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Nunes MH, Vaz MC, Camargo JLC, Laurance WF, de Andrade A, Vicentini A, Laurance S, Raumonen P, Jackson T, Zuquim G, Wu J, Peñuelas J, Chave J, Maeda EE. Edge effects on tree architecture exacerbate biomass loss of fragmented Amazonian forests. Nat Commun 2023; 14:8129. [PMID: 38097604 PMCID: PMC10721830 DOI: 10.1038/s41467-023-44004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Habitat fragmentation could potentially affect tree architecture and allometry. Here, we use ground surveys of terrestrial LiDAR in Central Amazonia to explore the influence of forest edge effects on tree architecture and allometry, as well as forest biomass, 40 years after fragmentation. We find that young trees colonising the forest fragments have thicker branches and architectural traits that optimise for light capture, which result in 50% more woody volume than their counterparts of similar stem size and height in the forest interior. However, we observe a disproportionately lower height in some large trees, leading to a 30% decline in their woody volume. Despite the substantial wood production of colonising trees, the lower height of some large trees has resulted in a net loss of 6.0 Mg ha-1 of aboveground biomass - representing 2.3% of the aboveground biomass of edge forests. Our findings indicate a strong influence of edge effects on tree architecture and allometry, and uncover an overlooked factor that likely exacerbates carbon losses in fragmented forests.
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Affiliation(s)
- Matheus Henrique Nunes
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA.
| | - Marcel Caritá Vaz
- Institute for Environmental Science and Sustainabilty, Wilkes University, Wilkes-Barre, PA, USA
| | - José Luís Campana Camargo
- Ecology Graduate Program, National Institute for Amazonian Research, (INPA), Manaus, Brazil
- Biological Dynamics of Forest Fragments Project (BDFFP) at National Institute for Amazonian Research (INPA), Manaus, Brazil
| | - William F Laurance
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Ana de Andrade
- Biological Dynamics of Forest Fragments Project (BDFFP) at National Institute for Amazonian Research (INPA), Manaus, Brazil
| | - Alberto Vicentini
- Biological Dynamics of Forest Fragments Project (BDFFP) at National Institute for Amazonian Research (INPA), Manaus, Brazil
- Coordenação de Pesquisas em Ecologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, AM, Brasil
| | - Susan Laurance
- Centre for Tropical Environmental and Sustainability Science, College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Pasi Raumonen
- Computing Sciences, Tampere University, Tampere, Finland
| | - Toby Jackson
- Plant Sciences and Conservation Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Gabriela Zuquim
- Amazon Research Team, Department of Biology, University of Turku, Turku, Finland
| | - Jin Wu
- School of Biological Sciences and Institute for Climate and Carbon Neutrality, The University of Hong Kong, Hong Kong, China
| | - Josep Peñuelas
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona, Catalonia, Spain
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique, CNRS, UPS, IRD, Université Paul Sabatier, Toulouse, France
| | - Eduardo Eiji Maeda
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
- Finnish Meteorological Institute, FMI, Helsinki, Finland.
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2
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Su C, Kokosza A, Xie X, Pěnčík A, Zhang Y, Raumonen P, Shi X, Muranen S, Topcu MK, Immanen J, Hagqvist R, Safronov O, Alonso-Serra J, Eswaran G, Venegas MP, Ljung K, Ward S, Mähönen AP, Himanen K, Salojärvi J, Fernie AR, Novák O, Leyser O, Pałubicki W, Helariutta Y, Nieminen K. Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem. Proc Natl Acad Sci U S A 2023; 120:e2308587120. [PMID: 37991945 PMCID: PMC10691325 DOI: 10.1073/pnas.2308587120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023] Open
Abstract
Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.
