Evaluation of 3D/2D Imaging and Image Processing Techniques for the Monitoring of Seed Imbibition

Seed imbibition is a very important process in plant biology by which, thanks to a simple water income, a dry seed may turn into a developing organism. In natural conditions, this process occurs in the soil, e.g., with difficult access for a direct observation. Monitoring the seed imbibition with non-invasive imaging techniques is therefore an important and possibly challenging task if one tries to perform it in natural conditions. In this report, we describe a set of four different imaging techniques that enable to addressing this task either in 3D or in 2D. For each technique, the following items are proposed. A detailed experimental protocol is provided to acquire images of the imbibition process. With the illustration of real data, the significance of the physical quantities measured in terms of their relation to the income of water in the seed is presented. Complete image analysis pipelines are then proposed to extract dynamic information on the imbibition process from such monitoring experiments. A final discussion compares the advantages and current limitations of each technique in addition to elements concerning the associated throughput and cost. These are criteria especially relevant in the field of plant phenotyping where large populations of plants are imaged to produce quantitatively significative traits after image processin

Automatic Assessment of Seed Germination Percentage

This research was designed to investigate an automatic seed germination rate for the top of paper germination method. Chili and guinea were adopted to be used in the experiment with a 4-time repetition and 2 sets of the germination group (4-separated plates with 50 seeds per plate, 2 sets per seed type, totally 400 seeds of chili and 400 seeds of quinea). Two detection methods were proposed binary thresholding and maximum likelihood; based on color analysis. An uncontrolled environment image taking was the way to collect image data. The results were compared to a hand-labeling groundtruth. Both methods achieved accuracy rate higher than 93% which was promising to implement this system. The binary thresholding was a lightweight method suitable for a very limited resource software environment system. The maximum likelihood was more complex. The method had more potential than the binary thresholding, it was flexible to the light condition, returned few false alarms per image (less than 3 false alarms per image). Maximum likelihood could be adopted to implement in a proper environment which still could be in a mobile device

Emerging thermal imaging techniques for seed quality evaluation: Principles and applications

Due to the massive progress occurred in the past few decades in imaging, electronics and computer science, infrared thermal imaging technique has witnessed numerous technological advancement and smart applications in non-destructive testing and quality monitoring of different agro-food produces. Thermal imaging offers a potential non-contact imaging modality for the determination of various quality traits based on the infrared radiation emitted from target foods. The technique has been moved from just an exploration method in engineering and astronomy into an effective tool in many fields for forming unambiguous images called thermograms eventuated from the temperature and thermal properties of the target objects. It depends principally on converting the invisible infrared radiation emitted by the objects into visible two-dimensional temperature data without making a direct contact with the examined objects. This method has been widely used for different applications in agriculture and food science and technology with special applications in seed quality assessment. This article provides an overview of thermal imaging theory, briefly describes the fundamentals of the system and explores the recent advances and research works conducted in quality evaluation of different sorts of seeds. The article comprehensively reviewed research efforts of using thermal imaging systems in seed applications including estimation of seed viability, detection of fungal growth and insect infections, detection of seed damage and impurities, seed classification and variety identification.info:eu-repo/semantics/acceptedVersio

Review of Microfluidic Devices and Imaging Techniques for Fluid Flow Study in Porous Geomaterials

Understanding transport phenomena and governing mechanisms of different physical and chemical processes in porous media has been a critical research area for decades. Correlating fluid flow behaviour at the micro-scale with macro-scale parameters, such as relative permeability and capillary pressure, is key to understanding the processes governing subsurface systems, and this in turn allows us to improve the accuracy of modelling and simulations of transport phenomena at a large scale. Over the last two decades, there have been significant developments in our understanding of pore-scale processes and modelling of complex underground systems. Microfluidic devices (micromodels) and imaging techniques, as facilitators to link experimental observations to simulation, have greatly contributed to these achievements. Although several reviews exist covering separately advances in one of these two areas, we present here a detailed review integrating recent advances and applications in both micromodels and imaging techniques. This includes a comprehensive analysis of critical aspects of fabrication techniques of micromodels, and the most recent advances such as embedding fibre optic sensors in micromodels for research applications. To complete the analysis of visualization techniques, we have thoroughly reviewed the most applicable imaging techniques in the area of geoscience and geo-energy. Moreover, the integration of microfluidic devices and imaging techniques was highlighted as appropriate. In this review, we focus particularly on four prominent yet very wide application areas, namely “fluid flow in porous media”, “flow in heterogeneous rocks and fractures”, “reactive transport, solute and colloid transport”, and finally “porous media characterization”. In summary, this review provides an in-depth analysis of micromodels and imaging techniques that can help to guide future research in the in-situ visualization of fluid flow in porous media

