1
|
Nauber T, Hodač L, Wäldchen J, Mäder P. Parametrization of biological assumptions to simulate growth of tree branching architectures. TREE PHYSIOLOGY 2024; 44:tpae045. [PMID: 38696364 PMCID: PMC11128038 DOI: 10.1093/treephys/tpae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Modeling and simulating the growth of the branching of tree species remains a challenge. With existing approaches, we can reconstruct or rebuild the branching architectures of real tree species, but the simulation of the growth process remains unresolved. First, we present a tree growth model to generate branching architectures that resemble real tree species. Secondly, we use a quantitative morphometric approach to infer the shape similarity of the generated simulations and real tree species. Within a functional-structural plant model, we implement a set of biological parameters that affect the branching architecture of trees. By modifying the parameter values, we aim to generate basic shapes of spruce, pine, oak and poplar. Tree shapes are compared using geometric morphometrics of landmarks that capture crown and stem outline shapes. Five biological parameters, namely xylem flow, shedding rate, proprioception, gravitysense and lightsense, most influenced the generated tree branching patterns. Adjusting these five parameters resulted in the different tree shapes of spruce, pine, oak, and poplar. The largest effect was attributed to gravity, as phenotypic responses to this effect resulted in different growth directions of gymnosperm and angiosperm branching architectures. Since we were able to obtain branching architectures that resemble real tree species by adjusting only a few biological parameters, our model is extendable to other tree species. Furthermore, the model will also allow the simulation of structural tree-environment interactions. Our simplifying approach to shape comparison between tree species, landmark geometric morphometrics, showed that even the crown-trunk outlines capture species differences based on their contrasting branching architectures.
Collapse
Affiliation(s)
- Tristan Nauber
- Data-intensive Systems and Visualization Group, Technische Universität Ilmenau, Ehrenbergstraße 29, Ilmenau 98693, Germany
| | - Ladislav Hodač
- Department Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena 07745, Germany
| | - Jana Wäldchen
- Department Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena 07745, Germany
- German Centre for Integrative Biodiversity Research, iDiv (Halle-Jena-Leipzig), Puschstraße 4, Leipzig 04103, Germany
| | - Patrick Mäder
- Data-intensive Systems and Visualization Group, Technische Universität Ilmenau, Ehrenbergstraße 29, Ilmenau 98693, Germany
- German Centre for Integrative Biodiversity Research, iDiv (Halle-Jena-Leipzig), Puschstraße 4, Leipzig 04103, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Fürstengraben 1, Jena 07737, Germany
| |
Collapse
|
2
|
Lin Y. Visual Functional-Structural Plant Modeling Innovatively as a Compound Eye: Opening a New Way for Advancing the Scientific Cognition of Plant Vision. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303399. [PMID: 37875392 PMCID: PMC10724382 DOI: 10.1002/advs.202303399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/07/2023] [Indexed: 10/26/2023]
Abstract
Plant vision is an interesting interdisciplinary branch of botany and vision science, and its emerging studies have composed an epic journey of discovery. However, there are few endeavors on modeling how a plant as an integrity sees. Inspired by the similarity between those discovered laws of plant vision and the visual performance of some insect species with compound eyes, the visual functional-structural plant modeling as a compound eye is innovatively proposed. Using this adapted basic-pattern-oriented modeling, we tried to validate its feasibility in terms of the structural support, visual pathway, and functional performance. First, for a diversity of woody plants, their crowns proved to show self-similar profiles, which render the omnidirectional surfaces for structurally supporting the proposed model. Second, for many plant species, their branching proved to abide by the Pareto front, which ensures the optimality of assuming the visual pathway along the branching network. Third, in canopies the varying, but existing horizontal and vertical modes of crown shyness are detected, which in functional performance accords with the panoramic visibility of the proposed model. Overall, the feasibility of compound eye modeling is validated preliminarily, with the implication of opening a way for advancing the scientific cognition of plant vision.
