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Segmentation of Electrocardiographic Signals Using Deep Learning Methods
Hejč, Jakub ; Černý, Martin (referee) ; Halámek, Josef (referee) ; Kolářová, Jana (advisor)
The thesis deals with deep learning methods for the segmentation of surface and intracardiac electrocardiographic recording with focus on atrial activity. The theoretical part introduces current segmentation aproaches of electrocardiographic signals. Issues related to the development of deep learning models in context of standard ECG databases were also discussed. We proposed a pipeling for processing multimodal electrophysiology data from interventional procedures in order to build reliable training datasets. A deep model for segmentation of intracardiac recordings based on a modified residual architecture was proposed. A series of experiments was conducted to evaluate the effect of both model and dataset properties on segmentation quality. The annotation methodology of recordings with atrial fibrillation proved to be a crucial factor. Properties of loss function and type of data augmentation were revealed as secondary important parameters. A novel P wave segmentation method for incomplete references was proposed in the thesis. The approach was inspired by the deep contrast learning. It was modified to distinguish local segments of signals at different levels of abstraction of the extracted feature maps. Results were analyzed using standard quality metrics and post-hoc visual analysis. In some cases, a statistical comparison of experiments for different settings was performed. The results of the work showed that it is possible to use intracardiac signals for embedding a vector representation of local atrial activation into deep models.
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Establishing Mutual Links among Brain Structures
Klimeš, Petr ; Hlinka,, Jaroslav (referee) ; Krajča,, Vladimír (referee) ; Halámek, Josef (advisor)
The Human brain consists of mutually connected neuronal populations that build anatomically and functionally separated structures. To understand human brain activity and connectivity, it is crucial to describe how these structures are connected and how information is spread. Commonly used methods often work with data from scalp EEG, with a limited number of contacts, and are incapable of observing dynamic changes during cognitive processes or different behavioural states. In addition, connectivity studies almost never analyse pathological parts of the brain, which can have a crucial impact on pathology research and treatment. The aim of this work is connectivity analysis and its evolution in time during cognitive tasks using data from intracranial EEG. Physiological processes in cognitive stimulation and the local connectivity of pathology in the epileptic brain during wake and sleep were analysed. The results provide new insight into human brain physiology research. This was achieved by an innovative approach which combines connectivity methods with EEG spectral power calculation. The second part of this work focuses on seizure onset zone (SOZ) connectivity in the epileptic brain. The results describe the functional isolation of the SOZ from the surrounding tissue, which may contribute to clinical research and epilepsy treatment.
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Analysis of Nonlinear Effects in Ultrasound Diagnostics
Čížek, Martin ; Hrazdíra,, Ivo (referee) ; Halámek, Josef (referee) ; Rozman, Jiří (advisor)
The model study of nonlinear effects in the ultrasound diagnostics is focused on developing and experimental verification of new computer algorithms for numerical modeling of the ultrasound field including nonlinear effects accompanying the ultrasound propagation in biological tissues. A theoretical analysis of nonlinearities in ultrasound propagation and their contribution to thermal and mechanical effects of diagnostic ultrasound applications was conducted. A numeric model of ultrasound propagating through a tissue model formed of a set of homogenous layers with defined physical parameters was developed in Matlab environment. The computation of ultrasound field spatial distribution is based on the angular spectrum method. For simulating of nonlinearities Burgers nonlinear wave equation is used. The resulting spatial distribution of the ultrasound field is described by the amplitudes of selected number of harmonic components of the acoustic pressure, by the mechanical index, by the harmonic distortion of the signal and by the spatial peak temporal average intensity of all considered components. The numerical model was experimentally verified using an unique ultrasound measurement system – the ultrasound measurement basin. The verified numeric model was used for assessing the veracity of mechanical index and tissue heating prediction during ultrasound applications in cases when the nonlinear effects are neglected in computations. The reliability of the mechanical index indicated by the diagnostic ultrasound instruments is also evaluated using the designed numeric model. The aim was to compare the indicated value usually obtained by derating the measurements in a water medium to the actual mechanical index present in the insonated tissue.
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Methods for the evaluation of heart rate and arterial blood pressure variability
Sedláčková, Gabriela ; Halámek, Josef (referee) ; Leinveber, Pavel (advisor)
The bachelor thesis deals with methods for description of heart rate variability and arterial blood pressure. An important mechanism for maintaining homoeostasis in the body is so called baroreflex feedback loop, which allows for a short-term regulation of blood pressure. The thesis contains description of methods which are currently used for baroreflex sensitivity evaluation. Analysis in time domain as well as in frequency domain was done using programs in Matlab environment. At the end of the thesis the influence of ventricular extrasystoles on output parameter is evaluated.
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Properties of pulse wave velocity in human body during various excitations
Matejková, Magdaléna ; Halámek, Josef (referee) ; Vondra, Vlastimil (advisor)
The thesis is concerned with the analysis of measuring pulse wave velocity in human body with the aid of whole-body multichannel bioimpedance which was developed at ISI AS CR, v.v.i.. The evaluation of pulse wave velocity can provide us with important information about the state of vessel compliance which is one of the basic parameters informing on their physiological state. The examination of the state of vascular system is a very important part of early diagnostics because its pathological states are the main contributor to the rise of cardiovascular diseases and disease mortality. The thesis is concerned with the theoretical analysis together with the available methods of valuation of the state of vascular system that use measuring of pulse wave velocity. The main part of the thesis deals with the analysis of the whole-body multichannel bioimpedance measurement. The proposed and programmed protocol that summarizes and visualizes all obtained information is a part of this thesis. This is currently used as an output of the experimental measurement by this method. Data file for statistical processing contains the values of the pulse wave velocity of 35 healthy volunteers and subsequently the properties of pulse wave are assessed at various excitations.