SeedGerm: a cost‐effective phenotyping platform for automated seed imaging and machine‐learning based phenotypic analysis of crop seed germination

Efficient seed germination and establishment are important traits for field and glasshouse crops. Large-scale germination experiments are laborious and prone to observer errors, leading to the necessity for automated methods. We experimented with five crop species, including tomato, pepper, Brassica, barley, and maize, and concluded an approach for large-scale germination scoring. Here, we present the SeedGerm system, which combines cost-effective hardware and open-source software for seed germination experiments, automated seed imaging, and machine-learning based phenotypic analysis. The software can process multiple image series simultaneously and produce reliable analysis of germination- and establishment-related traits, in both comma-separated values (CSV) and processed images (PNG) formats. In this article, we describe the hardware and software design in detail. We also demonstrate that SeedGerm could match specialists’ scoring of radicle emergence. Germination curves were produced based on seed-level germination timing and rates rather than a fitted curve. In particular, by scoring germination across a diverse panel of Brassica napus varieties, SeedGerm implicates a gene important in abscisic acid (ABA) signalling in seeds. We compared SeedGerm with existing methods and concluded that it could have wide utilities in large-scale seed phenotyping and testing, for both research and routine seed technology applications

HYDRAULIC PROPERTIES OF VARIABLY-SATURATED POROUS MEDIA DETERMINED USING QUANTITATIVE NEUTRON RADIOGRAPHY

The theoretical understanding of fluids in unsaturated porous media has improved substantially over the last several decades. Water retention curves remain a central pillar in the theoretical framework for modeling of water flow in unsaturated porous media. Use of the average water retention function in models to simulate water flow in porous media can result in inaccurate predictions due to the variations in water content and matric potential with elevation within the medium. As a result, point water retention curve data are needed for testing existing numerical and analytical models and for improving our ability to predict unsaturated water flow. Traditionally point water retention functions have been derived from average water retention curve data. The main objective of this research was to directly measure point water retention functions using neutron imaging. Neutron imaging provides a non-destructive tool for visualizing water flow in porous media due to its high sensitivity to hydrogen, and relative insensitivity to mineral solids. Using neutron imaging techniques we have explored the following research topics: (1) quantitative measurements of the equilibrium water content distribution in porous media, (2) measurement of average and point water retention functions using neutron radiography, (3) assessment of analytical models relating average and point water retention curves, and (4) investigation of the dynamics of unsaturated water flow. In the first two chapters of this dissertation we developed quantitative neutron imaging techniques to measure the 2-dimensional distribution of water in porous media and obtain the average water retention function for Flint sand by neutron radiography. In chapter III, point water retention functions were directly measured by neutron radiography and the resulting point functions were parameterized using the Brooks & Corey equation. The point water retention function constructed from the median values of the fitted Brooks and Corey parameters corresponded closely with the point curve for Flint sand obtained by inverse modeling of the average water retention curve data. In the final chapter of this dissertation we investigated capillary uptake of water in Berea Sandstone and estimated the sorptivity and unsaturated diffusivity function from analyses of the neutron radiographs

Investigating the impact of pre-harvesting sprouting on maize hardness using near infrared (NIR) hyperspectral imaging and X-ray micro-computed tomography (μCT)

