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Nástroje pro trojrozměrnou vizualizaci struktur v biologii
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
By consecutive scanning of layers of the biological specimen by a confocal microscope we obtain a stack of optical sections, i.e. a 3D digital representation of the specimen. Our research focuses, on volume reconstruction of large biological tissues, i.e. tissues greater than field of view and/or thicker than maximal depth of scanning of the confocal microscope. As a result of volume reconstruction we obtain a high resolution 3D image of the biological specimen. In order to visualize 3D objects on 2D computer screens we developed several tools including visualization by a specialized VolumePro board and by using consumer graphics cards supporting DirectX and OpenGL
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Objemová rekonstrukce velkých biologických tkáňových vzorků
Čapek, Martin ; Janáček, Jiří ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
Volume reconstruction is a technique for visualization of a biological specimen which is greater than the field of view of a used optical instrument - a confocal laser scanning microscope in our case. The first step of volume reconstruction is acquisition of sets of digital volume images (spatial tiles which overlap) from all studied physical slices. The second step is horizontal merging of overlapping spatial tiles of the same physical slice (mosaicking). The third reconstruction step is vertical merging of digital volumes of successive physical slices of the specimen. The resulting large digital volumes are visualized using a VolumePro hardware board that offers real-time 3D volume rendering. In this paper we show a reconstruction of a chick embryonic kidney
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Objemová vizualizace velkých biologických tkáňových vzorků
Čapek, Martin ; Kubínová, Lucie ; Janáček, Jiří ; Hána, K. ; Smrčka, P.
We apply volume reconstruction for visualization of a biological specimen greater than the field of view of a confocal laser scanning microscope. Prior to the volume reconstruction, large specimens are cut into thin physical slices. The first step of volume reconstruction is acquisition of digital volume images (spatial tiles which overlap) from all studied physical slices. The second step is horizontal merging of overlapping spatial tiles of the same physical slice using a registration algorithm based on a mutual information and translation. The third reconstruction step is vertical merging of digital volumes of successive physical slices using an elastic registration algorithm based on B-splines. The resulting large digital volumes are visualized by a VolumePro hardware board that provides volume rendering in real-time. In this paper we show a reconstruction of a chick embryonic kidney.
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3D vizualizace velkých biologických vzorků nasnímaných konfokálním mikroskopem
Čapek, Martin ; Janáček, Jiří ; Karen, Petr ; Kubínová, Lucie ; Smrčka, P. ; Hána, K.
Digital volume reconstruction is a technique for rendering and visualization of a biological specimen which is greater than the field of view of a used optical instrument - a confocal laser scanning microscope in our case. Prior to the volume reconstruction, large biological specimens are cut to thin physical slices. The first step of volume reconstruction is acquisition of sets of digital volume images (spatial tiles which overlap) from all studied physical slices. The second step is composition of neighbouring spatial tiles of the same physical slice. The third reconstruction step is registration and merging of digital volumes of neighbouring physical slices of the specimen. The resulting large digital volumes are rendered and visualized using a VolumePro hardware board that offers real-time 3D volume rendering. In this paper we show a reconstruction of a chick embryonic kidney
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Vizualizace velkých biologických tkáňových vzorků s použitím laserové konfokální mikroskopie
Čapek, Martin ; Kubínová, Lucie ; Hána, K. ; Smrčka, P.
In biology there is often necessary to visualize a biological specimen which size is greater when compared with the field of view of a used optical acquisition instrument. The visualization of such the specimen can be achieved by volume reconstruction. We study biological specimens by using a confocal laser scanning microscope which is able to capture a digital volume representation of the specimen. We investigate great specimens containing, for example, a human tooth pulp, an epithelial layer and a vascular bed of chick embryonic gut or chick embryonic kidneys
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Chaotic time-series prediction
Dědič, Martin ; Tichý, Vladimír (advisor) ; Smrčka, Pavel (referee)
This thesis focuses on possibility of chaotic (specially economic) time-series prediction. Chaotic time-series are unpredictable in long-term due to their high sensitivity on initial conditions. Nevertheless, their behavior should be more or less predictable in short-term. Goal of this thesis is to show, how much and if any prediction, is possible by non-linear prediction method, and try to reveal or to reject presence of chaotic behavior in them. Work is split into three chapters. Chapter One briefly introduces chosen important concepts and methods from this area. In addition, to describe some prediction methods, there are outlined which indicators and methods are possible to use in order to find possibilities and boundaries of this prediction. Chapter Two is focused on modifications of FracLab software, which is used for create this prediction. Last chapter is experimental. Besides the description of examined time-series and methods, it includes discussion of results.
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Fractal analysis of economic time series
Krýcha, Josef ; Tichý, Vladimír (advisor) ; Smrčka, Pavel (referee)
This thesis focuses on fractal analysis of economic time series. Chapter One introduces fractal analysis as a method of exploring time series and gathers information about progress and current state of understanding in this field. Chapter Two focuses on design and development of computer software, which will calculate selected fractal indices. Chapter Three is experimental and shows the results and discussion of economic time series (popular stock market indexes and currency exchange rate) analysis that have been obtained from the software developed in Chapter Two.
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