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Wavelet Based Filtering of Electrocardiograms
Smital, Lukáš ; Smékal, Zdeněk (referee) ; Halámek, Josef (referee) ; Kozumplík, Jiří (advisor)
This dissertation deals with possibilities of using wavelet transforms for elimination of broadband muscle noise in ECG signals. In this work, the characteristics of ECG signals and particularly the most frequently occurring type of interference are discussed firstly. The theory of wavelet transforms is also introduced and followed by design of the simple wavelet filter and the more sophisticated version with wiener filtering of wavelet coefficients. Next part is devoted to the design of our filter, which is based on wavelet wiener filtering and is complemented by algorithms that ensure full adaptability of its parameters when the properties of the input signal are changing. Suitable parameters of the proposed system are searched automatically and the algorithm is tested on the complete standard electrocardiograms database CSE, where it achieves significantly better results than other published methods.
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Detection of the repolarization parameters from ECG
Brandejs, Jakub ; Halámek, Josef (referee) ; Veselý, Petr (advisor)
A T wave peak and offset detector based on an unpublished lead transformation that can be briefly described as multilead linear regression was proposed and implemented afterwards. Potential of the transformation as a useful QRS detection tool was revealed later on. Proposed QRS detector was put to the test of CSE database. Results were compared with work of other authors. Results of T wave peak and offset detector were introduced in visual way.
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Study of Electrophysiological Function of the Heart in Experimental Cardiology
Ronzhina, Marina ; Tyšler, Milan (referee) ; Halámek, Josef (referee) ; Kolářová, Jana (advisor)
Srdeční poruchy, jejichž příkladem je ischemie myokardu, infarkt, hypertrofie levé komory a myokarditida, jsou v experimentální kardiologii obvykle studovány na modelu izolovaného srdce. Kritéria pro detekci srdečních poruch však nejsou pro zvířecí modely standardizována, což komplikuje srovnání a interpretaci výsledků různých experimentálních studií. Obzvlášť složitá situace nastává při současném výskytu několika patologických jevů, jejichž vzájemná součinnost komplikuje rozpoznání jejich individuálních účinků. Korektní posouzení stavu srdce vyžaduje také zohlednění mnoha faktorů spojených s akvizicí dat. Tato práce je věnována kvantitativnímu hodnocení elektrofyziologických změn způsobených globální ischemií myokardu. Vliv ischemie byl hodnocen pro fyziologická srdce a srdce se zvětšenou levou komorou a dále pro srdce nabarvená napěťově-citlivým barvivem di-4-ANEPPS. Přestože jsou oba fenomény často zastoupeny v animálních studiích, nebyl dosud popsán jejich vliv na manifestaci ischemie v elektrogramech (EG), ani nebyl kvantifikován jejich vliv na přesnost detekčních algoritmů pro identifikaci ischemie. Práce shrnuje kvantitativní změny srdeční funkce vyvolané ischemií (v normálních podmínkách, při hypertrofii levé komory, a při administraci barviva) založené na hodnocení EG a VKG parametrů. Dále práce obsahuje rozbor důležitých aspektů akvizice záznamů, jako je umístění snímacích elektrod, způsob výpočtu deskriptorů z EG a VKG (s použitím výsledků manuálního rozměření záznamů, nebo bez něj) a identifikace okamžiku vývoje ischemie v preparátu. Nedílnou součást práce tvoří návrh, realizace a ověření metod pro automatickou detekci ischemie v experimentálních záznamech. Výsledky práce dokazují, že dosažení opakovatelných a věrohodných výsledků je podmíněno zohledněním všech výše uvedených faktorů souvisejících jak se stavem srdce, tak s metodikou záznamu a analýzy dat.
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Model Study of Ultrasound Effects on Fetal Development
Jaroš, Josef ; Halámek, Josef (referee) ; Hrazdíra,, Ivo (referee) ; Rozman, Jiří (advisor)
The progress in ultrasound techniques goes hand in hand with increasing of diagnostic machine acoustic outputs. Ultrasound biological effects can adversely influence the development of human fetus. Recent studies of thermal effect on biological tissues are usually based on simulation of simple ultrasound transducers. The aim of this work is to build a flexible model of diagnostic system to simulate temperature increase during fetal development. Different types of ultrasound probes were used for generation of acoustic field with simulated piezoelectric element properties. Optimized linear and phased arrays were modeled with dynamic beam steering and focus. Computer simulations were concentrated on extreme conditions in obstetric ultrasonography and 3D tissue model was compared with real ultrasound probes measurements. To detect temperature increase, the bone tissue phantom was used. Results point out potential risks for fetus with diagnostic ultrasound probes. Based on the results of this work, practical recommendations increasing safety of obstetric examinations were drawn.
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