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Enhancing Reliability and Benchmarking Performance of Agar Plate Handling Algorithms for Laboratory Automation Robots
Kalivodová, Tereza ; Nohel, Michal (referee) ; Mézl, Martin (advisor)
Tato bakalářská práce zkoumá problematiku vzorkové přípravy v oblasti mikrobiologie a lékařské diagnostiky s důrazem na automatizovaný robotický systém MBT Pathfinder, vyvinutý firmou \bruker. S využitím digitálních obrazových technik a konvolučních neuronových sítí se práce zaměřuje na zdokonalení algoritmu pro identifikaci pozice mikrobiálních kolonií v systému MBT Pathfinder. Praktická část práce prezentuje inovativní přístupy k optimalizaci kritických kroků vzorkové přípravy s cílem eliminovat chyby a zvýšit efektivitu procesu. Výsledky této práce mohou posílit spolehlivost mikrobiologických analýz v oblasti lékařské diagnostiky a mikrobiologického výzkumu.
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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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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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