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Automatic detection of microcalcifications in mammogram images
Hývlová, Denisa ; Jakubíček, Roman (referee) ; Harabiš, Vratislav (advisor)
This bachelor thesis is focused on detection of microcalcification in mammography images. The introduction describes connection between their presence and breast cancer, principle of mammography and the DICOM standard used in radiology. In the following part the methods used for microcalcification enhancement and segmentation are explained. Detection algorithm based on wavelet transform, morphological closing and thresholding was designed in MATLAB. For evaluation of the results a graphical user interface was developed and an algorithm for automatic evaluation of the success rate in annotated mammography database was implemented.
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Movement correction in thoracic dynamic contrast CT data
Jakubíček, Roman ; Malínský, Miloš (referee) ; Walek, Petr (advisor)
This thesis deals with a nonrigid image registration for movement correction in thoracic dynamic contrast CT data. The deformation field is initialized by the analysis of disparities based on nonlinear matched filter, which defines local movement deformation. The values of control points are optimized by the Nelder-Mead method. The transformation model is based on a 4D (3D + time) free-form B-spline deformation for feature of movement distortion. The first part of the thesis briefly discusses the theory of image registration. Knowledge of this theory is necessary for understanding the remaining chapters, which describe the proposed method and its realization. The large part of this thesis is devoted to the geometrical image transformations, that is very important for the image registration. The thesis also describes a simplex method for function minimization. Three publicated methods of registration of medical 4D CT data are given. In the following chapter are individual parts of the purposed nonrigid registration including possible problems and their solution described.
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Software for visualization and processing of volumetric data
Viktorínová, Michaela ; Jakubíček, Roman (referee) ; Harabiš, Vratislav (advisor)
The work summarizes the possibilities of volume data displaying. It deals with the scalar type of volume algorithms, which are then divided into techniques of indirect and direct rendering of volume data. From indirect techniques the Marching Cubes method is mentioned. Direct techniques are further divided into trivial and advanced algorithms. The practical part describes the design, implementation and evaluation of the functionality of implemented program that uses trivial methods. The overall evaluation consists of partial evaluations of the computational complexity, the memory load and the quality of final rendering while using different methods and types of input volume data.
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3D reconstruction from multiple images
Řehoř, Jan ; Odstrčilík, Jan (referee) ; Jakubíček, Roman (advisor)
This thesis deals with 3D reconstruction of objects from multiple frames. Thesis is divided into five chapters. The first one is connected with theory, so, it is about 3D reconstruction, about camera geometry description and about reconstruction algorithms. The following are made up by practical parts, in which are described single steps of 3D reconstruction realization, so, it is about frame acquisition, camera calibration and about used algorithms. Last part of the thesis is made up by discussion and conclusion in which the results of the experiment are discussed and summarized.
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Classification of arteries and veins in retinal image data
Černohorská, Lucie ; Jakubíček, Roman (referee) ; Kolář, Radim (advisor)
This master's thesis deals with the classification of the retinal blood vessels in retinal image data. The thesis contains a description of anatomy of the human eye with focus on the blood circulation, and imaging and diagnostic methods of the retina are briefly mentioned further. The thesis also summarizes methods of the blood circulation classification with emphasis on the deep learning. The practical section was implemented in Python programming language and describes the pre-processing of the data with determination of AV ratio. Based on a literature search, the U-net architecture was chosen for the classification of the retinal blood vessels. The architecture was modified using the open-source Keras library and tested on images from the experimental video-ophthalmoscope. The modified architecture was initially used for classification of vessels into the corresponding classes and because of unsatisfying results was modified another architecture segmenting retinal vessels, arteries or veins and a proposition of a method of the blood vessels classification.
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Tissue characterisation in spectral CT data
Poláková, Veronika ; Jan, Jiří (referee) ; Jakubíček, Roman (advisor)
This bachelor thesis deals with tissue characterisation in virtual monoenergetic images (VMI). Firstly, literature survey presents spectral CT which allows reconstructing VMI. Secondly, statistical evaluation of tissue CT numbers was made for all energies of VMI which were reconstructed. It was found that with growing energy of VMI CT number increases or decreases with different steepness depending on a type of tissue. As a consequence, the suitable VMI offer better contrast resolution between selected pairs of tissues, which enables better tissue segmentation and classification in these images.
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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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Automatic rotational alignment of head CT scans
Karmazinová, Inna ; Kolář, Radim (referee) ; Jakubíček, Roman (advisor)
The aim of this thesis is automatic alignment of head CT scan. Currently, the alignment is performed manually by an expert, however this process is time consuming. Therefore, methods for automatization of this process are being developed. Two algorithms for alignment in axial and coronal plane were designed based on bilateral symmetry of head. Following an algorithm for alignment in sagittal plane which uses CG-TOB reference line for rotation angle detection. Algorithms were implemented in MATLAB and tested and validated using a database of manually annotated head CT scans.
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Ultrasound image registration based on active contours
Hesko, Branislav ; Jakubíček, Roman (referee) ; Harabiš, Vratislav (advisor)
This diploma thesis aims to implement an active contour method for ultrasound image segmentation. Properties of ultrasound images, basic segmentation approaches and a~principle of choosen active contour methods are described within theoretical part. Two different groups of active contour methods exists, methods with use of gradient and without use of gradient as image feature. For comparision, one method of each group is implemented in practical part and subsequently, segmentation efficiency and properties of methods are compared in evaluation part.
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