Thesis (MSc (Food Sc))--Stellenbosch University, 2016.ENGLISH ABSTRACT: Maize forms an integral part of the human energy intake in South Africa and its quality should always be maintained. A quality attribute important to the dry milling industry is maize hardness. In the milling industry, hard maize hybrids are described as kernels with a higher ratio of vitreous endosperm in comparison to floury endosperm. Certain circumstances such as agricultural conditions (e.g. pre-harvest germination), post-harvest conditions and improper treatments (e.g. no irrigation during periods of insufficient rain or improper drying procedures) will have a negative impact on maize hardness. This study focused on the impact of pre-germination on maize hardness, subsequently observations on the rate of the pre-germination process on three hardness variants (hard, intermediate and soft) were noted. Six maize hybrids with varying hardness levels were pre-germinated (from 0 – 22 h) bi-hourly and three imaging techniques (Scanning electron microscopy (SEM), near-infrared (NIR) h y p e r s p e c t r a l imaging and X -ray m i c r o computed tomography (X-ray μCT)) used to investigate the impact of the process on hardness. From the NIR hyperspectral imaging technique, principal component analysis (PCA) score plots and score images were employed in the investigations due to the amount of data obtained. Three types of endosperm (vitreous, intermediate or floury) were observed in the first principal component (PC1) of the score images. PCA classification plots revealed the three types of endosperm present within a maize kernel. Classification plots (both score plots and images) allowed for the isolation of the vitreous endosperm by removing the two clusters representing the floury and intermediate endosperm. PCA score images depicted decreasing trend in the content of the vitreous endosperm as pre-germination took place. Another observation from the PCA score images was that, the soft maize hybrids showed traces of vitreous endosperm after 8 h of pregermination. The intermediate hybrids showed a decrease in the endosperm content at 12 h and the hard hybrid was noted to be at 18 h. Pixel count (obtained from the PCA score plots) indicated a decreasing trend in all hybrids investigated. The graphs plotted from pixel counts of hard hybrids (i.e. H2 and H3), intermediate (H7) and soft (H9) depicted decreasing curvilinear plots. The rest of the hybrids’ graphs (H6 and H5) depicted a decreasing linear trend. X-ray μCT indicated fissures and shrinkage stress cracks occurring as a results of either or both of the pre-germination and drying processes. Larger fissures were assumed to have developed due to pre-germination and shrinkage stress cracks from the drying process. These (i.e. fissures and shrinkage stress cracks) were observed in all the 10 h and 22 h images, on 2D slices and 3D volumes. The side orientation 2D image slices depicted the intermediate and soft maize hybrids’ endosperm integrity as having deteriorated more than the hard hybrid at 10 h and 22 h incubation time period. The top orientation of the 2D slice images indicated the hard and intermediate deteriorated more than the soft hybrids. It was noted that the fissures and shrinkage stress cracks developed throughout the maize kernel. SEM was used to validate results obtained from the X-ray μCT imaging system, fissures could also be observed on SEM images. Starch and protein matrix deterioration was also observed. iii Stellenbosch University https://scholar.sun.ac.za Starch granules and protein matrix developed numerous pores on the surfaces indicating the extent of deterioration. Single kernel analysis using 2D slices at T8 = 21 h, crevices started to develop and propagated until the end of the pre-germination process at T19 = 143 h. Fissure measurement indicated an increment in all measured areas of the maize kernels, i.e. from the left side of the maize kernel fissures propagated from 1.51 mm at 99 h to 4.22 mm at 143 h, on the right side from 1.86 mm at 99 h to 3.65 mm at 143 h. At T15 = 123 h, a horizontal fissure was observed and measured to be 1.62 mm long while at T19 = 143 h it had propagated to 4.30 mm. The fissures were noted to be pathways used to transport hydrolytic enzymes and monomers (obtained from starch and protein hydrolysis) to the germ where the growing embryo utilises them as a source of nutrition. Volumes of the vitreous endosperm were also determined and a decreasing trend was noticed. At T1 = 0 h the content of the vitreous endosperm was 64.7 mm3 and at T19 = 143 h the content had decreased to 50.5 mm3. Endosperm deterioration due to pre-germination should thus be of great concern to the milling industry as it influences the desired end product.AFRIKAANSE OPSOMMING: Nie beskikbaar nie

Sugar beet

Sugar beet has entered the age of liberalism with the abolition of production quotas in Europe. It finds itself on the world market and on an equal footing with sugar cane. France has benefited from the “AKER - Sugar beet 2020, a competitive innovation” Investments for the Future Programme, which aims to double the annual growth rate of the sugar yield per hectare of beet. It has made a scientific breakthrough by researching all of the genetic diversity available worldwide, and by carrying out genotyping before phenotyping. It is developing new genetic material, available for introduction into future sugar beet varieties. It also offers innovative tools and methods in the fields of genotyping and phenotyping, supporting players in the sector - beet growers and sugar manufacturers - in their imperative improvement in competitiveness. This book is mainly intended for scientists and professionals, and all those interested in research, development and training in the plant sector. It has just completed eight years of multidisciplinary work bringing together a hundred scientists. The AKER programme puts for a long time sugar beet in the top tier of cultivated species and helps to provide the consumer with quality sugar produced locally and under environmentally friendly conditions

