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Root visualization software tools | Mathematical modeling

Root architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural…
RSML
Nontypeable

RSML Root System Markup Language

Facilitates the sharing of root architectures between software, experiments,…

Facilitates the sharing of root architectures between software, experiments, and research groups. RSML defines an XML file in which the topological, geometrical, and numerical information describing…

PRIMAL
Desktop

PRIMAL Pipeline of Root Image analysis using MAchine Learning

Allows users to analyze root images using machine learning techniques. PRIMAL…

Allows users to analyze root images using machine learning techniques. PRIMAL trains the Random Forest (RF) model and analyzes data. The software can be used to extract descriptors from large…

measuRoots
Desktop

measuRoots

Allows controlled experiments to be conducted on soil without compromising…

Allows controlled experiments to be conducted on soil without compromising factors such as exposure of roots to white light. measuRoots is an R package that presents an efficient pipeline for root…

OpenAlea
Desktop

OpenAlea

Allows researchers to build models using a visual programming interface.…

Allows researchers to build models using a visual programming interface. OpenAlea is based on a combination of the two families of approaches: a plant architecture analysis and a visual programming.…

R-SWMS
Desktop

R-SWMS Root-Soil Water Movement and Solute transport

Simulates solute transport and water flow in and between the soil and the plant…

Simulates solute transport and water flow in and between the soil and the plant systems. R-SWMS is based on the water potential gradient between soil and root nodes. It assumes that soil water is…

OpenSimRoot
Desktop

OpenSimRoot

Allows to model 3D architectural plant model. OpenSimRoot is based on…

Allows to model 3D architectural plant model. OpenSimRoot is based on interaction of minimodels, which encapsulate the simulation of a single state variable. It can represent the stele diameter,…

SimRoot
Desktop

SimRoot

Generates a realistic solid model of root geometry. SimRoot can modify the…

Generates a realistic solid model of root geometry. SimRoot can modify the functional form of the growth model of a simulated root system or simply the parameters of that model in order to change…

CRootBox
Web
Desktop

CRootBox

Models root architecture and its interactions with static and dynamic soil…

Models root architecture and its interactions with static and dynamic soil environments. CRootBox provides generic interfaces to interact with external models that simulate the soil environment or…

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