Previous research into microbial colonies and biofilms shows a significant gap in our current understanding of how bacterial structures develop. Despite the huge body of research undertaken into the formation, genetic makeup, composition, and optimal growth conditions of colonies, no study has been successful in identifying all individual bacteria in a colony in three-dimensions as a function of time. This lack of bacterial cell lineage in such a simple class of organisms is conspicuous in the light of what is known about other organisms, such as Caenorhabditis elegans [1]. In this thesis I show that using laser scanning confocal microscopy in conjunction with developments in sample preparation and post acquisition image analysis, it is possible to fully reconstruct all individual bacteria within an Escherichia coli (E. coli ) microcolony grown in viscoelastic media. Additionally, I show that by further pushing the resolution of confocal microscopes, commercial systems are capable of extracting three-dimensional information on protein structures inside bacteria at early stages of growth. This thesis is in three parts. The first part shows that by pushing the resolution of a commercial laser scanning confocal microscope system it is possible to achieve single cell resolution of a bacterial colony growing in three dimensions in a viscoelastic medium (agarose) from a seed bacterium. The growth of individual bacteria is examined as the concentration of agarose in the media is altered. Results show there is a nonlinear dependence between the rate of growth of a bacterium and the concentration of the agarose in the media with a peak in growth rate at 3% (weight) concentrations of agarose in M9 media. The second part of this work presents a study of how an initially two-dimensional colony growing between a glass slide and agarose gel suddenly invades the third spatial dimension by buckling. The results show that the cells within the centre of the colony flex and buckle, due to confinement by their neighbours, creating additional layers. Indeed, flexing is not limited to the buckling event but occurs throughout the early growth cycle of a colony. The final part of this thesis shows that by further pushing the resolution of confocal microscopes, commercial systems are capable of extracting three-dimensional information about the temporal evolution of the spatial distribution of the FtsZ septation ring within the cell. As the bacterial colony grows from a seed bacterium to a microcolony, the error in placing the division accurately at the cell centre is seen to increase as the number of bacteria within the colony increases and spatial confinement occurs.

This PhD work is dedicated to investigating the fringe effect of electrical capacitance tomography (ECT) and electrical resistance tomography (ERT) sensors systematically, exploring possible solutions and developing a novel 3D imaging technique by utilising the fringe effect of electrical tomography (ET) sensors. By referring to 2D simulation results, the fringe effect is investigated for 3D ERT and ECT sensor models with or without grounded guards, and with different axial lengths of electrodes. Simulation results reveal that increasing the electrode length or adopting grounded guards can reduce the fringe effect of ECT and ERT sensors. In this work, a voltage-excitation strategy is proposed and validated for ERT sensors instead of the conventional current-injection strategy. This approach enables ECT and ERT sensors to be integrated together as a common one to simplify the sensor design and reduce the interference between the ECT and ERT dual-modality measurements. For a conventional ERT sensor with the adjacent strategy, the fringe effect is evaluated for axially non-uniform central core and off-central core distributions at different axial positions and with different axial dimensions and conductivity contrasts. A method is proposed for compensating the fringe effect with the above typical distributions and a two-object distribution. A three-plane ERT sensor scheme is suggested for reducing the fringe effect induced by objects outside the sensor plane and the over-estimation by Landweber iteration. Both simulation and experiment have proved the effectiveness of the three-plane sensor scheme and the compensation method. Using the fringe effect, a novel 3D imaging method is proposed for ET with a single-plane sensor. It is explored to image metallic objects with ECT. The axial position of the object is derived by examining the corresponding fringe effect in a single-plane ECT sensor. Along with 2D imaging of the cross-sectional distribution, 3D imaging is achieved for a cylindrical metallic rod with known size. With this method, only the 3D position of the object needs to be calculated during the reconstruction which reduces the number of unknowns greatly and can improve the accuracy and stability of reconstruction.

It is well established that acquiring large amounts of range data with vision sensors can quickly lead to important data management challenges where processing capabilities become saturated and pre-empt full usage of the information available for autonomous systems to make educated decisions. While sub-sampling offers a naïve solution for reducing dataset dimension after acquisition, it does not capitalize on the knowledge available in already acquired data to selectively and dynamically drive the acquisition process over the most significant regions in a scene, the latter being generally characterized by variations in depth and surface shape in the context of 3D imaging. This thesis discusses the development of two formal improvement measures, the first based upon surface meshes and Ordinary Kriging that focuses on improving scene accuracy, and the second based upon probabilistic occupancy grids that focuses on improving scene coverage. Furthermore, three selection processes to automatically choose which locations within the field of view of a range sensor to acquire next are proposed based upon the two formal improvement measures. The first two selection processes each use only one of the proposed improvement measures. The third selection process combines both improvement measures in order to counterbalance the parameters of the accuracy of knowledge about the scene and the coverage of the scene. The proposed algorithms mainly target applications using random access range sensors, defined as sensors that can acquire depth measurements at a specified location within their field of view. Additionally, the algorithms are applicable to the case of estimating the improvement and point selection from within a single point of view, with the purpose of guiding the random access sensor to locations it can acquire. However, the framework is developed to be independent of the range sensing technology used, and is validated with range data of several scenes acquired from many different sensors employing various sensing technologies and configurations. Furthermore, the experimental results of the proposed selection processes are compared against those produced by a random sampling process, as well as a neural gas selective sensing algorithm.

