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Classification of Varying-Size Plankton Images with Convolutional Neural Network
Bureš, Jaroslav ; Juránek, Roman (referee) ; Zemčík, Pavel (advisor)
Tato práce pojednává o technikách automatické analýzy obrazu založené na konvolučních neuronových sítích (CNN), zaměřených na klasifikaci planktonu. V oblasti studování planktonu panuje velká diverzita v jeho tvarech a velikostech. Kvůli tomuto bývá klasifikace pomocí CNN náročná, jelikož CNN typicky požadují definovanou velikost vstupu. Běžné metody využívají škálování obrazu do jednotné velikosti. Avšak kvůli tomuto jsou ztraceny drobné detaily potřebné ke správné klasifikaci. Cílem práce bylo navrhnout a implementovat CNN klasifikátor obrazových dat planktonu a prozkoumat metody, které jsou zaměřené na problematiku různorodých velikostí obrázků. Metody, jako jsou patch cropping, využití spatial pyramid pooling vrstvy, zahrnutí metadat a sestavení multi-stream modelu jsou vyhodnoceny na náročném datasetu obrázků fytoplanktonu. Takto bylo dosaženo zlepšení o 1.0 bodů pro InceptionV3 architekturu s výslednou úspěšností 96.2 %. Hlavním přínosem této práce je vylepšení CNN klasifikátorů planktonu díky úspěšné aplikaci těchto metod.
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Classification of Varying-Size Plankton Images with Convolutional Neural Network
Bureš, Jaroslav ; Juránek, Roman (referee) ; Zemčík, Pavel (advisor)
Tato práce pojednává o technikách automatické analýzy obrazu založené na konvolučních neuronových sítích (CNN), zaměřených na klasifikaci planktonu. V oblasti studování planktonu panuje velká diverzita v jeho tvarech a velikostech. Kvůli tomuto bývá klasifikace pomocí CNN náročná, jelikož CNN typicky požadují definovanou velikost vstupu. Běžné metody využívají škálování obrazu do jednotné velikosti. Avšak kvůli tomuto jsou ztraceny drobné detaily potřebné ke správné klasifikaci. Cílem práce bylo navrhnout a implementovat CNN klasifikátor obrazových dat planktonu a prozkoumat metody, které jsou zaměřené na problematiku různorodých velikostí obrázků. Metody, jako jsou patch cropping, využití spatial pyramid pooling vrstvy, zahrnutí metadat a sestavení multi-stream modelu jsou vyhodnoceny na náročném datasetu obrázků fytoplanktonu. Takto bylo dosaženo zlepšení o 1.0 bodů pro InceptionV3 architekturu s výslednou úspěšností 96.2 %. Hlavním přínosem této práce je vylepšení CNN klasifikátorů planktonu díky úspěšné aplikaci těchto metod.
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Detekce a monitoring potenciálně toxických sinicových lipopeptidů
BÁRTOVÁ, Marie
The aim of this study was to design and optimize new PCR primers for detection of potential cyanobacterial producers of cytotoxic lipopeptides puwainaphycins and minutissamides in environmental samples. Samples from two distinct localities were tested, as suggested based on preliminary data. The first set of samples consisted of cyanobacterial soil biofilms from sheep pastures affected by Alveld illness in Norway. The other one contained samples of planktic cyanobacaterial blooms from Protected Landscape Area Třeboň and its vicinity. Three different approaches were used for evaluation of the presence of cyanobacterial lipopeptide producers: microscopy, PCR with the designed primeres, and liquid chromatography-mass spectrometry analysis. Results of this study confirmed the specificity of the newly designed PCR primers. The presence of producers of puwainaphycins/minutissamides was proven at both tested localities.
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You cannot step into the same fishpond twice - an evolution of fishpond ecosystems to hypertrophy
Vrba, Jaroslav ; Benedová, Z. ; Jezberová, Jitka ; Matoušů, Anna ; Musil, M. ; Nedoma, Jiří ; Pechar, L. ; Potužák, J. ; Řeháková, Klára ; Šimek, Karel ; Šorf, M. ; Zemanová, J.
Shallow manmade fishponds in south Bohemia were used for fish production for centuries, however, their ecosystems have changed dramatically due to excessive nutrient loading and fish stocking. Preliminary results of ten sampled fishponds suggested their hypertrophic status at present, while their plankton structure and dynamics reflected the actual size/age class of fish stock consisting predominantly of common carp. Planktivorous fish (both young carp and whitefish) remarkably reduced abundance, size, and species diversity of crustacean zooplankton, in particular large daphnids, whereas larger carp itself did not cause such a strong top-down effect. All other plankton components, i.e. phytoplankton, bacteria, protists, and rotifers showed rather high abundance and diversity, and suggested a reasonable impact of various microbial processes and interactions in the recent hypertrophic ecosystems.
