A computer-assisted approach to supporting taxonomical classification of freshwater green microalga images

• Autor(a) principal: Borges, Vinicius Ruela Pereira
• Data de Publicação: 2016
• Tipo de documento: Tese
• Idioma: eng
• Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
• Texto Completo: http://www.teses.usp.br/teses/disponiveis/55/55134/tde-07022017-163412/
• topic: Classificação visual incremental; Extração de características baseadas em forma; Green microalga images; Image segmentation; Imagens de microalgas verdes; Segmentação de imagens; Shape-based feature extraction; Visual incremental classification

The taxonomical identification of freshwater green microalgae is highly relevant problem in Phycology. In particular, the taxonomical identification of samples from the Selenastraceae family of algae is considered particularly problematic with many known inconsistencies. Biologists manually inspect and analyze microscope images of alga strains, and typically carry out several complex and time-consuming procedures that demand considerable expert knowledge. Such practical limitations motivated this investigation on the applicability of image processing, pattern recognition and visual data mining techniques to support the biologists in tasks of species identification. This thesis describes methodologies for the classification of green alga images, considering both traditional automated classification processes and also a user-assisted incremental classification process supported by Neighbor Joining tree visualizations. In this process, users can interact with the visualizations to introduce their knowledge into the classification process, e.g. by selecting suitable training sets and evaluate the results, thus steering the classification process. In order for visualization and classification to be feasible, accurate features must be obtained from the images capable of distinguishing between the different species of algae. As morphological shape properties are a fundamental property in identifying species, suitable segmentation and shape feature extraction strategies have been developed. This was particularly challenging, as different alga species share common morphological characteristics. Two segmentation methodologies are introduced, in which one relies on the level set method and the other is based on the region growing principle. Although the contour-based approach is capable of handling the uneven conditions of green alga images, its computation is time-consuming and not suitable for real time applications. A specialized formulation of the region-based methodology is proposed that considers the specific characteristics of the green alga images handled. This second formulation was shown to be more efficient than the level set approach and generates highly accurate segmentations. Once accurate alga segmentation is achieved, two descriptors are proposed that capture alga shape properties, and also an effective general shape descriptor that computes quantitative measures from two signatures associated to the shape properties. Experimental results are described that indicate that the proposed solutions can be useful to biologists conducting alga identification tasks once it reduces their effort and attains satisfactory discrimination among species.