2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT GreenLab is a functional-structural plant model that has already been applied to a numbe... more ABSTRACT GreenLab is a functional-structural plant model that has already been applied to a number of various plant species. Plant organogenesis is described by the dual-scale automaton formalism and growth is driven by source-sink relations between plant organs. The paper presents how the formalism of GreenLab and the growth process can be translated into the rule-based language XL. Currently essential parts of the deterministic and stochastic version of the GreenLab model are included. To provide a user-friendly way for parameter input, an additional graphical user interface was developed as part of the modelling platform GroIMP. Furthermore, the features provided by GroIMP can now be coupled with GreenLab, e.g., the integrated radiation model, based on Monte Carlo ray tracing, for computing the light distribution in the canopy.
Functional-structural plant models (FSPMs) simulate biological processes at different spatial sca... more Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming ...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to cr... more ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to crop modeling as a promising tool for the integration and exploration of experimental data from breeding and agronomy. Set up suitably, crop modeling can then also be used to predict performance of future high-yielding cultivars, e.g. of rice, which is one of the major food crops worldwide. Questions such as “Which combination of alleles is likely to have the strongest influence on the development of the individual phenotype?” or “In which way is QTL action modified by a particular environment?” can be tackled with the help of a crop modeling approach. As a further extension of a previously established Functional-Structural Plant model (FSPM) of rice we present here simulated “virtual” reproduction of individuals using QTL information, which can contribute to providing answers to these difficult questions. In this study, we briefly describe the way QTL information has been integrated into the rice model, and sketch the algorithmic implementation of processes leading to the creation of filial genotypes from parental genotypes via simulated sexual reproduction. The phenotype value, which in this case was plant height, was determined with the rules that specify the genetic processes operating on genotypes as intrinsic properties of each individual. The mapping results from the simulated population were compared with the input values for the parental lines. It is shown that the rice model faithfully reflected the genetic properties from the parental lines with low bias, which suggests a reasonable way to integrate QTLs into the plant eco-physiological model with the predictive properties. It could in the future be used as a supporting tool in breeding practice.
Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant m... more Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant material, management practice and environment. Plant structure is determined by bud break and shoot development while having an effect on local light climate. The aim of the present study is to cover selected aspects of the cut-rose system using functional -structural plant modelling (FSPM), in order to better understand processes contributing to produce quality and quantity. † Methods The model describes the production system in three dimensions, including a virtual greenhouse environment with the crop, light sources (diffuse and direct sun light and lamps) and photosynthetically active radiation (PAR) sensors. The crop model is designed as a multiscaled FSPM with plant organs (axillary buds, leaves, internodes, flowers) as basic units, and local light interception and photosynthesis within each leaf. A Monte-Carlo light model was used to compute the local light climate for leaf photosynthesis, the latter described using a biochemical rate model. † Key Results The model was able to reproduce PAR measurements taken at different canopy positions, different times of the day and different light regimes. Simulated incident and absorbed PAR as well as net assimilation rate in upright and bent shoots showed characteristic spatial and diurnal dynamics for different common cultivation scenarios. † Conclusions The model of cut-rose presented allowed the creation of a range of initial structures thanks to interactive rules for pruning, cutting and bending. These static structures can be regarded as departure points for the dynamic simulation of production of flower canes. Furthermore, the model was able to predict local ( per leaf ) light absorption and photosynthesis. It can be used to investigate the physiology of ornamental plants, and provide support for the decisions of growers and consultants.
As a first step towards a generic genotype-phenotype model of rice, we present here a model of th... more As a first step towards a generic genotype-phenotype model of rice, we present here a model of the growth and morphology of rice in combination with ecophysiological processes using the technique of functional-structural plant modelling (FSPM) and the interactive modelling platform GroIMP along with the graph-based Relational Growth Grammar formalism. The model constitutes a simple yet functionally coherent phenotype model of rice, consisting of a set of morphogenetic RGG rules describing an “average” developmental course and final morphology, partially linking yield traits to processes (tiller and grain number, stem length, grain filling rate, grain weight).
Maximizing photosynthesis at the canopy level is important for enhancing crop yield, and this req... more Maximizing photosynthesis at the canopy level is important for enhancing crop yield, and this requires insights into the limiting factors of photosynthesis. Using greenhouse cucumber (Cucumis sativus) as an example, this study provides a novel approach to quantify different components of photosynthetic limitations at the leaf level and to upscale these limitations to different canopy layers and the whole plant. A static virtual three-dimensional canopy structure was constructed using digitized plant data in GroIMP. Light interception of the leaves was simulated by a ray-tracer and used to compute leaf photosynthesis. Different components of photosynthetic limitations, namely stomatal (S(L)), mesophyll (M(L)), biochemical (B(L)) and light (L(L)) limitations, were calculated by a quantitative limitation analysis of photosynthesis under different light regimes. In the virtual cucumber canopy, B(L) and L(L) were the most prominent factors limiting whole-plant photosynthesis. Diffusional...
