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3D Slicer Extension for Tomographic Images Segmentation
Chalupa, Daniel ; Jakubíček, Roman (referee) ; Mikulka, Jan (advisor)
This work explores machine learning as a tool for medical images' classification. A literary research is contained concerning both classical and modern approaches to image segmentation. The main purpose of this work is to design and implement an extension for the 3D Slicer platform. The extension uses machine learning to classify images using set parameters. The extension is tested on tomographic images obtained by nuclear magnetic resonance and observes the accuracy of the classification and usability in practice.
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DESIGN OF FIBER-OPTIC BIOSENSOR WITH NEAR-INFRARED SPECTRAL ANALYSIS
Křepelka, Pavel ; Jakubec,, Martin (referee) ; Skládal, Petr (referee) ; Mikulka, Jan (advisor)
This thesis deals with a measurement and interpretation of NIR spectra of bacterial cells and design of biosensor using this analytical technique. In the first chapter, there is introduction of current state of knowledge in the field of NIR spectroscopy in microbiology and technology of fiber optic biosensors. The summary of this chapter shows that NIR is a suitable technique for direct molecular analysis of bacteria, but it suffers from low sensitivity and insufficient interpretation of bacterial spectra. In the next part of the thesis, there is a theoretical background of spectral analysis techniques and technology of fiber optic sensors. In the practical part of this work, there is suggested the elimination of disadvantages of NIR spectroscopy in microbiology by a series of experiments used for interpretation of NIR spectra of bacteria and design of fiber optic sensor to increase sensitivity of this technique. In this work, spectral regions important for the identification of bacterial strains were determined and partially interpreted and the sensor for bacterial analysis capable of classifying strains based on 105 captured cells was designed. Therefore, the objectives of this work were fulfilled.
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Measurement of tissue embryos by MR imaging methods
Vrba, Jan ; Mikulka, Jan (referee) ; Bartušek, Karel (advisor)
The aim of this work is to determine the volume of water in tissue cultures of spruce MR imaging methods and changes during growth. Was measured set of samples, where was found contain of cluster in each cuts. It describes spin-echo method, which was used for measurement. In this work is given a description of the acquisition, calculation, evaluation and graphical representation of measured values.
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Segmetation of tomographic data in 3D Slicer
Korčuška, Robert ; Dvořák, Pavel (referee) ; Mikulka, Jan (advisor)
This thesis contains basic theoretical information about SVM-based image segmentation and data classification. Basic information about 3D Slicer software are presented. Aspects of medical images segmentation are described. Workplan and implemetation of SVM method for MRI segmentation in 3D Slicer sofware as extension module is created. SVM method is compared with simple segmentation algorithms included in 3D Slicer. Quality of segmentation, based on SVM, tested on real subjects is experimentaly demonstrated.
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Open-source systems for image processing
Slinták, Vlastimil ; Zukal, Martin (referee) ; Mikulka, Jan (advisor)
The aim of this document is to describe open-source libraries for image processing — ITK, VTK and OpenCV. Their architectures are described and it is shown how to compile and use them in real applications. It also provides basic description of algorithms for image processing. In the second part of this document, we try to use ITK library with data-mining environment RapidMiner.
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THD Analyzer
Ha, Tuan ; Drexler, Petr (referee) ; Mikulka, Jan (advisor)
This thesis deals with design of a THD analyzer for audio frequency. In the interduction, there is a description of methods of THD calculation and realization of THD analyzer. Suitable computing platform must be chosen with capability to process audio data. The expansion board is designed for audio acquisition. Part of this design is complete program that is capable of displaying spectrum and computing THD.