Tracing back the source of contamination

From the time a contaminant is detected in an observation well, the question of where and when the contaminant was introduced in the aquifer needs an answer. Many techniques have been proposed to answer this question, but virtually all of them assume that the aquifer and its dynamics are perfectly known. This work discusses a new approach for the simultaneous identification of the contaminant source location and the spatial variability of hydraulic conductivity in an aquifer which has been validated on synthetic and laboratory experiments and which is in the process of being validated on a real aquifer

Pore network modelling of wettability effects on waterflood oil recovery from Agbada sandstone formation in the Niger Delta, Nigeria

A thesis Submitted to the School of Chemical and Metallurgical Engineering, Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Doctor of Philosophy Johannesburg, 2016Wettability of a porous reservoir rock is an important factor that affects oil recovery during waterflooding. It is recognized as being important for multiphase properties. Understanding the variation of these properties in the field, due to wettability trends and different pore structures, is very critical for designing efficient and reliable processes and projects for enhanced hydrocarbon recovery. After primary drainage the reservoir wettability changes: if it was oil-wet initially, it gradually changes to water-wet during waterflooding. This change in reservoir wettability towards water-wet will reduce the residual oil saturation and improve the oil displacement efficiency. However, knowledge of the constitutive relationship between the pore scale descriptors of transport in the porous system is required to adequately describe wettability trend and its impact on oil recovery, particularly during waterflooding. In this work, the petrophysical properties that define fluid flow in the Agbada, Nigeria sandstone reservoir were determined using conventional experimental and x-ray CT scanning methods. Experimentally measured average porosity is 0.28, average permeability is 1699 mD, while the initial and irreducible water saturation is 0.22. Permeability in the x, y and z directions, ranging from 50 to 200 mD, were calculated from the pore network extracted from the Agbada sandstone rock. Results obtained from the Amott-Harvey wettability measurement method indicate that the reservoir is strongly water-wet, with Amott-Harvey index of about 0.9. The cross-over between the water and oil relative permeabilities occurred at saturations of the samples above 0.5, giving an indication of strong water-wetness. The work summarizes the mechanism of wettability alteration and characterizes the performance of the reservoir during waterflooding from injecting water, and relates the residual oil saturation, relative permeability and volumes of water injected to wettability and its effects on oil recovery. Waterflood oil recovery is computed using the Buckley-Leverett method based on the reservoir rock and fluid properties. Computed waterflood oil recovery using this method was about 60% of the oil initially in place. Plots of spontaneous imbibition rate show that the injection rate for optimal oil recovery is 40 bbls of injected water per day. At this rate, both the mobility and shock front mobility ratios are less than 1, leading to a stable flood front and absence of viscous fingering. Waterflooding is by far the most widely applied method of improved oil recovery over the years with good results in conventional and unconventional (tight oil) reservoirs It is relatively simple and cost effective: abundance and availability of water. Waterflood oil recovery factor is affected by internal and external factors. The placement of the injection and production wells, for example, impacts on the effectiveness of the waterflooding process. I considered the placement of the wells in a five-spot pattern as elements of an unbounded double periodic array of wells and assumed the reservoir to be homogeneous, infinite and isotropic, with constant porosity and permeability. Both fluids are treated as having slight but constant compressibility and their flow governed by Darcy’s law. The average pressure in the reservoir satisfies quasi-static flow or diffusion equation. I then assumed piston-like displacement of oil by injected water that takes account of viscosity diffence between both fluids and proposed a model based on the theory of elliptic functions, in particular Weierstrass p-functions functions. Oil-water contact movement, dimensionless time for water breakthrough at the production well, areal sweep and average reservoir pressures were modeled. The model was tested using Wolfram Mathematica 10 software and the results are promising. The thesis has therefore established that the Agbada sandstone reservoir is strongly water-wet and that waterflooding is a viable option for enhanced oil recovery from the reservoir.MT201