SALT HRS (Southern African Large Telescope High Resolution Échelle Spectrograph) is a high-resolution, high-efficiency spectrograph for the 11m SALT telescope in Sutherland, South Africa. The initial optical design work was performed at the University of Canterbury, New Zealand. Revisions to the concept, the mechanical design, manufacture, assembly and testing have been handled by the Centre for Advanced Instrumentation, at Durham University in the United Kingdom. SALT HRS is a fibre-fed echelle grating spectrograph with four operational modes: low-, medium- and high-resolution and high-stability modes, having spectral resolutions of R ≈16000, 37000, 67000 and 67000 respectively over a wavelength range of 370-890nm. The instrument is of a dual channel, ‘white pupil’ design, in which the primary mirror acts to collimate light onto a single R4 echelle grating, and also to focus dispersed light to an intermediate focus. A dichroic beam-splitter separates the dispersed light into two separate spectral channels. Spherical pupil mirrors transfer the separated beams via a fold mirror to two wavelength-specific volume-phase holographic gratings (VPHGs) used as cross-dispersers. Cross-dispersed spectra are then imaged by two fully dioptric camera systems onto optimized CCD detectors. This thesis presents the results of the laboratory testing and specification of several critical sub-systems of SALT HRS, as well as the development of key software tools for the design verification and operation at the telescope. In Chapter 1 we first review the technical development of high-resolution spectroscopy and its specific implementation in SALT HRS. In Chapter 2 we develop a comprehensive throughput model of the entire system based on a combination of as-built performance and specific throughput measurements in the laboratory. This is used to make some specific predictions for the on-sky performance of SALT HRS and the magnitude limits for science targets. We also present a graphical exposure time calculator based on these measurements which can be used by an astronomer to plan their observations with SALT HRS. Chapter 3 contains a detailed treatise on the optical fibre system of SALT HRS. Considerations for the use of optical fibres in astronomy are provided, as are details of an optional double scrambler, and the various instrument fibre modes. Extensive measurements of focal ratio degradation (FRD) are also presented, with testing of input beam speed; wavelength; fibre bending; variable pupil mirror illumination; and vacuum tank pressure dependency. The systems for fibre management are reviewed, as is the fibre bundle assembly process. Testing of two further sub-systems is described in Chapter 4. Firstly the long-term stability of the mirror mounting mechanisms is determined. The advantages of cross-dispersion of echelle spectra using volume-phase holographic gratings are then discussed, and the results of diffraction efficiency measurements are given for both red and blue channel gratings. Modern CCD technologies are examined in Chapter 5, and the blue detector is experimentally characterized using photon transfer and quantum efficiency curves. It is also used for an investigation into cosmic ray events in CCDs. Results from shielding the detector using lead are described, as is an attempt to distinguish the source of the events based on their morphology. Finally, Chapter 6 deals with the handling of data produced by SALT HRS. Methods of wavelength calibration of the spectra are discussed, including the use of Thorium-Argon lamps and an iodine absorption cell. The implementation of a Python based quick-look data reduction pipeline is reviewed, with a description of the processes performed. A summary of the thesis is given in Chapter 7.

In this dissertation, we study the optical property of 2D graded photonic super-crystals (GPSCs) for photon management. We focused primarily on manipulation and control of light by using the newly discovered GPSCs which present great opportunity for electromagnetic wave control in photonic devices. The GPSC has been used to explore the superior capability of improving the light extraction efficiency of OLEDs. The enhancement of extraction efficiency has been explained in term of destructive interference of surface plasmon resonance and out-coupling of surface plasmon through phase matching provided by GPSC and verified by e-field intensity distributions. A large light extraction efficiency up to 75% into glass substrate has been predicted through simulation. We also study the light trapping enhancement in GPSCs. Broadband, wide incident angle, and polarization independent light trapping enhancement is achieved in silicon solar cells patterned with the GPSCs. In addition, novel 2D GPSCs were fabricated using holographic lithography through the interference lithography by two sets of multiple beams arranged in a cone geometry using a spatial light modulator (SLM). Finally, we also report a fabrication of GPSCs with a super-cell size of 12a×12a by using e-beam lithography. Diffraction pattern from GPSCs reveals unique diffraction properties. In an application aspect, light emitting diode arrays can be replaced by a single light emitting diode shinning onto the diffraction pattern for a uniform fluorescence.

