Bioinformatics Advance Access originally published online on April 1, 2004
Bioinformatics 2004 20(14):2189-2196; doi:10.1093/bioinformatics/bth213
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.
Extraction of fluorescent cell puncta by adaptive fuzzy segmentation
1 School of Computing and Information Technology, 2 Eskitis Institute for Cell and Molecular Therapies and 3 School of Biomolecular and Biomedical Sciences, Griffith University, Nathan Campus, QLD 4111, Australia
Received on November 24, 2003; revised on January 19, 2004; accepted on February 4, 2004
Advance Access Publication April 1, 2004
Motivation: The discrimination and measurement of fluorescent-labeled vesicles using microscopic analysis of fixed cells presents a challenge for biologists interested in quantifying the abundance, size and distribution of such vesicles in normal and abnormal cellular situations. In the specific application reported here, we were interested in quantifying changes to the population of a major organelle, the peroxisome, in cells from normal control patients and from patients with a defect in peroxisome biogenesis. In the latter, peroxisomes are present as larger vesicular structures with a more restricted cytoplasmic distribution. Existing image processing methods for extracting fluorescent cell puncta do not provide useful results and therefore, there is a need to develop some new approaches for dealing with such a task effectively.
Results: We present an effective implementation of the fuzzy c-means algorithm for extracting puncta (spots), representing fluorescent-labeled peroxisomes, which are subject to low contrast. We make use of the quadtree partition to enhance the fuzzy c-means based segmentation and to disregard regions which contain no target objects (peroxisomes) in order to minimize considerable time taken by the iterative process of the fuzzy c-means algorithm. We finally isolate touching peroxisomes by an aspect-ratio criterion. The proposed approach has been applied to extract peroxisomes contained in several sets of color images and the results are superior to those obtained from a number of standard techniques for spot extraction.
Availability: Image data and computer codes written in Matlab are available upon request from the first author.
Contact: t.pham{at}griffith.edu.au
* To whom correspondence should be addressed.
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