Collapse
Affiliation(s)
- Yi Lin
- School of Earth and Space SciencesPeking UniversityNo. 5 Yiheyuan RoadBeijing100871China
| |
Collapse
|
3
|
Zhu Y, Li D, Fan J, Zhang H, Eichhorn MP, Wang X, Yun T. A reinterpretation of the gap fraction of tree crowns from the perspectives of computer graphics and porous media theory. FRONTIERS IN PLANT SCIENCE 2023; 14:1109443. [PMID: 36814756 PMCID: PMC9939530 DOI: 10.3389/fpls.2023.1109443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The gap fraction (GF) of vegetative canopies is an important property related to the contained bulk of reproductive elements and woody facets within the tree crown volume. This work was developed from the perspectives of porous media theory and computer graphics techniques, considering the vegetative elements in the canopy as a solid matrix and treating the gaps between them as pores to guide volume-based GFvol calculations. Woody components and individual leaves were extracted from terrestrial laser scanning data. The concept of equivalent leaf thickness describing the degrees of leaf curling and drooping was proposed to construct hexagonal prisms properly enclosing the scanned points of each leaf, and cylinder models were adopted to fit each branch segment, enabling the calculation of the equivalent leaf and branch volumes within the crown. Finally, the volume-based GFvol of the tree crown following the definition of the void fraction in porous media theory was calculated as one minus the ratio of the total plant leaf and branch volume to the canopy volume. This approach was tested on five tree species and a forest plot with variable canopy architecture, yielding an estimated maximum volume-based GFvol of 0.985 for a small crepe myrtle and a minimal volume-based GFvol of 0.953 for a sakura tree. The 3D morphology of each compositional element in the tree canopy was geometrically defined and the canopy was considered a porous structure to conduct GFvol calculations based on multidisciplinary theory.
Collapse
Affiliation(s)
- Yunfeng Zhu
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Dongni Li
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Jiangchuan Fan
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Huaiqing Zhang
- Research Institute of Forestry Resource Information Techniques, Chinese Academy of Forestry, Beijing, China
| | - Markus P. Eichhorn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Xiangjun Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ting Yun
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
- Forestry College, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
4
|
Sun C, Huang C, Zhang H, Chen B, An F, Wang L, Yun T. Individual Tree Crown Segmentation and Crown Width Extraction From a Heightmap Derived From Aerial Laser Scanning Data Using a Deep Learning Framework. FRONTIERS IN PLANT SCIENCE 2022; 13:914974. [PMID: 35774816 PMCID: PMC9237566 DOI: 10.3389/fpls.2022.914974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/26/2022] [Indexed: 05/04/2023]
Abstract
Deriving individual tree crown (ITC) information from light detection and ranging (LiDAR) data is of great significance to forest resource assessment and smart management. After proof-of-concept studies, advanced deep learning methods have been shown to have high efficiency and accuracy in remote sensing data analysis and geoscience problem solving. This study proposes a novel concept for synergetic use of the YOLO-v4 deep learning network based on heightmaps directly generated from airborne LiDAR data for ITC segmentation and a computer graphics algorithm for refinement of the segmentation results involving overlapping tree crowns. This concept overcomes the limitations experienced by existing ITC segmentation methods that use aerial photographs to obtain texture and crown appearance information and commonly encounter interference due to heterogeneous solar illumination intensities or interlacing branches and leaves. Three generative adversarial networks (WGAN, CycleGAN, and SinGAN) were employed to generate synthetic images. These images were coupled with manually labeled training samples to train the network. Three forest plots, namely, a tree nursery, forest landscape and mixed tree plantation, were used to verify the effectiveness of our approach. The results showed that the overall recall of our method for detecting ITCs in the three forest plot types reached 83.6%, with an overall precision of 81.4%. Compared with reference field measurement data, the coefficient of determination R 2 was ≥ 79.93% for tree crown width estimation, and the accuracy of our deep learning method was not influenced by the values of key parameters, yielding 3.9% greater accuracy than the traditional watershed method. The results demonstrate an enhancement of tree crown segmentation in the form of a heightmap for different forest plot types using the concept of deep learning, and our method bypasses the visual complications arising from aerial images featuring diverse textures and unordered scanned points with irregular geometrical properties.
Collapse
Affiliation(s)
- Chenxin Sun
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Chengwei Huang
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Huaiqing Zhang
- Research Institute of Forest Resource Information Techniques, Chinese Academy of Forestry, Beijing, China
| | - Bangqian Chen
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Feng An
- Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Liwen Wang
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Ting Yun
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
5
|
Moulia B, Badel E, Bastien R, Duchemin L, Eloy C. The shaping of plant axes and crowns through tropisms and elasticity: an example of morphogenetic plasticity beyond the shoot apical meristem. THE NEW PHYTOLOGIST 2022; 233:2354-2379. [PMID: 34890051 DOI: 10.1111/nph.17913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
Shoot morphogenetic plasticity is crucial to the adaptation of plants to their fluctuating environments. Major insights into shoot morphogenesis have been compiled studying meristems, especially the shoot apical meristem (SAM), through a methodological effort in multiscale systems biology and biophysics. However, morphogenesis at the SAM is robust to environmental changes. Plasticity emerges later on during post-SAM development. The purpose of this review is to show that multiscale systems biology and biophysics is insightful for the shaping of the whole plant as well. More specifically, we review the shaping of axes and crowns through tropisms and elasticity, combining the recent advances in morphogenetic control using physical cues and by genes. We focus mostly on land angiosperms, but with growth habits ranging from small herbs to big trees. We show that generic (universal) morphogenetic processes have been identified, revealing feedforward and feedback effects of global shape on the local morphogenetic process. In parallel, major advances have been made in the analysis of the major genes involved in shaping axes and crowns, revealing conserved genic networks among angiosperms. Then, we show that these two approaches are now starting to converge, revealing exciting perspectives.
