National Repository of Grey Literature 35 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Analysis of meiotic spindle microscopy images captured with light-sheet microscope
Mikeštíková, Anna ; Schier, Jan (advisor) ; Zemčík, Pavel (referee)
Analysis of the meiotic spindle is an essential but time-consuming step in the research of the effects of the oocyte-meiosis regulating proteins. In this thesis, we propose a method for automated computation of the spindle volume as a step towards a more efficient analysis pipeline. The proposed method is based on convolutional neural networks. It consists of two steps: segmentation of the spindle on a microscopic image and calculation of its volume. The segmentation is performed by a modified 3D U-Net architecture, which is trained on an augmented dataset of volumetric images. The choice of architecture is supported by an in-depth analysis of the current state-of- the-art methods for image segmentation with a focus on biomedical images and volumetric data. The hyperparameters are tuned for the best performance on the dataset. The model is evaluated on the testing dataset with respect to the segmentation qual- ity and the volume estimation accuracy. The results demonstrate the feasibility of the proposed approach. 1
Acceleration of 2D Wavelet transform on parallel architectures
Kula, Michal ; Schier, Jan (referee) ; Sojka, Eduard (referee) ; Zemčík, Pavel (advisor)
I přesto, že byla 2D diskrétní vlnková transformace předmětem řady rozsáhlých studií, některé aspekty této problematiky byly doposud opomíjeny. Mezi takové aspekty lze zařadit techniky pro výpočet této transformace se zaměřením na vyvažování synchronizací, aritmetických instrukcí a využití paměti pro různé architektury. Tato práce ukazuje několik nových metod výpočtu této transformace s různě nastaveným vybalancováním těchto operací. Tyto metody jsou detailně popsány a jejich chování je vyhodnoceno na několika grafických adaptérech za použití GPGPU, zpracování pomocí grafické pipeliny a vícejádrových procesorů pomocí OpenMP.
Volumetric data processing for CT enterography
Horáček, Jan ; Pelikán, Josef (advisor) ; Czanner, Silvester (referee) ; Schier, Jan (referee)
Title: Volumetric data processing for CT enterography Author: Jan Horáček Department: Department of Software and Computer Science Education Supervisor: RNDr. Josef Pelikán, Department of Software and Computer Sci- ence Education Abstract: The overall goal of our work is to develop algorithms for efficient processing, segmentation and tracking of the small intestine in CT enterography scans. The small intestine is a complex organ, the shape of which can vary con- siderably between patients: and in addition to this, its location and shape can change significantly between subsequent scans of the same person. The CT en- terography process uses contrast agents to improve the visibility of the intestine, so that various potentially problematic features, such as inflammations, obstruc- tions and so on, can be properly seen. However, due to the convoluted shape of the organ, manual diagnosis of raw CT enterography data is still a difficult and time-consuming task, and is prone to diagnostic errors. We have prepared a set of methods for automatic preprocessing, segmentation and tracking of such data that aims at providing a much clearer data visualization: such tools can greatly improve the diagnostic process. Our first contribution is to make a high quality denoising method for volumet- ric data practically usable: so...
Technical report on multispectral imaging, multispectral applications and on libraries for multispectral/hyperspectral image processing
Schier, Jan
This report presents brief overview of multispectral and hyperspectral image acquisition methods, of applications of hyperspectral imaging and of basic methods of hyperspectral image processing. In the final part, we present an overview of Matlab and Python software libraries for hyperspectral image processing.
Volumetric data processing for CT enterography
Horáček, Jan ; Pelikán, Josef (advisor) ; Czanner, Silvester (referee) ; Schier, Jan (referee)
Title: Volumetric data processing for CT enterography Author: Jan Horáček Department: Department of Software and Computer Science Education Supervisor: RNDr. Josef Pelikán, Department of Software and Computer Sci- ence Education Abstract: The overall goal of our work is to develop algorithms for efficient processing, segmentation and tracking of the small intestine in CT enterography scans. The small intestine is a complex organ, the shape of which can vary con- siderably between patients: and in addition to this, its location and shape can change significantly between subsequent scans of the same person. The CT en- terography process uses contrast agents to improve the visibility of the intestine, so that various potentially problematic features, such as inflammations, obstruc- tions and so on, can be properly seen. However, due to the convoluted shape of the organ, manual diagnosis of raw CT enterography data is still a difficult and time-consuming task, and is prone to diagnostic errors. We have prepared a set of methods for automatic preprocessing, segmentation and tracking of such data that aims at providing a much clearer data visualization: such tools can greatly improve the diagnostic process. Our first contribution is to make a high quality denoising method for volumet- ric data practically usable: so...
Video analysis for entomology
Šerý, Martin ; Pelikán, Josef (advisor) ; Schier, Jan (referee)
Analysis of behavioral patterns of Drosophila Melanogaster species is a sub- ject of study of many laboratories. The behavior of individuals, for example in different gene lines, is monitored. In order for this analysis to be possible, it is necessary to have a device that is capable of tracking the fly and providing machine-readable data about them. These data are the output of a trace pro- gram FlyCatcher, which records the positions of the observed objects. Thanks to this, we can determine the location, the mutual position of individuals and other parameters. FlyCatcher is based on the use of the AForge library which handles multimedia files. FlyCatcher lets us process videos made in the lab and provide outputs in the .csv format. This format is further processed by external statistical programs.
Comparison and analysis of development of Greek and Latvian economy between years 2005 and 2014
Schier, Jan ; Vostrovská, Zdenka (advisor) ; Ševčíková, Michaela (referee)
The main topic of this bachelor thesis is development of the economy of Greece and Latvia. Period of observation is between years 2005 and 2014 because under this time both countries got into serious economic problems and it also incorporates period both before and after the main fall into recession influenced by global financial crisis. First part deals with theoretical basis of various indicators used to describe the economy of both countries. The analysis and comparison part examines the situation of both counties over the period to find causes of different evolution of economy in these countries that still overlaps into present time.
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.
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.
Použití Matlabu pro kvantitativní analýzu růstu kvasinek
Schier, Jan ; Kovář, Bohumil
Quantitative growth analysis is used in microbiology, genetics and medical re- search to determine the in uence of the tested substance on the growth of colonies of some organism (we focus on yeast colonies in this paper). Examples of the tested substance include antibiotics, mutagens or medical drugs. To evaluate the experiment, time series of images of the colonies inoculated on Petri dishes are taken by digital camera in a darkroom. Then, relative area and the number of the colonies in each image have to be determined for further statistical processing. In the current laboratory practice, these parameters have often been hand-counted in each image, which is an error-prone process of a limited precision. Also, given the time demands of this hand-counting, the number of snapshots that can reasonably be processed is rather limited. In this paper, we introduce a Matlab-based tool for semi-automated processing of the dish images.

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2 Schier, Jakub
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