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Detection of pathological vertebrae in spinal CTs utilised by machine learning methods
Tyshchenko, Bohdan ; Ronzhina, Marina (referee) ; Chmelík, Jiří (advisor)
This master's thesis focuses on detection of pathological vertebrae in spinal CT utilized by machine learning. Theoretical part describes anatomy of the spine and occurrence of pathologies in CT image data, contains an overview of existing methods intended for automated detection of pathological vertebrae. Practical part devotes to design a computer aided detection systems to identify pathological vertebrae and to classify a type of pathology. Designed classification system is based on using neural network, which performs classification step and on principal component analysis (PCA), which is used to reducing the original number of observation features. For completing this task were used real data. Conclusion contains evaluation of obtained results.
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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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Segmentation of soft tissues in facial part of mouse embryos from X-ray computed microtomography data
Janštová, Michaela ; Harabiš, Vratislav (referee) ; Chmelík, Jiří (advisor)
This diploma thesis deals with a segmentation of soft tissues in facial part of mouse embryos in Matlab. Segmentation of soft tissues of mouse embryos was not fully automated and every case needs a specific solution. Solving parts of this issues can provide valuable data for evolutionary biologists. Issues about staining and segmentation techniques are described. On the basis of accessible literature otsu thresholding, region growing, k-means clustering and segmentation with atlas were tested. In the end of this paper are those methods tested and evaluated on 3D microtomography data.
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Detection of biological structures in TEM microscope images
Cikánek, Martin ; Chmelík, Jiří (referee) ; Potočňák, Tomáš (advisor)
The aim of the first part of this thesis is to explain the theoretical basis of transmission electron microscopy and to mention fundamental parts of transmission electron microscopes. The next part of this work is focused on possible methods of image segmentation, the use of neural networks in the detection of objects in an image and the subsequent clustering of results. The theoretical part of the thesis is concluded with an explanation of some already published methods of automatic detection of biological structures in microscopic images and theoretical design of the algorithm, which will be subsequently developed. The process of training neural networks in order to automatically detect biological structures in an image is described at the beginning of the practical part. This is followed by an evaluation of the results achieved by these networks. Subsequently, cluster analysis methods are applied to these results, the products of which are compared with each other and also with the results obtained by already published methods.
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Identification of vertebrae type in CT data by machine learning methods
Matoušková, Barbora ; Kolář, Radim (referee) ; Chmelík, Jiří (advisor)
Identification of vertebrae type by machine learning is an important task to facilitate the work of medical doctors. This task is embarrassed by many factors. First, a spinal CT imagining is usually performed on patiens with pathologies such as lesions, tumors, kyphosis, lordosis, scoliosis or patients with various implants that cause artifacts in the images. Furthermore, the neighboring vertebraes are very similar which also complicates this task. This paper deals with already segmented vertebrae classification into cervical, thoracic and lumbar groups. Support vector machines (SVM) and convolutional neural networks (CNN) AlexNet and VGG16 are used for classification. The results are compared in the conclusion.
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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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Application of optimisation methods for MRI data segmentation
Olešová, Kristína ; Mézl, Martin (referee) ; Chmelík, Jiří (advisor)
This thesis deals with a segmentation of brain tissues from MRI image data and its implementation in MATLAB. Segmentation problematic is described with attention to formulating segmentation as optimization problem and segmentation of given images with different metaheuristic algorithm consequently. This approach was chosen due to information from last specialized publications, where it was accentuated for its fast computational speed and universality. This thesis tries to prove this statement with segmentation of brain images with brain tumours that have different types, number, stage of illness and phase of therapy.
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Using advanced segmentation methods for images from TEM microscopes
Mocko, Štefan ; Chmelík, Jiří (referee) ; Potočňák, Tomáš (advisor)
Tato magisterská práce se zabývá využitím konvolučních neuronových sítí pro segmentační účely v oblasti transmisní elektronové mikroskopie. Také popisuje zvolenou topologii neuronové sítě - U-NET, použíté augmentační techniky a programové prostředí. Firma Thermo Fisher Scientific (dříve FEI Czech Republic s.r.o) poskytla obrazová data pro účely této práce. Získané segmentační výsledky jsou prezentovány ve formě křivek (ROC, PRC) a ve formě numerických hodnot (ARI, DSC, Chybová matice). Zvolená UNET topologie dosáhla excelentních výsledků v oblasti pixelové segmentace. S největší pravděpodobností, budou tyto výsledky sloužit jako odrazový můstek pro interní firemní výzkum.
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Deep learning methods for image processing
Křenek, Jakub ; Chmelík, Jiří (referee) ; Kolář, Radim (advisor)
This master‘s thesis deals with the Deep Learning methods for image recognition tasks from the first methods to the modern ones. The main focus is on convolutional neural nets based models for classification, detection and image segmentation. These methods are used for practical implemetation – counting passing cars on video from traffic camera. After several test of available models, the YOLOv2 architecture was chosen and retrained on own dataset. The application also includes the addition of the SORT tracking algorithm.
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Image data shape analysis
Kylián, Jakub ; Harabiš, Vratislav (referee) ; Chmelík, Jiří (advisor)
Bachelor thesis is focused on shape analysis of image data. This thesis clarifies usage of methods, techniques and procedures that lead to such analysis. The content of this thesis is divided into three chapters – theory, analysis solution and conclusion. In the chapter theory, methods and general theory of the topic are introduced. The rule is, that every method used in subsequent sections is explained in detail, but this doesn't necessarily mean that it applies in reverse. Next chapter, following up the theory section is analysis solution. In this section, a problem is presented. This problem is then, with knowledge presented in chapter theory solved. The solution consists of many processes and preparations that are also explained in detail in this chapter.
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