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Correction of phase image background in the digital holographic microscope using convolution
Rudolfová, Zdena ; Malina, Radomír (referee) ; Uhlířová, Hana (advisor)
This bachelor thesis concentrates on a correction of background in the phase image of cells from a transmitted-light digital holographic microscope (TDHM). Optical aberrations in the optical systems of the object and reference arms cause "deformation" of the phase image. The cell is not displayed on a background with a constant value of phase, it is displayed on a background with phase values continuously changing between different places in the image. A method for removing the consequence of this imperfection from the image is described in this thesis. The principle lies in partial convolution of the phase image with a convolution kernel determined by a two-dimensional Gaussian function with the same variance in the both axes. To eliminate loss of information about the cells, the convolution is computed only from those parts of the phase image which contain no cells. The result of the convolution is considered to be an approximation of the background. This approximation is then subtracted from the phase image. The resulting phase image has a constant background, containing only noise. The necessary mathematical concepts are resumed in the introductory part of the thesis. The basic principle of the TDHM image reconstruction is also described. As a part of the thesis, a computer programme Odečet pozadí (Background subtraction) was created, which processes the phase images from the TDHM using this method.
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User programme for imaging and visualization of quantitative phase from the digital holographic microscope
Hladík, Lukáš ; Kvasnica, Lukáš (referee) ; Uhlířová, Hana (advisor)
This bachelor thesis deals with creation of an user computer program for processing of phase contrast images from a digital holographic microscope. The theoretical section of the thesis contains basic information about obtaining and evaluation of processed images, including a description of their digital representation in the computer. The experimental part deals with techniques and algorithms on which the program is built. This part also contains a description of the graphical user interface of the program and evaluate the impact of different user settings for output files properties.
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Coherence-controlled holographic microscope in cell's life cycle research
Křížová, Aneta ; Kozubek,, Michal (referee) ; Uhlířová, Hana (advisor)
The goal of this diploma thesis was using of a coherence-controlled holographic microscope in cell’s life research. A brief history of interference microscopy and it’s applications in biology is described. Also other microscopy techniques routinely used for transparent objects imaging are mentioned and the biology of cell’s life cycle briefly explained. Characteristics describing the shape of a cell were proposed and tested with respect to identification of particular phases of its life cycle. The method of dynamic phase differences was modified in order to distinguish the internal motion of cell’s mass from the movement of the whole cell. Selected characteristics were used to evaluate observations carried out with the holographic microscope and the possibilities of their further applications were depicted. In conclusion, obtained findings were summarized and modifications of microscope construction as well as data-processing software were suggested.
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Numerical refocusing in a digital holographic microscope with a partially coherent illumination
Slabá, Michala ; Komrska, Jiří (referee) ; Chmelík, Radim (advisor)
The bachelor thesis deals with issue of numerical refocusing in a holographic microscope with partially space coherent light. The numerical refocusing is a computation of the complex amplitude of an image wave in planes differing from the image plane. The calculation of the region where the numerical refocusing is usable is based on application of Rayleigh-Sommerfeld diffraction integral and the Fresnel approximation of a spherical wave. The description of coherence state and propagation of partially coherent light follows from statistical methods in optical coherence theory. In this thesis the thickness of field is calculated where the numerical refocusing is usable. The thickness depends on microscope parameters - the size of the light source and parameters of lenses in microscope. The result is applied to the microscope in the laboratory IPE FME BUT.
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A method for the visualization of high phase gradients in a microscopic image
Druckmüllerová, Hana ; Martišek, Dalibor (referee) ; Chmelík, Radim (advisor)
Holografická mikroskopie je nekonvenční mikroskopická technika, vhodná zvláště pro vzorky s malou optickou hustotou, která umožňuje zviditelnit index lomu pozorovaných objektů. Na Ústavu fyzikálního inženýrství Fakulty strojního inženýrství VUT v Brně byl sestrojen unikátní transmisní digitální holografický mikroskop (TDHM). Pořízené snímky (hologramy) jsou zpracovány metodou založenou na Fourierově ransformaci, čímž je zrekonstruována intenzita a fáze světelné vlny procházející pozorovaným objektem. Fáze popisuje index lomu a tloušťku pozorovaného objektu. V místech, kde se mění index lomu nebo tloušťka, dochází i ke změně fáze. Úkolem této bakalářské práce bylo najít metodu pro zviditelnění míst s vysokým gradientem fáze. Podařilo se vytvořit metodu, která nevyžaduje navazování fáze, a proto je vhodná pro libovolné obrazy pořízené TDHM. Tato metoda byla implementována do počítačového programu Gradient3D, který kromě výpočtu gradientu ve dvou a třech rozměrech umožňuje i vytváření barevných obrazů, jejichž složkami jsou kombinace intenzity, fáze a gradientu. Program též umožňuje odstranění falešných gradientů v místech s nízkou intenzitou, kde je hodnota fáze nespolehlivá. Program byl testován na několika souborech hologramů pořízených TDHM při pozorování biologických vzorků.
