Grow-cut based automatic cDNA microarray image segmentation

Stamos Katsigiannis, Eleni Zacharia, Dimitris Maroulis

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Complementary DNA (cDNA) microarray is a well-established tool for simultaneously studying the expression level of thousands of genes. Segmentation of microarray images is one of the main stages in a microarray experiment. However, it remains an arduous and challenging task due to the poor quality of images. Images suffer from noise, artifacts, and uneven background, while spots depicted on images can be poorly contrasted and deformed. In this paper, an original approach for the segmentation of cDNA microarray images is proposed. First, a preprocessing stage is applied in order to reduce the noise levels of the microarray image. Then, the grow-cut algorithm is applied separately to each spot location, employing an automated seed selection procedure, in order to locate the pixels belonging to spots. Application on datasets containing synthetic and real microarray images shows that the proposed algorithm performs better than other previously proposed methods. Moreover, in order to exploit the independence of the segmentation task for each separate spot location, both a multithreaded CPU and a graphics processing unit (GPU) implementation were evaluated.

Original languageEnglish
Pages (from-to)138-145
Number of pages8
JournalIEEE Transactions on Nanobioscience
Issue number1
Publication statusPublished - Jan 2015
Externally publishedYes


  • Algorithms
  • Image Processing, Computer-Assisted
  • Oligonucleotide Array Sequence Analysis
  • Journal Article


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