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Doctoral Thesis
DOI
10.11606/T.76.2011.tde-23052011-082033
Document
Author
Full name
Matheus Palhares Viana
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
São Carlos, 2011
Supervisor
Committee
Costa, Luciano da Fontoura (President)
Baccala, Luiz Antonio
Carvalho, André Carlos Ponce de Leon Ferreira de
Evsukoff, Alexandre Gonçalves
Lotufo, Roberto de Alencar
Title in Portuguese
Caracterização e modelagem de redes biológicas geográficas
Keywords in Portuguese
Processamento de imagem
Rede biológica
Rede geográfica
Teoria de grafo
Visualização 3D
Abstract in Portuguese
Nesta tese apresentamos uma metodologia de mapeamento capaz de gerar representações em termos de grafos para sistemas biológicos de conectividade complexa. Tais sistemas são inicialmente armazenados na forma de imagens digitais e em seguida submetidos a um pré-processamento com objetivo de padronizar as imagens. As imagens pré-processadas são então utilizadas para gerar modelos tridimensionais dos sistemas de interesse. Um algoritmo de propagação de rótulos é utilizado para extrair os esqueletos dos modelos volumétricos e estes esqueletos são por fim, representados por um grafo, composto por vértices e arestas. Os vértices e arestas desse grafo armazenam propriedades do sistema original, como posição, comprimento e diâmetro, bem como as características topológicas de tais sistemas. Finalmente, os grafos resultantes são estudados através da teoria das redes complexas, dentro de um contexto específico para cada sistema. Nossos procedimentos foram aplicados com sucesso a diferentes sistemas biológicos, como artérias caríotidas, árvores arteriais, estruturas mitocondriais e poros em amostras de solo.
Title in English
Characterization and modelling of biological networks
Keywords in English
3D visualization
Biologic network
Geographical network
Graph theory
Image processing
Abstract in English
In the present work, we developed a mapping methodology able to build a graph representation for biological branched systems. Initially, such systems are stored as digital images and then they undergo a pre-processing in order to standardize the images. The pre-processed imagens are used to build tridimensional models of the interested systems. A label-propagation algorithm is used to extract the skeleton from the volumetric models and these skeletons are then represented by a graph, composed by nodes and edges. The nodes and edges of these graphs store properties of the original system, such as spatial position, lengths and diameter, as well as the topological features of such systems. Finally, the graphs are studied by using the complex networks theory within a specific context for each system. Our procedures were apllied sucefully to different biological systems, such as carotid artery, arterial trees, mitocondrial structure and pores in soil samples.
 
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Publishing Date
2011-05-25
 
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