Design and Optimization of Four-dimensional Cone-beam Computed Tomography in Image-guided Radiation Therapy

The influence of respiratory motion on patient anatomy poses a challenge to accurate radiation therapy, especially in lung cancer treatment. Modern radiation therapy planning uses models of tumor respiratory motion to account for target motion in targeting. The tumor motion model can be verified on a per-treatment session basis with four-dimensional cone-beam computed tomography (4D-CBCT), which acquires an image set of the dynamic target throughout the respiratory cycle during the therapy session. 4D-CBCT is undersampled if the scan time is too short. However, short scan time is desirable in clinical practice to reduce patient setup time. This dissertation presents the design and optimization of 4D-CBCT to reduce the impact of undersampling artifacts with short scan times. This work measures the impact of undersampling artifacts on the accuracy of target motion measurement under different sampling conditions and for various object sizes and motions. The results provide a minimum scan time such that the target tracking error is less than a specified tolerance. This work also presents new image reconstruction algorithms for reducing undersampling artifacts in undersampled datasets by taking advantage of the assumption that the relevant motion of interest is contained within a volume-of-interest (VOI). It is shown that the VOI-based reconstruction provides more accurate image intensity than standard reconstruction. The VOI-based reconstruction produced 43% fewer least-squares error inside the VOI and 84% fewer error throughout the image in a study designed to simulate target motion. The VOI-based reconstruction approach can reduce acquisition time and improve image quality in 4D-CBCT.

Animations of micro-computed tomography of a pleistocene terebratulid brachiopod

The dorsal valve of a Pleistocene terebratulid brachiopod, Terebratula scillae Seguenza, 1871, has developed a malignant cyst due to colonization in vivo by an endolithic sponge.This trace fossil is a compound boring and bioclaustration structure, representing a boring that has grown in unison with the growth of the cyst. The brachiopod has grown to adult size and growthlines indicate that it was colonised by the sponge when about half grown. Malformation of the shell may not have caused the death of the brachiopod and the sponge does not appear to have outlived its host; both symbionts seem to have died more or less simultaneously. This minus-minus relationship of two symbionts is considered to be a case of 'accidental symbiosis'.

Detection and Differentiation of Intraretinal Hemorrhage in Spectral Domain Optical Coherence Tomography.

PURPOSE The purpose of this study was to classify and detect intraretinal hemorrhage (IRH) in spectral domain optical coherence tomography (SD-OCT). METHODS Initially the presentation of IRH in BRVO-patients in SD-OCT was described by one reader comparing color-fundus (CF) and SD-OCT using dedicated software. Based on these established characteristics, the presence and the severity of IRH in SD-OCT and CF were assessed by two other masked readers and the inter-device and the inter-observer agreement were evaluated. Further the area of IRH was compared. RESULTS About 895 single B-scans of 24 eyes were analyzed. About 61% of SD-OCT scans and 46% of the CF-images were graded for the presence of IRH (concordance: 73%, inter-device agreement: k = 0.5). However, subdivided into previously established severity levels of dense (CF: 21.3% versus SD-OCT: 34.7%, k = 0.2), flame-like (CF: 15.5% versus SD-OCT: 45.5%, k = 0.3), and dot-like (CF: 32% versus SD-OCT: 24.4%, k = 0.2) IRH, the inter-device agreement was weak. The inter-observer agreement was strong with k = 0.9 for SD-OCT and k = 0.8 for CF. The mean area of IRH detected on SD-OCT was significantly greater than on CF (SD-OCT: 11.5 ± 4.3 mm(2) versus CF: 8.1 ± 5.5 mm(2), p = 0.008). CONCLUSIONS IRH seems to be detectable on SD-OCT; however, the previously established severity grading agreed weakly with that assessed by CF.

Enhanced depth imaging optical coherence tomography of congenital cavitary optic disc anomaly (CODA).

AIM To report the finding of extension of the 4th hyper-reflective band and retinal tissue into the optic disc in patients with cavitary optic disc anomalies (CODAs). METHODS In this observational study, 10 patients (18 eyes) with sporadic or autosomal dominant CODA were evaluated with enhanced depth imaging optical coherence tomography (EDI-OCT) and colour fundus images for the presence of 4th hyper-reflective band extension into the optic disc. RESULTS Of 10 CODA patients (18 eyes), five patients (8 eyes) showed a definite 4th hyper-reflective band (presumed retinal pigment epithelium (RPE)) extension into the optic disc. In these five patients (seven eyes), the inner retinal layers also extended with the 4th hyper-reflective band into the optic disc. Best corrected visual acuity ranged from 20/20 to 20/200. In three patients (four eyes), retinal splitting/schisis was present and in two patients (two eyes), the macula was involved. In all cases, the 4th hyper-reflective band extended far beyond the termination of the choroid into the optic disc. The RPE extension was found either temporally or nasally in areas of optic nerve head excavation, most often adjacent to peripapillary pigment. Compared with eyes without RPE extension, eyes with RPE extension were more myopic (mean dioptres -0.9±2.6 vs -8.8±5, p=0.043). CONCLUSIONS The RPE usually stops near the optic nerve border separated by a border tissue. With CODA, extension of this hyper-reflective band and retinal tissue into the disc is possible and best evaluable using EDI-OCT or analogous image modalities. Whether this is a finding specific for CODA, linked to specific gene loci or is also seen in patients with other optic disc abnormalities needs further evaluation.

