Monitoring, tracking, and analyzing the dynamic growth of a living organism is essential to understanding its response to changes in its surrounding environment. Imaging tools to study these dynamics at spatial and temporal scales with optimal resolution rely on high-performance instrumentations. These systems are generally costly, stationary, and not flexible. In addition, performing non-destructive high-throughput phenotyping to extract roots' structural and morphological features remains challenging. We developed the MultipleXLab: a modular, mobile, and cost-effective robotic root imager to tackle these limitations. Among its advantages associated with a large field-of-view, integrated programmable plant-growth lighting, and high magnification with a high resolving power, the system is useful for a wide range of biological applications. We have also created the MultipleXLab Advanced; this configuration turns the system into a mobile environmental chamber by also featuring temperature control and automated irrigation. Another system we developed was the MultipleXLab Advanced Fluorescence to allow fluorescence imaging with a resolution that competes with a fluorescence binocular or even a fluorescence microscope. Furthermore, we have implemented various technologies and techniques to facilitate 3D imaging and quantification, ranging from X-ray micro-Computed Tomography to 3D segmentation of tissues, cells, and cellular compartments within the cell imaged using Confocal Laser Scanning Microscopy. For future research, we have conceptualized an upscaled system named MultipleXLabXL. This larger system will allow tracking, monitoring, and quantifying root growth of a much higher number of seedlings for more extended periods.

In tropical and subtropical countries with bad infrastructure there exists diseases which are often neglected and untreated. Some of these diseases are caused by parasitic intestinal worms which most often affect children severely. The worms spread through parasite eggs in human stool that end up in arable soil and drinking water. Over one billion people are infected with these worms, but medication is available. The problem is the ineffective diagnostic method hindering the medication to be distributed effectively. In the process of designing an automated microscope for increased effectiveness the solution for marking out the stool sample on the microscope slide is important for decreasing the time of diagnosis. This study examined the active contour model and four different semantic segmentation networks for the purpose of delineating the stool sample from the other parts of the microscope slide. The Intersection-over-Union (IoU) measurement was used to measure the performance of the models. Both active contour and the networks increased the IoU compared to the current implementation. The best model was the FCN-32 network which is a fully convolutional network created for semantic segmentation tasks. This network had an IoU of 95.2%, a large increase compared to the current method which received an IoU of 77%. The FCN-32 network showed great potential of decreasing the scanning time while still keeping precision of the diagnosis.

The inclusions have a different chemical composition and give the steel different mechanical properties. These inclusions affect several properties of steel. In order to understand how the inclusions will affect the steel properties, the electrolytic extraction of 3D investigate method is applied on the steel grade of 42CrMo4. Then follow with Scanning Electron Microscope (SEM) observation. Steel samples from both ingot and rolling with and without heat treatment are observed and compared with different ratios. The result shown that, heat treatment can be applied for removing carbides successfully. And most inclusions are belonging to Type RS which is rod like MnS. The percentage of broken particles can be up to 80%, which means that the reason for the inclusions broken should be find. And heat treatment can affect the characteristics of elongated MnS.

