In situ microscopy for analysis of filamentous bacteria: optics end image evalaution
In the activated sludge process, problems of foaming and filamentous bulking can occur due to overgrowth of certain filamentous bacteria. Nowadays, these microorganisms are typically monitored by means of light microscopy combined with staining techniques. As drawbacks, these methods are susceptible...
| Autor principal: | Dias, Philipe Ambrozio |
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| Formato: | Dissertação |
| Idioma: | Português |
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Universidade Tecnológica Federal do Paraná
2017
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riut-1-19992017-02-24T06:01:47Z In situ microscopy for analysis of filamentous bacteria: optics end image evalaution Microscopia in situ para análise de Bactérias filamentosas: ótica e processamento de imagens Dias, Philipe Ambrozio Schneider, Fábio Kurt http://lattes.cnpq.br/1463591813823167 Shur, Hajo Schneider, Fábio Kurt Belini, Valdinei Luis Vieira Neto, Hugo Águas residuais - Purificação - Processo de lodo ativado Microscopia Processamento de imagens - Técnicas digitais Bactérias Monitorização ambiental Métodos de simulação Engenharia biomédica Sewage - Purification - Activated sludge process Microscopy Image processing - Digital techniques Bacteria Environmental monitoring Simulation methods Biomedical engineering CNPQ::ENGENHARIAS::ENGENHARIA BIOMEDICA::BIOENGENHARIA In the activated sludge process, problems of foaming and filamentous bulking can occur due to overgrowth of certain filamentous bacteria. Nowadays, these microorganisms are typically monitored by means of light microscopy combined with staining techniques. As drawbacks, these methods are susceptible to human errors, subjectivity and limited by the use of discontinuous microscopy. The present project aims the application of an in situ microscope (ISM) for continuous monitoring of filamentous bacteria, providing real-time examination, automated analysis and elimination of sampling, preparation and transport of samples. The ISM previously developed at the Hochschule Mannheim required adaptations for use within wastewater environment, specially in terms of impermeability and development of a cleaning mechanism. With a new objective lens design, the system was simplified to a single tubus and an externally activated cleaning system based on magnetism was created. A proper image processing algorithm was designed for automated recognition and measurement of filamentous objects, allowing real-time evaluation of images without any staining, phase-contrast or dilution techniques. Three main operations are performed: preprocessing and binarization; recognition of filaments using distance-maps and shape descriptors; measurement and display of total extended filament length. A 3D-printed prototype was used for experiments with respect to the new ISM’s design, providing images with resolution very close to the ones acquired with the previous microscope. The designed cleaning system has shown to be effective, removing dirt settled above the lens during tests. For evaluation of the image processing algorithm, samples from an industrial activated sludge plant were collected weekly for a period of twelve months and imaged without any prior conditioning, replicating real environment conditions. Experiments have shown that the developed algorithm correctly identifies trends of filament growth rate, which is the most important parameter for decision making. For reference images whose filaments were marked by specialists, the algorithm correctly recognized 72% of the filaments pixels, with a false positive rate of at most 14%. An average execution time of 0.7 second per image was achieved, demonstrating the algorithm suitability for real-time monitoring. CAPES; CNPq Em processos de lodo ativado, problemas de foaming e filamentous bulking podem ocorrer devido ao crescimento exagerado de bactérias filamentosas. Atualmente, o monitoramento de tais micro-organismos é feito por meio de métodos baseados em microscopia ótica combinada com técnicas de marcadores, os quais apresentam limitações intrínsecas da microscopia descontínua, são subjetivos e suscetíveis a erro humano. O presente projeto visa a aplicação de um microscópio in situ (ISM) para monitoramento contínuo de bactérias filamentosas, de forma a possibilitar análise instantânea, computadorizada, sem necessidades de recolher, preparar e transportar amostras. O ISM previamente desenvolvido na Hochschule Mannheim teve que ser adaptado para análise de águas residuais, especialmente em termos de impermeabilidade e a criação de um mecanismo de limpeza. Com a utilização de uma nova objetiva, o novo ISM foi simplificado para um tubo único e um sistema de limpeza ativado externamente baseado em magnetismo foi criado. Um algoritmo de processamento de imagens foi elaborado para reconhecimento e medição de comprimento de estruturas filamentosas, permitindo avaliação em tempo real de imagens sem qualquer técnica de marcadores, contraste de fase ou diluição. O mesmo consiste em três operações principais: pré-processamento e binarização; reconhecimento de filamentos por meio de mapeamento de dis- tâncias e descritores de forma; e, finalmente, medição e visualização do comprimento de cada filamento. Um protótipo construído via impressão 3D foi utilizado para avaliação o novo design do microscópio, fornecendo imagens com resolução bastante próxima das adquiridas com a versão anterior do sistema. O mecanismo de limpeza desenvolvido mostrou-se efetivo, capaz de remover partículas sedimentadas acima das lentes durante os testes. Para avaliação do algoritmo de processamento de imagens, amostras de