doctor of Technical Sciences, Professor, Senior Researcher
Russian Federation, MoscowVladislav A. Berezhnoy
Belgorod State National Research University
Email: berezhnoy_v@bsu.edu.ru
Candidate of Engineering Sciences, Senior Lecturer
Russian Federation, BelgorodYuri N. Maslakov
Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
Email: u.maslakov@rgau-msha.ru
Junior Researcher of the Agrotechnologies for the Future World-Class Scientific Center
Russian Federation, MoscowVyacheslav I. Fedorov
Russian State Agrarian University – Moscow Timiryazev Agricultural Academy
Email: v.fedorov@rgau-msha.ru
Candidate of Engineering Sciences, Researcher of the Agrotechnologies for the Future World-Class Scientific Center
Russian Federation, MoscowReferences
- Chéné Y. On the use of depth camera for 3D phenotyping of entire plants / Y. Chéné, D. Rousseau, P. Lucidarme, J. Bertheloot, V. Caffier, P. Morel, F. Chapeau-Blondeau // Computers and Electronics in Agriculture, 2012. – Vol. 82. – P. 122-127.
- Chaudhury A. Machine vision system for 3D plant phenotyping / A. Chaudhury, C. Ward, A. Talasaz, A.G. Ivanov, M. Brophy, B. Grodzinski, J.L. Barron // IEEE/ACM transactions on computational biology and bioinformatics, 2018. – Vol. 16. – №. 6. – P. 2009-2022.
- Berezhnoy V.A. Approaches for Automated Monitoring and Evaluation of In Vitro Plant’s Morphometric Parameters / V.A. Berezhnoy, O.A. Ivashchuk, Y.N. Maslakov,
- V.I. Fedorov, V.M. Yacenko // Journal of Computational and Theoretical Nanoscience, 2020. – Vol. 17. – № 9-10. – P. 4725-4732.
- Berezhnoi V A Obzor metodov i algoritmov avtomatizirovannykh system fenotipirovaniia rastenii V A Berezhnoi O A Ivashchuk D S Semenov // Sovremennye naukoemkie tekhnologii. –2021. – 4. – Р. 111-116.
- Automatic plant leaf classification for a mobile field guide / D. Knight, J. Painter, M. Potter // Rapport technique. Université de Stanford, 2010. – URL: https://stacks.stanford.edu/file/druid:bj600br8916/Knight_ Painter_Potter_PlantLeafClassification.pdf (date of the application 20.10.2021).
- D leaf tracking for plant growth monitoring / W. Gélard, A. Herbulot, M. Devy, P. Casadebaig // 2018 25th IEEE International Conference on Image Processing (ICIP, Athens, Greece, 7-10 Oct. 2018 / IEEE Systems, Man, and Cybernetics Society, Institute of Electrical and Electronics Engineers. – Piscataway, New Jersey, 2018: conference proceedings – URL: https://ieeexplore.ieee.org/abstract/document/8451553 (date of the application 20.10.2021).
- Plant Species Recognition Methods using Leaf Image: Overview / S. Zhang, W. Huang, Y. A. Approaches to three-dimensional reconstruction of plant shoot topology and geometry / J. A. Gibbs, M. Pound, A. P. French [et al.] // Functional Plant Biology. – 2017. – Vol. 44, №. 1. – P. 62-75.
- Huang, C. Zhang // Neurocomputing. – 2020. – Vol. 408. – P. 246-272.
- D reconstruction methods for digital preservation of cultural heritage: A survey / L. Gomes, O. R. P. Bellon, L. Silva // Pattern Recognition Letters. – 2014. – Vol. 50. – P. 3-14.
- Shape-from-shading: A survey [Text] / R. Zhang, P. S. Tsai, J. E. Cryer, M. Shah // IEEE Transactions on Pattern Analysis and Machine Intelligence/ IEEE Systems, Man, and Cybernetics Society, Institute of Electrical and Electronics Engineers. – Piscataway, New Jersey, 1999. – URL: https://ieeexplore.ieee.org/abstract/document/784284 (date of the application 26.06.2021).
- Shape-from-silhouette across time part i: Theory and algorithms / S. Baker, T. Kanade // International Journal of Computer Vision. – 2005. – Vol. 62, №. 3. – P. 221247.
- The visual hull: A new tool for contour-based image understanding / A. Laurentini // In Proceedings of the Seventh Scandinavian Conference on Image Analysis. – 1991. – Vol. 993. – P. 1002.
- A stochastic approach to stereo vision / S. T Barnard // Readings in Computer Vision. – Morgan Kaufmann, 1987. – P. 21-25.
- Cheprasov, D. E. Postroenie 3D modeli po neuporiadochennoi kollektsii izobrazhenii / D. E. Cheprasov // Fundamentalnaia informatika i informatsionnye tekhnologii: SPbGU. 2016. – P. 1-47.
- Scene reconstruction from multiple uncalibrated views / T. Kanade, M. Han // Carnegie Mellon University: Pittsburgh, USA. – 2000. – URL: http://www.tka4.org/materials/study/5%20sem/%23Spec%20Sem/Mat%20Metody%20Obrabotki%20Izobrajeniy/Doklad%202/h4.pdf (date of the application 26.06.2021).
Supplementary files