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
This paper presents an easy and effective method to extract tree rings completely from images of ... more This paper presents an easy and effective method to extract tree rings completely from images of tree discs independent of their source. The method uses Active Contours, often used in medical image processing to detect organs, in combination with an optimised image filter based on the Sobel operator to automatically outline the tree rings. Special attention is given to eliminate critical physical irregularities caused by branches, cracks or colourisations. The work resulted in the implementation of a platform independent, free and open source software solution for semiautomatic tree ring segmentation. Comparison to manual measurements shows that the system is dependable and the results are reproducible. The system has been applied to several conifer species.
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
Functional-structural plant models (FSPMs) simulate biological processes at different spatial sca... more Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming ...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to cr... more ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to crop modeling as a promising tool for the integration and exploration of experimental data from breeding and agronomy. Set up suitably, crop modeling can then also be used to predict performance of future high-yielding cultivars, e.g. of rice, which is one of the major food crops worldwide. Questions such as “Which combination of alleles is likely to have the strongest influence on the development of the individual phenotype?” or “In which way is QTL action modified by a particular environment?” can be tackled with the help of a crop modeling approach. As a further extension of a previously established Functional-Structural Plant model (FSPM) of rice we present here simulated “virtual” reproduction of individuals using QTL information, which can contribute to providing answers to these difficult questions. In this study, we briefly describe the way QTL information has been integrated into the rice model, and sketch the algorithmic implementation of processes leading to the creation of filial genotypes from parental genotypes via simulated sexual reproduction. The phenotype value, which in this case was plant height, was determined with the rules that specify the genetic processes operating on genotypes as intrinsic properties of each individual. The mapping results from the simulated population were compared with the input values for the parental lines. It is shown that the rice model faithfully reflected the genetic properties from the parental lines with low bias, which suggests a reasonable way to integrate QTLs into the plant eco-physiological model with the predictive properties. It could in the future be used as a supporting tool in breeding practice.
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT GreenLab is a functional-structural plant model that has already been applied to a numbe... more ABSTRACT GreenLab is a functional-structural plant model that has already been applied to a number of various plant species. Plant organogenesis is described by the dual-scale automaton formalism and growth is driven by source-sink relations between plant organs. The paper presents how the formalism of GreenLab and the growth process can be translated into the rule-based language XL. Currently essential parts of the deterministic and stochastic version of the GreenLab model are included. To provide a user-friendly way for parameter input, an additional graphical user interface was developed as part of the modelling platform GroIMP. Furthermore, the features provided by GroIMP can now be coupled with GreenLab, e.g., the integrated radiation model, based on Monte Carlo ray tracing, for computing the light distribution in the canopy.
Functional-structural plant models (FSPMs) simulate biological processes at different spatial sca... more Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming ...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to cr... more ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to crop modeling as a promising tool for the integration and exploration of experimental data from breeding and agronomy. Set up suitably, crop modeling can then also be used to predict performance of future high-yielding cultivars, e.g. of rice, which is one of the major food crops worldwide. Questions such as “Which combination of alleles is likely to have the strongest influence on the development of the individual phenotype?” or “In which way is QTL action modified by a particular environment?” can be tackled with the help of a crop modeling approach. As a further extension of a previously established Functional-Structural Plant model (FSPM) of rice we present here simulated “virtual” reproduction of individuals using QTL information, which can contribute to providing answers to these difficult questions. In this study, we briefly describe the way QTL information has been integrated into the rice model, and sketch the algorithmic implementation of processes leading to the creation of filial genotypes from parental genotypes via simulated sexual reproduction. The phenotype value, which in this case was plant height, was determined with the rules that specify the genetic processes operating on genotypes as intrinsic properties of each individual. The mapping results from the simulated population were compared with the input values for the parental lines. It is shown that the rice model faithfully reflected the genetic properties from the parental lines with low bias, which suggests a reasonable way to integrate QTLs into the plant eco-physiological model with the predictive properties. It could in the future be used as a supporting tool in breeding practice.
Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant m... more Aims The production system of cut-rose (Rosa × hybrida) involves a complex combination of plant material, management practice and environment. Plant structure is determined by bud break and shoot development while having an effect on local light climate. The aim of the present study is to cover selected aspects of the cut-rose system using functional -structural plant modelling (FSPM), in order to better understand processes contributing to produce quality and quantity. † Methods The model describes the production system in three dimensions, including a virtual greenhouse environment with the crop, light sources (diffuse and direct sun light and lamps) and photosynthetically active radiation (PAR) sensors. The crop model is designed as a multiscaled FSPM with plant organs (axillary buds, leaves, internodes, flowers) as basic units, and local light interception and photosynthesis within each leaf. A Monte-Carlo light model was used to compute the local light climate for leaf photosynthesis, the latter described using a biochemical rate model. † Key Results The model was able to reproduce PAR measurements taken at different canopy positions, different times of the day and different light regimes. Simulated incident and absorbed PAR as well as net assimilation rate in upright and bent shoots showed characteristic spatial and diurnal dynamics for different common cultivation scenarios. † Conclusions The model of cut-rose presented allowed the creation of a range of initial structures thanks to interactive rules for pruning, cutting and bending. These static structures can be regarded as departure points for the dynamic simulation of production of flower canes. Furthermore, the model was able to predict local ( per leaf ) light absorption and photosynthesis. It can be used to investigate the physiology of ornamental plants, and provide support for the decisions of growers and consultants.
As a first step towards a generic genotype-phenotype model of rice, we present here a model of th... more As a first step towards a generic genotype-phenotype model of rice, we present here a model of the growth and morphology of rice in combination with ecophysiological processes using the technique of functional-structural plant modelling (FSPM) and the interactive modelling platform GroIMP along with the graph-based Relational Growth Grammar formalism. The model constitutes a simple yet functionally coherent phenotype model of rice, consisting of a set of morphogenetic RGG rules describing an “average” developmental course and final morphology, partially linking yield traits to processes (tiller and grain number, stem length, grain filling rate, grain weight).
Maximizing photosynthesis at the canopy level is important for enhancing crop yield, and this req... more Maximizing photosynthesis at the canopy level is important for enhancing crop yield, and this requires insights into the limiting factors of photosynthesis. Using greenhouse cucumber (Cucumis sativus) as an example, this study provides a novel approach to quantify different components of photosynthetic limitations at the leaf level and to upscale these limitations to different canopy layers and the whole plant. A static virtual three-dimensional canopy structure was constructed using digitized plant data in GroIMP. Light interception of the leaves was simulated by a ray-tracer and used to compute leaf photosynthesis. Different components of photosynthetic limitations, namely stomatal (S(L)), mesophyll (M(L)), biochemical (B(L)) and light (L(L)) limitations, were calculated by a quantitative limitation analysis of photosynthesis under different light regimes. In the virtual cucumber canopy, B(L) and L(L) were the most prominent factors limiting whole-plant photosynthesis. Diffusional...
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
This paper presents an easy and effective method to extract tree rings completely from images of ... more This paper presents an easy and effective method to extract tree rings completely from images of tree discs independent of their source. The method uses Active Contours, often used in medical image processing to detect organs, in combination with an optimised image filter based on the Sobel operator to automatically outline the tree rings. Special attention is given to eliminate critical physical irregularities caused by branches, cracks or colourisations. The work resulted in the implementation of a platform independent, free and open source software solution for semiautomatic tree ring segmentation. Comparison to manual measurements shows that the system is dependable and the results are reproducible. The system has been applied to several conifer species.
We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly... more We identified that in a two meter high greenhouse grown cucumber canopy, photosynthesis is mostly light-limited, and light interception and biochemical capacity are the major factors limiting photosynthesis. The diffusion pathways, stomatal and mesophyll conductance, are minor restrictions.
Functional-structural plant models (FSPMs) simulate biological processes at different spatial sca... more Functional-structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs. A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming ...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to cr... more ABSTRACT Crop plant researchers and agronomists have in the recent past increasingly turned to crop modeling as a promising tool for the integration and exploration of experimental data from breeding and agronomy. Set up suitably, crop modeling can then also be used to predict performance of future high-yielding cultivars, e.g. of rice, which is one of the major food crops worldwide. Questions such as “Which combination of alleles is likely to have the strongest influence on the development of the individual phenotype?” or “In which way is QTL action modified by a particular environment?” can be tackled with the help of a crop modeling approach. As a further extension of a previously established Functional-Structural Plant model (FSPM) of rice we present here simulated “virtual” reproduction of individuals using QTL information, which can contribute to providing answers to these difficult questions. In this study, we briefly describe the way QTL information has been integrated into the rice model, and sketch the algorithmic implementation of processes leading to the creation of filial genotypes from parental genotypes via simulated sexual reproduction. The phenotype value, which in this case was plant height, was determined with the rules that specify the genetic processes operating on genotypes as intrinsic properties of each individual. The mapping results from the simulated population were compared with the input values for the parental lines. It is shown that the rice model faithfully reflected the genetic properties from the parental lines with low bias, which suggests a reasonable way to integrate QTLs into the plant eco-physiological model with the predictive properties. It could in the future be used as a supporting tool in breeding practice.
Uploads
Papers by Michael Henke