Development and Application of 3D Reconstruction Technology at Different Scales in Plant Research
Received date: 2025-01-09
Accepted date: 2025-04-02
Online published: 2025-05-07
3D reconstruction technology involves using computer graphics and image processing technologies to extract the geometric and topological information of the target object from the two-dimensional image data. This information is then used to create a three-dimensional mathematical model that can be processed by a computer, enabling the virtual reconstruction of the target object. In plant science research, the construction of three-dimensional models has become an effective way to study plant growth and development, morphological structure and functional mechanism. These models provide robust support for multi-scale imaging, measurement and analysis, demonstrating significant application potential in the field of agriculture and forestry. In recent years, advancements in plant 3D reconstruction technology have led to diverse applications in botanical research, covering plant morphological structure modeling, growth and development dynamic monitoring, and plant breeding. In this paper, we summarize the development process of 3D reconstruction technology and its application in plant studies across different scales (from organs and tissues to cells). We focus on the basic principles and applications of these technologies, aiming to provide theoretical and technical support for multimodal cross-scale imaging and plant phenotypic and functional research. Additionally, this work offers a novel approach to understand the principles of plant growth and development and the mechanisms underlying their responses to environmental changes.
Key words: 3D reconstruction; different scales; imaging techniques; models; plants
Mengsha Huang , Lingdie Kong , Miao Yu , Chang Liu , Siqin Wang , Ruohan Wang . Development and Application of 3D Reconstruction Technology at Different Scales in Plant Research[J]. Chinese Bulletin of Botany, 2025 , 60(6) : 1005 -1016 . DOI: 10.11983/CBB25002
| [1] | Arshad MA, Jubery T, Afful J, Jignasu A, Balu A, Ganapathysubramanian B, Sarkar S, Krishnamurthy A (2024). Evaluating neural radiance fields for 3D plant geometry reconstruction in field conditions. Plant Phenomics 6, 0235. |
| [2] | Besl PJ, McKay ND (1992). A method for registration of 3-D shapes. IEEE Trans Pattern Anal Mach Intell 14, 239-256. |
| [3] | Bushby AJ, P'Ng KMY, Young RD, Pinali C, Knupp C, Quantock AJ (2011). Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy. Nat Protoc 6, 845-858. |
| [4] | Cai JR, Liang XX, Xu Q, Xia ZY, Sun L, Ma LX (2024). Detecting volumetric edible rate of thick-skinned citrus using X-ray three-dimensional reconstruction. Trans Chin Soc Agric Eng 40, 293-300. (in Chinese) |
| 蔡健荣, 梁小祥, 许骞, 夏中岩, 孙力, 马立鑫 (2024). 采用X射线三维重构技术检测厚皮柑橘的体积可食率. 农业工程学报 40, 293-300. | |
| [5] | Chen XJ (2015). Research on computer vision technology based on OpenCV. Comput Knowl Technol 11(30), 137-138, 141. (in Chinese) |
| 陈雪娇 (2015). 基于OpenCV的计算机视觉技术研究. 电脑知识与技术 11(30), 137-138, 141. | |
