Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

X-ray Imaging Techniques to Quantify Spray Characteristics in the Near Field

Liquid sprays play a key role in many engineering processes, including, but not limited to, food processing, coating and painting, 3D printing, fire suppression, agricultural production, and combustion systems. Spray characteristics can easily be assessed in the mid- and far-field regions, well after liquid sheet breakup and droplet formation, using various optical and/or laser diagnostic techniques. The conditions in the near-field region influence mid- and far-field characteristics; however, near-field measurements are extremely challenging because the spray in this region is typically optically dense where optical and laser diagnostics are generally ineffective. This paper provides an overview of the various X-ray imaging techniques that can be used to characterize the near-field region of a spray. X-rays produced with tube sources as well as synchrotron sources will be discussed. Using tube-source X-rays, 2D radiographic videos are possible showing qualitative spray information. The 2D radiographs can also provide quantitative measurements of the optical depth (OD) in the near-field region. Tube sources can also provide X-ray computed tomography imaging that can produce time-average 3D density (mass distribution) maps of the spray. X-rays from synchrotron radiation provide a high-flux X-ray beam that can be used to provide high spatial and temporal resolution of the spray equivalent path length (EPL) as well as other characteristics, but it is more challenging to implement than using a common tube source. Various examples of these X-ray imaging techniques will be discussed

Molecular Imaging

The present book gives an exceptional overview of molecular imaging. Practical approach represents the red thread through the whole book, covering at the same time detailed background information that goes very deep into molecular as well as cellular level. Ideas how molecular imaging will develop in the near future present a special delicacy. This should be of special interest as the contributors are members of leading research groups from all over the world

Bent Laue X-ray Beam Expander

Synchrotron imaging beamlines around the world all suffer from a similar limitation, namely a beam that is smaller in the vertical direction than the horizontal. This can produce a beam that is so small in the vertical direction that some imaging applications are limited or even impossible. At the BioMedical Imaging and Therapy (BMIT) beamline facility at the Canadian Light Source (CLS), the vertical beam sizes on the Bend Magnet (BM) and Insertion Device (ID) beamlines are 7 mm and 11 mm, respectively. This limited vertical beam size results in several limitations. Micro-computed-tomography experiments requiring multiple rotations to produce a full three-dimensional representation of the sample result in longer scan times and possible reconstruction errors due to misalignment between rotations. Similarly, projection images requiring vertical scans to cover the entire two dimensional field of view extend acquisition times and lead to potential stitching errors between exposures. Dynamic phase-based imaging (i.e. movies), which are being used for some of the most cutting edge biomedical imaging research taking place worldwide, is virtually impossible with samples larger than the vertical beam size. This problem has been solved at other synchrotrons by building very long beamlines and allowing the beam to naturally diverge to a larger field of view, however this was not possible for BMIT due to budgetary and geographical limitations. In order to vertically expand the beam, a bent Laue double crystal monochromator was used in a non-dispersive divergent geometry to ultimately produce a beam expansion of 12× the incident height. Improvements were made to the system to preserve the quality of transverse coherence in the beam, allowing phase-based imaging techniques to be performed with a larger field of view. This was achieved by carefully matching the geometric and single-ray focal points in the so-called “magic condition.” The quality of the expanded beam was compared to that produced by the beamline’s standard flat Bragg double crystal monochromator and was found to differ in divergence by less than 10% between the two monochromator systems. Further testing was done to evaluate the criticality of matching the two focal types, and to determine at least a minimum energy range over which the system could be used reliably. These tests showed that the system is much more flexible than previously believed, with energy ranges of at least ±5 keV producing images wherein the vertical and horizontal edge width differ by less than 1%, indicating that the expander does not adversely affect the beam in the diffraction plane. Despite the improvement to the diffraction and focus characteristics of the system, there was an ongoing issue with areas of missing intensity in the beam. The hypothesis that this was caused by imperfect bending of the second crystal has been confirmed using diffraction and mechanical measurement techniques

Dose ratio proton radiography using the proximal side of the Bragg peak

Purpose: In recent years there has been a movement towards single-detector proton radiography, due to its potential ease of implementation within the clinical environment. One such single-detector technique is the dose ratio method, in which the dose maps from two pristine Bragg peaks are recorded beyond the patient. To date, this has only been investigated on the distal side of the lower energy Bragg peak, due to the sharp fall-off. We investigate the limits and applicability of the dose ratio method on the proximal side of the lower energy Bragg peak, which has the potential to allow a much wider range of water-equivalent thicknesses (WET) to be imaged. Comparisons are made with the use of the distal side of the Bragg peak. Methods: Using the analytical approximation for the Bragg peak we generated theoretical dose ratio curves for a range of energy pairs, and then determined how an uncertainty in the dose ratio would translate to a spread in the WET estimate. By defining this spread as the accuracy one could achieve in the WET estimate, we were able to generate look-up graphs of the range on the proximal side of the Bragg peak that one could reliably use. These were dependent on the energy pair, noise level in the dose ratio image and the required accuracy in the WET. Using these look-up graphs we investigated the applicability of the technique for a range of patient treatment sites. We validated the theoretical approach with experimental measurements using a complementary metal oxide semiconductor active pixel sensor (CMOS APS), by imaging a small sapphire sphere in a high energy proton beam. Results: Provided the noise level in the dose ratio image was 1% or less, a larger spread of WETs could be imaged using the proximal side of the Bragg peak (max 5.31 cm) compared to the distal side (max 2.42 cm). In simulation it was found that, for a pediatric brain, it is possible to use the technique to image a region with a square field equivalent size of 7.6 cm2, for a required accuracy in the WET of 3 mm and a 1% noise level in the dose ratio image. The technique showed limited applicability for other patient sites. The CMOS APS demonstrated a good accuracy, with a root-mean-square-error of 1.6 mm WET. The noise in the measured images was found to be σ =1.2% (standard deviation) and theoretical predictions with a 1.96σ noise level showed good agreement with the measured errors. Conclusions: After validating the theoretical approach with measurements, we have shown that the use of the proximal side of the Bragg peak when performing dose ratio imaging is feasible, and allows for a wider dynamic range than when using the distal side. The dynamic range available increases as the demand on the accuracy of the WET decreases. The technique can only be applied to clinical sites with small maximum WETs such as for pediatric brains