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Affiliation(s)
- Chang Su
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
| | - Andrzej Kokosza
- Mathematics and Computer Science, Adam Mickiewicz University, Poznań61-614, Poland
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya321-8505, Japan
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, OlomoucCZ-78371, Czech Republic
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
- Center of Plant Systems Biology and Biotechnology, 4000Plovdiv, Bulgaria
| | - Pasi Raumonen
- Mathematics, Tampere University, Tampere33720, Finland
| | - Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Sampo Muranen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
| | - Melis Kucukoglu Topcu
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
| | - Juha Immanen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Production Systems, Natural Resources Institute Finland (Luke), Helsinki00790, Finland
| | - Risto Hagqvist
- Production Systems, Natural Resources Institute Finland (Luke), Helsinki00790, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
| | - Juan Alonso-Serra
- Laboratoire de Reproduction et Développement des Plantes, École Normale Supérieure de Lyon, Institut National de la Recherche Agronomique, Lyon69342, France
| | - Gugan Eswaran
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
| | - Mirko Pavicic Venegas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN37830
- National Plant Phenotyping Infrastructure, Helsinki Institute of Life Science, University of Helsinki, Biocenter Finland, Helsinki00014, Finland
| | - Karin Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90183Umeå, Sweden
| | - Sally Ward
- Sainsbury Laboratory, University of Cambridge, CambridgeCB2 1LR, United Kingdom
| | - Ari Pekka Mähönen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
| | - Kristiina Himanen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- National Plant Phenotyping Infrastructure, Helsinki Institute of Life Science, University of Helsinki, Biocenter Finland, Helsinki00014, Finland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore637551, Singapore
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm14476, Germany
- Center of Plant Systems Biology and Biotechnology, 4000Plovdiv, Bulgaria
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, Faculty of Science of Palacký University, OlomoucCZ-78371, Czech Republic
- Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University and Institute of Experimental Botany of the Academy of Sciences of the Czech Republic, Olomouc78371, Czech Republic
| | - Ottoline Leyser
- Sainsbury Laboratory, University of Cambridge, CambridgeCB2 1LR, United Kingdom
| | - Wojtek Pałubicki
- Mathematics and Computer Science, Adam Mickiewicz University, Poznań61-614, Poland
| | - Ykä Helariutta
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki00014, Finland
- Sainsbury Laboratory, University of Cambridge, CambridgeCB2 1LR, United Kingdom
| | - Kaisa Nieminen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki00014, Finland
- Production Systems, Natural Resources Institute Finland (Luke), Helsinki00790, Finland
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Terryn L, Calders K, Åkerblom M, Bartholomeus H, Disney M, Levick S, Origo N, Raumonen P, Verbeeck H. Analysing individual 3D tree structure using the R package ITSMe. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Louise Terryn
- CAVElab – Computational and Applied Vegetation Ecology, Department of Environment Ghent University Ghent Belgium
| | - Kim Calders
- CAVElab – Computational and Applied Vegetation Ecology, Department of Environment Ghent University Ghent Belgium
| | | | - Harm Bartholomeus
- Wageningen University & Research, Laboratory of Geo‐Information Science and Remote Sensing Wageningen The Netherlands
| | - Mathias Disney
- UCL Department of Geography London UK
- NERC National Centre for Earth Observation (NCEO‐UCL) Leicester UK
| | - Shaun Levick
- CSIRO Land and Water Winnellie Northwest Territories Australia
| | - Niall Origo
- Climate and Earth Observation group ‐ National Physical Laboratory Teddington UK
| | - Pasi Raumonen
- Computing Sciences, Tampere University Tampere Finland
| | - Hans Verbeeck
- CAVElab – Computational and Applied Vegetation Ecology, Department of Environment Ghent University Ghent Belgium
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4
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Herrero-Huerta M, Raumonen P, Gonzalez-Aguilera D. 4DRoot: Root phenotyping software for temporal 3D scans by X-ray computed tomography. Front Plant Sci 2022; 13:986856. [PMID: 36212319 PMCID: PMC9539560 DOI: 10.3389/fpls.2022.986856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Currently, plant phenomics is considered the key to reducing the genotype-to-phenotype knowledge gap in plant breeding. In this context, breakthrough imaging technologies have demonstrated high accuracy and reliability. The X-ray computed tomography (CT) technology can noninvasively scan roots in 3D; however, it is urgently required to implement high-throughput phenotyping procedures and analyses to increase the amount of data to measure more complex root phenotypic traits. We have developed a spatial-temporal root architectural modeling software tool based on 4D data from temporal X-ray CT scans. Through a cylinder fitting, we automatically extract significant root architectural traits, distribution, and hierarchy. The open-source software tool is named 4DRoot and implemented in MATLAB. The source code is freely available at https://github.com/TIDOP-USAL/4DRoot. In this research, 3D root scans from the black walnut tree were analyzed, a punctual scan for the spatial study and a weekly time-slot series for the temporal one. 4DRoot provides breeders and root biologists an objective and useful tool to quantify carbon sequestration throw trait extraction. In addition, 4DRoot could help plant breeders to improve plants to meet the food, fuel, and fiber demands in the future, in order to increase crop yield while reducing farming inputs.