| [6] | Collevatti RG, Casta?eda M, Silva-Caminha SAF, Jaramillo C (2024). Application of confocal laser microscopy for identification of modern and fossil pollen grains, an example in palm Mauritiinae. Rev Palaeobot Palynol 327, 105140. |
| [7] | Cooley JW, Tukey JW (1965). An algorithm for the machine calculation of complex Fourier series. Math Comput 19, 297-301. |
| [8] | Crumpton-Taylor M, Grandison S, Png KMY, Bushby AJ, Smith AM (2012). Control of starch granule numbers in Arabidopsis chloroplasts. Plant Physiol 158, 905-916. |
| [9] | Cui Y, Cao WH, He YL, Zhao Q, Wakazaki M, Zhuang XH, Gao JY, Zeng YL, Gao CJ, Ding Y, Wong HY, Wong WS, Lam HK, Wang PF, Ueda T, Rojas-Pierce M, Toyooka K, Kang BH, Jiang LW (2019). A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells. Nat Plants 5, 95-105. |
| [10] | Davies HE, Wathen CG, Gleeson FV (2011). The risks of radiation exposure related to diagnostic imaging and how to minimise them. BMJ 342, d947. |
| [11] | Drummy LF, Yang JY, Martin DC (2004). Low-voltage electron microscopy of polymer and organic molecular thin films. Ultramicroscopy 99, 247-256. |
| [12] | Du Z, Hu YG, Ali Buttar N, Mahmood A (2019). X-ray computed tomography for quality inspection of agricultural products: a review. Food Sci Nutr 7, 3146-3160. |
| [13] | Fink S (2006). The use of laser scanning confocal microscopy in the study of wound healing phenomena in plants. Isr J Plant Sci 54, 265-271. |
| [14] | Gao T, Zhu FY, Paul P, Sandhu J, Doku HA, Sun JX, Pan Y, Staswick P, Walia H, Yu HF (2021). Novel 3D imaging systems for high-throughput phenotyping of plants. Remote Sens 13, 2113. |
| [15] | Gómez-Felipe A, de Folter S (2019). A simple protocol for imaging floral tissues of Arabidopsis with confocal microscopy. In: de Folter, ed. Plant MicroRNAs. New York: Humana Press. pp. 187-195. |
| [16] | Guo JS, Wang G, Xie L, Wang XQ, Feng LC, Guo WB, Tao XR, Humbel BM, Zhang ZK, Hong J (2023). Three-dimensional analysis of membrane structures associated with tomato spotted wilt virus infection. Plant Cell Environ 46, 650-664. |
| [17] | He YP, Zhou NS, Ziemczonok M, Wang YJ, Lei L, Duan LT, Zhou RJ (2023). Standardizing image assessment in optical diffraction tomography. Opt Lett 48, 395-398. |
| [18] | Hériché M, Arnould C, Wipf D, Courty PE (2022). Imaging plant tissues: advances and promising clearing practices. Trends Plant Sci 27, 601-615. |
| [19] | Herppich WB, Matsushima U, Graf W, Zabler S, Dawson M, Choinka G, Manke I (2015). Synchrotron X-ray CT of rose peduncles-evaluation of tissue damage by radiation. Mater Test 57, 59-63. |
| [20] | Herremans E, Melado-Herreros A, Defraeye T, Verlinden B, Hertog M, Verboven P, Val J, Fernández-Valle ME, Bongaers E, Estrade P, Wevers M, Barreiro P, Nicola? BM (2014). Comparison of X-ray CT and MRI of watercore disorder of different apple cultivars. Postharvest Biol Technol 87, 42-50. |
| [21] | Herremans E, Verboven P, Verlinden BE, Cantre D, Abera M, Wevers M, Nicola? BM (2015). Automatic analysis of the 3-D microstructure of fruit parenchyma tissue using X-ray micro-CT explains differences in aeration. BMC Plant Biol 15, 264. |
