Chinese Bulletin of Botany ›› 2025, Vol. 60 ›› Issue (6): 1-0.DOI: 10.11983/CBB25002 cstr: 32102.14.CBB25002
Huang Mengsha, Kong Lingdie, Yu Miao, Liu Chang, Wang Siqin, Wang Ruohan*
Received:
2025-01-09
Revised:
2025-03-27
Online:
2025-11-10
Published:
2025-05-07
Contact:
Ruohan Wang
Huang Mengsha, Kong Lingdie, Yu Miao, Liu Chang, Wang Siqin, Wang Ruohan. Development and Application of 3D Reconstruction Technology at Different Scales in Plant Research[J]. Chinese Bulletin of Botany, 2025, 60(6): 1-0.
[1]Andrea G-F, Stefan d F(2019).A Simple Protocol for Imaging Floral Tissues of Arabidopsis with Confocal Microscopy.Methods Mol Biol, 1932:187-195.[2]Arshad M A, 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, 0235.[3]Bernd Z, Stefan M, Günther Z(2022).Volumetric 3D reconstruction of plant leaf cells using SEM,ion milling,TEM,and serial sectioning.Planta, 255:118-118.[4]Besl P J, McKay N D(1992).A method for registration of 3-D shapes.IEEE Trans Pattern Anal Mach Intell, 14:239-256.[5]Bushby A J, P' ng K M Y, Young R D, Young R D, Pinali C, Knupp C, Quantock A J(2011).Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy.Nat Protoc, 6:845-858.[6]Cai JR, Liang XX, Xu Q, Xia ZY, Sun L, Ma LX(2024).X-ray three-dimensional reconstruction technology was used to detect the volumetric edibility of thick-skinned citrus.Transactions of the CSAE, 40:293-300.[7]蔡健荣, 梁小祥, 许骞, 夏中岩, 孙力, 马立鑫(2024).采用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.[8]Chen XJ(2015).Research on computer vision technology based on OpenCV.Computer Knowledge and Technology, 11:137-141.[9]陈雪娇(2015).基于的计算机视觉技术研究.电脑知识与技术,11(30):137-141.[10]Collevatti R G, Casta?eda M, Caminha S A F S, Jaramillo C(2024).Application of confocal laser microscopy for identification of modern and fossil pollen grains,an example in palm Mauritiinae.Rev Palaeobot Palynol, 327:105140-105140.[11]Cooley J W, Tukey J W(1965).An algorithm for the machine calculation of complex Fourier series.Math Comput, 19:297-301.[12]Crumpton-Taylor M, Grandison S, Png K M Y, Bushby A J, Smith A M(2012).Control of starch granule numbers in Arabidopsis chloroplasts.Plant Physiol, 158:905-916.[13]Cui Y, Cao W, He Y, Zhao Q, Wakazaki M, Zhuang XH, Gao JY, Zeng YL, Gao CJ, Ding Y, Wong HY, Wong WS, Lam H K, 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.[14]Davies H E, Wathen C G, Gleeson F V(2011).The risks of radiation exposure related to diagnostic imaging and how to minimise them.BMJ, 342:947-947.[15]Guo JS, Wang G, Xie L, Wang XQ, Feng LC, Guo WB, Tao XR, Humbel B M, Zhang ZK, Hong J ( 2022).Three-Dimensional Analysis of Membrane Structures Associated with Tomato Spotted Wilt Virus Infection. Plant Cell Environ 46(2).[17]Herppich W B, 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.[18]Herremans E, Melado-Herreros A, Defraeye T, Verlinden Bert, Hertog M, Verboven P, Val J, Fernández-Valle M E, Bongaers E, Estrade P, Wevers M, Barreiro P, Nicola? B M(2014).Comparison of X-ray CT and MRI of watercore disorder of different apple cultivars.Postharvest Biol Technol, 87:42-50.[19]Herremans E, Verboven P, Verlinden B E, Cantre D, Abera M, Wevers M, Nicola? B M(2015).Automatic analysis of the 3-D microstructure of fruit parenchyma tissue using X-ray micro-CT explains differences in aeration.BMC Plant Biol, 264.[20]Heymann J A W, Hayles M, Gestmann I, Giannuzzi L A, Lich B, Subramaniam S(2006).Site-specific 3D imaging of cells and tissues with a dual beam microscope.J Struct Biol, 155:63-73.