Rentgenová počítačová mikrotomografie (CT) je metoda pro trojrozměrné (3D) zobrazování vnitřní struktury objektů. Laboratoř rentgenové počítačové mikro a nanotomografie na CEITEC VUT (Středoevropský technologický institut, Vysoké učení technické v Brně) se zaměřuje zejména na nedestruktivní analýzu v průmyslovém odvětví. Ukázalo se ale, že tato metoda nachází široké uplatnění i v dalších vědeckých oblastech včetně vývojové biologie. Tato práce poskytuje propojení mezi materiálovými a živými vědami. Kompletní proces vedoucí k vytvoření 3D modelu různých anatomických struktur je detailně popsán. Tento postup zahrnuje kontrastování vzorků, samotné CT měření a analýzu dat. Právě zpracování dat je mnohdy považováno za nejdůležitější část v rentgenové počítačové tomografii a proto je této oblasti věnována v práci největší část. Úpravou měřicích parametrů byl dále optimalizován CT přístroj GE v|tome|x L 240 za účelem umožnění automatické segmentace. Navíc je diskutována možnost měření na synchrotronu za účelem zvýšení prostorového rozlišení a diferenciálního kontrastu. Předpokládá se, že v blízké budoucnosti získají průmyslové CT přístroje podobné zobrazovací vlastnosti, a to jak díky nedávnému vývoji v oblasti hardwaru, tak v oblasti zpracování dat.

Footwear and tire impressions are critical evidence commonly found at a crime scene. However, they are often undervalued because they are hard to be captured and documented. Traditional 2D evidence quality photographs do not adequately provide metric depth information, and physical casts destroy the evidence afterward. Therefore, the forensic science community raised the need for improved evidence recognition, collection, and visualization analytical instrumentation for field and lab use. While the 3D optical techniques for imaging static objects have been extensively studied, there is still a major gap between current knowledge and collecting high-quality footwear and tire impressions evidence. Among optical means for 3D imaging, digital fringe projection (DFP) techniques reconstruct 3D shape from phase information, achieving camera-pixel spatial resolution. This paper presents a high-resolution 3D imaging technology using DFP techniques dedicated to footwear and tire impression capture. We developed fully automated software algorithms and a graphical user interface (GUI) that allow anyone without training to operate for high-quality 3D data capture. We performed accuracy evaluations and comparisons comparing with the commercial high-end 3D scanner and carried out qualitative tests for various impressions comparing with the current practices. Overall, our technology achieves similar levels of accuracy and resolution with a high-end commercially available 3D scanner, while having the merits of being 1) more affordable; 2) much easier to operate, and 3) more robust. Compared with the current practice of casting, our technology demonstrates its superiority because it 1) is non-destructive; 2) collects more evidence detail than casts, especially when an impression is fragile; 3) requires less time and money to collect each piece of evidence, and 4) results in a digital file that can easily be shared with other examiners.<br>

<p>This thesis describes the development of a low-cost, low-power, accurate sensor designed for precise, feedback control of an autonomous vehicle to a hitch. Few studies have been completed on the hitching problem, yet it is an important challenge to be solved for vehicles in the agricultural and transportation industries. Existing sensor solutions are high cost, high power, and require modification to the hitch in order to work. Other potential sensor solutions such as LiDAR and Digital Fringe Projection suffer from these same fundamental problems. </p> <p>The solution that has been developed uses an active stereo vision system, combining classical stereo vision with a laser speckle projection system, which solves the correspondence problem experienced by classic stereo vision sensors. A third camera is added to the sensor for texture mapping. As a whole, the system cost is $188, with a power usage of 2.3 W.</p> <p>To test the system, a model test of the hitching problem was developed using an RC car and a target to represent a hitch. In the application, both the stereo system and the texture camera are used for measurement of the hitch, and a control system is implemented to precisely control the vehicle to the hitch. The system can successfully control the vehicle from within 35⁰ of perpendicular to the hitch, to a final position with an overall standard deviation of 3.0 mm of lateral error and 1.5⁰ of angular error. Ultimately, this is believed to be the first low power, low cost hitching system that does not require modification of the hitch in order to sense it. </p>