Technical developments for computed tomography on the CENBG nanobeam line

The use of ion microbeams as probes for computedtomography has proven to be a powerful tool for the three-dimensional characterization of specimens a few tens of micrometers in size. Compared to other types of probes, the main advantage is that quantitative information about mass density and composition can be obtained directly, using specific reconstruction codes. At the Centre d’Etudes Nucléaires de Bordeaux Gradignan (CENBG), this technique was initially developed for applications in cellular biology. However, the observation of the cell ultrastructure requires a sub-micron resolution. The construction of the nanobeamline at the Applications Interdisciplinaires des Faisceaux d’Ions en Region Aquitaine (AIFIRA) irradiation facility has opened new perspectives for such applications. The implementation of computedtomography on the nanobeamline of CENBG has required a careful design of the analysis chamber, especially microscopes for precise sample visualization, and detectors for scanning transmission ion microscopy (STIM) and for particle induced X-ray emission (PIXE). The sample can be precisely positioned in the three directions X, Y, Z and a stepper motor coupled to a goniometer ensures the rotational motion. First images of 3D tomography were obtained on a reference sample containing microspheres of certified diameter, showing the good stability of the beam and the sample stage, and the precision of the motion.

Automatic quantification of matrix cracking and fiber rotation by X-ray computed tomography in shear-deformed carbon fiber-reinforced laminates

The deformation and damage mechanisms of carbon fiber-reinforced epoxy laminates deformed in shear were studied by means of X-ray computed tomography. In particular, the evolution of matrix cracking, interply delamination and fiber rotation was ascertained as a function of the applied strain. In order to provide quantitative information, an algorithm was developed to automatically determine the crack density and the fiber orientation from the tomograms. The investigation provided new insights about the complex interaction between the different damage mechanisms (i.e. matrix cracking and interply delamination) as a function of the applied strain, ply thickness and ply location within the laminate as well as quantitative data about the evolution of matrix cracking and fiber rotation during deformation

Geometrical characterization of undisturbed soil samples using X-ray computed tomography image analysis. Effect of soil management on soil structure

El estudio de la estructura del suelo es de vital importancia en diferentes campos de la ciencia y la tecnología. La estructura del suelo controla procesos físicos y biológicos importantes en los sistemas suelo-planta-microorganismos. Estos procesos están dominados por la geometría de la estructura del suelo, y una caracterización cuantitativa de la heterogeneidad de la geometría del espacio poroso es beneficiosa para la predicción de propiedades físicas del suelo. La tecnología de la tomografía computerizada de rayos-X (CT) nos permite obtener imágenes digitales tridimensionales del interior de una muestra de suelo, proporcionando información de la geometría de los poros del suelo y permitiendo el estudio de los poros sin destruir las muestras. Las técnicas de la geometría fractal y de la morfología matemática se han propuesto como una poderosa herramienta para analizar y cuantificar características geométricas. Las dimensiones fractales del espacio poroso, de la interfaz poro-sólido y de la distribución de tamaños de poros son indicadores de la complejidad de la estructura del suelo. Los funcionales de Minkowski y las funciones morfológicas proporcionan medios para medir características geométricas fundamentales de los objetos geométricos tridimensionales. Esto es, volumen, superficie, curvatura media de la superficie y conectividad. Las características del suelo como la distribución de tamaños de poros, el volumen del espacio poroso o la superficie poro-solido pueden ser alteradas por diferentes practicas de manejo de suelo. En este trabajo analizamos imágenes tomográficas de muestras de suelo de dos zonas cercanas con practicas de manejo diferentes. Obtenemos un conjunto de medidas geométricas, para evaluar y cuantificar posibles diferencias que el laboreo pueda haber causado en el suelo. ABSTRACT The study of soil structure is of vital importance in different fields of science and technology. Soil structure controls important physical and biological processes in soil-plant-microbial systems. Those processes are dominated by the geometry of soil pore structure, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. The technology of X-ray computed tomography (CT) allows us to obtain three-dimensional digital images of the inside of a soil sample providing information on soil pore geometry and enabling the study of the pores without disturbing the samples. Fractal geometry and mathematical morphological techniques have been proposed as powerful tools to analyze and quantify geometrical features. Fractal dimensions of pore space, pore-solid interface and pore size distribution are indicators of soil structure complexity. Minkowski functionals and morphological functions provide means to measure fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. Soil features such as pore-size distribution, pore space volume or pore-solid surface can be altered by different soil management practices. In this work we analyze CT images of soil samples from two nearby areas with contrasting management practices. We performed a set of geometrical measures, some of them from mathematical morphology, to assess and quantify any possible difference that tillage may have caused on the soil.

