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Airway analysis of prematurely born babies based on X-ray CT and MRI scans
Lázňovský, Jakub ; Harabiš, Vratislav (referee) ; Chmelík, Jiří (advisor)
Předkládaná Diplomová práce se zabývá analýzou a tvorbou modelů dýchacích cest předčasně narozených dětí. Nejprve je položen teoretický základ v oblasti vývoje dýchacího ústrojí a tvorby modelů dýchacích cest. Poté jsou představeny využité zobrazovací modality a popsány metody pro práci s obrazovými daty. Praktická část práce se zabývá vytvořením modelů dýchacích cest tří novorozenců. Všechny tyto modely jsou vytvořeny na základě klinických CT a MRI dat novorozenců narozených ve 30. týdnu gestačního věku. U těchto vytvořených modelů jsou dále analyzovány vybrané parametry související s anatomickou strukturou dýchacích cest. Na základě analýzy těchto parametrů byl následně navrhnut reprezentativní model, odpovídající dýchacím cestám novorozence daného gestačního věku.
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Affine registration of native and contrast-enhanced CT brain images
Chmelík, Jiří ; Mézl, Martin (referee) ; Walek, Petr (advisor)
This thesis is dealing with problem of brain images registration aquired by computed tomography. At the beginning is explanation of image geometrical transformation methods, notably affine transformation. Following part of text the is dealing with interpolation methods issues, calculation of similarity criterion and subsequent optimalization. All issues are handled especially for three-dimensional data. Second part of this work is practical sample of MatLab® program enviroment for registration of acquired frames by affine tranformation. In this program is algorithm for removement of stair-step artefact, under head pillow and patient’s desk, too. As an optimalization algorithm is used control random search (CRS) methode. Due to medical images type, which are distributed in DICOM format, is included process for their load and save at this work.
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Method for Extending the Field of View for X-ray Computed Tomography with Submicron Resolution
Zemek, Marek ; Chmelík, Jiří (referee) ; Mézl, Martin (advisor)
Výpočetní tomografie je nástroj pro nedestruktivní inspekci vzorků, který je běžně používán v mnoha oblastech průmyslu a výzkumu. Některé tomografické přístroje umožňují snímání obrazů s prostorovým rozlišením pod jeden mikrometr. Zorné pole takovýchto přístrojů bývá malé, v rozsahu jednotek milimetrů či méně. Tím jsou omezeny rozměry vzorků, což je značně limitující. Toto omezení lze překonat pomocí různých technik pro rozšíření zorného pole. Jedna takováto dříve publikovaná metoda byla v této práci upravena a implementována pro přístroj Rigaku Nano3DX. Tato technika téměř zdvojnásobuje zorné pole přístroje bez nutnosti většího detektoru. Implementovaný přístup byl testován pomocí umělých i skutečných dat, a jeho účinnost byla zhodnocena subjektivně i objektivně, pomocí vizuální kontroly a metrik kvality obrazu. Hodnocení je převážně založeno na srovnání obrazů rekonstruovaných pomocí této metody s obrazy získanými pomocí většího detektoru. Implementovaná technika rozšíření zorného pole poskytuje věrné rekonstrukce vzorku, srovnatelné se zmíněnými protějšky.
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Pupil and iris center detection
Prosser, Jan ; Chmelík, Jiří (referee) ; Kolář, Radim (advisor)
This thesis is aimed at image processing to obtain informations about the center of pupil and iris,the pupillar and limbic boundary from grayscale images of the eye. An introduction describes general research in topic of pupil, iris and changes in size of pupil. There are mentioned articles dealing with the detection of the center of pupil and iris. These articles were used as an inspiration for proposal of detection methods used in this work. The introduction ends with description of designed approaches of detection of parameters of pupil and iris in images of CASIA-Iris-Interval database. The second, practical part of this work, is dedicated to description of acquisition system, which was compiled to obtain proper images of eye. Individual analysis of methods used to obtain parameters of pupil and iris follows after that. There are two methods of detection of center of pupil and pupillar boundary, one method determines center of iris and limbic boundary. Last method detects centers and boundaries of pupil and iris at one time. The end of this work is dedicated to analysis of results of designed methods. Analysis includes score of successfulness of detection, statistical analysis, discussion of changes in pupillary diameter depending on the light conditions and changes in position of center of pupil during constriction and dilatation of pupil.
