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Using blind image filtering for images from TEM microscopes
Nováková, Kateřina ; Mézl, Martin (referee) ; Potočňák, Tomáš (advisor)
Předložená práce se zabývá problematikou slepé filtrace obrazů z transmisního elektronového mikroskopu. V úvodu práce je uveden popis transmisního elektronového mikroskopu. Navazující část popisuje mechanismy interakce elektronů se zkoumaným vzorkem a z toho vyplývající zobrazovací techniky elektronové mikroskopie. Poslední kapitola teoretické části práce zahrnuje popis vybraných metod slepé filtrace obrazu zejména s využitím dekompozice obrazu na charakteristické složky. Taktéž je zde uveden výčet metod pro zhodnocení úspěšnosti filtrace. V praktické části jsou popsány aplikované metody slepé filtrace obrazů a výsledky filtrování. Jednotlivé metody jsou mezi sebou porovnány. Získané výsledky a využitelnost aplikovaných metod jsou zhodnoceny v diskuzi.
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Detection and measurement of electron beam in TEM images
Polcer, Simon ; Vičar, Tomáš (referee) ; Chmelík, Jiří (advisor)
This diploma thesis deals with automatic detection and measurement of the electron beam in the images from a transmission electron microscope (TEM). The introduction provides a description of the construction and the main parts of the electron microscope. In the theoretical part, there are summarized modes of illumination from the fluorescent screen. Machine learning, specifically convolution neural network U-Net is used for automatic detection of the electron beam in the image. The measurement of the beam is based on ellipse approximation, which defines the size and dimension of the beam. Neural network learning requires an extensive database of images. For this purpose, the own augmentation approach is proposed, which applies a specific combination of geometric transformations for each mode of illumination. In the conclusion of this thesis, the results are evaluated and summarized. This proposed algorithm achieves 0.815 of the DICE coefficient, which describes an overlap between two sets. The thesis was designed in Python programming language.
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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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Segmentation of carbon nanocones in TEM images using generalized Hough transform
Sladký, Vladimír ; Odstrčilík, Jan (referee) ; Walek, Petr (advisor)
Bachelor thesis deals with automatic detection of carbon nanostructures in TEM images using generalized Hough transform. There is described the theory of Hough transform in order to detect analytic as well as general structures in images. According to the characteristics of carbon nanostructures TEM images synthetic test images, that are preprocessed by morphological operations and thresholding with global threshold, are created. Hough transform algorithm that detects nanocones in synthetic images of carbon nanocone structures is created. Success and accuracy of detection is tested changing the parameters of artificial images or level of preprocessing.
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Comparison of microscopic diagnostic methods
Veselý, Jakub ; Tihlaříková, Eva (referee) ; Čudek, Pavel (advisor)
This thesis deals with the description and comparison of diagnostic methods, transmission electron microscopy, scanning electron microscopy and atomic force microscopy. The introduction is a description of diagnostic methods. The following experimental section dealing with the diagnosis of ferritic chromium steel sample methods of scanning electron microscopy, atomic force microscopy, transmission electron microscopy and the evaluation and interpretation of measured results. The conclusion provides a comparison, the advantages and disadvantages of diagnostic methods.
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Microscopy: tool for material analysis
Pleskalová, Kateřina ; Řehořek, Lukáš (referee) ; Čupera, Jan (advisor)
This thesis deals with description of the microscopic techniques that are used to analyse materials. The introductory part briefly summarizes the history of microscopy. The first part of the thesis is focused on light microscopy and the confocal microscopy technique is more elaborated here. The second part of the thesis is focused on basic techniques of electron microscopy, which means transmission electron microscopy and scanning electron microscopy. At the end of each chapter, there is summarization of limits and advantages of these techniques. The preparation of metallographic samples is also briefly described for these microscopic techniques.