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Obsah biogenů (N,P) ve vodě a sedimentu vybraných rybníků
Horák, Filip
The aim of presented diploma thesis was 7-months monitoring of biogenous elements (P, N) in water and its determination in bottom sediments within selected fihsponds assigned by Rybníkářství Pohořelice a.s. Studied fihsponds were Šumický horní, Šumický dolní and Pohořelický. Sampling of water was carried out twice a month from two separate sampling spots, both near the fishpond dam. Basic physicochemical parameters of water were measured in locality, samples for laboratory chemical analysis and plankton analysis were transported to the Department of Fisheries and Hydrobiology for further analysing. The main aim of this project was to account for massive fish kill in summer season in the fishpond Pohořelický dolní on which was Rybníkářství Pohořelice a.s. focused mainly. Realized monitoring showed rapid decrease in dissolved oxygen amount in water which caused mainly the fish kill. Based on this result, decreasing of fish stock intensity and lower fertilization with manure within fishpond management was suggested as suitable. Subsequently, the mud removal of fishpond and use of superphosphate when the level of dissolved oxygen goes below the critical limit was suggested as well.
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The role of microhabitats in spatio-temporal differentiation of phytoplankton flagellates
Pusztai, Martin ; Němcová, Yvonne (advisor) ; Bílý, Michal (referee)
This thesis deals with factors structuring phytoplankton flagellates. The aim of the thesis was to investigate the role of microhabitats in spatio-temporal differentiation of lentic communities of these flagellates, which has not been rigorously examined to date. The study was conducted during 2010-2013 in the shallow littoral sites of Horní rybník, Rybníčky u Podbořánek Nature Reserve. Phytoplankton flagellates showed cyclic seasonal dynamics, which was reflected by significantly different community structure and species richness during the season. In contrast, silica-scaled chrysophytes showed a non- cyclic seasonal dynamics. The impact of the season was strongly correlated with the impact of fluctuating environmental factors - pH, conductivity and temperature. Gradient of interrelated environmental factors between the northern and southern shore together with microhabitat - substrate type played the major role and accounted for 64.4 - 75.8 % variability in the data. Microhabitat type (plankton, metaphyton, epipelon) significantly affected species richness and community structure also in the course of the season. A large number of species was assessed to prefer a certain type of microhabitat. These preferences were observed at both species and generic levels, and even at the level of the main taxonomic...
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Iron fertilization of the Southern ocean
Přibylová, Petra ; Koblížek, Michal (advisor) ; Nedbalová, Linda (referee)
This thesis summarizes the current knowledge of the effect of iron on the growth of plankton in relation to lowering the concentration of CO2 in the atmosphere. Iron is a limiting factor for phytoplankton growth in large parts of the Pacific Ocean and the Southern Ocean. This thesis is focused on the Southern ocean, where it chronologically describes natural and artificial experiments, where the objective was to uncover the possibilities of artificial iron fertilization of the ocean. The iron fertilization experiments were based on supplying the upper layer of the ocean with an iron solution, which resulted in an increase in phytoplankton growth and chlorophyll concentration. The reaction of plankton to a natural iron input via upwelling was also observed. In these cases an increase of phytoplankton and chlorophyll was observed. Nowadays, the lively discussed possibility of large-scale fertilization is restricted by the United Nations due to insufficient knowledge and concerns of geoengineering.
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Vývoj softwarové aplikace pro zpracování vzorků planktonu
KROČÁK, Vladimír
This bachelor thesis deals with the implementation of a new application for quantitative processing of zooplankton samples and replaces current application in use developed by prof. RNDr. Adam Petrusek, Ph.D. The application will also be used as a framework for further needs of the Department of Ecosystem Biology, Faculty of Science, University of South Bohemia. The application and its source code will be released under MIT license to allow its further development.
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The assessment of the NPR Řežabinec pond ecosystem stability.
ŠRÁMEK, Pavel
The first part is characterized by a pond ecosystem and National Nature Reserve Řežabinec in terms of its historical development and creation. Are mentioned methods , the method and system of protection of the site. The paper describes a method of fish farming during the period of the individual plans of care farming in the last five years and the water conditions in the area . The ecosystem is assessed on the basis of available data in the literature to me In our own work we focus on monitoring water chemistry and state recovery tank , especially in terms of development and biomass of zooplankton species representation in the course of one growing season. He also details the fishing and agricultural management and water management conditions in the locality. Marginally judging submerged and littoral vegetation and the presence of water birds. This work demonstrated the dependence of the size of the fish stock on the frequency of a generic representation of zooplankton and the positive impact of lower stocking on the development and stability of the entire ecosystem. Contributes to the stability and sensitive farming in the last period.
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