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Toolbox for neuronal datasets
Malý, Lukáš ; Harabiš, Vratislav (referee) ; Lamoš, Martin (advisor)
The aim of this bachelor's thesis was to create toolbox for functional magnetic resonance (fMRI) and electroencefalography (EEG) data processing in MATLAB enviroment using SPM software package. The first part describes the physiological origin of these data at neuronal level, basics of magnetic resonance imaging, principles of fMRI experiment, preprocessing and processing of fMRI data, their interpretation, then function and principles of EEG are described and at the end is simultaneous EEG-fMRI described. In the second part of the thesis features of each tool from Neural Data Toolbox (NDTb) are described.
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Application of Interferometry in VT UHV SPM
Šulc, Dalibor ; Klapetek, Petr (referee) ; Fejfar, Antonín (referee) ; Spousta, Jiří (advisor)
The thesis is aimed at the development of Scanning Probe Microscopes (SPM). It describes design and development of modular controll electronics to be applied eectively on more microscopes SPM. Control electronics consist of stabilized power source, high–voltage amplier and probe signal amplier. The open–source project GXSM has been introduced. It contains a logic control unit which controls scanning, acquiring data and feedback control. GXSM provides a graphical user interface based on linux operation system. Second part of the thesis is aimed at design and development of interferometric deection sensing system for SPM cantilevers and applications at SPM in general. Designed interferometer has been assembled and tested. It can clearly distinguish a signal of amplitude 2 nm. At the end of the thesis the design of interferometric system implementation is presented.
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Self-sensing SPM probes for measuring electrical properties of materials
Očkovič, Adam ; Vařeka, Karel (referee) ; Pavera, Michal (advisor)
The bachelor's thesis is focused on the modification of probes with an integrated sensor usable for measuring conductivity characteristics of surfaces in atomic force microscopy. The first part presents the theory concerning atomic force microscopy, conductivity measurement and deposition using an ion beam. Furthermore, the method of production and limitation of the use of electrically conductive probes with optically read deflection is described. The practical part presents the main problems of probes with integrated sensors in conductivity measurements. Furthermore, the modification of the probes themselves, the measurements made with these probes and suggestions for improving the properties of the probes are described.
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Scanning probe microscopy scanner with high resonant frequency
Krupa, Matyáš ; Dostál, Zbyněk (referee) ; Pavera, Michal (advisor)
The thesis deals with the design of the scanning probe microscopy scanner with a higher resonant frequency. The first part of the thesis is focused on theory as the principle of atomic force microscopy, function of the scanner and its properties. The second part describes the gradual development of a new microscope. The mechanical simulations used to determine the properties of scanners are introduced first. Furthermore, the thesis deals with the design for the x, y axis and then also for the z axis. In conclusion, the final design of a three-axis scanner with a higher resonant frequency is presented.
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Advanced SPM techniques for measuring electrical properties of materials
Kramář, Jan ; Konečný, Martin (referee) ; Pavera, Michal (advisor)
This bachelor thesis is concerned about development of local electric properties characterization technique of sample in contact mode of Atomic Force Microscopy. The research part describes the most expanded techniques of characterization of local electric properties using Scanning Probe Microscopy. For realization was chosen Scanning Spreading Resistance Microscopy. Important part of this technique is current amplifier. For that reason, operational amplifiers, circuits with them and implementation of new amplifier on microscop are described. Last chapter is dedicated to description of samples, which were used to test functionality of the amplifier and technique.
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Nonlinear phenomena in optical fibers
Burian, Radek ; Horváth, Tomáš (referee) ; Münster, Petr (advisor)
The subject of this thesis is to describe nonlinear phenomena in the optic fiber. The theoretical part describes a principle of transmission in optical fibers. Optics modules, fibers and their parameters are described marginally. Except nonlinear phenomena, there is also described linear phenomena such as attenuation, dispersion, scattering. In terms of nonlinear phenomena there is described second order phenomena such as Second harmonic generation (SHG), Sum and difference harmonic generation (SFG and DFG) and third order phenomena, such as Kerr effect, Third harmonic generation (THG), Four-wave mixing (FWM) and Cross phase modulation (XPM). There are also described nonlinear scattering, such as Raman´s and Brillouin´s scattering. The Four-wave mixing is simulated in the first half of the practical part. Four-wave mixing occurs in DWMD systems, where can invoke cross-talks between channels. In the second half of the practical part is measured this nonlinear phenomenon. The aim of the measurement is to understand the behaviour of the FWM and find the way how to eliminate its power. The Four-wave mixing measurement is based on the simulation. Second measurement is designed for Brillouin scattering. The conclusion from simulated and laboratory part from both measurements are compared with theoretical knowledge.
