Development and Application of 3D Reconstruction Technology at Different Scales in Plant Research

doi:10.11983/CBB25002

Abstract

Abstract: 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.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB25002

https://www.chinbullbotany.com/EN/Y2025/V60/I6/1005

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References 80

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尺度	植物物种	方法	应用部位	参考文献
器官	水稻(Oryza sativa)	Micro-CT	茎	吴迪, 2019
	银杏(Ginkgo biloba)、拟南芥(Arabidopsis thaliana)和榆树(Ulmus pumila)	Micro-CT、LSFM、Auto CUTS-SEM和X-CT	种子	马灵玉, 2021; 祁晓红, 2022; Ma et al., 2024
	柑橘(Citrus reticulata ‘Bu Zhi Huo’)、苹果(Malus pumila)、梨(Pyrus spp.)、茄子(Solanum melongena)、萝卜(Raphanus sativus)和葡萄(Vitis vinifera)	X-CT	果实	Herremans et al., 2014; Nugraha et al., 2019; Janssen et al., 2020; Van de Looverbosch et al., 2020; 蔡健荣等, 2024
	拟南芥(A. thaliana)和大麦(Hordeum vulgare)	X-CT	花	Ijiri et al., 2014; Tracy et al., 2017; Xiao et al., 2021
组织	雪松(Cedrus deodara)、苹果(M. pumila)和月季(Rosa hybrida)	FIB-SEM和X-CT	输导组织	Herppich et al., 2015; Herremans et al., 2015; Nugraha et al., 2019; 王静等, 2022
	拟南芥(A. thaliana)	CLSM	分生组织	Gómez-Felipe and de Folter, 2019
	橡树(Quercus palustris)	X-CT	保护组织	Morisset et al., 2012
	橡树(Q. palustris)	CLSM和X-CT	营养组织	Fink, 2006; Morisset et al., 2012
细胞	拟南芥(A. thaliana)、狗尾草(Setaria viridis)、青杄(Picea wilsonii)、红松(Pinus densiflora)和黑松(P. thunbergii)	ODT、ssTEM、 FIB-SEM和CLSM	叶肉细胞、花粉粒细胞、下胚轴细胞和雄蕊细胞	Jackson et al., 2017; Kim et al., 2018; Cui et al., 2019; Wang et al., 2020; Silveira et al., 2022; Zechmann et al., 2022; Guo et al., 2023; Yamakawa et al., 2023; Collevatti et al., 2024; Hu et al., 2024

尺度	植物物种	方法	应用部位	参考文献
器官	水稻(Oryza sativa)	Micro-CT	茎	吴迪, 2019
	银杏(Ginkgo biloba)、拟南芥(Arabidopsis thaliana)和榆树(Ulmus pumila)	Micro-CT、LSFM、Auto CUTS-SEM和X-CT	种子	马灵玉, 2021; 祁晓红, 2022; Ma et al., 2024
	柑橘(Citrus reticulata ‘Bu Zhi Huo’)、苹果(Malus pumila)、梨(Pyrus spp.)、茄子(Solanum melongena)、萝卜(Raphanus sativus)和葡萄(Vitis vinifera)	X-CT	果实	Herremans et al., 2014; Nugraha et al., 2019; Janssen et al., 2020; Van de Looverbosch et al., 2020; 蔡健荣等, 2024
	拟南芥(A. thaliana)和大麦(Hordeum vulgare)	X-CT	花	Ijiri et al., 2014; Tracy et al., 2017; Xiao et al., 2021
组织	雪松(Cedrus deodara)、苹果(M. pumila)和月季(Rosa hybrida)	FIB-SEM和X-CT	输导组织	Herppich et al., 2015; Herremans et al., 2015; Nugraha et al., 2019; 王静等, 2022
	拟南芥(A. thaliana)	CLSM	分生组织	Gómez-Felipe and de Folter, 2019
	橡树(Quercus palustris)	X-CT	保护组织	Morisset et al., 2012
	橡树(Q. palustris)	CLSM和X-CT	营养组织	Fink, 2006; Morisset et al., 2012
细胞	拟南芥(A. thaliana)、狗尾草(Setaria viridis)、青杄(Picea wilsonii)、红松(Pinus densiflora)和黑松(P. thunbergii)	ODT、ssTEM、 FIB-SEM和CLSM	叶肉细胞、花粉粒细胞、下胚轴细胞和雄蕊细胞	Jackson et al., 2017; Kim et al., 2018; Cui et al., 2019; Wang et al., 2020; Silveira et al., 2022; Zechmann et al., 2022; Guo et al., 2023; Yamakawa et al., 2023; Collevatti et al., 2024; Hu et al., 2024

方法	分辨率	成像速度	样品制备	定位水平	参考文献
LSCM	200-500 nm	秒级/分级, 快	需荧光标记和透明化处理	细胞、亚细胞和分子水平	李叶等, 2015; 李成辉等, 2020; 路姣等, 2023
X-CT	250 μm以下	分级, 较快	需稳定固定	器官、组织、细胞和亚细胞水平	Du et al., 2019; Piovesan et al., 2021; Karahara et al., 2023
Micro-CT	50 μm以下	分级/小时级, 较快, 越精细越慢且越清晰	采用冷冻或化学固定	器官、组织、细胞和亚细胞水平	Wang et al., 2018; Karahara et al., 2023
ODT	200-600 nm	秒级/分级, 快	无需荧光标记, 透明化处理	器官、组织、细胞和亚细胞水平	He et al., 2023; Zhou et al., 2023
FIB-SEM	1-10 nm	小时级, 慢	制备方法复杂, 常温树脂包埋方法、高压冷冻及冷冻等	细胞及亚细胞水平	Heymann et al., 2006; Wei et al., 2012; 贾星等, 2022
TEM	0.1-2 nm	小时级, 慢	化学固定、常温脱水、包埋、切片、染色后观察	细胞、亚细胞、分子和原子水平	Drummy et al., 2004; 李斗星, 2004

方法	分辨率	成像速度	样品制备	定位水平	参考文献
LSCM	200-500 nm	秒级/分级, 快	需荧光标记和透明化处理	细胞、亚细胞和分子水平	李叶等, 2015; 李成辉等, 2020; 路姣等, 2023
X-CT	250 μm以下	分级, 较快	需稳定固定	器官、组织、细胞和亚细胞水平	Du et al., 2019; Piovesan et al., 2021; Karahara et al., 2023
Micro-CT	50 μm以下	分级/小时级, 较快, 越精细越慢且越清晰	采用冷冻或化学固定	器官、组织、细胞和亚细胞水平	Wang et al., 2018; Karahara et al., 2023
ODT	200-600 nm	秒级/分级, 快	无需荧光标记, 透明化处理	器官、组织、细胞和亚细胞水平	He et al., 2023; Zhou et al., 2023
FIB-SEM	1-10 nm	小时级, 慢	制备方法复杂, 常温树脂包埋方法、高压冷冻及冷冻等	细胞及亚细胞水平	Heymann et al., 2006; Wei et al., 2012; 贾星等, 2022
TEM	0.1-2 nm	小时级, 慢	化学固定、常温脱水、包埋、切片、染色后观察	细胞、亚细胞、分子和原子水平	Drummy et al., 2004; 李斗星, 2004