Práce se zabývá interpretací kvantitativního fázového zobrazení pomocí techniky koherencí řízené holografické mikroskopie. Vzhledem k tomu, že tato technika generuje velké množství kvantitativních fázových obrazů o nezanedbatelné velikosti, manuální analýza by byla časově náročná a neefektivní Za účelem urychlení analýzy obrazů získaných pomocí koherencí řízené holografické mikroskopie je v této práci navržena metodika automatizované interpretace kvantitativních fázových obrazů pomocí strojového učení s učitelem. Kvantitativní fázové obrazy umožňují extrakci parametrů charakterizujících distribuci suché hmoty v buňce a poskytují tak cennou informaci o buněčném chování. Cílem této práce je navrhnout metodologii pro automatizovanou klasifikaci buněk při využití této kvantitativní informace jak ze statických, tak z časosběrných kvantitativních fázových obrazů. Navržená metodika byla testována v experimentech s živými buňkami, jimiž byla vyhodnocena výkonnost klasifikace a významnost parametrů získaných z kvantitativních fázových obrazů.

This master’s thesis deals with the design of methodology for measurement of refractive index and thickness of living cells by coherence-controlled holographic microscope. The theoretical part summarises the holographic microscopy and its development at IPE FME BUT in Brno. The thesis focuses on the multimodal holographic microscope, its description, the principle, the procedure of work and data processing. Confocal microscopy is also described, which serves to compare the acquired values with the proposed methodology. The last part of the theoretical part deals with the testing of statistical hypotheses, which is needed for the processing of measured data. Experiments were designed for the verification of methodology for determination of the refractive index and cell thickness. The experimental part of the thesis deals with the sample preparation and measurement. The procedure and results of the proposed experiments and their evaluation follows.

Diplomová práca sa zaoberá rozptylom elektromagnetického žiarenia na biologickej bunke použitím metódy konečných diferencií v časovej oblasti (FDTD), Bornovej aproximácie a Rytovovej aproximácie. Metóda FDTD dáva presné výsledky v širokej škále problémov. Je spravené porovnanie Bornovej aproximácie a Rytovovej aproximácie prostredníctvom FDTD metódy. Ďaľšia časť práce zahrnuje krátky popis koherenciou riadeného holografického mikroskopu CCHM. Záverečná časť sa venuje zobrazeniu rozptýleného poľa získaného z jednotlivých simulácií pomocou simulácie objektového ramena mikroskopu CCHM.

The Digital Micromirror Device (DMD) technology has been developed especially for Digital Light Processing projectors, which allow the image projection. After this succesful implementation, and thanks to the commercial availibility and low initial cost of the DMD chip, a wide range of other applications became possible. Besides, it may be used in microscopy as a spatial light modulator. For example in Coherence-Controlled Holographic Microscope (CCHM) that finds its use especially for imaging and measurement of live-cell dynamic processes. The DMD chip placed in the illumination part of CCHM allows for broadening the application possibilities. Namely it could be different illumination mode experiments or tomographic applications. The master's thesis deals with the optical design of CCHM with digital optics, i. e. DMD chip. The selection of optical elements for CCHM, the experimental verification of the imaging setup and the process of designing the illumination part are described in detail. In the end, the analysis of different designs for illumination setup with the digital optics in object arm is carried out and the results are compared.

The new arrangement of the off-axis holographic module, which is using polarizationactive diffraction grating divides signal into reference and subject wave of an interferometer based on their polarization. However, current design of the module does not have a possibility to tune a length of the optical paths. Thus the inability to tune optical paths leads to a reduced quality of interference structure during observation of biological samples. The current module is only suitable for technical applicating due to this limitation. Possibility of tuning branches is key step in biological applications. Therefore a new computer-controlled module is created in order to enable use for biological samples.

The Coherence Controlled Holographic Microscope (CCHM) was developed at BUT Brno for a quantitative phase imaging of living cells. Nowadays it ocurres that its imaging properties are enhanced by the use of additional modules. In the present the microscope is equipped with the epifluorescence module, which allows observation of fluorescently marked living cells. This thesis is going to follow up on the development of this module and is going to extend its options by confocal imaging. The disadvantage of current multi-channel confocal microscopes is a mechanical rotation of the Nipkow discs, which causes undesired mechanical vibrations. That is why in this thesis it is replaced by Digital Micromirror Device. With its use was developed optical system of the whole confocal model, whose correct funcion was simulated in optical CAD. The experimentally verified prototype serves to test the imaging properties. On this basis is designed an application idea of the fluorescence confocal module, which will be possible to connect to the CCHM microscope.

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.

This diploma thesis describes the design of the illumination system for a Coherence--Controlled Holographic Microscope (CCHM). The theoretical part mentions the history of microscopy, the principle of holography and individual types of interference microscopy. To get closer to the topic, individual light sources and an overview of current illumination systems are mentioned. The diploma thesis also describes the procedure of designing a fiber-optic illumination module for microscopy from optical design through design of construction to the last step, which is assembly and testing of the module.