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Multifunctional SNOM probes of new generation for correlative SEM/SPM measurements
Zezulka, Lukáš ; Kolíbal, Miroslav (referee) ; Spousta, Jiří (advisor)
Práce se věnuje návrhu multifunkční SNOM sondy pro korelativní SEM/SPM měření využívající dutého optického vlákna s plným jádrem. V rešerši jsou prozkoumány možné způsoby výroby SNOM hrotů na dutém optickém vlákně, využití dutých kapilár pro přívod pracovních tekutin ke vzorku a možnosti přívodu potenciálového rozdílu ke vzorku pomocí kapilár vyplněných vodivým materiálem. Dále je v práci prezentován vyvinutý způsob výroby unikátních SNOM hrotů a celý koncept je ověřen provedenými korelativními měřeními. Následně jsou diskutované problémy spojené s výrobou a měřeními.
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Correlated probe and electron microscopy for the study of modern magnetic nanomaterials
Novotný, Ondřej ; Flajšman, Lukáš (referee) ; Pavera, Michal (advisor)
High pressure on the development of new magnetic materials and their miniaturization also emphasizes the development of new analytical techniques. This diploma thesis deals with the development and demonstration of correlated magnetic force and electron microscopy, which is a promising tool for the characterization of magnetic nanomaterials. The first part of this thesis describes the fundamental physics of micromagnetism with a focus on cylindrical nanofibers. The following pages describe optic, probe, electron, and synchrotron methods for mapping the magnetic properties of materials. The next part describes magnetic domain wall motion in cylindrical nanowires performed as a part of a more extensive material study. The last part of the thesis describes the development of correlated magnetic force and electron microscopy on LiteScope device. A production of magnetic probes was designed and successfully tested. Probes were fabricated by focused electron beam-induced deposition from the Co2(CO)8 precursor. Further, the developed correlated microscopy is demonstrated on a multilayer PtCo sample, magnetic cylindrical nanofibers, NiFe vortex structures, and FeRh metamagnetic nano-islands.
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Processing of MREG MRI data
Lampert, Frederik ; Mikl, Michal (referee) ; Gajdoš, Martin (advisor)
MR-encephalography (MREG) is an innovative method of ultrafast magnetic resonance imaging. Most of the publications about this method are concerning about acquisition and reconstruction of raw data. Studies dedicated to standardization of preprocessing MREG data have not been published yet, which led to motivation of creating this bachelor thesis. The main goal of this thesis is to set an optimal way of preprocessing MREG data, which could be advised for future studies utilizing this method. The main goal of this work was divided into several subgoals, consisting of making a literary review, implementation of general method for data preprocessing and suggesting an alternative ways of data preprocessing and their implementation into MATLAB programming language. Suggested ways of data preprocessing were evaluated by created criteria, described in this work. Results of the evaluation were discussed and interpreted by graphs. Based on the results of the evaluation, an optimal way for preprocessing data was set. It consists of movement and geometric distortion correction accomplished by SPM Realign & UNWARP function, spatial normalisation to EPI MNI template and spatial smoothing by Gaussian kernel.
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Correlative measurement of cathodoluminescence using SEM and SPM techniques
Černek, Ondrej ; Knápek, Alexandr (referee) ; Spousta, Jiří (advisor)
The diploma thesis deals with the combined use of SEM and SPM techniques using optical fiber, which is used to collect the cathodoluminescent signal in close proximity to the sample. The thesis also includes a research section, which lists description of CPEM technique, the techniques used to modify the optical fiber, theoretical introduction to cathodoluminescence and techniques used to measure it. The practical part discusses the obtained measurement results and the problems that occurred in the process of modification of the optical fiber, its use as an SPM probe and in the measurement of cathodoluminescence active materials.
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