Collapse
Affiliation(s)
- Bruno Moulia
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
| | - Eric Badel
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
| | - Renaud Bastien
- Université Clermont Auvergne, INRAE, PIAF, F-63000, Clermont-Ferrand, France
- INSERM U1284, Center for Research and Interdisciplinarity (CRI), Université de Paris, F-75004, Paris, France
| | - Laurent Duchemin
- Physique et Mécanique des Milieux Hétérogenes, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, F-75005, Paris, France
| | - Christophe Eloy
- Aix Marseille Univ, CNRS, Centrale Marseille, IRPHE, F-13013, Marseille, France
| |
Collapse
|
6
|
Li HH, Cheng YC, Yang KJ, Chu CR, Hong TM. Role of the crown in tree resistance against high winds. Phys Rev E 2021; 104:025006. [PMID: 34525538 DOI: 10.1103/physreve.104.025006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/28/2021] [Indexed: 11/07/2022]
Abstract
Rather than using wooden sticks to simulate the breakage of trees in high winds as in most research, we employ fresh samples from camphor and Formosa gum with branches and leaves to certify the crucial role of the tree crown. By using a blowdown wind tunnel with a maximum wind speed of 50 m/s, we purposely reduce the number of leaves and show that the drag force will drop by as much as two thirds when half pruned. Based on real observations, we model the leaf by an open and full cone in the presence of light and strong winds, and calculate how their corresponding cross-sectional area A and drag force F vary with wind speed v. Different slopes before and after the formation of a full cone are predicted and confirmed when these two quantities are plotted in full-log scale. Compared to the empirical value, our simple model gave α=2/5 and 2/3 for A∝v^{-α} and β=4/5 and 2/3 for F∝v^{β} at low and high winds. Discrepancies can be accounted for by including further details, such as the reorientation of open cones and the movement of branches.
Collapse
Affiliation(s)
- Hsin-Huei Li
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan 30043, Republic of China
| | - Yu-Chuan Cheng
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan 30043, Republic of China
| | - Kai-Jie Yang
- Department of Civil Engineering, National Central University, Taoyuan, Taiwan 32001, Republic of China
| | - Chia-Ren Chu
- Department of Civil Engineering, National Central University, Taoyuan, Taiwan 32001, Republic of China
| | - Tzay-Ming Hong
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan 30043, Republic of China
| |
Collapse
|
7
|
Moulia B, Douady S, Hamant O. Fluctuations shape plants through proprioception. Science 2021; 372:372/6540/eabc6868. [PMID: 33888615 DOI: 10.1126/science.abc6868] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Plants constantly experience fluctuating internal and external mechanical cues, ranging from nanoscale deformation of wall components, cell growth variability, nutating stems, and fluttering leaves to stem flexion under tree weight and wind drag. Developing plants use such fluctuations to monitor and channel their own shape and growth through a form of proprioception. Fluctuations in mechanical cues may also be actively enhanced, producing oscillating behaviors in tissues. For example, proprioception through leaf nastic movements may promote organ flattening. We propose that fluctuation-enhanced proprioception allows plant organs to sense their own shapes and behave like active materials with adaptable outputs to face variable environments, whether internal or external. Because certain shapes are more amenable to fluctuations, proprioception may also help plant shapes to reach self-organized criticality to support such adaptability.
Collapse
Affiliation(s)
- Bruno Moulia
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France.
| | - Stéphane Douady
- Laboratoire Matières et Systèmes Complexes (MSC), Université de Paris, CNRS, 75205 Paris Cedex 13, France.