[21]House A, Balkwill K(2013).FIB-SEM: An Additional Technique for Investigating Internal Structure of Pollen Walls.Microsc Microanal, 19:1535-1541.[22]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.[23]Jackson M D B, Xu H, Duran-Nebreda S, Stamm P, Bassel G W(2017).Topological analysis of multicellular complexity in the plant hypocotyl.ELife, 6.[24]Janes G, Daniel v W, Cowling S, Kerr I, Band L, French A P, Bishopp A(2018).Cellular Patterning of Arabidopsis Roots Under Low Phosphate Conditions.Front Plant Sci, 735.[25]Janssen S, Verboven P, Nugraha B, Boone M, Josipovic I, Nicola? B M(2020).D pore structure analysis of intact ‘Braeburn’ apples using X-ray micro-CT.Postharvest Biol Tec, 159:111014-111014.[26]Jin D, Zhou RJ, Yaqoob Z, So P T C(2017).Tomographic phase microscopy: principles and applications in bioimaging [Invited].J Opt Soc Am B, 34:64-77.[27]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-UK, 8:-.[28]Kim K, Chung J M, Lee S, Jung H S(2015).The Effects of Electron Beam Exposure Time on Transmission Electron Microscopy Imaging of Negatively Stained Biological Samples.Appl Microsc, 45:150-154.[29]Leo S, Sovanna T, Sarah R, Langdale J A(2022).Flip-Flap: A Simple Dual-View Imaging Method for 3D Reconstruction of Thick Plant Samples.Plants, 11:506-506.[30]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, (04):33-38.[31]李亮, 陈志强, 张丽, 邢宇翔(2006).潘晓川教授的反投影滤波新型重建算法介绍.理论与应用研究, (03):68-73.[32]李青, 李润睿, 强彦, 成煜斌, 王涛(2023).人工智能在医学图像重建中的研究进展.太原理工大学学报, 54:1-16.[33]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.[34]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, :169-176.[35]Looverbosch T V D, Bhuiyan M H R, Verboven P, Dierick M, Loo D V, Beenbouwer J D, Sijbers J, Nicola? B(2020).Nondestructive internal quality inspection of pear fruit by X-ray CT using machine learning.Food Control, 113:107170-107170.[36]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, 25-29.[37]Luo LY, Jiang XT, Yang Y, Samy E R A, Lefsrud M, HoyosV V, Sun SP(2023).Eff-3DPSeg: 3D Organ-Level Plant Shoot Segmentation Using Annotation-Efficient Deep Learning.Plant phenomics, 5:0080-0080.[38]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1-101.[39]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).D reconstruction and multi-omics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.Plant, Physiol.[40]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, 98-110..,:-.[41]Maizel A, Daniel v W, Federici F, Haseloff J, Stelzer E H K(2011).High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy.Plant J, 68(2):377-385.[42]Masters B R, Gonzalez R C, Woods R(2009).Book Review: Digital Image Processing,Third Edition.J Biomed Opt, 029901..,:-.[43]Masyutin A G, Tarasova E K, Onishchenko G E, Erokhina M V(2023).Identifying Carbon Nanoparticles in Biological Samples by Means of Transmission Electron Microscopy.Bull Russ Acad Sci Phys, 87(10):1443-1448.[44]Mathilde H, Christine A, Daniel W, PierreEmmanuel C(2022).Imaging plant tissues: advances and promising clearing practices.Trends Plant Sci, 27(6):601-615.[45]Montenegro-Johnson T D, Stamm P, Strauss S, Topham A T, Tsagris M, Wood A T A, Smith R S, Bassel G W(2015).Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas.Plant Cell, 27(4):1018-1033.[46]Morisset J-B, 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.