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Phase plates for transmission electron microscopy
Špičáková, Tereza ; Sháněl, Ondřej (referee) ; Konečná, Andrea (advisor)
Vzorky tvořené atomy lehčích prvků, jako jsou například biologické preparáty, dosahují na snímcích z transmisních elektronových mikroskopů nízkého kontrastu. Pokud však vneseme mezi elektrony nesoucí informaci o zkoumaném vzorku a elektrony pozadí dodatečný fázový posun, dojde k výraznému navýšení kontrastu bez negativních dopadů na kvalitu obrazu. Tohoto efektu lze v mikroskopech dosáhnout s pomocí fázových destiček. V konvenčních transmisních elektronových mikroskopech se běžně využívají fázové destičky založené na tenkých vrstvách amorfního uhlíku. V posledních letech byly detailně zkoumány různé pokročilé designy fázových destiček. Jen několik málo studií se však věnuje alternativním materiálům, které by bylo možné použít jako tenkovrstvé fázové destičky. Hlavním cílem této diplomové práce je tedy navrhnout způsoby měření fázových vlastností různých materiálů. V první části práce je nejprve popsána teorie zobrazování elektronovou vlnou v transmisních elektronových mikroskopech. Dále jsou zde prezentovány a porovnány různé druhy fázových destiček. Ve druhé části práce jsou představeny čtyři návrhy experimentálního uspořádání, z nichž dva byly experimentálně otestovány. Tato měření byla provedena na sadách vzorků různých materiálů a tlouštěk a vhodně zpracována. Na závěr bylo kvalitativní chování těchto návrhů porovnáno s teoretickými výpočty.
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Comparison of microscopic diagnostic methods
Veselý, Jakub ; Tihlaříková, Eva (referee) ; Čudek, Pavel (advisor)
This thesis deals with the description and comparison of diagnostic methods, transmission electron microscopy, scanning electron microscopy and atomic force microscopy. The introduction is a description of diagnostic methods. The following experimental section dealing with the diagnosis of ferritic chromium steel sample methods of scanning electron microscopy, atomic force microscopy, transmission electron microscopy and the evaluation and interpretation of measured results. The conclusion provides a comparison, the advantages and disadvantages of diagnostic methods.
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Characterization of PHA producing microbial cells by advanced microscopic and cytometric techniques
Dlouhá, Karolína ; Nováčková, Ivana (referee) ; Obruča, Stanislav (advisor)
The aim of this bachelor thesis is to document production of polyhydroxyalkanoates in selected bacterial strains, which were Pseudomonas thermotolerans, Chelatococcus daeguensis, Tepidiphilus thermophilus and Chelatococcus thermostellatus. In the case of the microorganisms Tepidiphilus thermophilus and Pseudomonas thermotolerans, the production of PHA´s has not yet been described, and in the Chelatococcus bacteria, which were analysed in this work, the production has not yet been documented by electron microscopy. In this work, the selected producers were analysed by flow cytometry first, using BODIPY and Nile Red as fluorescence probes. Selected producers, for which was production confirmed, were analysed by other methods, such as fluorescence microscopy, cryo scanning electron microscopy and transmission electron microscopy. In the bacterial culture of Pseudomonas thermotolerans, PHA´s production wasn´t confirmed by the first analysis by flow cytometer. For other microorganisms was production confirmed. Chelatococcus bacteria clearly proved to be better producers. Bacterial cells of Tepidiphilus thermophilus produced smaller granules and in lower amount.
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Techniques using beam of charged particles for imaging and material analysis
Lamborová, Leona ; Kičmerová, Dina (referee) ; Čupera, Jan (advisor)
This bachelor´s thesis deals with techniques using beam of charged particles for imaging and material analysis. There are two types of charged particles that are used for this purpose, electrons and ions. This research study is divided into principles of electron optics and principles of ion optics. Further, there is mentioned function, construction and detectors used for imaging and chemical analysis of scanning electron microscopy, transmission electron microscopy and focused ion beam.
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