Microwave Breast Models Through T1-weighted 3-d Mri Data

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2013Thesis (M.Sc.) -- İstanbul Technical University, Institute of Science and Technology, 2013Son yıllarda, meme kanserinin erken teşhisi konusunda mikrodalga görüntüleme alanında yapılan çalışmalar popülerlik kazanmıştır. Bu bağlamda, insan memesinin elektromanyetik sayısal modelleri bu konuda çalışan araştırmacılara, hızlı deneysel analizler yaparak yeni teknolojilerin fizibilitesinin artırılması ve böylece daha iyi görüntüleme tekniklerinin ve aygıtlarının geliştirilmesi konularında yardımcı olmaktadır. Literatürde özel olarak sayısal mikrodalga meme modellerini konu alan bu ilk çalışmada arzu edilen türde bir model üretilebilmesi için 3 ana adım içeren bir yöntem öne sürülmüştür. Bu yöntemin alt adımları kısaca: MRI verisindeki gürültünün homomorfik filtreleme ile giderilmesi, dokuların Gauss Karışım Modeli (GMM) ile segmentasyonu ve elektromanyetik özelliklerin parçalı-doğrusal eşleme fonksiyonları ile eşlenmesi olarak tarif edilebilir. Bu çalışmada, mikrodalga meme görüntülemesi çalışmalarında kullanılmak üzere değişik şekil, ebat ve radyografik yoğunluklarda 3-boyutlu sayısal mikrodalga meme modelleri üretilmesi için etkin ve kendi kendine işleyebilen bir yöntem sunulmuştur. Memenin heterojen yapısının mekânsal bilgisi, memelerinde bir anomaliye rastlanmayan değişik hastaların yüz üstü pozisyonda alınmış T1-ağırlıklı 3-boyutlu MRI verileri kullanılarak elde edilmiştir. Dokulara ait her bir sınıf ile elektromanyetik özellikler arasında tekdüze parçalı kübik Hermitte interpolasyon yöntemi kullanılarak doğrusal olmayan bir ilişki kurulmuştur. İlgili meme dokularının elektromanyetik özellikleri Debye and Cole-Cole dağılım modelleri üzerinden tercih edilen çalışma frekansına göre belirlenmiş, böylece MRI verisindeki her bir voksel değeri uygun bağıl geçirgenlik ve iletkenlik değerleri ile eşlenmiştir. Bağıl geçirgenlik ve iletkenlik dağılımlarına dönüştürülen MRI kesitleri, doğrusal interpolasyon ile 3-boyutlu ve gerçekçi bir yapıya dönüştürülmüştür.Recent years, early detection of breast cancer in the field of electromagnetic imaging has gained high popularity. In this context, computational electromagnetic models of the human breast are used to help researchers develope better techniques and instruments for imaging, increasing the feasibility of new technologies, and doing fast experimental analysis. In this study, an effective and automated methodology for realistic numerical 3-D breast phantom development of different shapes, size and radiographic density in order to be used for different electromagnetic simulation models in microwave breast imaging research is presented. The spatial information of heterogeneity of the breast structure is collected from T1-weighted MRI slices of different patients’ in prone position with normal breast tissue (not malignant or abnormal). Each voxel in MRI data was mapped to the appropriate dielectric properties using several steps. First, bias field appears on each slice in MRI data was estimated and eliminated. After filtering of all slices, voxels belong to adipose and glandular tissues were classified into four categories. Then those tissue categories were related to electromagnetic properties of relative permittivity and conductivity by monotone piecewise polynomial cubic Hermite interpolation. Electromagnetic properties of the breast tissue are expanded to desired frequency using Debye dispersion models. Each voxel intensity value is nonlinearly mapped to the appropriate electromagnetic properties of the corresponding breast tissue. Later, the resultant slices of permittivity and conductivity are linearly interpolated to form a proper 3-D breast structure.Yüksek LisansM.Sc

Animating jellyfish through numerical simulation and symmetry exploitation

This thesis presents an automatic animation system for jellyfish that is based on a physical simulation of the organism and its surrounding fluid. Our goal is to explore the unusual style of locomotion, namely jet propulsion, which is utilized by jellyfish. The organism achieves this propulsion by contracting its body, expelling water, and propelling itself forward. The organism then expands again to refill itself with water for a subsequent stroke. We endeavor to model the thrust achieved by the jellyfish, and also the evolution of the organism's geometric configuration. We restrict our discussion of locomotion to fully grown adult jellyfish, and we restrict our study of locomotion to the resonant gait, which is the organism's most active mode of locomotion, and is characterized by a regular contraction rate that is near one of the creature's resonant frequencies. We also consider only species that are axially symmetric, and thus are able to reduce the dimensionality of our model. We can approximate the full 3D geometry of a jellyfish by simulating a 2D slice of the organism. This model reduction yields plausible results at a lower computational cost. From the 2D simulation, we extrapolate to a full 3D model. To prevent our extrapolated model from being artificially smooth, we give the final shape more variation by adding noise to the 3D geometry. This noise is inspired by empirical data of real jellyfish, and also by work with continuous noise functions from the graphics community. Our 2D simulations are done numerically with ideas from the field of computational fluid dynamics. Specifically, we simulate the elastic volume of the jellyfish with a spring-mass system, and we simulate the surrounding fluid using the semi-Lagrangian method. To couple the particle-based elastic representation with the grid-based fluid representation, we use the immersed boundary method. We find this combination of methods to be a very efficient means of simulating the 2D slice with a minimal compromise in physical accuracy

Modelling and peeling extended sources with shapelets: a Fornax A case study

To make a power spectrum (PS) detection of the 21 cm signal from the Epoch of Reionisation (EoR), one must avoid/subtract bright foreground sources. Sources such as Fornax A present a modelling challenge due to spatial structures spanning from arc seconds up to a degree. We compare modelling with multi-scale (MS) CLEAN components to 'shapelets', an alternative set of basis functions. We introduce a new image-based shapelet modelling package, SHAMFI. We also introduce a new CUDA simulation code (WODEN) to generate point source, Gaussian, and shapelet components into visibilities. We test performance by modelling a simulation of Fornax A, peeling the model from simulated visibilities, and producing a residual PS. We find the shapelet method consistently subtracts large-angular-scale emission well, even when the angular-resolution of the data is changed. We find that when increasing the angular-resolution of the data, the MS CLEAN model worsens at large angular-scales. When testing on real MWA data, the expected improvement is not seen in real data because of the other dominating systematics still present. Through further simulation we find the expected differences to be lower than obtainable through current processing pipelines. We conclude shapelets are worthwhile for subtracting extended galaxies, and may prove essential for an EoR detection in the future, once other systematics have been addressed.Comment: 17 pages, 11 Figures, accepted for publication in Publications of the Astronomical Society of Australia (18/05/2020). "For the SHAMFI code, see: https://github.com/JLBLine/SHAMFI" . "For the SHAMFI documentation, see: https://shamfi.readthedocs.io/" . "For the WODEN code and documentation see: https://github.com/JLBLine/WODEN