[47]Nugraha B, Verboven P, Janssen S, Wang Z, Nicola? B M(2019).Non-destructive porosity mapping of fruit and vegetables using X-ray CT.Postharvest Biol Tech, 150:80-88.[48]Ove?ka M, Ji?í S, Michaela T, George K, Jasim B, Cintia M, ?amajová O, Kuběnová L, ?amaj J(2022).Imaging plant cells and organs with light-sheet and super-resolution microscopy.Plant Physiol, 188(2):683-702.[49]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. 1-123.[50]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, 271:153639-153639.[51]Roberts L G (2022).Machine Perception of Three-Dimensional Solids.[52]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.1-124.[53]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.[54]Silveira S R, Le G C, GómezFelipe A, RoutierKierzkowska A, Kierzkowski D(2021).Live-imaging provides an atlas of cellular growth dynamics in the stamen.Plant physiol, 188(2):769-781.[55]Stevens K(2014).The Vision of David Marr.Perception, 41:1061-1072.[56]Takashi I, Shin Y, Hideo Y, Takeo I(2014).Flower modeling via X-ray computed tomography.ACM Trans Graphics, 33(4):1-10.[57]Tian G, Feiyu Z, Puneet P, Jaspreet Sandhu, Akrofi D H, Sun JX, Yu Pan, Paul S, Harkamal W, Yu HF (2021).Novel 3D Imaging Systems for High-Throughput Phenotyping of Plants. Remote Sens-Basel 13(11) 2113-2113.[58]Tracy S R, Gomez J F, Sturrock C J, Wilson Z A, Ferguson A C(2017).Non-destructive determination of floral staging in cereals using X-ray micro computed tomography (μCT).Plant Methods, 13.[59]Trueba S, Theroux-Rancourt G, Earles J M, Buckley T N, Love D, Johnson D M, Brodersen C(2022).The three-dimensional construction of leaves is coordinated with water use efficiency in conifers.New Phytol, 233(2):851-861.[60]Truernit E, Bauby H, Dubreucq B, Grandjean O, Runions J, Barthélémy J, Palauqui J C(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(6):1494-1503.[61]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, 66-71.[62]Wang Q, Huang YG, Ren Z J, Zhang XX, Ren J, Su JQ, Zhang C, Tian J, Yu YJ, Gao G F, Li LG, Kong Z S(2020).Transfer cells mediate nitrate uptake to control root nodule symbiosis.Nat Plants, 6(7):800-808.[63]Wei D, Jacobs S, Modla S, Zhang S, Young C L, 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(1):41-48.[64]Wen WL, Wang JL, Zhao YX, Wang CY, Liu K, Chen B, Wang YQ, Duan MX, Guo XY(2024).D Morphological Feature Quantification and Analysis of Corn Leaves.Plant Phenomics, 0225.[65]吴迪(2019).基于-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. 1-128.[66]Xiao Z, StaitGardner T, Willis S A, Price W S, Moroni F J, Pagay V, Tyerman S D, Schmidtke L M, Rogiers S Y(2021).D visualisation of voids in grapevine flowers and berries using X‐ray micro computed tomography.Aust J Grape Wine Res, 27(2):141-148.[67]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.[68]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.[69]Zhang X, Man Y, Zhuang XH, Shen J B, Zhang Y, Cui Y N, Yu M, Xing JJ, Wang GC, Lian N, Hu Z J, Ma L Y, 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(09):1392-1422.[70]Zhu YY(2023).D Reconstruction of Ancient Building Structure Scene Based on Computer Image Recognition.Int J Inf Technol Sy, 16(3).[71]Zi W, Pieter V, Bart N(2017).Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques.Plant Methods,105. |
[1] |
Xiao Wang, Changwen Xu, Hongping Qian, Sibo Li, Jinxing Lin, Yaning Cui.