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Affiliation(s)
- Monica Herrero-Huerta
- Department of Cartographic and Land Engineering, Higher Polytechnic School of Ávila, Universidad de Salamanca, Ávila, Spain
| | - Pasi Raumonen
- Department of Computing Sciences, Tampere University, Tampere, Finland
| | - Diego Gonzalez-Aguilera
- Department of Cartographic and Land Engineering, Higher Polytechnic School of Ávila, Universidad de Salamanca, Ávila, Spain
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Guzmán E, Fernández MP, Alcalde JA, Contreras S, Raumonen P, Picco L, Montalba C, Tejos C. Phyllotaxis transition over the lifespan of a palm tree using Magnetic Resonance Imaging (MRI) and Terrestrial Laser Scanning (TLS): the case of Jubaea chilensis. Plant Methods 2022; 18:88. [PMID: 35752854 PMCID: PMC9233369 DOI: 10.1186/s13007-022-00920-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/09/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Jubaea chilensis (Molina) Baillon, is a uniquely large palm species endemic to Chile. It is under threatened status despite its use as an ornamental species throughout the world. This research seeks to identify the phyllotaxis of the species based on an original combination of non-destructive data acquisition technologies, namely Magnetic Resonance Imaging (MRI) in saplings and young individuals and Terrestrial Laser Scanning (TLS) in standing specimens, and a novel analysis methodology. RESULTS Two phyllotaxis parameters, parastichy pairs and divergence angle, were determined by analyzing specimens at different developmental stages. Spiral phyllotaxis patterns of J. chilensis progressed in complexity from parastichy pairs (3,2) and (3,5) in juvenile specimens and (5,3), (8,5) and (8,13) for adult specimens. Divergence angle was invariable and averaged 136.9°, close to the golden angle. Phyllotactic pattern changes associated with establishment phase, the adult vegetative and the adult reproductive phases were observed. Both technologies, MRI and TLS proved to be adequate for the proposed analysis. CONCLUSIONS Understanding phyllotactic transitions may assist identification of developmental stages of wild J. chilensis specimens. The proposed methodology may also be useful for the study of other palm species.
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Affiliation(s)
- Eduardo Guzmán
- Master Program in Natural Resources, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M. Paulina Fernández
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro Nacional de Excelencia para la Industria de la Madera (CENAMAD), Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro UC de Innovación en Madera, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José-Antonio Alcalde
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Samuel Contreras
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pasi Raumonen
- Computing Sciences, Tampere University, Tampere, Finland
| | - Lorenzo Picco
- Department of Land, Environment, Agriculture and Forestry, Universitá degli Studi di Padova, Padua, Italy
| | - Cristián Montalba
- Biomedical Imaging Center, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Radiology Department, School of Medicine, Pontificia Universidad Católica de Chile, Santiago Centro, Santiago, Chile
| | - Cristián Tejos
- Biomedical Imaging Center, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Department of Electrical Engineering, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Millennium Institute for Intelligent Healthcare Engineering (iHEALTH), Santiago, Chile
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O’Sullivan H, Raumonen P, Kaitaniemi P, Perttunen J, Sievänen R. Integrating terrestrial laser scanning with functional-structural plant models to investigate ecological and evolutionary processes of forest communities. Ann Bot 2021; 128:663-684. [PMID: 34610091 PMCID: PMC8557364 DOI: 10.1093/aob/mcab120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Woody plants (trees and shrubs) play an important role in terrestrial ecosystems, but their size and longevity make them difficult subjects for traditional experiments. In the last 20 years functional-structural plant models (FSPMs) have evolved: they consider the interplay between plant modular structure, the immediate environment and internal functioning. However, computational constraints and data deficiency have long been limiting factors in a broader application of FSPMs, particularly at the scale of forest communities. Recently, terrestrial laser scanning (TLS), has emerged as an invaluable tool for capturing the 3-D structure of forest communities, thus opening up exciting opportunities to explore and predict forest dynamics with FSPMs. SCOPE The potential synergies between TLS-derived data and FSPMs have yet to be fully explored. Here, we summarize recent developments in FSPM and TLS research, with a specific focus on woody plants. We then evaluate the emerging opportunities for applying FSPMs in an ecological and evolutionary context, in light of TLS-derived data, with particular consideration of the challenges posed by scaling up from individual trees to whole forests. Finally, we propose guidelines for incorporating TLS data into the FSPM workflow to encourage overlap of practice amongst researchers. CONCLUSIONS We conclude that TLS is a feasible tool to help shift FSPMs from an individual-level modelling technique to a community-level one. The ability to scan multiple trees, of multiple species, in a short amount of time, is paramount to gathering the detailed structural information required for parameterizing FSPMs for forest communities. Conventional techniques, such as repeated manual forest surveys, have their limitations in explaining the driving mechanisms behind observed patterns in 3-D forest structure and dynamics. Therefore, other techniques are valuable to explore how forests might respond to environmental change. A robust synthesis between TLS and FSPMs provides the opportunity to virtually explore the spatial and temporal dynamics of forest communities.