The morphology of the craniofacial complex is prone to alterations resulting from a wide range of external factors. In the first part of the presented thesis, we analysed the influence of slow long- term changes of the environment and population genome by comparing historical (11-12th century AD) and contemporary skulls using cephalometric X-ray images. The second part focuses on the effects of orthodontic treatment on bone thickness in relevant areas, with the analysis being based on Cone Beam computed tomography. A comparison of the palatal angle of 115 historical and 75 contemporary skulls revealed a statistically significant decrease of this parameter. The follow-up of 58 patients utilizing three- dimensional diagnostic imaging measurements before and after treatment revealed a statistically significant decrease in vestibular bone thickness, without changes of total alveolar width. Our analysis revealed a substantial bone response to respective forces, with relevant clinical implications - respecting the anatomical limits of the range of motion is essential to achieve therapeutic success and to avoid alveolar defects. Keywords: 3D imaging, CBCT, cephalometry, orthodontics, dentistry

<p>Multiphase fields find wide applications in the fields of combustion, sprays, turbomachinery, heating and cooling systems, blasts, energetic materials, and several more areas of engineering interest. As the efficiency and performance of these systems depend heavily on the underlying multiphase field, studying their intricate structural features becomes important. The current study follows the development of a three-dimensional Wide-Angle Relay Plenoptic (WARP) imaging system with two image quadruplers for the tomographic imaging of multiphase fields. 3D printed targets were used to simulate both semi-transparent as well as opaque particle fields to emulate multiphase systems. Tomographic reconstruction of the targets was performed using the iterative MART reconstruction algorithm in a commercial image processing software. Reconstructions were performed at different angular separations between the cameras as well as for varied separation distance between the object and the imaging system. Quantitative analysis of the reconstruction quality of the developed system was performed to study the effectiveness and accuracy of this system in imaging multiphase fields. The effect of varying different system parameters on reconstruction quality has been studied to evaluate the best system configuration for imaging multiphase fields.</p>

Shape and size of rocks are important physical characteristics of aggregates used in engineering and for interpretation of the genesis of naturally occurring sediment. Several image processing programs are available for measure the size and shape of various types of objects. The accuracy and reproducibility of results of a new imaging method and new matlab based 3D imaging program has been studied. 3D results are obtained by coupling two images of particles one of their largest and one of the smallest projected areas. The accuracy of results depends on the focal length used for imaging as well as the positioning of particles in the view field.

<p>  </p> <p>Congenital diseases of the kidney are the leading cause of chronic kidney disease in pediatric patients. Tissue engineering models used to investigate these diseases are limited by an immature phenotype. Models cultured in an extracellular matrix (ECM), a network of proteins and glycosaminoglycans surrounding cells and providing structural support that mimic the matrix found in development will be likely more mature. However, developing kidney ECM composition and structural dynamics are unknown. To address this gap, we studied ECM composition using mass spectrometry and organization by visualizing the ECM in 3D.</p> <p>In this work, we used mass spectrometry to resolve ECM basement membrane and interstitial matrix dynamics between embryonic, perinatal, and adult kidneys. Surprisingly, we observed a transient upregulation of interstitial matrix structures that corresponded to dynamic 3D structures in the cortex (vertical fibers) and at the corticomedullary junction (medullary ray sheath fibers). Notably, in a model of abnormal <em>Foxd1</em>+ stromal cells, the vertical fibers were disorganized, and medullary ray sheath fibers were no longer associated with blood vessels, suggesting the dynamic 3D structures depended on stromal cell modulation.</p> <p>One of the effects of abnormal kidney development is decreased amniotic fluid, which limits embryonic movement and subsequent limb development. In additional studies, we looked at the implications of the lost motility in the muscular dysgenesis (<em>mdg</em>) mouse on the development of the myotendinous junction (MTJ). The MTJ links contractile muscle with tendon. We found the ECM protein COL22A1 was specific to the developing MTJ as early as embryonic day (E)13.5. The development of the MTJ from a linear structure to a cap-like structure with invaginations in adolescent mice depended on muscle contraction. Furthermore, we used a model to decouple the muscle-tendon-bone complex at an ectopic lateral triceps insertion (<em>Prrx1Cretg/+; Tbx3fl/fl</em>). We observed disorganized tendon and MTJ markers at the termination of the ectopic lateral triceps muscle but negligible cartilage markers. Together, this indicated MTJ maturation depended on motility but not on the enthesis.</p> <p>The information gleaned from our studies on how stromal cells affect dynamic 3D interstitial ECM structures and composition change during kidney development can be used as a template for 3D kidney culture systems. Combined with forelimb MTJ development, our results indicate the importance of the interstitial matrix in tissue morphogenesis.</p>