Lipid molecule is well known natural building block to form different supramolecular structures with specific shape, size and functionality. In my thesis work, I have used DC8,9PC 1,2-bis(tricosa-10,12-dinoyl)-sn-glycero-3-phosphocholine), a type of chiral lipid to form the vesicles, tubules and ribbons . By using Atomic Force Microscope, I have studied the morphological features of these particular structures. Also, the mechanical properties of lipid tubules have been studied using AFM. Softlithography has been used to pattern the lipid vesicles and tubules into 2-dimensional and 3-dimensional ordered arrays. The structure of self-assembled hollow spherical vesicles was studied using AFM. The applications of soft lithography in patterning polymerized lipid vesicles of DC8,9PC on glass substrates are reported. It has been demonstrated that the lipid vesicles can be used as a high-molecular weight ink to be transferred from a PDMS stamp onto a glass substrate to form two-dimensional stripes with a controlled separation over a large area. By combining channel flow with dewetting within microfluidic networks, vesicles were assembled into one-dimension lines on a glass substrate. The vesicle lines can also be selectively removed from the substrate with lift-up process. The direct and precise assembly of lipid vesicles on solid substrates will open up the possibility of integrating them in biosensors and microelectronic devices. Lipid tubules and helices are other extremely interesting superstructures that have captured the imagination of scientists in disciplines from biology through material science to chemistry and physics. Lipid tubules are self-assembled hollow cylindrical structures with opened ends, composed of rolled-up bilayers. They have been used as a template for the synthesis of inorganic materials, a substrate for the crystallization of proteins, a controlled release system for drug deliver, and a colorimetric material for chemical sensors. However, due to the high aspect ratio, the formation of ordered arrays of lipid tubules on substrates still remains to be challenging. In this thesis work, the application of well-known soft lithography techniques in assembling and manipulating lipid tubules on substrates has been reported. I show that lipid nano- and microtubules can be assembled into two-dimensional (2-D) parallel arrays with controlled separations by combining fluidic alignment with dewetting, which occur within microchannels. It has also been shown that lipid tubules can be assembled into 3-D crossbar arrays with fluidic alignment, which occurs within microfluidic networks. The deposition experiments with silica colloidal particles show that the 2-D parallel-aligned tubules can be used as a template to synthesize silica films with controlled morphologies and patterns on substrates in a single-step process. Atomic force microscopy studies show that the resulting silica films replicate the shape, orientation, and pattern of aligned tubule templates. Though, the structures of the lipid tubules have been extensively studied, but very little is known about their mechanical properties. In my work, the mechanical properties of the lipid tubules of DC8,9PC were studied with atomic force microscope. The deformation of the lipid tubules with different outer diameters is directly observed in both tapping and contact modes with increasing loading forces.

A part of the Ph.D. project focused on growth and characterization of metal multilayers is presented in this licentiate thesis. The main interest in carrying out this research is to develop highly reflective normal-incidence condenser mirrors for soft X-ray microscopy studies in the water window (λ=2.4-4.2 nm) wavelength regime. Transition metals like Sc, Ti V, etc. have been considered because of the presence of their 2p-absorption edges within the water window. An anomalous dispersion at absorption edges has been utilized to get enhanced reflectance of soft X-rays. Since a single surface exhibits a very poor X-ray reflectivity, Cr/Sc, Cr/Ti, and Ni/V multilayers were grown in order to coherently add many reflections from several interfaces. The selection of Cr and Ni, as spacer layer, was made on the basis of their X-ray optical contrasts with the above-mentioned transition metals. The multilayer design, i.e., the individual layer thicknesses and the total number of bilayers, directly influences the resultant reflectance and careful determination was therefore made with the aid of computer simulations. All multilayers were grown on chemically cleaned Si substrates by ion-assisted dual target magnetron sputtering under high vacuum (~10-7 Torr) conditions. The effect of low and high ion-flux bombardment of low energy (&lt;50 eV) Ar ions, on growing surfaces was studied for all material systems. Furthermore, a two-stage deposition of each individual layer with modulated ion-energies was applied in order to obtain smooth and abrupt interfaces with as small intermixing as possible. Ion-surface interactions were also theoretically considered for estimating an appropriate ion-flux and ion-energy range desired for sufficient ad-atom mobilities. X-ray reflectivity and transmission electron microscopy have been the main probes for multilayer characterization in this work. For the Cr/Ti multilayer designed for normal incidence and grown with optimized two-stage ion-energy modulation, a peak reflectance of 2.1% was achieved at the Ti-2p absorption edge (λ=2.74 nm). For a multilayer mirror designed for the Brewster angle a maximum reflectance of 4.3% was accomplished. These measurements were made at the synchrotron radiation source BESSY in Berlin. Specular reflectivity and diffuse scattering scans were utilized for quantitative and qualitative analysis of the vertical and lateral structure of the multilayers. At-wavelength measurements of a series of Cr/Ti multilayers revealed the accumulation of roughness with increasing number of bilayers (N&gt;100) for this material system. Hard X-ray reflectivity and diffractometry were used for quality checks of the multilayers for rapid feedback to the deposition. In-situ annealing using hard X-ray reflectivity was also performed to assess the thermal stability of Cr/Ti multilayers. It was found that probably due to a strong thermal diffusion the degradation of multilayers (with bilayer period of 1.37 nm) in this material system occurs just above the growth temperature (~40°C). The accumulation of a low spatial frequency "waviness" with increasing number of layers in Cr/Ti multilayers was investigated by transmission electron microscopy. The influence of process conditions on multilayer structure with different periodicities was investigated by TEM analyses of a series of three samples for each of the above-mentioned material system. The Cr/Sc multilayers have shown the most flat and abrupt interface structure without any significant roughness evolution when grown with optimum process parameters. / <p>Report code: LiU-TEK-LIC-2005:48. On the day of the defence data the status of article I was: Accepted.</p>

