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Meta-analysis of bone tumorous lesions in spinal CT data using convolutional neural networks
Nantl, Ondřej ; Jakubíček, Roman (referee) ; Chmelík, Jiří (advisor)
This bachelor thesis deals with the use of convolutional neural networks in the meta-analysis of bone tumor lesions in CT image data. The theoretical part describes the anatomy and pathology of bone tissue, machine learning, discusses the functionality of convolutional neural networks and summarizes selected existing methods for computer-aided diagnosis of vertebra bone lesions. In the practical part, various types of models using convolutional neural networks were implemented and the networks were trained on an available augmented dataset. Finally, the results of various types of models were statistically evaluated, compared with available articles and discussed.
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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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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 cranial bone after craniectomy
Vavřinová, Pavlína ; Chmelík, Jiří (referee) ; Jakubíček, Roman (advisor)
This thesis deals with the segmentation of cranial bone in CT patient’s data after craniectomy. The U-Net architecture in 2D and 3D variant were selected for the intention of solving this problem. Jaccard index for 2D U-Net was evaluate as 89,4 % and for 3D U-Net it was 67,1 %. In the area after surgical intervention evaluating index has smaller difference between both variant, the average success rate of skull classification was 98,4 % for 2D U-Net and 97,0 % for 3D U-Net.
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Artificial intelligence for predicting sepsis from clinical signals
Šidlo, David ; Chmelík, Jiří (referee) ; Vičar, Tomáš (advisor)
This bachelor thesis deals with the issue of predicting sepsis from clinical data using artificial intelligence methods. In the theoretical part, a literature research is made on the basic principles and functioning of various methods of artificial intelligence. Greater emphasis was placed on recurrent neural networks. The aim of the practical part was to implement a suitable method in the chosen programming environment. The LSTM network and the temporal convolutional network TCN were chosen as suitable methods. The best results of the normalized value of the utility score were achieved by TCN, namely 0.377 and seven-layer LSTM 0.356.
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Segmentation of biological samples in cryo-electron microscopy images using machine learning methods
Sokol, Norbert ; Vičar, Tomáš (referee) ; Chmelík, Jiří (advisor)
Zobrazovanie pomocou kryo-elektrónovej mikroskopie má svoje nezastúpiteľné miesto v analýze viacerých biologických štruktúr. Lokalizácia buniek kultivovaných na mriežke a ich segmentácia voči pozadiu alebo kontaminácii je základom. Spolu s vývojom viacerých metód hlbokého učenia sa podstatne zvýšila úspešnosť úloh sémantickej segmentácie. V tejto práci vyvinieme hlbokú konvolučnú neurónovú sieť pre úlohu sémantickej segmentácie buniek kultivovaných na mriežke. Dátový súbor pre túto prácu bol vytvorený pomocou dual-beam kryo-elektónového mikroskopu vyvinutého spoločnosťou Thermo Fisher Scientific Brno.
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Automatic classification of Petri dish colony images
Herodes, Jakub ; Odstrčilík, Jan (referee) ; Chmelík, Jiří (advisor)
The thesis describe issue of segmentation and classification of Petri dishes colored images. There is proposed a segmentation method that extracts positions of cells from the image. Another techniques focues on classification to groups according to the parameters obtained from images. Reliability of each optimalized algorithm is tested on database containing 250 colored images received from company BioVendor Instruents a.s.
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Negative Photoresist Exposition with LED Application
Chmelík, Jiří ; Novák, Vítězslav (referee) ; Starý, Jiří (advisor)
The purpose of this work is conception and realization of exposition unit for negative photoresist with ultra violet light emitting diodes application. For conception of this unit is necessary understanding of physical laws about light and radiation. The major part of this work is dealing with conception and construction of LED matrix array. Second step is testing of this array. Next parts are aimed to conception or choose of power source, vacuum frame, timer controller, control unit and other support systems. Final part is devoted to device description and service manual.
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Utilization of convolutional neural networks for segmentation of mouse embryos cartilaginous tissue in micro-CT data
Poláková, Veronika ; Vičar, Tomáš (referee) ; Chmelík, Jiří (advisor)
Automatická segmentace biologických struktur v mikro-CT datech je stále výzvou, protože často objekt zájmu (v našem případě obličejová chrupavka) není charakterizovaný unikátním jasem či ostrými hranicemi. V posledních letech se konvoluční neuronové sítě (CNNs) staly mimořádně populárními v mnoha oblastech počítačového vidění. Konkrétně pro segmentaci biomedicínských obrazů je široce používaná architektura U-Net. Nicméně v případě mikro-CT dat vyvstává otázka, zda by nebylo výhodnější použít 3D CNN. Diplomová práce navrhla CNN architekturu založenou na síti V-Net včetně metodologie pro předzpracování a postprocessing dat. Základní architektura byla dále optimalizována pomocí pokročilých architektonických modifikací jako jsou pyramidální modul dilatovaných konvolucí (ASPP modul), škálovatelná exponenciálně-lineární jednotka (SELU aktivační funkce), víceúrovňová kontrola učení (multi-output supervision) či bloky s hustými propojeními (Dense blocks). Pro učení sítě byly použity moderní přístupy jako zahřívání kroku učení (learning rate warmup) či AdamW optimalizátor. I přes to, že 3D CNN v úloze segmentace obličejové chrupavky nepřekonala U-Net, optimalizace zvýšila medián Dice koeficientu z 69,74 % na 80,01 %. Používání těchto pokročilých architektonických modifikací v dalším výzkumu je proto vřele doporučováno, jelikož můžou být přidány do libovolné architektury typu U-Net a zároveň výrazně zlepšit výsledky.
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Classification of glioma grading in brain MRI
Olešová, Kristína ; Mézl, Martin (referee) ; Chmelík, Jiří (advisor)
This thesis deals with a classification of glioma grade in high and low aggressive tumours and overall survival prediction based on magnetic resonance imaging. Data used in this work is from BRATS challenge 2019 and each set contains information from 4 weighting sequences of MRI. Thesis is implemented in PYTHON programming language and Jupyter Notebooks environment. Software PyRadiomics is used for calculation of image features. Goal of this work is to determine best tumour region and weighting sequence for calculation of image features and consequently select set of features that are the best ones for classification of tumour grade and survival prediction. Part of thesis is dedicated to survival prediction using set of statistical tests, specifically Cox regression
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