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Three-Dimensional Reconstruction of Image in Digital Holographic Microscopy
Týč, Matěj ; Karásek,, Vítězslav (referee) ; Martišek, Dalibor (referee) ; Chmelík, Radim (advisor)
This thesis deals with the topic of 3D image processing for digital holographic microscopy - numerical refocusing. This method allows to perform mathematically accurate defocus correction on image of a sample captured away from the sample plane and it was applicable only for images that were made made using coherent illumination source. It has been generalized to a form in which it is also applicable to devices that use incoherent (non-monochromatic or extended) illumination sources. Another presented achievement concerns hologram processing. The advanced hologram processing method enables obtaining more data mainly concerning precision of quantities from one hologram — normally, one would have to capture multiple holograms to get those. Both methods have been verified experimentally.
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Three-dimensional reconstruction of image in digital holographic microscopy
Týč, Matěj ; Chmelík, Radim (advisor)
This thesis deals with the topic of 3D image processing for digital holographic microscopy - numerical refocusing. This method allows to perform mathematically accurate defocus correction on image of a sample captured away from the sample plane and it was applicable only for images that were made made using coherent illumination source. It has been generalized to a form in which it is also applicable to devices that use incoherent (non-monochromatic or extended) illumination sources. Another presented achievement concerns hologram processing. The advanced hologram processing method enables obtaining more data mainly concerning precision of quantities from one hologram — normally, one would have to capture multiple holograms to get those. Both methods have been verified experimentally.
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Advanced signal processing methods in dynamic contrast enhanced magnetic resonance imaging
Bartoš, Michal ; Flusser,, Jan (referee) ; Mlynárik,, Vladimír (referee) ; Jiřík, Radovan (advisor)
Tato dizertační práce představuje metodu zobrazování perfúze magnetickou rezonancí, jež je výkonným nástrojem v diagnostice, především v onkologii. Po ukončení sběru časové sekvence T1-váhovaných obrazů zaznamenávajících distribuci kontrastní látky v těle začíná fáze zpracování dat, která je předmětem této dizertace. Je zde představen teoretický základ fyziologických modelů a modelů akvizice pomocí magnetické rezonance a celý řetězec potřebný k vytvoření obrazů odhadu parametrů perfúze a mikrocirkulace v tkáni. Tato dizertační práce je souborem uveřejněných prací autora přispívajícím k rozvoji metodologie perfúzního zobrazování a zmíněného potřebného teoretického rozboru.
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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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Restoration of optical coherence tomography image data
Smékal, Ondřej ; Odstrčilík, Jan (referee) ; Jan, Jiří (advisor)
Restoration of image data has become an essential part of the processing of medical images obtained by any system. The same applies in the case of optical coherence tomography. The aim of this work is to study the first restoration methods. Second, the description of the data representation from optical coherence tomography and subsequent discussions that restoration methods based on deconvolution would potentially find application in processing of Optical coherence tomography. Finally, the third to create a program solution of the OCT data restoration process in MATLAB environment and followed by discussion of effectiveness of the presented solutions.
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Deconvolution of hemodynamic response from fMRI data
Bartoň, Marek ; Kolář, Radim (referee) ; Havlíček, Martin (advisor)
This paper deals with the variability of HRF, which may have crucial impact on outcomes of fMRI neuronal activation detection in some cases. There are three methods described - averaging, regression deconvolution and biconjugate gradient method - which provide HRF shape estimation. In frame of simulations regression method, which uses B-spline curves of 4-th order for window length of 30 s, was chosen as the most robust method. Deconvolution estimates was used as HRF models for classic analyse of fMRI data, concretely visual oddball paradigm, via general linear model. Enlargement of localizated areas was observed and after expert consultation with scientific employees from neurology clinic, outcomes was evaluated as relevant. Furthermore Matlab application, which provides confortable observation of HRF variability among brain areas, was made.
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Deconvolution in perfusion imaging
Líbal, Marek ; Havlíček, Martin (referee) ; Bartoš, Michal (advisor)
The purpose of this study is to introduce the methods of the deconvolution and to programme some of them. For the simulation, the tissue homogeneity model and the model of arterial input fiction were used. These models were engaged as the test procedures with the aim of verify the functionality and utility of the Wiener filter, the Lucy-Richardson algorithm and the Singular value decomposition.
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On Validation of Algorithms for Dynamic Medical Data Separation
Tichý, Ondřej
The problem of dynamic medical image sequence separation is studied. We introduced the state of the art algorithms for medical sequence decomposition together with those that are proposed by us. The validation and the comparison of the algorithms are nontrivial and challenging task. We propose to use a synthetic data where a ground truth is available so it is possible to compute a significant statistics for comparison reason. Moreover, we proposed a comparison on 99 real data from renal scintigraphy where relative renal functions are automatically computed and compared with those obtained by physician.
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Elastodynamic Properties and Signal Propagation in Materials within Time Reversal Acoustics
Farová, Zuzana ; Převorovský, Zdeněk ; Kůs, V. ; Dos Santos, S.
In this paper we present related parts of elastodynamic theory, which are a keynote for the wave propagation through the medium. We describe the basic material characteristics - strain tensor and stress tensor, also we provide the relations of these tensors and describe the derivation of the well-know Lame's parameters. Further, we deal with the theory of Green functions, its properties, and its form for di®erent sources. Finally, we propose and explain the so-called experimental deconvolution, quite newly developed technique, based on time reversal acoustics with the knowledge of Green function and using the Fourier transform.
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Odhad hloubkové mapy a současná slepá dekonvoluce obrazů rozmazaných defokuzací
Šorel, Michal ; Flusser, Jan
We present an algorithm that uses two or more defocused images of the same scene for recovery of scene structure and simultaneous restoration of sharp image. Defocousation is modeled by convolution with arbitrary known spatially-variant mask unlike the vast majority of published algorithms that used cylindrical or Gaussian masks. In this way it is able to deal with aberrations present in real optical systems. The mask can be given analytically ro by a table or a ray tracing algorithm.
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