<p> In this thesis the results of optical and scanning electron microscopic investigations of the evaporation morphology of zinc single crystals are presented. Dislocation etch pits developed on (0001) zinc cleavage surfaces. A mechanism is proposed to account for enhanced evaporation at decorated dislocations. The observation of macroledges on pit faces is reported and attributed to impurity-induced bunching of monatomic ledges, the impurities having out-diffused from the bulk. A proposed model for evaporation of faceted surfaces is used to interpret the ledge morphology which developed when samples were evaporated in an oxygen environment. Finally, a correlation between the effects of bulk impurities and gaseous impurities on ledge morphology is demonstrated.</p> / Thesis / Doctor of Philosophy (PhD)

<p> Dramatic advances over the past decade have occurred in the use of cryogenic electron microscopy (cryoEM) to elucidate the structures of macromolecules at atomic resolution. Unfortunately, the sample preparation process is one of the most time-consuming and empirical methods in the cryoEM workflow. Each sample must be tediously optimized to resolve issues with particle aggregation, ice quality, particle orientation, and particle density to enable high-resolution reconstruction analysis. Post-polymerization modifications of synthetic aqueous bottlebrushes offer a promising approach to streamline the workflow for cryoEM sample preparation. Our approach utilizes synthetic bottlebrush materials comprised of flexible polymer scaffolds bearing grafted side-chains, armed with high affinity ligands at the distal termini of the grafted polymers along the polymer core. Development of water-soluble one-dimensional (1D) synthetic bottlebrush polymers has led to new advancements in the biomaterials, antimicrobial, nanomedicine, and responsive materials fields. These synthetic bottlebrush materials are favorable as they confer properties that linear polymers and small molecules cannot achieve. Moreover, structural manipulations employed during post-polymerization processes can afford bottlebrush polymers with distinguishable topologies for advanced functions. These 1D constructs can be synthesized by atom transfer radical polymerization (ATRP), reversible addition- fragmentation chain-transfer polymerization (RAFT), ring-opening polymerization (ROP), cationic ring-opening polymerization (CROP), anionic ring-opening polymerization (AROP) or ring opening metathesis polymerization (ROMP). The chemical composition of the molecule, number of monomer repeats, grafting density and topology influence the morphology and function of polymer brushes. Elongated, vesicular or micellar morphologies can be specifically tuned for the desired application of the material. The morphology of the polymers can also be manipulated by concentration effects. The morphologies of amphiphilic bottlebrush materials specifically, can typically be influenced by structural topology, solvent choice, or external conditions. ROMP is a living polymerization mechanism that can suffer from catalytic backbiting, causing a loss of livingness. The synthesis of aqueous bottlebrush polymers and the comparison of morphologies via AUC, DLS, AFM and TEM will be presented in this dissertation. The synthetic amphiphilic bottlebrush polymer family presented suffered a loss of livingness and ultimately displayed distinct morphologies, relative to chemical composition, solvent, and ultimately polymerization time. Post-polymerization 11 modifications such as backbone hydrolysis and single-walled carbon nanotube complexation promoted even more unique morphologies of bottlebrushes. These synthetic materials indicate use as promising reagents for cryoEM sample preparation.  </p>

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