The Insight Segmentation and Registration Toolkit (ITK) is a highly utilized open source medical imaging library. Written in C++, ITK provides chiefly the functionality to register, segment, and filter medical images. Although extremely powerful, ITK has a very steep learning curve for users with little or no background in programming. It was for this reason that SimITK was developed. SimITK wraps ITK into the model driven engineering environment Simulink, a part of the Matlab development suite. The first released version of SimITK was a proof of concept, and demonstrated that ITK could be wrapped successfully in Simulink. Very few segmentation and registration functions were available and the system was based on ITK version 3 with a semi-automatic wrapping procedure. In this thesis a new version of SimITK is presented that includes thirty-seven image filter, twelve optimizer, and nineteen transform classes from ITK version 4 which are successfully wrapped and tested. These classes were chosen to represent a broad range of usability (in the case of the filters) and to allow for greater flexibility when creating registration pipelines by having more options for optimizers, transforms, and metrics. Many usability improvements were also implemented for the registration pipeline, including providing the user with the metric value while executing a registration model and allowing the output image size to be specified for certain filters. In order for SimITK to transition to a usable research tool, several usability improvements were needed. These included transitioning from wrapping ITK version 3 to ITK version 4, fully automating the wrapping process, and usability modifications to the registration pipeline including a metric value output. These implementations of an automated wrapping procedure for ITK version 4, and improved usability of the registration pipeline have propelled SimITK on a path towards a usable research tool. The author will be creating a release of these changes, updating installation documentation, and updating tutorials which are available at www.SimITKVTK.com / Thesis (Master, Computing) -- Queen's University, 2013-08-05 10:15:16.607

<p> Patients receiving Intensity Modulated Radiation Therapy (IMRT) for late stage head and neck (HN) cancer often experience anatomical changes due to weight loss, tumor regression, and positional changes of normal anatomy (1). As a result, the actual dose delivered may vary from the original treatment plan. The purpose of this study was (a) to evaluate the dosimetric consequences of the parotid glands during the course of treatment, and (b) to determine if there would be an optimal timeframe for replanning. Nineteen locally advanced HN cancer patients underwent definitive IMRT. Each patient received an initial computerized tomography simulation (CT-SIM) scan and weekly cone beam computerized tomography (CBCT) scans. A Deformable Image Registration (DIR) was performed between the CT-SIM and CBCT of the parotid glands and Planning Target Volumes (PTVs) using the Eclipse treatment planning system (TPS) and the Velocity deformation software. A recalculation of the dose was performed on the weekly CBCTs using the original monitor units. The parameters for evaluation of our method were: the changes in volume of the PTVs and parotid glands, the dose coverage of the PTVs, the lateral displacement in the Center of Mass (COM), the mean dose, and Normal Tissue Complication Probability (NTCP) of the parotid glands. The studies showed a reduction of the volume in the PTVs and parotids, a medial displacement in COM, and alterations of the mean dose to the parotid glands as compared to the initial plans. Differences were observed for the dose volume coverage of the PTVs and NTCP of the parotid gland values between the initial plan and our proposed method utilizing deformable registration-based dose calculations.</p>

No description available.

Neurosurgery is an effective method for prolonging life and improving outcomes for patients with brain tumors. However, this option bears the risk of damaging areas of eloquent cortex, areas associated with motor and language tasks that, when lesioned, will result in a functional deficit for the patient. Functional magnetic resonance imaging (fMRI) is a valuable tool in the localization of eloquent cortex for preoperative neurosurgical planning. Through use of this modality of functional neuroimaging, the neurosurgeon can adjust the surgical trajectory to incur the least amount of damage to sites of functional activity. The supplementary motor area (SMA) is one such site of eloquent cortex that must be visualized preoperatively due to the risk of postoperative deficit with lesions in this area. However, due to both the effects of tumor pathology and naturally occurring interindividual variability, the SMA’s location and functional fingerprint can be highly variable. We present a study in which patients with frontal tumor (n=46) underwent task-based fMRI for motor and language network mapping. The patient-specific functional data were normalized and evaluated using ROI analysis to illustrate group-level activation patterns within the SMA during the language and motor tasks. The results illustrate a distinct pattern of activation including a rostro-caudal organization of language and motor activation, overlapping extent cluster volumes throughout the two functional subdivisions of the SMA, the pre-SMA and SMA proper, and discrete activation foci.