| [22] | Heymann JAW, Hayles M, Gestmann I, Giannuzzi LA, Lich B, Subramaniam S (2006). Site-specific 3D imaging of cells and tissues with a dual beam microscope. J Struct Biol 155, 63-73. |
| [23] | House A, Balkwill K (2013). FIB-SEM: an additional technique for investigating internal structure of pollen walls. Microsc Microanal 19, 1535-1541. |
| [24] | Hu ZJ, Liu JZ, Shen SY, Wu WQ, Yuan JB, Shen WW, Ma LY, Wang GC, Yang SY, Xu XP, Cui YN, Li ZC, Shen LJ, Li LL, Bian JH, Zhang X, Han H, Lin JX (2024). Large-volume fully automated cell reconstruction generates a cell atlas of plant tissues. Plant Cell 36, 4840-4861. |
| [25] | Ijiri T, Yoshizawa S, Yokota H, Igarashi T (2014). Flower modeling via X-ray computed tomography. ACM Trans Graphics 33, 48. |
| [26] | Jackson MDB, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017). Topological analysis of multicellular complexity in the plant hypocotyl. eLife 6, e26023. |
| [27] | Janes G, Von Wangenheim D, Cowling S, Kerr I, Band L, French AP, Bishopp A(2018). Cellular patterning of Arabidopsis roots under low phosphate conditions. Front Plant Sci 9, 735. |
| [28] | Janssen S, Verboven P, Nugraha B, Wang Z, Boone M, Josipovic I, Nicola? BM (2020). 3D pore structure analysis of intact ‘Braeburn’ apples using X-ray micro-CT. Postharvest Biol Technol 159, 111014. |
| [29] | Jia X, Sun F, Ji G (2022). Advances in cryo-focused ion beam-scanning electron microscopy imaging technology. Chin Bull Bot 57, 24-29. (in Chinese) |
| 贾星, 孙飞, 季刚 (2022). 冷冻聚焦离子束-扫描电镜成像技术研究进展. 植物学报 57, 24-29. | |
| [30] | Jiang ZG (2016). How many species are there on Earth? Chin Sci Bull 61, 2337-2343. (in Chinese) |
| 蒋志刚 (2016). 地球上有多少物种? 科学通报 61, 2337-2343. | |
| [31] | Jin D, Zhou RJ, Yaqoob Z, So PTC (2017). Tomographic phase microscopy: principles and applications in bioimaging. J Opt Soc Am B 34, B64-B77. |
| [32] | Karahara I, Yamauchi D, Uesugi K, Mineyuki Y (2023). Three-dimensional visualization of plant tissues and organs by X-ray micro-computed tomography. Microscopy (Oxf) 72, 310-325. |
| [33] | Katsevich A (2002). Analysis of an exact inversion algorithm for spiral cone-beam CT. Phys Med Biol 47, 2583-2597. |
| [34] | Kim G, Lee S, Shin S, Park Y (2018). Three-dimensional label-free imaging and analysis of Pinus pollen grains using optical diffraction tomography. Sci Rep 8, 1782. |
| [35] | Kim K, Chung JM, Lee S, Jung HS (2015). The effects of electron beam exposure time on transmission electron microscopy imaging of negatively stained biological samples. Appl Microsc 45, 150-154. |
| [36] | Li CH, Tian YF, Yan SG (2020). Laser scanning confocal microscopy technology and application. Exp Sci Technol 18(4), 33-38. (in Chinese) |
| 李成辉, 田云飞, 闫曙光 (2020). 激光扫描共聚焦显微成像技术与应用. 实验科学与技术 18(4), 33-38. | |
| [37] | Li DX (2004). New progress in transmission electron microscopy I. Development and application of transmission electron microscopy and related components. J Chin Electron Microsc Soc 3, 269-277. (in Chinese) |
| 李斗星 (2004). 透射电子显微学的新进展I. 透射电子显微镜及相关部件的发展及应用. 电子显微学报 3, 269-277. | |