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Affiliation(s)
- Hannah O’Sullivan
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Pasi Raumonen
- Mathematics, Tampere University, Korkeakoulunkatu 7, FI-33720 Tampere, Finland
| | - Pekka Kaitaniemi
- Hyytiälä Forestry Field Station, Faculty of Agriculture and Forestry, University of Helsinki, Hyytiäläntie 124, FI-35500 Korkeakoski, Finland
| | - Jari Perttunen
- Natural Resources Institute Finland, Latokartanontie 9, 00790 Helsinki, Finland
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7
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Martin-Ducup O, Mofack G, Wang D, Raumonen P, Ploton P, Sonké B, Barbier N, Couteron P, Pélissier R. Evaluation of automated pipelines for tree and plot metric estimation from TLS data in tropical forest areas. Ann Bot 2021; 128:753-766. [PMID: 33876194 PMCID: PMC8557371 DOI: 10.1093/aob/mcab051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Terrestrial LiDAR scanning (TLS) data are of great interest in forest ecology and management because they provide detailed 3-D information on tree structure. Automated pipelines are increasingly used to process TLS data and extract various tree- and plot-level metrics. With these developments comes the risk of unknown reliability due to an absence of systematic output control. In the present study, we evaluated the estimation errors of various metrics, such as wood volume, at tree and plot levels for four automated pipelines. METHODS We used TLS data collected from a 1-ha plot of tropical forest, from which 391 trees >10 cm in diameter were fully processed using human assistance to obtain control data for tree- and plot-level metrics. KEY RESULTS Our results showed that fully automated pipelines led to median relative errors in the quantitative structural model (QSM) volume ranging from 39 to 115 % at the tree level and 10 to 134 % at the 1-ha plot level. For tree-level metrics, the median error for the crown-projected area ranged from 46 to 59 % and that for the crown-hull volume varied from 72 to 88 %. This result suggests that the tree isolation step is the weak link in automated pipeline methods. We further analysed how human assistance with automated pipelines can help reduce the error in the final QSM volume. At the tree scale, we found that isolating trees using human assistance reduced the error in wood volume by a factor of 10. At the 1-ha plot scale, locating trees with human assistance reduced the error by a factor of 3. CONCLUSIONS Our results suggest that in complex tropical forests, fully automated pipelines may provide relatively unreliable metrics at the tree and plot levels, but limited human assistance inputs can significantly reduce errors.
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Affiliation(s)
| | - Gislain Mofack
- Plant Systematics and Ecology Laboratory, Higher Teacher’s Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - Di Wang
- Department of Built Environment, School of Engineering, Aalto University, Helsinki, Finland
| | - Pasi Raumonen
- Mathematics, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Pierre Ploton
- AMAP, Univ. Montpellier, IRD, CNRS, CIRAD, INRAE, Montpellier, France
| | - Bonaventure Sonké
- Plant Systematics and Ecology Laboratory, Higher Teacher’s Training College, University of Yaoundé I, Yaoundé, Cameroon
| | - Nicolas Barbier
- AMAP, Univ. Montpellier, IRD, CNRS, CIRAD, INRAE, Montpellier, France
| | - Pierre Couteron
- AMAP, Univ. Montpellier, IRD, CNRS, CIRAD, INRAE, Montpellier, France
| | - Raphaël Pélissier
- AMAP, Univ. Montpellier, IRD, CNRS, CIRAD, INRAE, Montpellier, France
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Beyer RM, Basler D, Raumonen P, Kaasalainen M, Pretzsch H. Do trees have constant branch divergence angles? J Theor Biol 2020; 512:110567. [PMID: 33359208 DOI: 10.1016/j.jtbi.2020.110567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 10/22/2022]
Abstract
Many herbaceous plants feature remarkably regular arrangements of lateral organs along the central axis. These phyllotactic patterns are generated by a constant divergence angle between successive buds (or whorls thereof) that first appears at the shoot apircal meristem and is maintained across later ontogentic stages when it can be observed at the macroscopic scale. Do the branches along a tree trunk exhibit similar patterns? Here we use branch skeleton data derived from terrestrial laser scans to empirically estimate the distributions of the divergence angles between successive branches along the trunks of mature European beech, Norway spruce, and Scots pine trees. We find that rather than clustering around a particular value, species-specific branch divergence angles feature statistical properties characteristic of a uniform distribution. We hypothesise this to be the result of the stochasticity in bud development and branch shedding, and provide a rigorous mathematical proof that even when the divergence angle between successive lateral buds is constant, the observed distribution of branch divergence angles will approximate a uniform distribution if bud mortality and branch shedding rates are high.
