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Intensity-based segmentation of microarray images.

Radhakrishnan Nagarajan1

  • 1Center on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA. nagarajanradhakrish@uams.edu

IEEE Transactions on Medical Imaging
|August 9, 2003
PubMed
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Clustering-based segmentation effectively extracts gene expression data from microarray images by analyzing pixel intensity distributions. This method accurately quantifies spot intensity, crucial for gene expression analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Microarray image analysis relies on spot intensity to measure gene expression.
  • Accurate gene expression quantification depends on reliable spot segmentation.
  • Pixel intensity distribution is a key factor in microarray spot analysis.

Purpose of the Study:

  • To develop and evaluate clustering-based segmentation techniques for microarray image analysis.
  • To extract target spot intensities by analyzing pixel intensity distributions.
  • To compare clustering methods with existing region-growing approaches.

Main Methods:

  • Utilized k-means clustering and Partitioning Around Medoids (PAM) for pixel intensity distribution analysis.
  • Applied manual adjustment of rectilinear grids to define approximate spot boundaries.

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  • Modeled pixel intensity distribution as a superposition of foreground and local background.

    • Main Results:

    • Clustering-based segmentation successfully extracted target intensities from microarray spots.
    • The k-means and PAM methods provided effective binary partitions of pixel intensity distributions.
    • Results were comparable to the region-growing (SPOT) approach, demonstrating robustness.

    Conclusions:

    • Clustering-based segmentation is a viable and effective method for microarray image analysis.
    • The approach accurately quantifies gene expression by analyzing pixel intensity distributions.
    • Further investigation into the impact of noise on segmentation performance is warranted.