Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Tipo de documento: | Dissertação |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | https://hdl.handle.net/1822/37076 |
Resumo: | The yeast Saccharomyces cerevisiae is one of the microorganisms with increased use at industrial, academic and scientific level. The easy growth in any culture medium, as well as the complete sequencing of its genome, are two of the main interesting factors, making this microorganism one of the most important worldwide. The morphological analysis of yeast using optical microscopy is a research area of great interest. Over the last decades, significant advances have been made in digital image processing as well in the analysis of microscopic images of cells. In this context, the development of specific software such as ImageJ is of particular interest since it is free access and open source. The main goal of this work was to develop a computer program, in the form of an extension module (plugin), in order to add certain features to ImageJ software. For this purpose, programming and processing methods were applied for a more reliable evaluation of cell and finally implemented as an ImageJ plugin. The plugin code was carried out using the Java programming language, since certain required functions were not present in the main program source code. Results presented as .xls file included the identification of cells, as well as counting and cataloguing after images processing and analysis. The features developed in this work allowed the user to process and analyse different microscopic images of S. cerevisiae cells. Finally, the plugin code was tested using multiple images of S. cerevisiae. The final version has shown high efficiency in S. cerevisiae culture images with different exposure times. Nevertheless, the plugin code was able to detect almost all cells in the images and classify them as large, normal, small and bud. |
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Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJS. cerevisiaeImageJImage analysisThe yeast Saccharomyces cerevisiae is one of the microorganisms with increased use at industrial, academic and scientific level. The easy growth in any culture medium, as well as the complete sequencing of its genome, are two of the main interesting factors, making this microorganism one of the most important worldwide. The morphological analysis of yeast using optical microscopy is a research area of great interest. Over the last decades, significant advances have been made in digital image processing as well in the analysis of microscopic images of cells. In this context, the development of specific software such as ImageJ is of particular interest since it is free access and open source. The main goal of this work was to develop a computer program, in the form of an extension module (plugin), in order to add certain features to ImageJ software. For this purpose, programming and processing methods were applied for a more reliable evaluation of cell and finally implemented as an ImageJ plugin. The plugin code was carried out using the Java programming language, since certain required functions were not present in the main program source code. Results presented as .xls file included the identification of cells, as well as counting and cataloguing after images processing and analysis. The features developed in this work allowed the user to process and analyse different microscopic images of S. cerevisiae cells. Finally, the plugin code was tested using multiple images of S. cerevisiae. The final version has shown high efficiency in S. cerevisiae culture images with different exposure times. Nevertheless, the plugin code was able to detect almost all cells in the images and classify them as large, normal, small and bud.A levedura Saccharomyces cerevisiae é um dos microrganismos com maior utilização a nível industrial, académico e científico. A facilidade de crescimento em qualquer meio de cultura, assim como a completa sequenciação do seu genoma, são dois dos principais fatores que tornam este microrganismo dos mais importantes no mundo. A análise morfológica de leveduras é uma das áreas. Nas últimas décadas, foram feitos avanços significativos no processamento de imagens digitais, bem como na análise de imagens microscópicas de células. Neste contexto, o desenvolvimento de software específico, tal como o ImageJ é de particular importância, uma vez que é de acesso livre e possui implementação livre e aberta (open source). Este trabalho teve como principal objectivo o desenvolvimento de um programa de computador na forma de módulo de extensão (plugin) com a finalidade de adicionar determinadas funcionalidades ao software ImageJ. Para permitir ao utilizador do ImageJ uma avaliação fidedigna de imagens de células obtidas por microscopia, foram aplicados diversos métodos de processamento. O código do plugin foi desenvolvido utilizando a linguagem de programação Java, uma vez que certas funções exigidas não estavam presentes no código fonte do programa. Os resultados apresentados como tipo de arquivo .xls incluíram a identificação de células, bem como a contagem e catalogação após o processamento e análise de imagens. As funcionalidades desenvolvidas durante a execução deste trabalho permitem ao utilizador processar e analisar diferentes imagens de células de S. cerevisiae obtidas por microscopia. O código do plugin foi testado utilizando várias imagens de S. cerevisiae. A versão final revelou uma elevada eficiência na caracterização de imagens de culturas de S. cerevisiae com diferentes tempos de exposição. Foi ainda possível detetar quase todas as células presentes nas imagens e classificá-las como grandes, normais, pequenas e germinadas.Ferreira, Eugénio C.Mesquita, D. P.Universidade do MinhoSilva, Vitor Damião Baixinho da2014-11-202014-11-20T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttps://hdl.handle.net/1822/37076eng201196387info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:34:14Zoai:repositorium.sdum.uminho.pt:1822/37076Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:29:52.546820Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
title |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
spellingShingle |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ Silva, Vitor Damião Baixinho da S. cerevisiae ImageJ Image analysis |
title_short |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
title_full |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
title_fullStr |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
title_full_unstemmed |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
title_sort |
Image analysis of Saccharomyces cerevisiae cells: development of a plugin for IMAGEJ |
author |
Silva, Vitor Damião Baixinho da |
author_facet |
Silva, Vitor Damião Baixinho da |
author_role |
author |
dc.contributor.none.fl_str_mv |
Ferreira, Eugénio C. Mesquita, D. P. Universidade do Minho |
dc.contributor.author.fl_str_mv |
Silva, Vitor Damião Baixinho da |
dc.subject.por.fl_str_mv |
S. cerevisiae ImageJ Image analysis |
topic |
S. cerevisiae ImageJ Image analysis |
description |
The yeast Saccharomyces cerevisiae is one of the microorganisms with increased use at industrial, academic and scientific level. The easy growth in any culture medium, as well as the complete sequencing of its genome, are two of the main interesting factors, making this microorganism one of the most important worldwide. The morphological analysis of yeast using optical microscopy is a research area of great interest. Over the last decades, significant advances have been made in digital image processing as well in the analysis of microscopic images of cells. In this context, the development of specific software such as ImageJ is of particular interest since it is free access and open source. The main goal of this work was to develop a computer program, in the form of an extension module (plugin), in order to add certain features to ImageJ software. For this purpose, programming and processing methods were applied for a more reliable evaluation of cell and finally implemented as an ImageJ plugin. The plugin code was carried out using the Java programming language, since certain required functions were not present in the main program source code. Results presented as .xls file included the identification of cells, as well as counting and cataloguing after images processing and analysis. The features developed in this work allowed the user to process and analyse different microscopic images of S. cerevisiae cells. Finally, the plugin code was tested using multiple images of S. cerevisiae. The final version has shown high efficiency in S. cerevisiae culture images with different exposure times. Nevertheless, the plugin code was able to detect almost all cells in the images and classify them as large, normal, small and bud. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-11-20 2014-11-20T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://hdl.handle.net/1822/37076 |
url |
https://hdl.handle.net/1822/37076 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
201196387 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799132800276758528 |