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Affiliation(s)
- Robert M Beyer
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
| | - David Basler
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, United States; Department of Environmental Sciences - Botany, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland
| | - Pasi Raumonen
- Mathematics, Tampere University, FI-33014 Tampere, Finland
| | | | - Hans Pretzsch
- TUM School of Life Sciences Weihenstephan, Technische Universität München, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
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9
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Kunz M, Fichtner A, Härdtle W, Raumonen P, Bruelheide H, von Oheimb G. Neighbour species richness and local structural variability modulate aboveground allocation patterns and crown morphology of individual trees. Ecol Lett 2019; 22:2130-2140. [PMID: 31625279 DOI: 10.1111/ele.13400] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 01/22/2023]
Abstract
Local neighbourhood interactions are considered a main driver for biodiversity-productivity relationships in forests. Yet, the structural responses of individual trees in species mixtures and their relation to crown complementarity remain poorly understood. Using a large-scale forest experiment, we studied the impact of local tree species richness and structural variability on above-ground wood volume allocation patterns and crown morphology. We applied terrestrial laser scanning to capture the three-dimensional structure of trees and their temporal dynamics. We found that crown complementarity and crown plasticity increased with species richness. Trees growing in species-rich neighbourhoods showed enhanced aboveground wood volume both in trunks and branches. Over time, neighbourhood diversity induced shifts in wood volume allocation in favour of branches, in particular for morphologically flexible species. Our results demonstrate that diversity-mediated shifts in allocation pattern and crown morphology are a fundamental mechanism for crown complementarity and may be an important driver of overyielding.
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Affiliation(s)
- Matthias Kunz
- Institute of General Ecology and Environmental Protection, Technische Universität Dresden, PF 1117, 01735, Tharandt, Germany
| | - Andreas Fichtner
- Institute of Ecology, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany
| | - Werner Härdtle
- Institute of Ecology, Leuphana University Lüneburg, Universitätsallee 1, 21335, Lüneburg, Germany
| | - Pasi Raumonen
- Department of Mathematics, Tampere University, FI-33014 Tampere University, Tampere, Finland
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle- Wittenberg, Am Kirchtor 1, 06108, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103, Leipzig, Germany
| | - Goddert von Oheimb
- Institute of General Ecology and Environmental Protection, Technische Universität Dresden, PF 1117, 01735, Tharandt, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103, Leipzig, Germany
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10
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Jackson T, Shenkin A, Moore J, Bunce A, van Emmerik T, Kane B, Burcham D, James K, Selker J, Calders K, Origo N, Disney M, Burt A, Wilkes P, Raumonen P, Gonzalez de Tanago Menaca J, Lau A, Herold M, Goodman RC, Fourcaud T, Malhi Y. An architectural understanding of natural sway frequencies in trees. J R Soc Interface 2019; 16:20190116. [PMID: 31164076 DOI: 10.1098/rsif.2019.0116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.
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Affiliation(s)
- T Jackson
- 1 Environmental Change Institute, School of Geography and the Environment, University of Oxford , Oxford OX1 3QY , UK
| | - A Shenkin
- 1 Environmental Change Institute, School of Geography and the Environment, University of Oxford , Oxford OX1 3QY , UK
| | - J Moore
- 2 Scion , 49 Sala Street, Rotorua 3010 , New Zealand
| | - A Bunce
- 3 Department of Natural Resources, University of Connecticut , Mansfield, CT 06269 , USA
| | - T van Emmerik
- 4 Water Resources Section, Delft University of Technology , Stevinweg 1, 2628 CN, Delft , The Netherlands.,5 Hydrology and Quantitative Water Management Group, Wageningen University , Wageningen , The Netherlands
| | - B Kane
- 6 Department of Environmental Conservation, University of Massachusetts , Amherst, MA 01003 , USA
| | - D Burcham
- 7 Centre for Urban Greenery and Ecology , National Parks Board, 259569 Singapore
| | - K James
- 8 School of Ecosystem and Forest Sciences, Faculty of Science, University of Melbourne , Melbourne , Australia
| | - J Selker
- 9 Oregon State University , Corvallis, OR 97331 , USA
| | - K Calders
- 10 CAVElab - Computational and Applied Vegetation Ecology, Ghent University , Ghent , Belgium
| | - N Origo
- 11 Earth Observation, Climate and Optical Group, National Physical Laboratory , Hampton Road, Teddington, Middlesex TW11 0LW , UK.,12 Department of Geography, University College London , London WC1E 6BT , UK
| | - M Disney
- 12 Department of Geography, University College London , London WC1E 6BT , UK.,13 NERC National Centre for Earth Observation (NCEO) , Leicester , UK
| | - A Burt
- 12 Department of Geography, University College London , London WC1E 6BT , UK
| | - P Wilkes
- 12 Department of Geography, University College London , London WC1E 6BT , UK.,13 NERC National Centre for Earth Observation (NCEO) , Leicester , UK