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

Development of 3D-Printed Cartilage Constructs and Their Non-Invasive Assessment by Synchrotron-Based Inline-Phase Contrast Imaging Computed Tomography

One goal of cartilage tissue engineering (CTE) is to create constructs for regeneration of hyaline cartilage. Three-dimensional (3D)-printed cartilage constructs fabricated from polycaprolactone (PCL) and chondrocyte-impregnated alginate mimic the biphasic nature of articular cartilage and offers great promise for CTE applications. However, ensuring that these constructs provide biologically conducive environment and mechanical support for cellular activities and articular cartilage regeneration is still a challenge. That said, the regulatory pathway for medical device development requires validation of implants such as these through in vitro bench test and in vivo preclinical examination prior to their premarket approval. Furthermore, mechano-transduction and secretion of cartilage-specific ECM are influenced by mechanical stimuli directed at chondrocytes. Thus, ensuring that these cartilage constructs have mechanical properties similar to that of human articular cartilage is crucial to their success. Non-invasive imaging techniques are required for effective evaluation of progression of these cartilage constructs. However, current non-invasive techniques cannot decipher components of the cartilage constructs, nor their time-dependent structural changes, because they contain hydrophobic and hydrophilic biomaterials with different X-ray refractive indices. The aims of this thesis were to develop 3D-printed cartilage constructs that biologically and mechanically mimic human articular cartilage and to investigate synchrotron radiation inline phase contrast computed tomography (SR-inline-PCI-CT) as a non-invasive imaging technique to characterize components of these constructs and associated time-dependent structural changes. The first objective was to determine in vitro biological functionality of the cartilage constructs over a 42-day period with regards to cell viability and secretion of extracellular matrix by traditional invasive assays. In parallel, performance of SR-inline-PCI-CT for non-invasive visualization of components and associated structural changes within the constructs in vitro over a 42-day was examined. To achieve this objective, three sample-to-detector distances (SDDs): 0.25 m, 1 m and 3 m were investigated. Then, the optimal SDD with better phase contrast and edge enhancement fringes for characterization of the multiple refractive indices within the constructs was utilized to visualize their structural changes over a 42-day culture period. Like the first objective, the second objective was to examine in vivo biological functionality of the cartilage constructs by traditional invasive assays and utilize SR-inline-PCI-CT to non-invasively visualize components of the hybrid cartilage constructs over a 21-day period post-implantation in mice. The third objective was to modulate mechanical properties of PCL framework of the 3D-printed PCL-based cartilage constructs to mimic mechanical properties of human articular cartilage. To achieve this, effect of modulation of PCL's molecular weight (MW) and scaffold's pore geometric configurations: strand size (SZ), strand spacing (SS), and strand orientation (SO), on mechanical properties of 3D-printed PCL scaffolds were studied. Then, regression models showing the effect of SZ, SS, and SO on porosity, tensile moduli and compressive moduli of scaffold were developed. Compressive and tensile properties of these scaffolds were compared with those of human articular cartilage. Then, “modulated PCL scaffolds” with mechanical and biomimetic properties that better mimic human articular cartilage was identified and recommended for fabrication of PCL-based cartilage constructs. This thesis demonstrated effective in vitro and in vivo biological performance of the 3D-printed hybrid cartilage constructs studied and presented a significant advancement in CTE applications. To be precise, cell viability was at a minimum of 77 % and secretion of sulfated GAGs and Col2 increased progressively within cartilage constructs over a 42-day in vitro. Similarly, cell viability was consistently above 70 %, and secretion of sulfated GAGs and Col2 increased post-implantation of constructs in mice over a 21-day period. Furthermore, SR-inline-PCI-CT demonstrated phase contrast and edge-enhancement fringes effective for visualization of the different components and subtle variations within the biphasic cartilage constructs, and thus, offers great potential for their non-invasive and three-dimensional visualization. Lastly, this thesis presented a significant advancement towards development of PCL constructs with mechanical behavior that mimic that of human articular cartilage. The statistical regression models developed showed the effect of SZ, SS, and SO on porosity, tensile moduli and compressive moduli of scaffolds and recommended sets of parameters for fabrication of “modulated PCL scaffolds” with mechanical properties that better mimic mechanical behavior of human articular cartilage. These “modulated PCL scaffolds” could serve as a better framework and could guide more effective secretion of cartilage-specific ECM within PCL-based constructs for CTE applications