| [38] | Li L, Chen ZQ, Zhang L, Xing YX (2006). Xiaochuan Pan’s new BPF-type algorithms for computed tomography image reconstruction. CT Theory Appl 15(3), 68-73. (in Chinese) |
| 李亮, 陈志强, 张丽, 邢宇翔 (2006). 潘晓川教授的反投影滤波(BPF)新型重建算法介绍. CT理论与应用研究 15 (3), 68-73. | |
| [39] | Li Q, Li RR, Qiang Y, Cheng YB, Wang T (2023). Research and progress of artificial intelligence in medical CT image reconstruction. J Taiyuan Univ Technol 54, 1-16. (in Chinese) |
| 李青, 李润睿, 强彦, 成煜斌, 王涛 (2023). 人工智能在医学CT图像重建中的研究进展. 太原理工大学学报 54, 1-16. | |
| [40] | Li XX, Ji G, Chen X, Ding W, Sun L, Xu W, Han H, Sun F (2017). Large scale three-dimensional reconstruction of an entire Caenorhabditis elegans larva using AutoCUTS- SEM. J Struct Biol 200, 87-96. |
| [41] | Li Y, Huang HP, Lin PQ, Cui YM, Li QF, Zheng YQ (2015). The fundamentals and techniques in laser scanning confocal microscopy. J Chin Electron Microsc Soc 34, 169-176. (in Chinese) |
| 李叶, 黄华平, 林培群, 崔艳梅, 李勤奋, 郑勇奇 (2015). 激光扫描共聚焦显微镜的基本原理及其使用技巧. 电子显微学报 34, 169-176. | |
| [42] | Lu J, Meng GL, Yu LZ (2023). Imaging techniques and application of super-resolution laser scanning confocal microscope. Exp Sci Technol 21, 25-29. (in Chinese) |
| 路姣, 孟国龙, 余凌竹 (2023). 超高分辨率激光扫描共聚焦显微镜的成像技术与应用. 实验科学与技术 21, 25-29. | |
| [43] | Luo LY, Jiang XT, Yang Y, Samy ERA, Lefsrud M, Hoyos-Villegas V, Sun SP (2023). Eff-3DPSeg: 3D organ-level plant shoot segmentation using annotation-effi-cient deep learning. Plant Phenomics 5, 0080. |
| [44] | Ma LY (2021). Multiscale 3D Reconstruction of Ginkgo Biloba Embryo and Arabidopsis Thaliana Seed. PhD dissertation. Beijing: Beijing Forestry University. pp. 1-101. (in Chinese) |
| 马灵玉 (2021). 银杏种胚和拟南芥种子多尺度三维重构研究. 博士论文. 北京: 北京林业大学. pp. 1-101. | |
| [45] | Ma LY, Hu ZJ, Shen WW, Zhang YY, Wang GC, Chang B, Lu JK, Cui YN, Xu HM, Feng Y, Jin B, Zhang X, Wang L, Lin JX (2024). Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba. Plant Physiol 196, 95-111. |
| [46] | Ma LY, Qi XH, Hu ZJ, Shen WW, Wang GC, Zhang BL, Zhang X, Lin JX (2022). Applications of optical clearing technique in multi-scale imaging. Chin Bull Bot 57, 98-110. (in Chinese) |
| 马灵玉, 祁晓红, 胡子建, 沈微微, 王广超, 张柏林, 张曦, 林金星 (2022). 光学透明技术在植物多尺度成像中的应用. 植物学报 57, 98-110. | |
| [47] | Maizel A, Von Wangenheim D, Federici F, Haseloff J, Stelzer EHK (2011). High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy. Plant J 68, 377-385. |
| [48] | Masters BR, Gonzalez RC, Woods R (2009). Book review: digital image processing, third edn. J Biomed Opt 14, 029901. |
| [49] | Masyutin AG, Tarasova EK, Onishchenko GE, Erokhina MV (2023). Identifying carbon nanoparticles in biological samples by means of transmission electron microscopy. Bull Russ Acad Sci Phys 87, 1443-1448. |
| [50] | Montenegro-Johnson TD, Stamm P, Strauss S, Topham AT, Tsagris M, Wood ATA, Smith RS, Bassel GW (2015). Digital single-cell analysis of plant organ development using 3D Cell Atlas. Plant Cell 27, 1018-1033. |
| [51] | Morisset JB, Mothe F, Colin F (2012). Observation of Quercus petraea epicormics with X-ray CT reveals strong pith-to-bark correlations: silvicultural and ecological implications. Forest Ecol Manag 278, 127-137. |
