scholarly journals Model selection and parameter estimation for root architecture models using likelihood-free inference

2019 ◽  
Vol 16 (156) ◽  
pp. 20190293
Author(s):  
Clare Ziegler ◽  
Rosemary J. Dyson ◽  
Iain G. Johnston
Keyword(s):  
Root System ◽  
Approximate Bayesian Computation ◽  
Growth Parameters ◽  
Plant Root ◽  
System Architectures ◽  
Mechanistic Insight ◽  
Approximate Bayesian ◽  
Plant Root Systems ◽  
Model Structures ◽  
Insight Into

Plant root systems play vital roles in the biosphere, environment and agriculture, but the quantitative principles governing their growth and architecture remain poorly understood. The ‘forward problem’ of what root forms can arise from given models and parameters has been well studied through modelling and simulation, but comparatively little attention has been given to the ‘inverse problem’: what models and parameters are responsible for producing an experimentally observed root system? Here, we propose the use of approximate Bayesian computation (ABC) to infer mechanistic parameters governing root growth and architecture, allowing us to learn and quantify uncertainty in parameters and model structures using observed root architectures. We demonstrate the use of this platform on synthetic and experimental root data and show how it may be used to identify growth mechanisms and characterize growth parameters in different mutants. Our highly adaptable framework can be used to gain mechanistic insight into the generation of observed root system architectures.

scholarly journals Recovering complete plant root system architectures from soil via X-ray μ-Computed Tomography

Plant Methods ◽  
2013 ◽  
Vol 9 (1) ◽  
pp. 8 ◽  
Author(s):  
Stefan Mairhofer ◽  
Susan Zappala ◽  
Saoirse Tracy ◽  
Craig Sturrock ◽  
Malcolm John Bennett ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Root System ◽  
Plant Root ◽  
System Architectures ◽  
X Ray ◽  
Complete Plant ◽  
Plant Root System

scholarly journals An Ultra-Wideband Frequency System for Non-Destructive Root Imaging

Sensors ◽  
2018 ◽  
Vol 18 (8) ◽  
pp. 2438 ◽  
Author(s):  
Thomas Truong ◽  
Anh Dinh ◽  
Khan Wahid
Keyword(s):  
Image Processing ◽  
Root System ◽  
Plant Root ◽  
Ultra Wideband ◽  
Soil Conditions ◽  
System Architectures ◽  
Image Processing And Analysis ◽  
Processing Module ◽  
Data Acquisition Module ◽  
Non Destructive

Understanding the root system architecture of plants as they develop is critical for increasing crop yields through plant phenotyping, and ultra-wideband imaging systems have shown potential as a portable, low-cost solution to non-destructive imaging root system architectures. This paper presents the design, implementation, and analysis of an ultra-wideband imaging system for use in imaging potted plant root system architectures. The proposed system is separated into three main subsystems: a Data Acquisition module, a Data Processing module, and an Image Processing and Analysis module. The Data Acquisition module consists of simulated and experimental implementations of a non-contact synthetic aperture radar system to measure ultra-wideband signal reflections from concealed scattering objects in a pot containing soil. The Data Processing module is responsible for interpreting the measured ultra-wideband signals and producing an image using a delay-and-sum beamforming algorithm. The Image Processing and Analysis module is responsible for improving image quality and measuring root depth and average root diameter in an unsupervised manner. The Image Processing and Analysis module uses a modified top-hat transformation alongside quantization methods based on energy distributions in the image to isolate the surface of the imaged root. Altogether, the proposed subsystems are capable of imaging and measuring concealed taproot system architectures with controlled soil conditions; however, the performance of the system is highly dependent on knowledge of the soil conditions. Smaller roots in difficult imaging conditions require future work into understanding and compensating for unwanted noise. Ultimately, this paper sought to provide insight into improving imaging quality of ultra-wideband (UWB) imaging systems for plant root imaging for other works to be followed.

scholarly journals Interpreting scratch assays using pair density dynamics and approximate Bayesian computation

