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3D analysis of biological samples using focused ion beam electron microscopy
Petrovský, Jan ; Sobola, Dinara (referee) ; Hrubanová,, Kamila (advisor)
Understanding the three-dimensional information inside biological microscopic structures is easier and more intuitive than a set of two-dimensional images. The aim of this thesis is to create a 3D model of the bacterium Rubrum rhodospirillum that allows the observation of structural changes with respect to the whole experiment. To successfully image the cells, it is essential to fix their ultrastructures. In our case, chemical fixation followed by heavy metal staining and embedding in resin is used. The final acquisition of a good quality dataset for the creation of the three-dimensional model is preceded by the optimization of the image acquisition parameters. Emphasis is placed on the parameters of the electron and ion beam used. In this work, several different microscope settings are tested and compared and their influence on the final image is examined. Subsequently, several datasets are imaged using the software Auto Slice and View 4 and then whole cells and PHB granules inside these cells are segmented. From this modified data, a 3D model of the bacteria in the studied volume was created using selected reconstruction techniques.
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Surface Wave Analysis and Inversion-Application to the Bohemian Massif
Kolínský, Petr ; Prokop Brokešová, Johana (advisor) ; Novotný, Oldřich (referee) ; Růžek, Bohuslav (referee)
title: Surface Wave Analysis and Inversion Application to the Bohemian Massif author: Mgr. Petr Kolínský, DiS. author's e-mail address: kolinsky@irsm.cas.cz departments: Department of Geophysics Faculty of Mathematics and Physics Charles University Prague V Holešovičkách 2, Praha 8 - 180 00, Czech Republic and Department of Seismology Institute of Rock Structure and Mechanics, v.v.i. Academy of Sciences of the Czech Republic V Holešovičkách 41, Praha 8 - 182 09, Czech Republic supervisor: RNDr. Johana Brokešová, CSc. supervisor's e-mail address: johana.brokesova@mff.cuni.cz consultant: RNDr. Jiří Málek, PhD. consultant's e-mail address: malek@irsm.cas.cz keywords: surface waves, group velocity, phase velocity, frequency-time analysis, multiple filtering, tomography, inversion problems, Earth crust structure, Bohemian Massif An overview of surface wave analysis methods as well as of inversion techniques is given. Special attention is paid to the multiple filtering method for dispersion curve estimation, which is described by two different ways in detail. The isometric method is used for dispersion curve inversion and its description and tests are presented. Described methods are further used in applications. The applications show examples of surface wave analysis and inversion for 1D and 2D...
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Tomographical analysis of semiconductor devices by FIB-SIMS
Mičulka, Martin ; Voborný, Stanislav (referee) ; Bábor, Petr (advisor)
This thesis deals with a tomographic analysis of the structure of through-silicon via utilizing TOF-SIMS; a method used in electrotechnical industry. A focused ion beam isused to create a cross section of a semiconductor to reveal its inner structure. Afterwards a newly created surface is analysed by TOF-SIMS to determine its chemical composition. A series of 2D images is created which are used for tomographic reconstruction of the through-silicon via. Moreover, the thesis deals with an optimization of FIB-SIMS method by employing oxygen ion beam for improvement of ionized sputter yield and for artifacts reduction. A measurement of instability of bismuth ion beam is demonstrated as well.
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Supervised Segmentation For 3D Slicer
Chalupa, Daniel
The purpose of this work is to introduce an extendable framework for training and usage of machine learning algorithms. This framework is bundled in an extension for 3D Slicer that is to be used for medical images segmentation. An example usage of the extension is also provided.
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Automatic smoothing 3D models of cranial embryonic mouse cartilage
Kočendová, Kateřina ; Harabiš, Vratislav (referee) ; Jakubíček, Roman (advisor)
The focus of this thesis is the smoothing of manually segmented 3D models of mouse embryo craniofacial cartilege. During the process of manual segmentation, artefacts and other imperfections appear in the final models and need to be repaired. Firstly, manual segmentation is corrected using gradients and thresholding. Subsequent smoothing methods are constructed based on theoretical research. Algorithmizing is executed in the MATLAB environment. All the designed algorithms are then tested on selected models. Statistical evaluation is determined using the Srensen–Dice coefficient, where manually smoothened models cleared of all artefacts are used as the gold standard.
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2D and 3D analysis of semiconductor devices by SIMS
Vařeka, Karel ; Šamořil, Tomáš (referee) ; Bábor, Petr (advisor)
The chemical analysis of semiconductor structures using the SIMS method is the main part of this bachelor thesis. It allows the user to make a depth profiling and a creation of 2D or 3D material images. During the analysis of the chip from the TIGBT semiconductor, there is a sputtering of a heterogeneous structure in the material with different sputtering rates. It is convenient to make a cut through the material using a focused ion beam to create a profile, which grants the user to perform a tomographic measurement. This new surface enables a chemical analysis of a depth profile of semiconductor structures without the need for sputtering beam in dynamic SIMS mode. By reconstructing individual two-dimensional images, it is possible to assemble a three-dimensional pattern of the analysed sample area. Also, the preparation and removal of the lamella from the TIGBT chip were accomplished and analysed via a detector of transmission electrons.
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3D tomography of thin film catalysts by means of FIB/SEM techniques
Dinhová, Thu Ngan ; Matolínová, Iva (advisor) ; Khalakhan, Ivan (referee)
One of the actual problems of today society are decreasing sources of fossil fuels. They are raw minerals and by their burning is energy produced. Regarding to the importance of energy in todays world, it's necessary to find an alternative way how to generate energy. A possible solution to this problem are fuel cells, which work on the principle of converting chemical energy into electric energy. At this moment, the development of fuel cells is in progress. In this bachelor thesis, we are concerned with morphology of catalytic layers Pt/CeO2 deposed on a polymer membrane for hydrogen fuel cells. By using of tomography method with focused ion beam system (FIB) we are creating three-dimensional models of their surface structures. 1
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Surface Wave Analysis and Inversion-Application to the Bohemian Massif
Kolínský, Petr ; Prokop Brokešová, Johana (advisor) ; Novotný, Oldřich (referee) ; Růžek, Bohuslav (referee)
title: Surface Wave Analysis and Inversion Application to the Bohemian Massif author: Mgr. Petr Kolínský, DiS. author's e-mail address: kolinsky@irsm.cas.cz departments: Department of Geophysics Faculty of Mathematics and Physics Charles University Prague V Holešovičkách 2, Praha 8 - 180 00, Czech Republic and Department of Seismology Institute of Rock Structure and Mechanics, v.v.i. Academy of Sciences of the Czech Republic V Holešovičkách 41, Praha 8 - 182 09, Czech Republic supervisor: RNDr. Johana Brokešová, CSc. supervisor's e-mail address: johana.brokesova@mff.cuni.cz consultant: RNDr. Jiří Málek, PhD. consultant's e-mail address: malek@irsm.cas.cz keywords: surface waves, group velocity, phase velocity, frequency-time analysis, multiple filtering, tomography, inversion problems, Earth crust structure, Bohemian Massif An overview of surface wave analysis methods as well as of inversion techniques is given. Special attention is paid to the multiple filtering method for dispersion curve estimation, which is described by two different ways in detail. The isometric method is used for dispersion curve inversion and its description and tests are presented. Described methods are further used in applications. The applications show examples of surface wave analysis and inversion for 1D and 2D...
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