| [52] | Nugraha B, Verboven P, Janssen S, Wang Z, Nicola? BM (2019). Non-destructive porosity mapping of fruit and vegetables using X-ray CT. Postharvest Biol Technol 150, 80-88. |
| [53] | Ove?ka M, Sojka J, Tichá M, Komis G, Basheer J, Marchetti C, ?amajová O, Kuběnová L, ?amaj J (2022). Imaging plant cells and organs with light-sheet and super-resolution microscopy. Plant Physiol 188, 683-702. |
| [54] | Piovesan A, Vancauwenberghe V, Van De Looverbosch T, Verboven P, Nicola? B (2021). X-ray computed tomography for 3D plant imaging. Trends Plant Sci 26, 1171-1185. |
| [55] | Qi XH (2022). Multiscale 3D Reconstruction, Metabolism and Transcriptome Analysis of Ulmus Pumila Seeds During Late-maturation Stage. PhD dissertation. Beijing: Beijing Forestry University. pp. 1-123. (in Chinese) |
| 祁晓红 (2022). 榆树种子发育后期多尺度三维重构及代谢和转录组分析研究. 博士论文. 北京: 北京林业大学. pp. 1-123. | |
| [56] | Qi XH, Chen LL, Hu ZJ, Shen WW, Xu HM, Ma LY, Wang GC, Jing YP, Wang XD, Zhang BL, Lin JX (2022). Cytology, transcriptomics, and mass spectrometry imaging reveal changes in late-maturation elm (Ulmus pumila) seeds. J Plant Physiol 271, 153639. |
| [57] | Roberts LG (1963). Machine Perception of Three-dimensional Solids. PhD dissertation. Cambridge: Massachusetts Institute of Technology. pp. 1-82. |
| [58] | Serra L, Tan S, Robinson S, Langdale JA (2022). Flip- Flap: a simple dual-view imaging method for 3D reconstruction of thick plant samples. Plants 11, 506. |
| [59] | Shen RH (2021). New Methods for Three-dimensional Reconstruction in the Transmission Electron Microscope. PhD dissertation. Changsha: Hunan University. pp. 1-124. (in Chinese) |
| 沈若涵 (2021). 透射电子显微镜中的三维重构新方法. 博士论文. 长沙: 湖南大学. pp. 1-124. | |
| [60] | Shi BR, Huang XP, Fu XL, Wang BJ (2022). Advances in the plant multicellular network analysis. Chin J Biotechnol 38, 2798-2810. (in Chinese) |
| 施般若, 黄小萍, 付秀荣, 王邦俊 (2022). 植物多细胞网络分析研究进展. 生物工程学报 38, 2798-2810. | |
| [61] | Silveira SR, Le Gloanec C, Gómez-Felipe A, Routier-Kierzkowska AL, Kierzkowski D (2022). Live-imaging provides an atlas of cellular growth dynamics in the stamen. Plant Physiol 188, 769-781. |
| [62] | Stevens KA (2012). The vision of David Marr. Perception 41, 1061-1072. |
| [63] | Tracy SR, Gómez JF, Sturrock CJ, Wilson ZA, Ferguson AC (2017). Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (μCT). Plant Methods 13, 9. |
| [64] | Trueba S, Théroux-Rancourt G, Earles JM, Buckley TN, Love D, Johnson DM, Brodersen C (2022). The three- dimensional construction of leaves is coordinated with water use efficiency in conifers. New Phytol 233, 851-861. |
| [65] | Truernit E, Bauby H, Dubreucq B, Grandjean O, Runions J, Barthélémy J, Palauqui JC (2008). High-resolution whole-mount imaging of three-dimensional tissue organization and gene expression enables the study of phloem development and structure in Arabidopsis. Plant Cell 20, 1494-1503. |
| [66] | Van De Looverbosch T, Bhuiyan MHR, Verboven P, Dierick M, Van Loo D, De Beenbouwer J, Sijbers J, Nicola? B (2020). Nondestructive internal quality inspection of pear fruit by X-ray CT using machine learning. Food Control 113, 107170. |
