Visual exploration of feature spaces to support Green Algae Taxonomic Classification

• Grant number: 12/00269-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Effective date (Start): April 01, 2012
• Effective date (End): February 16, 2016
• Field of knowledge: Physical Sciences and Mathematics - Computer Science - Computing Methodologies and Techniques
• Principal Investigator: Maria Cristina Ferreira de Oliveira
• Grantee: Vinícius Ruela Pereira Borges
• Host Institution: Instituto de Ciências Matemáticas e de Computação (ICMC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated scholarship(s): 13/26647-0 - Visual exploration to support green algae taxonomic classification, BE.EP.DR

Abstract

This Ph.D. project has the objective of employing Information Visualization and Multidimensional Visualization techniques to support biologists in tasks involved in the taxonomic classification of fresh water green algae. Taxonomical classification of such organisms is problematic due to their feature variations. Similar features may be identify multiple algae species, which introduces errors and inconsistencies in manual classification. It is expected that employing appropriate multidimensional data visualization techniques can collaborate to improve the quality of the overall process, minimizing drawbacks and offering an improved alternative over manual classification. Features currently employed for classification include shape descriptors manually extracted from microscopy images of the algae and other taxonomical keys. In order to improve the classification process in terms of efficiency, reliability and robustness, we shall investigate and develop automatic shape-based feature extraction from images, and integrate tehm with other availablefeatures. The proposed solutions shall be initially evaluated comparing the classification results obtained with the proposed methods with those obtained with standard processes currently employed by the biology experts who collaborate in this project.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BORGES, VINICIUS R. P.; DE OLIVEIRA, MARIA CRISTINA F.; SILVA, THAIS GARCIA; HENRIQUES VIEIRA, ARMANDO AUGUSTO; HAMANN, BERND. Region Growing for Segmenting Green Microalgae Images. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, v. 15, n. 1, p. 257-270, JAN-FEB 2018. (11/22749-8, 13/26647-0, 12/00269-7)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

BORGES, Vinícius Ruela Pereira. A computer-assisted approach to supporting taxonomical classification of freshwater green microalga images. 2016. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Ciências Matemáticas e de Computação (ICMC/SB) São Carlos.