Mechanisms of Plant Cell Wall Involvement in the Immune Response and its in situ non-labelled Imaging Technique [J]. Chinese Bulletin of Botany, 2025, 60(5): 1-0. |
[2] | Tao Xie, Yifan Zhang, Yunhui Liu, Huiyu You, Jibenben Xia, Rong Ma, Chunni Zhang, Xuejun Hua. Research Progress on the Iron-sulfur Cluster Synthesis System and Regulation in Plant Mitochondria [J]. Chinese Bulletin of Botany, 2025, 60(4): 499-514. |
[3] | Xiong Lianglin, Liang Guolu, Guo Qigao, Jing Danlong. Advances in the Regulation of Alternative Splicing of Genes in Plants in Response to Abiotic Stress [J]. Chinese Bulletin of Botany, 2025, 60(3): 435-448. |
[4] | Jing Xuan, Qidi Fu, Gan Xie, Kai Xue, Hairui Luo, Ze Wei, Mingyue Zhao, Liang Zhi, Huawei Wan, Jixi Gao, Min Li. An Artificial Intelligence Model for Identifying Grassland Plants in Northern China [J]. Chinese Bulletin of Botany, 2025, 60(1): 74-80. |
[5] | Yan Deng, Limin Lu, Qiang Zhang, Zhiduan Chen, Haihua Hu. A Comprehensive Evaluation of the Plastid DNA Data Gaps of Vascular Plants in Species and Geographic Area [J]. Chinese Bulletin of Botany, 2025, 60(1): 1-16. |
[6] | Chunjiao Xia, Yunguang Li, Shu Xia, Wei Pang, Chunli Chen. Flow Cytometric Analysis and Sorting in Plant Genomics [J]. Chinese Bulletin of Botany, 2024, 59(5): 774-782. |
[7] | Jiahang Che, Weinan Li, Yingzhi Qin, Jinhuan Chen. Research Progress of Leaf Color Variation Mechanism in Woody Plants [J]. Chinese Bulletin of Botany, 2024, 59(2): 319-328. |
[8] | Lansha Luo, Wenpei Song, Qingzhu Hua, Dawei Li, Hong Liang, Xianzhi Zhang. Research Progress on Plant Sex-determination Genes and Their Epigenetic Regulation [J]. Chinese Bulletin of Botany, 2024, 59(2): 278-290. |
[9] | Yi Li, Xi Zhang, Yanhui Yuan, Pichang Gong, Jinxing Lin. Aptamers and Their Applications in Plant Science Researches [J]. Chinese Bulletin of Botany, 2023, 58(6): 935-945. |
[10] | Hao Xuefeng, Wu Zhangjing, Ma Tian, Jin Zhuping, Pei Yanxi. Alternative Splicing of Plant Genes: Full of Change, Sail with Wind [J]. Chinese Bulletin of Botany, 2022, 57(5): 661-672. |
[11] | He Xiaoling, Liu Pengcheng, Ma Bojun, Chen Xifeng. Advance in Gene-editing Technology Based on CRISPR/Cas9 and Its Application in Plants [J]. Chinese Bulletin of Botany, 2022, 57(4): 508-531. |
[12] | Qian Luo, Yansha Zhang, Jing Ou. Callus Induction and Plant Regeneration of Cerasus serrulata var. lannesiana cv. ‘Grandiflora’ [J]. Chinese Bulletin of Botany, 2021, 56(4): 451-461. |
[13] | Yanmin Li, Hui Jiang, Zhenzhu Fu, Jing Zhang, Xin Yuan, Huijuan Wang, Jie Gao, Xiaoyu Dong, Limin Wang, Hechen Zhang. Callus Induction and Somatic Embryogenesis in Anther Culture of Paeonia lactiflora [J]. Chinese Bulletin of Botany, 2021, 56(4): 443-450. |
[14] | Binbin Hu, Zhihui Xue, Cui Zhang. Protocols for Small RNA FISH in Plants [J]. Chinese Bulletin of Botany, 2021, 56(3): 330-338. |
[15] | Jing Li,Liang Guo,Haixin Cui,Bo Cui,Guoqiang Liu. Research Progress on Uptake and Transport of Nanopesticides in Plants [J]. Chinese Bulletin of Botany, 2020, 55(4): 513-528. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||