| | - P Raumonen
- 14 Tampere University of Technology , Korkeakoulunkatu 10, 33720 Tampere , Finland
| | - J Gonzalez de Tanago Menaca
- 15 Laboratory of Geo-Information Science and Remote Sensing, Wageningen University , Droevendaalsesteeg 3, 6708 PB Wageningen , The Netherlands.,16 Center for International Forestry Research (CIFOR) , PO Box 0113 BOCBD, Bogor 16000 , Indonesia
| | - A Lau
- 15 Laboratory of Geo-Information Science and Remote Sensing, Wageningen University , Droevendaalsesteeg 3, 6708 PB Wageningen , The Netherlands.,16 Center for International Forestry Research (CIFOR) , PO Box 0113 BOCBD, Bogor 16000 , Indonesia
| | - M Herold
- 15 Laboratory of Geo-Information Science and Remote Sensing, Wageningen University , Droevendaalsesteeg 3, 6708 PB Wageningen , The Netherlands
| | - R C Goodman
- 17 Department of Forest Ecology and Management, Swedish University of Agricultural Sciences , Umeå , Sweden
| | - T Fourcaud
- 18 AMAP, University of Montpellier, CIRAD, CNRS, INRA, IRD , Montpellier , France
| | - Y Malhi
- 1 Environmental Change Institute, School of Geography and the Environment, University of Oxford , Oxford OX1 3QY , UK
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11
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Sievänen R, Raumonen P, Perttunen J, Nikinmaa E, Kaitaniemi P. A study of crown development mechanisms using a shoot-based tree model and segmented terrestrial laser scanning data. Ann Bot 2018; 122:423-434. [PMID: 29800102 PMCID: PMC6110348 DOI: 10.1093/aob/mcy082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims Functional-structural plant models (FSPMs) allow simulation of tree crown development as the sum of modular (e.g. shoot-level) responses triggered by the local environmental conditions. The actual process of space filling by the crowns can be studied. Although the FSPM simulations are at organ scale, the data for their validation have usually been at more aggregated levels (whole-crown or whole-tree). Measurements made by terrestrial laser scanning (TLS) that have been segmented into elementary units (internodes) offer a phenotyping tool to validate the FSPM predictions at levels comparable with their detail. We demonstrate the testing of different formulations of crown development of Scots pine trees in the LIGNUM model using segmented TLS data. Methods We made TLS measurements from four sample trees growing in a forest on a relatively poor soil from sapling size to mature stage. The TLS data were segmented into internodes. The segmentation also produced information on whether needles were present in the internode. We applied different formulations of crown development (flushing of buds and length of growth of new internodes) in LIGNUM. We optimized the parameter values of each formulation using genetic algorithms to observe the best fit of LIGNUM simulations to the measured trees. The fitness function in the estimation combined both tree-level characteristics (e.g. tree height and crown length) and measures of crown shape (e.g. spatial distribution of needle area). Key Results Comparison of different formulations against the data indicates that the Extended Borchert-Honda model for shoot elongation works best within LIGNUM. Control of growth by local density in the crown was important for all shoot elongation formulations. Modifying the number of lateral buds as a function of local density in the crown was the best way to accomplish density control. Conclusions It was demonstrated how segmented TLS data can be used in the context of a shoot-based model to select model components.
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Affiliation(s)
| | - Pasi Raumonen
- Laboratory of Mathematics, Tampere University of Technology, Tampere, Finland
| | | | - Eero Nikinmaa
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Pekka Kaitaniemi
- Hyytiälä Forestry Field Station University of Helsinki, Korkeakoski, Finland
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12
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Raumonen P, Tarvainen T. Segmentation of vessel structures from photoacoustic images with reliability assessment. Biomed Opt Express 2018; 9:2887-2904. [PMID: 29984073 PMCID: PMC6033551 DOI: 10.1364/boe.9.002887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 05/20/2023]
Abstract
Photoacoustic imaging enables the imaging of soft biological tissue with combined optical contrast and ultrasound resolution. One of the targets of interest is tissue vasculature. However, the photoacoustic images may not directly provide the information on, for example, vasculature structure. Therefore, the images are improved by reducing noise and artefacts, and processed for better visualisation of the target of interest. In this work, we present a new segmentation method of photoacoustic images that also straightforwardly produces assessments of its reliability. The segmentation depends on parameters which have a natural tendency to increase the reliability as the parameter values monotonically change. The reliability is assessed by counting classifications of image voxels with different parameter values. The resulting segmentation with reliability offers new ways and tools to analyse photoacoustic images and new possibilities for utilising them as anatomical priors in further computations. Our MATLAB implementation of the method is available as an open-source software package [P. Raumonen, Matlab, 2018].