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Segmentation and morphological analysis of mouse embryo choroid plexus
Parobková, Viktória ; Jakubíček, Roman (referee) ; Chmelík, Jiří (advisor)
Choroidálny plexus je regulovanou bránou medzi krvou a mozgovomiechovým mokom a má niekoľko funkcií spojených s nervovým systémom. Mnohé funkcie sú však stále neznáme, čo je spôsobené krehkosťou, umiestnením a tvarom plexu. Preto sa na prístup k tejto kľúčovej súčasti mozgu, ktorá sa nachádza v komorách, používajú neinvazívne techniky. Okrem toho existuje súvislosť medzi jeho tvarom a patologickými stavmi mozgu. Cieľom tohto projektu bolo extrahovať ChP 4. komory implementáciou segmentačných metód a následnou morfologickou analýzou s cieľom odhaliť zákonitosti medzi tvarom a ochorením.
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Friction and lubrication of fascia
Chmelík, Jiří ; Daniel, Matej (referee) ; Vrbka, Martin (advisor)
The diploma thesis was part of the project "Regeneration and lubrication of fascia with hyaluronan" of the company Contipro a.s., whose main goal is the development of an injectable medicinal product. The number of patients suffering from so-called myofascial lower back pain is increasing. The cause of the pain is increased hyaluronic acid, which is produced between the layers of the fascia. If the viscosity is low, the fascia layers are not affected and the coefficient of friction is low. The purpose of the product is to improve the sliding movement of the fascia and relieve patients of pain. The main component of the medicine is hyaluronic acid. The project included rheological and tribological analysis of hyaluronic acid samples. A tribological model of fascia in a pin-on-plate configuration was created for the analysis of the coefficient of friction. Based on the fascia models used, the dependence between the coefficient of friction and viscosity of native hyaluronic acid solutions was found. For models and real fascias, the native solution (Bonharen) was found to have better friction properties than hyaluronic acid derivatives. These analyzes have contributed not only to the development of the drug, but also to the emergence of other studies that would like to address the biotribology of fascia.
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Microposition control device
Chmelík, Jan ; Magát, Martin (referee) ; Kadlec, Jaroslav (advisor)
This thesis deals with control of a micropositioning device. Aim of this study was to design a device that will control the piezzo-shift in three dimensions with adjustable speed and step-size. A further goal was to create a software for which allow to employ a user-defined shift profile to control the device. Actual construction of the device, based on a microcontroler Microchip 18F4550, is described in the practical section of the work.
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Segmentation of cartilage tissue of mouse embryos in 3D micro CT data
Matula, Jan ; Vičar, Tomáš (referee) ; Chmelík, Jiří (advisor)
Manual segmentation of cartilage tissue in micro CT images of mouse embryos is a very time consuming process and significantly increases the time required for the research of mammal facial structure development. This problem might be solved by using a fully-automatic segmentation algorithm. In this diploma thesis a fully-automatic segmentation method is proposed using a convolutional neural network trained on manually segmented data. The architecture of the proposed convolutional network is based on the U-Net architecture with it's encoding part substituted for the encoding part of the VGG16 classification convolutional neural network pretrained on the ImageNet database of labeled images. The proposed network achieves Dice coefficient 0.8731 ± 0.0326 in comparison to manually segmented images.
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Noise reduction for low dose CT data
Holub, Zbyněk ; Odstrčilík, Jan (referee) ; Chmelík, Jiří (advisor)
The aim of this work is comparing of methods which are used for filtration of low dose CT images. This filtration is realized due to suppress of noise in final image and better visble of details. This work contains design and realization of selected filtration methods. Wiener´s correction coefficient and filtration with usage of WAVELET TRANSFORM are introduced in detail view. These methods are created in Matlab®; with the option to set para-meters of filteres. The filters are tested on 3D CT lungs image data. In the end of this work is a ranking of filter‘s quality and choosen of the most optimal approach.
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Algorithms for the image reconstruction from projections
Zemek, Marek ; Chmelík, Jiří (referee) ; Mézl, Martin (advisor)
This work focuses on the task of reconstructing an image from its projections, particularly in relation to the CT medical imaging modality, and the evaluation of the quality of this reconstruction using various types of algorithms. First, the theory behind contemporary reconstruction algorithms is discussed. Next, this paper deals with the implementation of several simple methods of image reconstruction in Matlab, their application on simulated as well as real data, and subsequent evaluation in terms of reconstruction quality and computational complexity.
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