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Study of the influence of magnetic fields on biological tissue
Vlachová Hutová, Eliška ; Fiala, Pavel (referee) ; Bartušek, Karel (advisor)
The aim of this research is to explore the influence of magnetic field on early somatic embryos (ESEs) of spruce and pine. The magnetic field is gradual. This is important for the experiment, each cluster of ESE was exposed to magnetic field of different intensity. The resulting report of this experiment consists of the comparison between various methods of image analysis and the difference in growth of ESEs due to different exposure to magnetic field and surrounding temperature. Enclosed is a proposal of ESE size computing algorithm from a given image.
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Processing of Images of Petri Dishes
Adámek, Jakub ; Hradiš, Michal (referee) ; Zemčík, Pavel (advisor)
This master thesis deals with image processing of Petri dishes. The first part is about terms and procedures in laboratory practice. The following part is about devices and algorithms for image analysis of Petri dishes. The second part is about draft and implementation of own colony counting application, which was developed in cooperation with the microbiological laboratory. The application is developed for mobile devices running Android OS. The master thesis also includes the design and creation of two lighting units, which uses as an accessory for better results in the analysis of Petri dishes. In conclusion are presented results, compared lighting units and various types of mobile devices, on which the application was tested.
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Detection and localization of microbial colonies by means of deep learning algorithms
Čičatka, Michal ; Vičar, Tomáš (referee) ; Mézl, Martin (advisor)
Due to massive expansion of the mass spectrometry and constant price growth of the human labour the optimalisation of the microbial samples preparation comes into question. This master thesis deals with design and implementation of a machine learning algorithm for segmentation of images of microbial colonies cultivated on Petri dishes. This algorithm is going to be a part of a controlling software of a MBT Pathfinder device developed by the company Bruker s. r. o. that automates the process of smearing microbial colonies onto a MALDI target plates. In terms of this thesis a several models of neural networks based on the UNet, UNet++ and ENet architecture were implemented. Based on a number of experiments investigating various configurations of the networks and pre-processing of the training datatset there was chosen an ENet model with quadruplet filter count and additional convolutional block of the encoder trained on a dataset pre-processed with round mask.
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Image-Based Clustering of Microbial Colonies
Láncoš, Jan ; Kišš, Martin (referee) ; Beneš, Karel (advisor)
Laboratorní analýza mikrobiálních kolonií pěstovaných na Petriho miskách je v současné době předmětem intenzivního výzkumu ve snaze o dosažení totální laboratorní automatizace. Jádro tohoto problému spočívá v přesné lokalizaci kolonií při obrazové analýze. Současná řešení nejčastěji využívají strojové učení, které je však obecně závislé na kvalitních datech, kterých je v tomto odvětví k dispozici jen velmi málo. Abych adresoval tento problém, vytvořil jsem víceúčelový generátor syntetických dat. Úspěšně jsem jej aplikoval jak při segmentaci tak při shlukování kolonií. Výsledné segmentační F1 skóre se mi podařilo navýšit z 0,518 na 0,729 a při shlukování jsem s využitím této segmentace dosáhl V-measure skóre 0,830. Prací navržený přístup ke generování syntetických dat nás posouvá o krok blíže k plné laboratorní automatizaci.
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Detection and localization of microbial colonies by means of deep learning algorithms
Čičatka, Michal ; Vičar, Tomáš (referee) ; Mézl, Martin (advisor)
Due to massive expansion of the mass spectrometry and constant price growth of the human labour the optimalisation of the microbial samples preparation comes into question. This master thesis deals with design and implementation of a machine learning algorithm for segmentation of images of microbial colonies cultivated on Petri dishes. This algorithm is going to be a part of a controlling software of a MBT Pathfinder device developed by the company Bruker s. r. o. that automates the process of smearing microbial colonies onto a MALDI target plates. In terms of this thesis a several models of neural networks based on the UNet, UNet++ and ENet architecture were implemented. Based on a number of experiments investigating various configurations of the networks and pre-processing of the training datatset there was chosen an ENet model with quadruplet filter count and additional convolutional block of the encoder trained on a dataset pre-processed with round mask.
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Processing of Images of Petri Dishes
Adámek, Jakub ; Hradiš, Michal (referee) ; Zemčík, Pavel (advisor)
This master thesis deals with image processing of Petri dishes. The first part is about terms and procedures in laboratory practice. The following part is about devices and algorithms for image analysis of Petri dishes. The second part is about draft and implementation of own colony counting application, which was developed in cooperation with the microbiological laboratory. The application is developed for mobile devices running Android OS. The master thesis also includes the design and creation of two lighting units, which uses as an accessory for better results in the analysis of Petri dishes. In conclusion are presented results, compared lighting units and various types of mobile devices, on which the application was tested.
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Study of the influence of magnetic fields on biological tissue
Vlachová Hutová, Eliška ; Fiala, Pavel (referee) ; Bartušek, Karel (advisor)
The aim of this research is to explore the influence of magnetic field on early somatic embryos (ESEs) of spruce and pine. The magnetic field is gradual. This is important for the experiment, each cluster of ESE was exposed to magnetic field of different intensity. The resulting report of this experiment consists of the comparison between various methods of image analysis and the difference in growth of ESEs due to different exposure to magnetic field and surrounding temperature. Enclosed is a proposal of ESE size computing algorithm from a given image.
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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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