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Affiliation(s)
- Pasi Raumonen
- Laboratory of Mathematics, Tampere University of Technology, PO Box 527, 33101 Tampere,
Finland
| | - Tanja Tarvainen
- Department of Applied Physics, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio,
Finland
- Department of Computer Science, University College London, Gower Street, London WC1E 6BT,
UK
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13
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Åkerblom M, Raumonen P, Casella E, Disney MI, Danson FM, Gaulton R, Schofield LA, Kaasalainen M. Non-intersecting leaf insertion algorithm for tree structure models. Interface Focus 2018; 8:20170045. [PMID: 29503724 PMCID: PMC5829186 DOI: 10.1098/rsfs.2017.0045] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 11/29/2022] Open
Abstract
We present an algorithm and an implementation to insert broadleaves or needleleaves into a quantitative structure model according to an arbitrary distribution, and a data structure to store the required information efficiently. A structure model contains the geometry and branching structure of a tree. The purpose of this work is to offer a tool for making more realistic simulations of tree models with leaves, particularly for tree models developed from terrestrial laser scanning (TLS) measurements. We demonstrate leaf insertion using cylinder-based structure models, but the associated software implementation is written in a way that enables the easy use of other types of structure models. Distributions controlling leaf location, size and angles as well as the shape of individual leaves are user definable, allowing any type of distribution. The leaf generation process consist of two stages, the first of which generates individual leaf geometry following the input distributions, while in the other stage intersections are prevented by carrying out transformations when required. Initial testing was carried out on English oak trees to demonstrate the approach and to assess the required computational resources. Depending on the size and complexity of the tree, leaf generation takes between 6 and 18 min. Various leaf area density distributions were defined, and the resulting leaf covers were compared with manual leaf harvesting measurements. The results are not conclusive, but they show great potential for the method. In the future, if our method is demonstrated to work well for TLS data from multiple tree types, the approach is likely to be very useful for three-dimensional structure and radiative transfer simulation applications, including remote sensing, ecology and forestry, among others.
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Affiliation(s)
- Markku Åkerblom
- Laboratory of Mathematics, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland
| | - Pasi Raumonen
- Laboratory of Mathematics, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland
| | - Eric Casella
- Centre for Sustainable Forestry and Climate Change, Forest Research, Farnham GU10 4LH, UK
| | - Mathias I Disney
- Department of Geography, University College London, Gower Street, London WC1E 6BT, UK.,NERC National Centre for Earth Observation (NCEO), UK
| | - F Mark Danson
- School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Rachel Gaulton
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Lucy A Schofield
- School of Humanities, Religion and Philosophy, York St John University, York YO31 7EX, UK
| | - Mikko Kaasalainen
- Laboratory of Mathematics, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland
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14
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Disney MI, Boni Vicari M, Burt A, Calders K, Lewis SL, Raumonen P, Wilkes P. Weighing trees with lasers: advances, challenges and opportunities. Interface Focus 2018; 8:20170048. [PMID: 29503726 PMCID: PMC5829188 DOI: 10.1098/rsfs.2017.0048] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 11/15/2022] Open
Abstract
Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.