Previous studies have shown the connection between aortic stiffness, cerebral microbleeds (CMBs) and increased cognitive decline in both human and mouse studies (Akoudad et al., 2016; Mitchell, 2015; Wang, 2018). However, most studies have been done only on males, leaving out a clear understanding of sex differences in CMBs. The purpose of the present study is to identify the changes in CMB levels in aging C57BL/6 female mice and compare this to the aging male mouse model. There were two hypotheses the study aimed to test: (1) female mice would show an increase in CMBs with age and (2) the level of CMBs in females would be less than in males until old age where both sexes will have similar levels of microbleeds. To test the hypotheses, histology via Prussian Blue staining was used to detect CMBs in the perfused C57BL/6 aging female mice and then compared to CMB levels in the males, found previously (Wang, 2018). The results support the first hypothesis that CMBs increase with age in the female mouse model. However, the level of CMBs is decreased in the old age female compared to the old male. The present study is the first to show sex differences in cerebral microbleeds with age. This is relevant to researchers and clinicians as it shows that sex differences need to be accounted for when identifying mechanisms and developing cures for diseases such as dementia. / 2021-06-18T00:00:00Z

No description available.

Phase-contrast imaging is a method of imaging widely used in biomedical research and applications. It is a label-free method that exploits intrinsic differences in the refractive index of different tissues to differentiate between biological structures under analysis. The basic principle of phase-contrast imaging has inspired a lot of implementations that are suited for different applications. This thesis explores multiple novel implementations of phase-contrast imaging in the following order. 1, We combined scanning Oblique Back-illumination Microscope (sOBM) and confocal microscope to produce phase and fluorescence contrast images in an endomicroscopy configuration. This dual-modality design provides co-registered, complementary labeled and unlabeled contrast of the sample. We further miniaturized the probe by dispensing the two optical fibers in our old design. And we presented proof of principle demonstrations with ex-vivo mouse colon tissue. 2, Then we explored sOBM-based phase and amplitude contrast imaging under different wavelengths. Hyperspectral imaging is achieved by multiplexing a wide-range supercontinuum laser with a Michaelson interferometer (similar to Fourier transform spectroscopy). It features simultaneous acquisition of hyperspectral phase and amplitude images with arbitrarily thick scattering biological samples. Proof-of-principle demonstrations are presented with chorioallantoic membrane of a chick embryo, illustrating the possibility of high-resolution hemodynamics imaging in thick tissue. 3, We focused on increasing the throughput of flow cytometry with principle of phase-contrast imaging and compressive sensing. By utilizing the linearity of scattered patterns under partially coherent illumination, our cytometer can detect multiple objects in the same field of view. By utilizing an optimized matched filter on pupil plane, it also provides increased information capacity of each measurement without sacrificing speed. We demonstrated a throughput of over 10,000 particles/s with accuracy over 91% in our results. 4, A fourth part, which describes the principle and preliminary results of a computational fluorescence endomicroscope is also included. It uses a numerical method to achieve sectioning effect and renders a pseudo-3D image stack with a single shot. The results are compared with true-3D image stack acquired with a confocal microscope.

Frequently, testing of Single Photon Emission Computed Tomography (SPECT) motion correction algorithms is done either by using simplistic deformations that do not accurately simulate true patient motion or by applying the algorithms directly to data acquired from a real patient, where the true internal motion is unknown. In this work, we describe a way to combine these two approaches by using imaging data acquired from real volunteers to simulate the data that the motion correction algorithms would normally observe. The goal is to provide an assessment framework which can both: simulate realistic SPECT acquisitions that incorporate realistic body deformations and provide a ground truth volume to compare against. Every part of the motion correction algorithm needs to be exercised: from parameter estimation of the motion model, to the final reconstruction results. In order to build the ground truth anthropomorphic numerical phantoms, we acquire high resolution MRI scans and motion observation data of a volunteer in multiple different configurations. We then extract the organ boundaries using thresholding, active contours, and morphology. Phantoms of radioactivity uptake and density inside the body can be generated from these boundaries to be used to simulate SPECT acquisitions. We present results on extraction of the ribs, lungs, heart, spine, and the rest of the soft tissue in the thorax using our segmentation approach. In general, extracting the lungs, heart, and ribs in images that do not contain the spine works well, but the spine could be better extracted using other methods that we discuss. We also go in depth into the software development component of this work, describing the C++ coding framework we used and the High Level Interactive GUI Language (HLING). HLING solved a lot of problems but introduced a fair bit of its own. We include a set of requirements to provide a foundation for the next attempt at developing a declarative and minimally restrictive methodology for writing interactive image processing applications in C++ based on lessons learned during the development of HLING.

