Bioinformatics Vol. 19 no. 5 2003
Pages 553-562
© 2003 Oxford University Press
Automatic analysis of DNA microarray images using mathematical morphology
Centre de Morphologie Mathématique, Ecole des Mines de Paris, 77305 Fontainebleau, France
Received on January 14, 2002
; revised on November 12, 2002
; accepted on November 14, 2002
Motivation: DNA microarrays are an experimental technology which consists in arrays of thousands of discrete DNA sequences that are printed on glass microscope slides. Image analysis is an important aspect of microarray experiments. The aim of this step is to reduce an image of spots into a table with a measure of the intensity for each spot. Efficient, accurate and automatic analysis of DNA spot images is essential in order to use this technology in laboratory routines.
Results: We present an automatic non-supervised set of algorithms for a fast and accurate spot data extraction from DNA microarrays using morphological operators which are robust to both intensity variation and artefacts. The approach can be summarised as follows. Initially, a gridding algorithm yields the automatic segmentation of the microarray image into spot quadrants which are later individually analysed. Then the analysis of the spot quadrant images is achieved in five steps. First, a pre-quantification, the spot size distribution law is calculated. Second, the background noise extraction is performed using a morphological filtering by area. Third, an orthogonal grid provides the first approach to the spot locus. Fourth, the spot segmentation or spot boundaries definition is carried out using the watershed transformation. And fifth, the outline of detected spots allows the signal quantification or spot intensities extraction; in this respect, a noise model has been investigated. The performance of the algorithm has been compared with two packages: ScanAlyze and Genepix, showing its robustness and precision.
Availability: A prototype system integrated in PDI32 (an image processing software for Windows) may be obtained from the authors on request.
Contact: angulo,serra{at}cmm.ensmp.fr
Supplementary Information: http://cmm.ensmp.fr/~angulo/
* To whom correspondence should be addressed.
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