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Detection algorithms of moving objects
Novotný, Josef ; Mikulka, Jan (referee) ; Marcoň, Petr (advisor)
This work deals with detection methods of moving objects. This thesis contains a research of available solutions for further implementation on the Raspberry Pi using the OpenCV library. The aim of the thesis is to realize a module that is capable of detecting and recognizing moving objects in the sky. Required objects can be detected in static or dynamic mode. In the theoretical part of the thesis are methods divided into motion detection, object detection and object recognition. In the practical part were for detection of undesired objects selected a background subtraction method and the localization of significant ORB points. Haar feature-based cascade classifiers was for recognition of learned objects chosen. In the practical part, methods were of computational difficulty and detection success tested. The result is an automatic detection device that allows to watch and distinguish unwanted objects in the sky.
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Measurement of conifers needles surface by MR tomography
Hladík, Roman ; Kubásek, Radek (referee) ; Mikulka, Jan (advisor)
This bachelor thesis deals with the tomography based on magnetic resonance and evaluation of scanned images of conifers needles. At first, it is described the physical basis and methods of magnetic resonance scanning of objects. Another part is devoted to graphical preprocessing, which consist of noise suppression and image segmentation. After that there are described the design and algorithm for parameter estimation implemented to the application. The first experimental measurements were lightly discussed and evaluated in the last part of the work. In the last part there are discussed results of the experimental measurement. The attached documents contain the source code in Matlab language.
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Wireless transmission interference modeling (AWGN, Rayleigh, Rice fading channels)
Hloušek, Tomáš ; Gleissner, Filip (referee) ; Mikulka, Jan (advisor)
This thesis describes and models wirelesss transmission intereferences in real communication channels. A signal received on a fading channel is subjected to a multiplicative distortion and to the usual additive noise. Real channel adds to the signal noise and fadings. Gaussian noise is a result of channel awgn. Fadings is implicated by multipath propagation of signal in Rayleigh and Rician channels. Main goal of this project is to program BERsolve, which is created in tool GUIDE in Matlab. User program BERsolve makes it possible to analyse bit error rate and symbol error rate for some types of channel models, which are defined by standard COST207. BERsolve offers some other functions i.e. display time behaviour, constellation diagram and spectrum. This program provides us with an overview representation of problem by multipath interferences in communication channels.
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Implementation of restoring method for reading bar code
Kadlčík, Libor ; Bartušek, Karel (referee) ; Mikulka, Jan (advisor)
Bar code stores information in the form of series of bars and gaps with various widths, and therefore can be considered as an example of bilevel (square) signal. Magnetic bar codes are created by applying slightly ferromagnetic material to a substrate. Sensing is done by reading oscillator, whose frequency is modulated by presence of the mentioned ferromagnetic material. Signal from the oscillator is then subjected to frequency demodulation. Due to temperature drift of the reading oscillator, the demodulated signal is accompanied by DC drift. Method for removal of the drift is introduced. Also, drift-insensitive detection of presence of a bar code is described. Reading bar codes is complicated by convolutional distortion, which is result of spatially dispersed sensitivity of the sensor. Effect of the convolutional distortion is analogous to low-pass filtering, causing edges to be smoothed and overlapped, and making their detection difficult. Characteristics of convolutional distortion can be summarized into point-spread function (PSF). In case of magnetic bar codes, the shape of the PSF can be known in advance, but not its width of DC transfer. Methods for estimation of these parameters are discussed. The signal needs to be reconstructed (into original bilevel form) before decoding can take place. Variational methods provide effective way. Their core idea is to reformulate reconstruction as an optimization problem of functional minimization. The functional can be extended by other functionals (regularizations) in order to considerably improve results of reconstruction. Principle of variational methods will be shown, including examples of use of various regularizations. All algorithm and methods (including frequency demodulation of signal from reading oscillator) are digital. They are implemented as a program for a microcontroller from the PIC32 family, which offers high computing power, so that even blind deconvolution (when the real PSF also needs to be found) can be finished in a few seconds. The microcontroller is part of magnetic bar code reader, whose hardware allows the read information to be transferred to personal computer via the PS/2 interface or USB (by emulating key presses on virtual keyboard), or shown on display.
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