There are unmet needs in evaluating treatment response of hepatocellular carcinoma in research protocols. Early predictors, such as imaging biomarkers, could allow for earlier judgment of treatment effect. Currently RECIST is the most widely accepted criterion in clinical trials. A modified RECIST (mRECIST) criterion was developed to take into account the unique imaging characteristics of HCC lesions. Much discussion has occurred regarding linear measurements and their appropriateness for evaluating change in tumor burden over time. The simplicity of currently accepted criteria differs with the increasing sophistication of imaging techniques. Tumor volume change on 3D imaging can provide insight into actual action of treatment rather than an estimate of action as shown by linear and bi-dimensional measurements. It was the aim of this study to determine whether linear, bi-dimensional, and volumetric percent changes of HCC lesions, in both the arterial and portal venous phases, are significantly comparable. 27 HCC lesions (identified on 25 subjects) were measured at two timepoints by each method on 3D GRE MRI scans in both phases. Percent change was calculated per lesion for each measurement type in both the arterial and portal venous phases. Signed rank tests, paired t tests, and comparison of change tests were run to evaluate the data. Significant differences between the percent changes of linear measurements versus volumetric measurements were observed using a Wilcoxon signed-rank test which showed p = 0.0000. A simple correlation assessment showed positive correlations for all measurements, with the lowest being correlations 0.8679 for the arterial linear percent change versus the arterial volumetric percent change and 0.8434 for the portal venous linear percent change versus the portal venous volumetric percent change. Differences between percent changes of linear versus bi-dimensional measurements and bi-dimensional versus volumetric measurements were significant as well (Linear versus bi-dimensional p = 0.0001, bi-dimensional versus volumetric p = 0.0004). To conclude, the differences in the percent changes when comparing the measurement types are statistically significant, particularly when comparing linear and volumetric measurements. Establishing a reproducible volumetric criterion could lead to improvements in the implementation of clinical trials.

PURPOSE: Extremely low gestation age newborns (ELGANs) are at high risk for developmental brain abnormalities, which can lead to cognitive, physical, emotional and behavioral deficits. This study is to determine potential brain volumetric abnormalities of ELGAN children at 9 to 10 years of age. METHODS: High-resolution magnetic resonance imaging (MRI) scans were obtained from 82 ELGAN children using a dual-echo turbo spin-echo (DE-TSE) pulse sequence at 3.0T (or 1.5T at only one site). The DICOM MR images were processed with quantitative MRI algorithms programmed in Mathcad. The brain gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) volumes were quantified using semi-automated clustering segmentation algorithms. RESULTS: Total brain volumes (GM+WM) of ELGAN children showed a large distribution range from 400 to 1500 mL. About 63% of the children had smaller brain volumes while 5% of them had larger brain volumes compared to the published data from normal children at the same ages1. Smaller brain volumes were observed more often in males (74%) than in females (50%). WM reduction was the major change in ELGANs with over 90% of them (86% of males and 92% of females) having reduced WM volumes. GM volumes were either reduced (15%) or enlarged (32%); GM reduction was observed more often in males (31%) than in females (4.8%), while GM enlargement was more frequently observed in females (35%) than in males (28%). Intracranial CSF volumes range from 25 mL to 600 mL, with 16% of ELGAN children (9% of males and 21% of females) having smaller CSF volume, while 38% of them (53% of males and 27% of females) having larger CSF volume. Correlation analysis revealed a positive correlation between total intracranial matter (ICM) and CSF volumes (male: r = 0.4972, p = 0.0014 and female: r = 0.3233, p = 0.0125), but a negative correlation was found between brain volumes and CSF volumes (male: r = - 0.2998, p = 0.0424 and female: r = - 0.2279, p = 0.0596). Further analysis demonstrated a negative correlation between GM and CSF both in absolute (male: r = - 0.4489, p = 0.0039 and female: r = - 0.3769, p = 0.0041) and in relative (male: r = - 0.8675, p = 0.0000 and female: r = - 0.8350, p = 0.0000) volumes, while WM volumes did not correlate with CSF volumes. CONCLUSION: ELGAN children had mostly smaller brain volumes while some of them displayed larger brain volumes at ages of 9 to 10 years. The reduction of WM was a characteristic change in ELGAN children and contributed to smaller brain volumes. GM volumes either increased or decreased. Larger intracranial CSF volumes were associated with larger intracranial matter (ICM) volume.