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Simulation of imaging in Reflected-light Holographic Microscope with optical aberrations
Effenberger, Adam ; Kvasnica, Lukáš (referee) ; Týč, Matěj (advisor)
The aim of this work is the simulation of a moving cell on a noisy backgroud. Experience gained during this work was used for correction of artificially created data. Subsequently it was used for the correction of real experiment a data. Spyder, open source cross-platform IDE for scientific programming in the Python language, was used for it. The simulation was successful, as well as the correction of artificially created data. The correction of real experiment data was only partly suscessfull . It gives us enough room for further improvement.
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Automatization of method of surface structure measurement by means of reflection mode digital holographic microscope.
Vacula, Daniel ; Šerý, Mojmír (referee) ; Lovicar, Luděk (advisor)
Reflected-light digital holographic microscope developed at IPE FME BUT uses off-axis holography principle and low spatial and temporal coherence illumination. Microscope allows reconstruction of the image amplitude and the image phase, which can be handled in real time. The only limiting factors are imaging speed of the detector and computer performance when processing holograms. Reconstruction of image phase and amplitude allows high-resolution profilometric measurements in the vertical axis direction. This thesis deals with the automatization of profilometric measurement method proposed in [2]. Proposed method uses the combination of the image phase and the image amplitude for the measurement of specimens with surface structure the vertical size of which cause the uncertainty of the image phase by a factor of 2pí. Futher the thesis deals with the construction design of the illumination system of the microscope and its realization together with experimental verification of functionality of proposed method automatization.
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Theoretical description of imaging by a digital holographic microscope
Slabá, Michala ; Komrska, Jiří (referee) ; Chmelík, Radim (advisor)
The diploma thesis deals with theory of imaging in a transmitted-light digital holographic microscope using partially coherent illumination. The influence of spatial and temporal coherence state on optical sectioning property is solved. The coherent transfer function is calculated. From this function imaging characteristics for a two-dimensional scattering object are derived depending on its defocus. Two different designs of microscopes developed in the Laboratory of optical microscopy in IPE FME BUT are considered.
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Coherence-controlled holographic microscope in cell's life cycle research
Křížová, Aneta ; Kozubek,, Michal (referee) ; Uhlířová, Hana (advisor)
The goal of this diploma thesis was using of a coherence-controlled holographic microscope in cell’s life research. A brief history of interference microscopy and it’s applications in biology is described. Also other microscopy techniques routinely used for transparent objects imaging are mentioned and the biology of cell’s life cycle briefly explained. Characteristics describing the shape of a cell were proposed and tested with respect to identification of particular phases of its life cycle. The method of dynamic phase differences was modified in order to distinguish the internal motion of cell’s mass from the movement of the whole cell. Selected characteristics were used to evaluate observations carried out with the holographic microscope and the possibilities of their further applications were depicted. In conclusion, obtained findings were summarized and modifications of microscope construction as well as data-processing software were suggested.
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Theoretical description of imaging by a digital holographic microscope
Slabá, Michala ; Komrska, Jiří (referee) ; Chmelík, Radim (advisor)
The diploma thesis deals with theory of imaging in a transmitted-light digital holographic microscope using partially coherent illumination. The influence of spatial and temporal coherence state on optical sectioning property is solved. The coherent transfer function is calculated. From this function imaging characteristics for a two-dimensional scattering object are derived depending on its defocus. Two different designs of microscopes developed in the Laboratory of optical microscopy in IPE FME BUT are considered.
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