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, 69007 Lyon, France.
| |
Collapse
|
8
|
Rivière M, Corre Y, Peaucelle A, Derr J, Douady S. The hook shape of growing leaves results from an active regulatory process. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6408-6417. [PMID: 32816036 DOI: 10.1093/jxb/eraa378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
The rachis of most growing compound leaves observed in nature exhibits a stereotypical hook shape. In this study, we focus on the canonical case of Averrhoa carambola. Combining kinematics and mechanical investigation, we characterize this hook shape and shed light on its establishment and maintenance. We show quantitatively that the hook shape is a conserved bent zone propagating at constant velocity and constant distance from the apex throughout development. A simple mechanical test reveals non-zero intrinsic curvature profiles for the rachis during its growth, indicating that the hook shape is actively regulated. We show a robust spatial organization of growth, curvature, rigidity, and lignification, and their interplay. Regulatory processes appear to be specifically localized: in particular, differential growth occurs where the elongation rate drops. Finally, impairing the graviception of the leaf on a clinostat led to reduced hook curvature but not to its loss. Altogether, our results suggest a role for proprioception in the regulation of the leaf hook shape, likely mediated via mechanical strain.
Collapse
Affiliation(s)
- Mathieu Rivière
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, Paris Cedex, France
| | - Yoann Corre
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, Paris Cedex, France
| | - Alexis Peaucelle
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, Paris Cedex, France
- Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, Versailles Cedex, France
| | - Julien Derr
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, Paris Cedex, France
| | - Stéphane Douady
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, Paris Cedex, France
| |
Collapse
|
9
|
Retrieval of Aerodynamic Parameters in Rubber Tree Forests Based on the Computer Simulation Technique and Terrestrial Laser Scanning Data. REMOTE SENSING 2020. [DOI: 10.3390/rs12081318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Rubber trees along the southeast coast of China always suffer severe damage from hurricanes. Quantitative assessments of the capacity for wind resistance of various rubber tree clones are currently lacking. We focus on a vulnerability assessment of rubber trees of different clones under wind disturbance impacts by employing multidisciplinary approaches incorporating scanned points, aerodynamics, machine learning and computer graphics. Point cloud data from two typical rubber trees belonging to different clones (PR107 and CATAS 7-20-59) were collected using terrestrial laser scanning, and a connection chain of tree skeletons was constructed using a clustering algorithm of machine learning. The concept of foliage clumps based on the trunk and first-order branches was first proposed to optimize rubber tree plot 3D modelling for simulating the wind field and assessing the wind-related parameters. The results from the obtained phenotypic traits show that the variable leaf area index and included angle between the branches and trunk result in variations in the topological structure and gap fraction of tree crowns, respectively, which are the major influencing factors relevant to the rubber tree’s capacity to resist hurricane strikes. The aerodynamics analysis showed that the maximum dynamic pressure, wind velocity and turbulent intensity of the wind-related parameters in rubber tree plots of clone PR107 (300 Pa, 30 m/s and 15%) are larger than that in rubber tree plots of clone CATAS-7-20-59 (120 Pa, 18 m/s and 5%), which results in a higher probability of local strong cyclone occurrence and a higher vulnerability to hurricane damage.
Collapse
|
10
|
Moulia B, Bastien R, Chauvet-Thiry H, Leblanc-Fournier N. Posture control in land plants: growth, position sensing, proprioception, balance, and elasticity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3467-3494. [PMID: 31305901 DOI: 10.1093/jxb/erz278] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
The colonization of the atmosphere by land plants was a major evolutionary step. The mechanisms that allow for vertical growth through air and the establishment and control of a stable erect habit are just starting to be understood. A key mechanism was found to be continuous posture control to counterbalance the mechanical and developmental challenges of maintaining a growing upright structure. An interdisciplinary systems biology approach was invaluable in understanding the underlying principles and in designing pertinent experiments. Since this discovery previously held views of gravitropic perception had to be reexamined and this has led to the description of proprioception in plants. In this review, we take a purposefully pedagogical approach to present the dynamics involved from the cellular to whole-plant level. We show how the textbook model of how plants sense gravitational force has been replaced by a model of position sensing, a clinometer mechanism that involves both passive avalanches and active motion of statoliths, granular starch-filled plastids, in statocytes. Moreover, there is a transmission of information between statocytes and other specialized cells that sense the degree of organ curvature and reset asymmetric growth to straighten and realign the structure. We give an overview of how plants have used the interplay of active posture control and elastic sagging to generate a whole range of spatial displays during their life cycles. Finally, a position-integrating mechanism has been discovered that prevents directional plant growth from being disrupted by wind-induced oscillations.
Collapse
Affiliation(s)
- Bruno Moulia
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
| | - Renaud Bastien
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
- Department of Collective Behaviour, Max Planck Institute for Ornithology and Department of Biology, University of Konstanz, Konstanz, Germany
| | - Hugo Chauvet-Thiry
- Université Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France
- Aix-Marseille Université, CNRS, IUSTI, Marseille, France
| | | |
Collapse
|