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Affiliation(s)
- M I Disney
- UCL Department of Geography, Gower Street, London WC1E 6BT, UK.,NERC National Centre for Earth Observation (NCEO), UK
| | - M Boni Vicari
- UCL Department of Geography, Gower Street, London WC1E 6BT, UK
| | - A Burt
- UCL Department of Geography, Gower Street, London WC1E 6BT, UK
| | - K Calders
- Earth Observation, Climate and Optical Group, National Physical Laboratory, Teddington TW11 0LW, UK
| | - S L Lewis
- UCL Department of Geography, Gower Street, London WC1E 6BT, UK.,School of Geography, University of Leeds, Leeds LS2 9JT, UK
| | - P Raumonen
- Tampere University of Technology, Laboratory of Mathematics, Korkeakoulunkatu 10, 33720 Tampere, Finland
| | - P Wilkes
- UCL Department of Geography, Gower Street, London WC1E 6BT, UK.,NERC National Centre for Earth Observation (NCEO), UK
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15
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Gonzalez de Tanago J, Lau A, Bartholomeus H, Herold M, Avitabile V, Raumonen P, Martius C, Goodman RC, Disney M, Manuri S, Burt A, Calders K. Estimation of above‐ground biomass of large tropical trees with terrestrial LiDAR. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12904] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jose Gonzalez de Tanago
- Laboratory of Geo‐Information Science and Remote SensingWageningen University & Research Wageningen The Netherlands
- Center for International Forestry Research (CIFOR) Bogor Indonesia
| | - Alvaro Lau
- Laboratory of Geo‐Information Science and Remote SensingWageningen University & Research Wageningen The Netherlands
- Center for International Forestry Research (CIFOR) Bogor Indonesia
| | - Harm Bartholomeus
- Laboratory of Geo‐Information Science and Remote SensingWageningen University & Research Wageningen The Netherlands
| | - Martin Herold
- Laboratory of Geo‐Information Science and Remote SensingWageningen University & Research Wageningen The Netherlands
| | - Valerio Avitabile
- Laboratory of Geo‐Information Science and Remote SensingWageningen University & Research Wageningen The Netherlands
| | - Pasi Raumonen
- Laboratory of MathematicsTampere University of Technology Tampere Finland
| | | | - Rosa C. Goodman
- Department of Forest Ecology and ManagementSwedish University of Agricultural Sciences (SLU) Umeå Sweden
| | - Mathias Disney
- Department of GeographyUniversity College London London UK
- NERC National Centre for Earth Observation (NCEO) Leicester UK
| | - Solichin Manuri
- Fenner School of Environment and SocietyAustralian National University Canberra ACT Australia
| | - Andrew Burt
- Department of GeographyUniversity College London London UK
| | - Kim Calders
- Department of GeographyUniversity College London London UK
- Earth ObservationClimate and Optical groupNational Physical Laboratory Teddington UK
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16
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Potapov I, Järvenpää M, Åkerblom M, Raumonen P, Kaasalainen M. Bayes Forest: a data-intensive generator of morphological tree clones. Gigascience 2017; 6:1-13. [PMID: 29020742 PMCID: PMC5632294 DOI: 10.1093/gigascience/gix079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/08/2017] [Accepted: 08/13/2017] [Indexed: 12/04/2022] Open
Abstract
Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree "clones" based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research.
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Affiliation(s)
- Ilya Potapov
- Mathematics Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland
| | - Marko Järvenpää
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076, Espoo, Finland
| | - Markku Åkerblom
- Mathematics Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland
| | - Pasi Raumonen
- Mathematics Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland
| | - Mikko Kaasalainen
- Mathematics Department, Tampere University of Technology, P.O. Box 553, 33101, Tampere, Finland
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17
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Calders K, Newnham G, Burt A, Murphy S, Raumonen P, Herold M, Culvenor D, Avitabile V, Disney M, Armston J, Kaasalainen M. Nondestructive estimates of above‐ground biomass using terrestrial laser scanning. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12301] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kim Calders
- Laboratory of Geo‐Information Science and Remote Sensing Wageningen University Droevendaalsesteeg 3 Wageningen 6708 PBThe Netherlands
| | - Glenn Newnham
- CSIRO Land and Water Private Bag 10 Clayton South Vic.3169Australia
| | - Andrew Burt
- Department of Geography University College London Gower Street London WC1E 6BTUK
| | - Simon Murphy
- Melbourne School of Land and Environment University of Melbourne 500 Yarra Boulevard Richmond Vic. 3121Australia
| | - Pasi Raumonen
- Department of Mathematics Tampere University of Technology P.O. Box 553 FI‐33101Tampere Finland
| | - Martin Herold
- Laboratory of Geo‐Information Science and Remote Sensing Wageningen University Droevendaalsesteeg 3 Wageningen 6708 PBThe Netherlands
| | - Darius Culvenor
- Environmental Sensing Systems 16 Mawby Road Bentleigh East Vic.3165 Australia
| | - Valerio Avitabile
- Laboratory of Geo‐Information Science and Remote Sensing Wageningen University Droevendaalsesteeg 3 Wageningen 6708 PBThe Netherlands
| | - Mathias Disney
- Department of Geography University College London Gower Street London WC1E 6BTUK
- NERC National Centre for Earth Observation UK
| | - John Armston
- Remote Sensing Centre Department of Science Information Technology, Innovation and the Arts Ecosciences Precinct 41 Boggo Road Dutton Park Qld4102Australia
- Joint Remote Sensing Research Programme School of Geography, Planning and Environmental Management University of Queensland Brisbane Qld4072Australia
| | - Mikko Kaasalainen
- Department of Mathematics Tampere University of Technology P.O. Box 553 FI‐33101Tampere Finland
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