uma planta industrial de lodo ativado foram coletadas semanalmente por um período de doze meses e imageadas sem qualquer condicionamento prévio, replicando condições reais de ambiente. Experimentos demonstraram que o algoritmo desenvolvido identifica corretamente tendências de aumento/decréscimo da concentração de filamentos, o que constitui o principal parâmetro para tomadas de decisão. Para imagens de referência cujos filamentos foram marcados por especialistas, o algoritmo reconheceu corretamente 80% dos pixels atribuídos a filamentos, com uma taxa de falso positivos de até 24%. Um tempo de execução médio de 0,7 segundo por imagem foi obtido, provando sua aptidão para formar uma ferramenta de monitoramento em tempo real. 2017-02-23T19:20:00Z 2017-02-23T19:20:00Z 2016-02-29 masterThesis DIAS, Philipe Ambrozio. In situ microscopy for analysis of filamentous bacteria: optics and image evaluation. 2016. 72 f. Dissertação (Mestrado em Engenharia Elétrica e Informática Industrial) - Universidade Tecnológica Federal do Paraná, Curitiba, 2016. http://repositorio.utfpr.edu.br/jspui/handle/1/1999 por openAccess application/pdf Universidade Tecnológica Federal do Paraná Curitiba Brasil Programa de Pós-Graduação em Engenharia Elétrica e Informática Industrial UTFPR |
| institution |
Universidade Tecnológica Federal do Paraná |
| collection |
RIUT |
| language |
Português |
| topic |
Águas residuais - Purificação - Processo de lodo ativado Microscopia Processamento de imagens - Técnicas digitais Bactérias Monitorização ambiental Métodos de simulação Engenharia biomédica Sewage - Purification - Activated sludge process Microscopy Image processing - Digital techniques Bacteria Environmental monitoring Simulation methods Biomedical engineering CNPQ::ENGENHARIAS::ENGENHARIA BIOMEDICA::BIOENGENHARIA |
| spellingShingle |
Águas residuais - Purificação - Processo de lodo ativado Microscopia Processamento de imagens - Técnicas digitais Bactérias Monitorização ambiental Métodos de simulação Engenharia biomédica Sewage - Purification - Activated sludge process Microscopy Image processing - Digital techniques Bacteria Environmental monitoring Simulation methods Biomedical engineering CNPQ::ENGENHARIAS::ENGENHARIA BIOMEDICA::BIOENGENHARIA Dias, Philipe Ambrozio In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| description |
In the activated sludge process, problems of foaming and filamentous bulking can occur due to overgrowth of certain filamentous bacteria. Nowadays, these microorganisms are typically monitored by means of light microscopy combined with staining techniques. As drawbacks, these methods are susceptible to human errors, subjectivity and limited by the use of discontinuous microscopy. The present project aims the application of an in situ microscope (ISM) for continuous monitoring of filamentous bacteria, providing real-time examination, automated analysis and elimination of sampling, preparation and transport of samples. The ISM previously developed at the Hochschule Mannheim required adaptations for use within wastewater environment, specially in terms of impermeability and development of a cleaning mechanism. With a new objective lens design, the system was simplified to a single tubus and an externally activated cleaning system based on magnetism was created. A proper image processing algorithm was designed for automated recognition and measurement of filamentous objects, allowing real-time evaluation of images without any staining, phase-contrast or dilution techniques. Three main operations are performed: preprocessing and binarization; recognition of filaments using distance-maps and shape descriptors; measurement and display of total extended filament length. A 3D-printed prototype was used for experiments with respect to the new ISM’s design, providing images with resolution very close to the ones acquired with the previous microscope. The designed cleaning system has shown to be effective, removing dirt settled above the lens during tests. For evaluation of the image processing algorithm, samples from an industrial activated sludge plant were collected weekly for a period of twelve months and imaged without any prior conditioning, replicating real environment conditions. Experiments have shown that the developed algorithm correctly identifies trends of filament growth rate, which is the most important parameter for decision making. For reference images whose filaments were marked by specialists, the algorithm correctly recognized 72% of the filaments pixels, with a false positive rate of at most 14%. An average execution time of 0.7 second per image was achieved, demonstrating the algorithm suitability for real-time monitoring. |
| format |
Dissertação |
| author |
Dias, Philipe Ambrozio |
| author_sort |
Dias, Philipe Ambrozio |
| title |
In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| title_short |
In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| title_full |
In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| title_fullStr |
In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| title_full_unstemmed |
In situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| title_sort |
in situ microscopy for analysis of filamentous bacteria: optics end image evalaution |
| publisher |
Universidade Tecnológica Federal do Paraná |
| publishDate |
2017 |
| citation |
DIAS, Philipe Ambrozio. In situ microscopy for analysis of filamentous bacteria: optics and image evaluation. 2016. 72 f. Dissertação (Mestrado em Engenharia Elétrica e Informática Industrial) - Universidade Tecnológica Federal do Paraná, Curitiba, 2016. |
| url |
http://repositorio.utfpr.edu.br/jspui/handle/1/1999 |
| _version_ |
1805316930185199616 |
| score |
10,814766 |