WheatSpikeNet: an improved wheat spike segmentation model for accurate estimation from field imaging.

Phenotyping is used in plant breeding to identify genotypes with desirable characteristics, such as drought tolerance, disease resistance, and high-yield potentials. It may also be used to evaluate the effect of environmental circumstances, such as drought, heat, and salt, on plant growth and development. Wheat spike density measure is one of the most important agronomic factors relating to wheat phenotyping.

Modelling of PFAS-surface interactions: Effect of surface charge and solution ions.

PER-: and poly-fluoroalkyl substances (PFAS) are a class of substances of increasing concern as environmental contaminants. The interactions between PFAS and surfaces play an important role in PFAS transport and remediation. Previous studies have found PFAS adsorption to be dependent upon properties including pH, organic matter and particle size, along with PFAS functional group and carbon chain length.

A Whole Leaf Comparative Study of Stomatal Conductance Models.

We employed a detailed whole leaf hydraulic model to study the local operation of three stomatal conductance models distributed on the scale of a whole leaf. We quantified the behavior of these models by examining the leaf-area distributions of photosynthesis, transpiration, stomatal conductance, and guard cell turgor pressure. We gauged the models' local responses to changes in environmental conditions of carbon dioxide concentration, relative humidity, and light irradiance.

Density functional theory of confined ionic liquids: the influence of power-law attractions on molecule distributions and surface forces.

Interaction energies and density profiles for two model ionic liquids, [Cmim][BF ] and [Cmim][TFSI], confined between charged planar walls are studied within a density functional theory framework. The results of these simulations are also compared with results assuming a simpler linear hexamer-monomer, cation-anion system. We focus attention on the effect on the atom site distributions and the surface forces of an additional, specific attractive potential between oppositely charged molecules.

Interrogating the relationship between the microstructure of amphiphilic poly(ethylene glycol-b-caprolactone) copolymers and their colloidal assemblies using non-interfering techniques.

Understanding the microstructural parameters of amphiphilic copolymers that control the formation and structure of aggregated colloids (e.g., micelles) is essential for the rational design of hierarchically structured systems for applications in nanomedicine, personal care and food formulations.

On the Efficacy of Water Transport in Leaves. A Coupled Xylem-Phloem Model of Water and Solute Transport.

In this paper, we present and use a coupled xylem/phloem mathematical model of passive water and solute transport through a reticulated vascular system of an angiosperm leaf. We evaluate the effect of leaf width-to-length proportion and orientation of second-order veins on the indexes of water transport into the leaves and sucrose transport from the leaves. We found that the most important factor affecting the steady-state pattern of hydraulic pressure distribution in the xylem and solute concentration in the phloem was leaf shape: narrower/longer leaves are less efficient in convecting xylem water and phloem solutes than wider/shorter leaves under all conditions studied.

A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. III. Quantifying the Energy Costs of Ion Transport in Salt-Stressed Roots of .

Salt stress defense mechanisms in plant roots, such as active Na efflux and storage, require energy in the form of ATP. Understanding the energy required for these transport mechanisms is an important step toward achieving an understanding of salt tolerance. However, accurate measurements of the fluxes required to estimate these energy costs are difficult to achieve by experimental means.

Statistical analysis and modeling of the geometry and topology of plant roots.

The root is an important organ of a plant since it is responsible for water and nutrient uptake. Analyzing and modeling variabilities in the geometry and topology of roots can help in assessing the plant's health, understanding its growth patterns, and modeling relations between plant species and between plants and their environment. In this article, we develop a framework for the statistical analysis and modeling of the geometry and topology of plant roots.

A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. II. Clarifying the Roles of SOS1 in the Salt-Stress Response in .

SOS1 transporters play an essential role in plant salt tolerance. Although is known to encode a plasma membrane Na/H antiporter, the transport mechanisms by which these transporters contribute to salt tolerance at the level of the whole root are unclear. Gene expression and flux measurements have provided conflicting evidence for the location of SOS1 transporter activity, making it difficult to determine their function.

An Automatic Field Plot Extraction Method From Aerial Orthomosaic Images.

Unmanned aerial vehicles have an immense capacity for remote imaging of plants in agronomic field research trials. Traits extracted from the plots can explain development of the plants coverage, growth, flowering status, and related phenomenon. An important prerequisite step to obtain such information is to find the exact position of plots to extract them from an orthomosaic image.

High-Throughput Field Imaging and Basic Image Analysis in a Wheat Breeding Programme.

Visual assessment of colour-based traits plays a key role within field-crop breeding programmes, though the process is subjective and time-consuming. Digital image analysis has previously been investigated as an objective alternative to visual assessment for a limited number of traits, showing suitability and slight improvement to throughput over visual assessment. However, easily adoptable, field-based high-throughput methods are still lacking.

Density functional theory of confined ionic liquids: A survey of the effects of ion type, molecular charge distribution, and surface adsorption.

Ionic liquids confined between two planar charged walls are explored using density functional theory. The effort represents a study of the effects of the molecular structure, molecular charge distribution, and degree of surface adsorption on forces between the surfaces and on the inhomogeneous atom density profiles. Surface adsorption was found to significantly affect both the magnitude and sign of the surface forces, while differences in the distribution of molecular charge did not.