Neural-network-based classification of cognitively normal, demented, Alzheimer disease and vascular dementia from single photon emission with computed tomography image data from brain.

Single photon emission with computed tomography (SPECT) hexamethylphenylethyleneamineoxime technetium-99 images were analyzed by an optimal interpolative neural network (OINN) algorithm to determine whether the network could discriminate among clinically diagnosed groups of elderly normal, Alzheimer disease (AD), and vascular dementia (VD) subjects. After initial image preprocessing and registration, image features were obtained that were representative of the mean regional tissue uptake. These features were extracted from a given image by averaging the intensities over various regions defined by suitable masks. After training, the network classified independent trials of patients whose clinical diagnoses conformed to published criteria for probable AD or probable/possible VD. For the SPECT data used in the current tests, the OINN agreement was 80 and 86% for probable AD and probable/possible VD, respectively. These results suggest that artificial neural network methods offer potential in diagnoses from brain images and possibly in other areas of scientific research where complex patterns of data may have scientifically meaningful groupings that are not easily identifiable by the researcher.

Spectral-domain optical coherence tomography study of macular structure as prognostic and determining factor for macular hole surgery outcome

Purpose: To evaluate postoperative spectral-domain optical coherence tomography findings after macular hole surgery. Methods: Retrospective, interventional, nonrandomized study. Overall, 164 eyes of 157 patients diagnosed with macular hole were operated on by vitrectomy and internal limiting membrane peeling. Preoperative and postoperative best-corrected visual acuity and spectral-domain optical coherence tomography images were obtained. Two groups were considered on the basis of the postoperative integrity of the back reflection line from the ellipsoid portion of the photoreceptor inner segment: group A (disruption of ellipsoid portion of the inner segment line, 60 eyes) and group B (restoration of ellipsoid portion of the inner segment line, 104 eyes). Results: Logarithm of the minimum angle of resolution best-corrected visual acuity improved significantly after the surgery of macular hole from a mean preoperative value of 0.79 ± 0.37 (range, 0.15–2.00) to a mean postoperative value of 0.35 ± 0.31 (range, 0.00–1.30) at the last follow-up visit (P < 0.01). Best-corrected visual acuity improved significantly in the 2 groups analyzed (all P < 0.01). A larger improvement was found in group B than in group A (P < 0.01). Conclusion: Ellipsoid portion of the inner segment line reconstruction seems to be a good prognostic factor for visual rehabilitation after macular hole surgery.

Long time remodeling during retinal degeneration evaluated by optical coherence tomography, immunocytochemistry and fundus autofluorescence

Purpose: To characterize the relationship between fundus autofluorescence (FAF), Optical Coherence Tomography (OCT) and immunohistochemistry (IHC) over the course of chronic retinal degeneration in the P23H rat. Methods: Homozygous albino P23H rats, Sprague–Dawley (SD) rats as controls and pigmented Long Evans (LE) rats were used. A Spectralis HRA OCT system was used for scanning laser ophthalmoscopy (SLO) imaging OCT and angiography. To determine FAF, fluorescence was excited using diode laser at 488 nm. A fast retina map OCT was performed using the optic nerve as a landmark. IHC was performed to correlate with the findings of OCT and FAF changes. Results: During the course of retinal degeneration, the FAF pattern evolved from some spotting at 2 months old to a mosaic of hyperfluorescent dots in rats 6 months and older. Retinal thicknesses progressively diminished over the course of the disease. At later stages of degeneration, OCT documented changes in the retinal layers, however, IHC better identified the cell loss and remodeling changes. Angiography revealed attenuation of the retinal vascular plexus with time. Conclusion: We provide for the first time a detailed long-term analysis of the course of retinal degeneration in P23H rats using a combination of SLO and OCT imaging, angiography, FAF and IHC. Although, the application of noninvasive methods enables longitudinal studies and will decrease the number of animals needed for a study, IHC is still an essential tool to identify retinal changes at the cellular level.