| [67] | Wang J, Wang J, Guo J, Feng Y, Li XX, Zhang JG, Jiang XM, Yin YF, Li S (2022). The three-dimensional structure of bordered pit in xylem of Cedrus deodara base on focused ion beam scanning electron microscopy. J Chin Electron Microsc Soc 41, 66-71. (in Chinese) |
| 王静, 王杰, 郭娟, 冯韵, 李喜霞, 张建国, 姜笑梅, 殷亚方, 李姗 (2022). 基于聚焦离子束-扫描电子显微技术的雪松木质部具缘纹孔三维重构. 电子显微学报 41, 66-71. | |
| [68] | Wang Q, Huang YG, Ren ZJ, Zhang XX, Ren J, Su JQ, Zhang C, Tian J, Yu YJ, Gao GF, Li LG, Kong ZS (2020). Transfer cells mediate nitrate uptake to control root nodule symbiosis. Nat Plants 6, 800-808. |
| [69] | Wang Z, Herremans E, Janssen S, Cantre D, Verboven P, Nicola? B (2018). Visualizing 3D food microstructure using tomographic methods: advantages and disadvantages. Annu Rev Food Sci Technol 9, 323-343. |
| [70] | Wang Z, Verboven P, Nicolai B (2017). Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques. Plant Methods 13, 105. |
| [71] | Wei DG, Jacobs S, Modla S, Zhang S, Young CL, Cirino R, Caplan J, Czymmek K (2012). High-resolution three- dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy. BioTechniques 53, 41-48. |
| [72] | Wen WL, Wang JL, Zhao YX, Wang CY, Liu K, Chen B, Wang YQ, Duan MX, Guo XY (2024). 3D morphological feature quantification and analysis of corn leaves. Plant Phenomics 6, 0225. |
| [73] | Wu D (2019). Nondestructive Extraction of Rice Tiller Traits Based on Micro-CT. PhD dissertation. Wuhan: Huazhong Agricultural University. pp. 1-128. (in Chinese) |
| 吴迪 (2019). 基于Micro-CT的水稻茎部性状无损提取关键技术研究. 博士论文. 武汉: 华中农业大学. pp. 1-128. | |
| [74] | Xiao Z, Stait-Gardner T, Willis SA, Price WS, Moroni FJ, Pagay V, Tyerman SD, Schmidtke LM, Rogiers SY (2021). 3D visualisation of voids in grapevine flowers and berries using X-ray micro computed tomography. Aust J Grape Wine Res 27, 141-148. |
| [75] | Yamakawa S, Kato Y, Taniguchi M, Oi T (2023). Intracellular positioning of mesophyll chloroplasts following to aggregative movement in Setaria viridis analysed three- dimensionally with a confocal laser scanning microscope. Flora 306, 152364. |
| [76] | Zechmann B, M?stl S, Zellnig G (2022). Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning. Planta 255, 118. |
| [77] | Zhang K, Zhang Y, Hu ZJ, Ji G, Sun F (2010). Development and frontier of electron microscopy 3D reconstruction. Acta Biophys Sin 26, 533-559. (in Chinese) |
| 张凯, 张艳, 胡仲军, 季刚, 孙飞 (2010). 电子显微三维重构技术发展与前沿. 生物物理学报 26, 533-559. | |
| [78] | Zhang X, Man Y, Zhuang XH, Shen JB, Zhang Y, Cui YN, Yu M, Xing JJ, Wang GC, Lian N, Hu ZJ, Ma LY, Shen WW, Yang SY, Xu HM, Bian JH, Jing YP, Li XJ, Li RL, Mao TL, Jiao YL, Sodmergen, Ren HY, Lin JX (2021). Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. Sci China Life Sci 64, 1392-1422. |
| [79] | Zhou N, Sun JS, Zhang RN, Ye R, Li JJ, Bai ZD, Zhou S, Chen Q, Zuo C (2023). Quasi-isotropic high-resolution Fourier ptychographic diffraction tomography with opposite illuminations. ACS Photonics 10, 2461-2466. |
| [80] | Zhu YY (2023). 3D reconstruction of ancient building structure scene based on computer image recognition. Int J Inf Technol Syst Approach 16, 1-14. |
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