Open Biology ◽  
2014 ◽  
Vol 4 (9) ◽  
pp. 140097 ◽  
Author(s):  
Stuart T. Johnston ◽  
Matthew J. Simpson ◽  
D. L. Sean McElwain ◽  
Benjamin J. Binder ◽  
Joshua V. Ross
Keyword(s):  
Approximate Bayesian Computation ◽  
Chronic Wounds ◽  
Essential Element ◽  
Cell Spreading ◽  
Bayesian Computation ◽  
Potential Treatment ◽  
Pair Density ◽  
Approximate Bayesian ◽  
The Impact ◽  
Insight Into

Quantifying the impact of biochemical compounds on collective cell spreading is an essential element of drug design, with various applications including developing treatments for chronic wounds and cancer. Scratch assays are a technically simple and inexpensive method used to study collective cell spreading; however, most previous interpretations of scratch assays are qualitative and do not provide estimates of the cell diffusivity, D , or the cell proliferation rate, λ . Estimating D and λ is important for investigating the efficacy of a potential treatment and provides insight into the mechanism through which the potential treatment acts. While a few methods for estimating D and λ have been proposed, these previous methods lead to point estimates of D and λ , and provide no insight into the uncertainty in these estimates. Here, we compare various types of information that can be extracted from images of a scratch assay, and quantify D and λ using discrete computational simulations and approximate Bayesian computation. We show that it is possible to robustly recover estimates of D and λ from synthetic data, as well as a new set of experimental data. For the first time, our approach also provides a method to estimate the uncertainty in our estimates of D and λ . We anticipate that our approach can be generalized to deal with more realistic experimental scenarios in which we are interested in estimating D and λ , as well as additional relevant parameters such as the strength of cell-to-cell adhesion or the strength of cell-to-substrate adhesion.

scholarly journals The Application of Contrast Media for In Vivo Feature Enhancement in X-Ray Computed Tomography of Soil-Grown Plant Roots

2017 ◽  
Vol 23 (3) ◽  
pp. 538-552 ◽  
Author(s):  
Samuel D. Keyes ◽  
Neil J. Gostling ◽  
Jessica H. Cheung ◽  
Tiina Roose ◽  
Ian Sinclair ◽  
...  
Keyword(s):  
Contrast Media ◽  
Plant Root ◽  
Root Systems ◽  
System Architectures ◽  
X Ray ◽  
Iodinated Contrast ◽  
Seminal Roots ◽  
X Ray Computed ◽  
Plant Root Systems

AbstractThe use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.

Utilization of a hydrate cellulose film for investigation of Arabidopsis thaliana L. root system growth and development

2020 ◽  
Vol 36 (1) ◽  
pp. 36-43
Author(s):  
I.O. Konovalova ◽  
T.N. Kudelina ◽  
S.O. Smolyanina ◽  
A.I. Lilienberg ◽  
T.N. Bibikova
Keyword(s):  
Arabidopsis Thaliana ◽  
Root System ◽  
Life Support ◽  
Higher Plants ◽  
Plant Root ◽  
Lateral Roots ◽  
Basic Research ◽  
Cellulose Film ◽  
A New Technique ◽  
Basic Research Project

A new technique for Arabidopsis thaliana cultivation has been proposed that combines the use of a phytogel-based nutrient medium and a hydrophilic membrane of hydrate cellulose film, separating the root system of the plant from the medium thickness. Growth rates of both main and lateral roots were faster in the plants cultivated on the surface of hydrate cellulose film than in the plants grown in the phytogel volume. The location of the root system on the surface of the transparent hydrate film simplifies its observation and analysis and facilitates plant transplantation with preservation of the root system configuration. The proposed technique allowed us to first assess the effect of exogenous auxin on the growth of lateral roots at the 5-6 developmental stage. methods to study plant root systems, hydrate cellulose film, A. thaliana, lateral roots, differential root growth rate, auxin The work was financially supported by the Russian Foundation for Basic Research (Project Bel_mol_a 19-54-04015) and the basic topic of the Russian Academy of Sciences - IBMP RAS «Regularities of the Influence of Extreme Environmental Factors on the Processes of Cultivation of Higher Plants and the Development of Japanese Quail Tissues at Different Stages of its Ontogenesis under the Conditions of Regenerative Life Support Systems».

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