Ultrasonic and X-ray computed tomography characterization of progressive fracture damage in low-porous carbonate rocks

This paper studies the fracturing process in low-porous rocks during uniaxial compressive tests considering the original defects and the new mechanical cracks in the material. For this purpose, five different kinds of rocks have been chosen with carbonate mineralogy and low porosity (lower than 2%). The characterization of the fracture damage is carried out using three different techniques: ultrasounds, mercury porosimetry and X-ray computed tomography. The proposed methodology allows quantifying the evolution of the porous system as well as studying the location of new cracks in the rock samples. Intercrystalline porosity (the smallest pores with pore radius < 1 μm) shows a limited development during loading, disappearing rapidly from the porosimetry curves and it is directly related to the initial plastic behaviour in the stress–strain patterns. However, the biggest pores (corresponding to the cracks) suffer a continuous enlargement until the unstable propagation of fractures. The measured crack initiation stress varies between 0.25 σp and 0.50 σp for marbles and between 0.50 σp and 0.85 σp for micrite limestone. The unstable propagation of cracks is assumed to occur very close to the peak strength. Crack propagation through the sample is completely independent of pre-existing defects (porous bands, stylolites, fractures and veins). The ultrasonic response in the time-domain is less sensitive to the fracture damage than the frequency-domain. P-wave velocity increases during loading test until the beginning of the unstable crack propagation. This increase is higher for marbles (between 15% and 30% from initial vp values) and lower for micrite limestones (between 5% and 10%). When the mechanical cracks propagate unstably, the velocity stops to increase and decreases only when rock damage is very high. Frequency analysis of the ultrasonic signals shows clear changes during the loading process. The spectrum of treated waveforms shows two main frequency peaks centred at low (~ 20 kHz) and high (~ 35 kHz) values. When new fractures appear and grow the amplitude of the high-frequency peak decreases, while that of the low-frequency peak increases. Besides, a slight frequency shift is observed towards higher frequencies.

Analysis of analogue models by helical X-ray computed tomography

The aim of analogue model experiments in geology is to simulate structures in nature under specific imposed boundary conditions using materials whose rheological properties are similar to those of rocks in nature. In the late 1980s, X-ray computed tomography (CT) was first applied to the analysis of such models. In early studies only a limited number of cross-sectional slices could be recorded because of the time involved in CT data acquisition, the long cooling periods for the X-ray source and computational capacity. Technological improvements presently allow an almost unlimited number of closely spaced serial cross-sections to be acquired and calculated. Computer visualization software allows a full 3D analysis of every recorded stage. Such analyses are especially valuable when trying to understand complex geological structures, commonly with lateral changes in 3D geometry. Periodic acquisition of volumetric data sets in the course of the experiment makes it possible to carry out a 4D analysis of the model, i.e. 3D analysis through time. Examples are shown of 4D analysis of analogue models that tested the influence of lateral rheological changes on the structures obtained in contractional and extensional settings.

SPECTRAL DOMAIN-OPTICAL COHERENCE TOMOGRAPHY IMAGE CONTRAST AND BACKGROUND COLOR SETTINGS INFLUENCE IDENTIFICATION OF RETINAL STRUCTURES.

PURPOSE To evaluate image contrast and color setting on assessment of retinal structures and morphology in spectral-domain optical coherence tomography. METHODS Two hundred and forty-eight Spectralis spectral-domain optical coherence tomography B-scans of 62 patients were analyzed by 4 readers. B-scans were extracted in 4 settings: W + N = white background with black image at normal contrast 9; W + H = white background with black image at maximum contrast 16; B + N = black background with white image at normal contrast 12; B + H = black background with white image at maximum contrast 16. Readers analyzed the images to identify morphologic features. Interreader correlation was calculated. Differences between Fleiss-kappa correlation coefficients were examined using bootstrap method. Any setting with significantly higher correlation coefficient was deemed superior for evaluating specific features. RESULTS Correlation coefficients differed among settings. No single setting was superior for all respective spectral-domain optical coherence tomography parameters (P = 0.3773). Some variables showed no differences among settings. Hard exudates and subretinal fluid were best seen with B + H (κ = 0.46, P = 0.0237 and κ = 0.78, P = 0.002). Microaneurysms were best seen with W + N (κ = 0.56, P = 0.025). Vitreomacular interface, enhanced transmission signal, and epiretinal membrane were best identified using all color/contrast settings together (κ = 0.44, P = 0.042, κ = 0.57, P = 0.01, and κ = 0.62, P ≤ 0.0001). CONCLUSION Contrast and background affect the evaluation of retinal structures on spectral-domain optical coherence tomography images. No single setting was superior for all features, though certain changes were best seen with specific settings.

Functional Optical Coherence Tomography: In Vivo Applications in Dermatology and Neuroscience

Thesis (Ph.D.)--University of Washington, 2016-06