This master's thesis is focused on in situ observation of the negative electrode of the lead acid accumulator using atomic force microscopy AFM. Discussed topics are lead acid accumulator, atomic force microscopy, cyclic voltammetry and current knowledge of the in situ observation of the lead acid accumulator using AFM. The main task of this project is assembling the experimental cells, make in situ observation of the negative electrode surface of the lead acid accumulator. In the end evaluate if this method is suitable for the lead acid battery observation.

This thesis is pointed on simulation of electron microscope. It uses knowledge  from ray-tracing methods and physically based rendering with physics of electron microscopy. The main object of this thesis is to create realistic simulator for electron microscope which can generate satisfying realistic images. This output can be used for another research in range of machine learning or microscope application development. This method should replace long and more expensive way of getting test images from real system for those research activities.

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.

Control of cultivation conditions in the~live cell imaging extends the possibilities of biological experiments and makes the experimental results more reliable. In order to change the~cultivation conditions in a controlled manner and increase the reproducibility of the experiments, it is necessary to reduce the amount of manual operations and replace them with automated procedures. Therefore, the concept of a new automated culture device (bioreactor) was created. This device controls the exchange of medium in the observation chamber, ensures the circulation and exchange of the atmosphere and controls its composition. The bioreactor is intended for use in the Laboratory of Experimental Biophotonics. This laboratory is equipped with coherence-controlled holographic microscope (CCHM), which uses quantitative phase imaging (QPI) method. Thus, the bioreactor is adapted to the current requirements of this laboratory and optical elements of the bioreactor meet the requirements of the QPI method. This text specifies the cultivation conditions of the living cells and summarizes, how the conditions could be controlled in the live cell microscopy. Next some commercially available culture devices are described and assessed, whether they are convenient for the~use in Laboratory of Experimental Biophotonics. The crucial part of the thesis is the~design, construction and testing of the new bioreactor.

Magnetické materiály a z nich vyrobené nanostruktury jsou v průběhu posledních let studovány pro jejich aplikace v např. záznamových médiích a logických obvodech. Tato práce navazuje na náš předchozí výzkum tohoto oboru s hlavním zaměřením na statické a dynamické vlastnosti nanostrukturovaných magnetických materiálů, jako například NiFe, CoFeB a YIG. Práce začíná teoretickým úvodem s popisem mikromagnetických systémů, dynamiky magnetických vortexů, feromagnetické rezonance (FMR) a spinových vln včetně jejich disperzních vlastností. Následuje popis použitých experimentálních metod a první experimentální část zabývající se nukleačním procesem magnetického vortexu, jinými slovy procesem transformace ze saturovaného stavu do spinové konfigurace magnetického vortexu v průběhu snižování magnetického pole. Jsou použity mikroskopické metody zobrazující magnetickou strukturu materiálu, jmenovitě Lorentzova transmisní elektronová mikroskopie a rentgenová transmisní mikroskopie. Výsledky jsou poté korelovány s měřením elektrické odezvy pomocí jevu anizotropní magnetorezistence. Výhodou elektrických měření je, že plně elektrická detekce dovoluje použití tohoto systému v uzavřených systémech integrovaných obvodů. Výsledky oblasti nukleací magnetických vortexů ukazují, že při tomto procesu prochází magnetizace v nano- a mikrometrových magnetických discích několika fázemi s růsnými typy spinových konfigurací nazvaných nukleační stavy. Dále je představeno měření magnetických materiálů pomocí vektorového síťového analyzátoru (VNA), což je aplikováno na měření resonance magnetických vortexů (určení gyrotropické frekvence a měření vysokofrekvenčních módů), feromagnetické rezonance tenkých vrstev (získání základních magnetických materiálových parametrů) a spektroskopii spinových vln. Právě spektroskopie spinových vlna je rozvinuta za účelem měření disperzních relací tenkých magnetických vrstev, což je základní charakteristika, jejíž znalost je důležitá v návrhu aplikací. Nakonec je představeno anténní zařízení, díky kterému lze oddělit magnetické buzení od vzorku samotného bez nutnosti absolvovat proces elektronové litorafie, což je zapotřebí v klasickém přístupu antény na vzorku a kontaktování vysokofrekvenční sondou. Toto zařízení se skládá ze skleněného kantilívru, na kterém je vyrobena budící anténa, konektoru a spojovacího prvku v podobě plošného spoje. Celé zařízení je díky umístění na x-y-z stolek s náklonem pozicovatelné a lze tedy měřit v jakémkoliv místě vzorku. Umístění antény na sklo umožňuje navigaci pomocí mikroskopu a optické měření, např. metodou Brillouinova světelného rozptylu (BLS) nebo Kerrova jevu.

The demountable splicing of optical fibres uses different types of connectors which ensures accurate position of connected fibres. If the optical fibres are aligned in free space, a view from two perpendicular viewing directions is necessary for a maximum aligning accuracy. The method of direct monitoring of optical fibres provides this possibility however, it is necessary to use two imaging systems. This problem can be solved by a special microscope, which is designed in this thesis. The microscope can visualize the alignment of optical fibres from two mutually perpendicular directions by moving the objective lens and inclined mirror. The diploma thesis also describes the procedure of designing an optical simulation of the connection of optical fibres. Based on it, the microscope is designed, adjusted and tested with various optical fibres.

This diploma thesis deals with electron microscopy. Examined equipment is environmental scanning electron microscope (ESEM), namely scintillation a detector of the microscope. There is solved the influence of the profile of holes in diaphragms to the resulting pressure and gas flow on the path of secondary electrons at the detector. Introductory part of thesis informs about microscopy in general, with concentration on electron microscopy; especially on scanning microscope, because research is taken just on the environmental scanning electron microscope. Another part informs about both general principles of dynamics of gases and with finite volume method. Another part deals with concrete used software and with setting of individual parameters for calculation. At the beginning of calculation are used five basic profiles of holes in diaphragms for pressure 1000 Pa in the chamber of the sample. For modelling individual shapes is used 3D parametric modeller SolidWorks. Analysis of circulation of secondary electrons through detector is made by using Cosmos FloWorks module. The most suitable type of diaphragms is chosen from measured models. Another part of diploma thesis deals with measuring of chosen types of diaphragms for more pressures in the chamber of the sample; the pressure is 200, 400, 600, 800 and 1000 Pa. The outcomes of this research are both models of pressure and speed of circulation inside the detector and graphically processed values by using different diaphragms, respectively one type of a diaphragm in different pressures. Production drawings of each diaphragm, together with calculated models, are enclosed.

The semestral project will focus on using Computer Aided Engineering for analysis of the ESEM differential chamber. The instruments used for the analysis, evaluation and scrutiny of the given issue will be the CAD and CAE systems (Computer Aided Design and Computer Aided Engineering).

This master's thesis deals with the ways of cell viability determination and its measuring. The first part of this thesis has a brief introduction into the theory of cell viability, also the methods of cell viability measurement and different types of fluorescent probes are described. The thesis further includes a brief description of the image processing methods, as well as the fluorescent microscope and applied filters are described. In the practical part the system implemented at a graphical programming environment LabVIEW used for the cell viability evaluation is described, functions of applied units are explained. The program is checked on model data.

This thesis is focused on the environmental scanning electron microscopes including a description of the basic physical mechanisms. It describes the design and realization of the electrode ionization detector system suitable for the detection of signal electrons with a greater proportion of secondary electrons. It also deals with simulations of trajectories of electrons in the electrostatic field of the detector, and with verification of the functionality of the detector in the environment of water vapors in the specimen chamber of the electron microscope.