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Methodology of Dictyostelium discoideum imaging with the transmission digital holographic microscope
Křížová, Aneta ; Ježek, Jan (referee) ; Uhlířová, Hana (advisor)
The task of this bachelor’s thesis was to image Dictyostelium discoideum with a transmission digital holographic microscope and compare this imaging with a commonly used microscopy technique. This bachelor's thesis is structured into a theoretical part and an experimental part. The theoretical part describes the setting of the transmission digital holographic microscope, basic operation and physical principles of imaging with this microscope. Further the process of image reconstruction and numerical process of phase reconstruction is illustrated. At the end of this part, basic biological characteristics of observed cells of Dictyostelium discoideum are introduced. The experimental part describes the cultivation and preparation of Dictyostelium discoideum for the observations, and further the process of performed experiments. The cells of Dictyostelium discoideum have been imaged in couple experiments by a method of the classical phase contrast. By the transmission digital holographic microscope the cells of Dictyostelium discoideum have been imaged in two mediums. Images captured by the transmission digital holographic microscope were processed by a method of Dynamic phase differences and analysed.
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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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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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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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Digital Image Analysis of Mitotic Chromosomes
Buchta, M.
The present work describes the cytogenetic from the point of view of image processing. We propose an algorithm which is able to treat every aspect of this analysis such as segmentation and separation of chromosomes. Moreover, our algorithm is tested on images of chromosomes labelled with 2 different methods coming from various free databases.
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Autonomous Car Path Optimalization
Vladyka, V.
This paper deals with path search and optimalisation of model car in unknown space. All data from sensors are processed in real-time onboard at ARM Cortex M4 microcontroller. Model’s main sensor is line-scan camera.
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Analysis of computer vision and its aplication in systems of quality management
Nguyen, Cuong Manh ; Plášková, Alena (advisor) ; Urban, Jan (referee)
The main goals of my thesis is to provide closer look into issue of computer vision and its potential in quality management. The main reason for writing this thesis is to prove that there are simple methods of controling by computer vision, that even start-ups in production sector can afford. Hereafter I am compering two methods of controling. Firsty method of controling by computer vision and secondly method of controling by human eye. I am primarily focused on its cost of implementation and operation, its speed of controling units and measurement accuracy of each methods. For this purpose I use a practical simulation of control station in fictional production line to get real comparable resuts of both methods. To costruct successful simulation with relevant results it is essential to understad principles of the issue.
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Tools for image processing in ecology
DOMIN, Daniel
This thesis deals with automated image processing in biology and ecology. Based on the analysis of image processing steps and most common cases of application in biology and ecology, the main outcome of this thesis is a modular application framework prototype. It allows modeling of the whole process of image analysis which can be applied on a large batch of input data. Moreover, it can be extended by modules with new features so it can be used generally for any sequential data processing.
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GenExLib C/C++ library, Reference Manual
Kovář, Bohumil ; Schier, Jan ; Kuneš, Michal
This technical report contains reference manual for the GenExLib C++ software library. for analysis of FISH microscopy images. The purpose of this library is to detect cell nuclei and fluorescence signals contained in the images and to evaluate their shape and intensity parameters. The reference manual describes in detail the installation of the library as well as methodology of image processing for the FISH images and application of the library in the user code.
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GenEx Software library for object detection in genetical analysis evaluation: User manual
Schier, Jan ; Kovář, Bohumil ; Kuneš, Michal
This technical report contains user manual for the GenEx library for evaluation of FISH microscopy images. The purpose of the library is to find and filter objects in images from fluorescence microscope and to detect fluorescence signals contained in these objects. The library has been designed to be used for diagnostics of the Turner syndrome chromosome aneuploidies in chromosome X, in other words, to find the (roughly round) interphase nuclei and to count the associated hybridization signals. It is characterized by the following features: - separate processing channels for DAPI and for the fluorescence signals. - no restrictions on the number of the signal channels - output in the form of a CSV-file.
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