Energy costs of salt tolerance in crop plants.

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed.

Correction to: Detection and analysis of wheat spikes using Convolutional Neural Networks.

[This corrects the article DOI: 10.1186/s13007-018-0366-8.].

Detection and analysis of wheat spikes using Convolutional Neural Networks.

Background: Field phenotyping by remote sensing has received increased interest in recent years with the possibility of achieving high-throughput analysis of crop fields. Along with the various technological developments, the application of machine learning methods for image analysis has enhanced the potential for quantitative assessment of a multitude of crop traits. For wheat breeding purposes, assessing the production of wheat spikes, as the grain-bearing organ, is a useful proxy measure of grain production.

Land-based crop phenotyping by image analysis: consistent canopy characterization from inconsistent field illumination.

Background: One of the main challenges associated with image-based field phenotyping is the variability of illumination. During a single day's imaging session, or between different sessions on different days, the sun moves in and out of cloud cover and has varying intensity. How is one to know from consecutive images alone if a plant has become darker over time, or if the weather conditions have simply changed from clear to overcast? This is a significant problem to address as colour is an important phenotypic trait that can be measured automatically from images.

Land-based crop phenotyping by image analysis: Accurate estimation of canopy height distributions using stereo images.

In this paper we report on an automated procedure to capture and characterize the detailed structure of a crop canopy by means of stereo imaging. We focus attention specifically on the detailed characteristic of canopy height distribution-canopy shoot area as a function of height-which can provide an elaborate picture of canopy growth and health under a given set of conditions. We apply the method to a wheat field trial involving ten Australian wheat varieties that were subjected to two different fertilizer treatments.

Pre-processing by data augmentation for improved ellipse fitting.

Ellipse fitting is a highly researched and mature topic. Surprisingly, however, no existing method has thus far considered the data point eccentricity in its ellipse fitting procedure. Here, we introduce the concept of eccentricity of a data point, in analogy with the idea of ellipse eccentricity.

Estimation of vegetation indices for high-throughput phenotyping of wheat using aerial imaging.

Background: Unmanned aerial vehicles offer the opportunity for precision agriculture to efficiently monitor agricultural land. A vegetation index (VI) derived from an aerially observed multispectral image (MSI) can quantify crop health, moisture and nutrient content. However, due to the high cost of multispectral sensors, alternate, low-cost solutions have lately received great interest.

Detecting spikes of wheat plants using neural networks with Laws texture energy.

Background: The spike of a cereal plant is the grain-bearing organ whose physical characteristics are proxy measures of grain yield. The ability to detect and characterise spikes from 2D images of cereal plants, such as wheat, therefore provides vital information on tiller number and yield potential.

Results: We have developed a novel spike detection method for wheat plants involving, firstly, an improved colour index method for plant segmentation and, secondly, a neural network-based method using Laws texture energy for spike detection.

Convective and diffusive effects on particle transport in asymmetric periodic capillaries.

We present here results of a theoretical investigation of particle transport in longitudinally asymmetric but axially symmetric capillaries, allowing for the influence of both diffusion and convection. In this study we have focused attention primarily on characterizing the influence of tube geometry and applied hydraulic pressure on the magnitude, direction and rate of transport of particles in axi-symmetric, saw-tooth shaped tubes. Three initial value problems are considered.

A Comprehensive Biophysical Model of Ion and Water Transport in Plant Roots. I. Clarifying the Roles of Endodermal Barriers in the Salt Stress Response.

In this paper, we present a detailed and comprehensive mathematical model of active and passive ion and water transport in plant roots. Two key features are the explicit consideration of the separate, but interconnected, apoplastic, and symplastic transport pathways for ions and water, and the inclusion of both active and passive ion transport mechanisms. The model is used to investigate the respective roles of the endodermal Casparian strip and suberin lamellae in the salt stress response of plant roots.

Phenotyping of plants in competitive but controlled environments: a study of drought response in transgenic wheat.

In recent years, the interest in new technologies for wheat improvement has increased greatly. To screen genetically modified germplasm in conditions more realistic for a field situation we developed a phenotyping platform where transgenic wheat and barley are grown in competition. In this study, we used the platform to (1) test selected promoter and gene combinations for their capacity to increase drought tolerance, (2) test the function and power of our platform to screen the performance of transgenic plants growing in competition, and (3) develop and test an imaging and analysis process as a means of obtaining additional, non-destructive data on plant growth throughout the whole growth cycle instead of relying solely on destructive sampling at the end of the season.

Scaling exponent and dispersity of polymers in solution by diffusion NMR.

Molecular mass distribution measurements by pulsed gradient spin echo nuclear magnetic resonance (PGSE NMR) spectroscopy currently require prior knowledge of scaling parameters to convert from polymer self-diffusion coefficient to molecular mass. Reversing the problem, we utilize the scaling relation as prior knowledge to uncover the scaling exponent from within the PGSE data. Thus, the scaling exponent-a measure of polymer conformation and solvent quality-and the dispersity (M/M) are obtainable from one simple PGSE experiment.