Skip to Main content Skip to Navigation
Journal articles

Polar Modelling And Segmentation Of Genomic Microarray Spots Using Mathematical Morphology

Abstract : Robust image analysis of spots in microarrays (quality control + spot segmentation + quantification) is a requirement for automated software which is of fundamental importance for a high-throughput analysis of genomics microarray-based data. This paper deals with the development of model-based image processing algorithms for qualifying/segmenting/quantifying adaptively each spot according to its morphology. A series of morphologicalmodels for spot intensities are introduced. The spot typologies representmost of the possible qualitative cases identified from a large database (different routines, techniques, etc.). Then, based on these spot models, a classification framework has been developed. The spot feature extraction and classification (without segmenting) is based on converting the spot image to polar coordinates and, after computing the radial/angular projections, the calculation of granulometric curves and derived parameters from these projections. Spot contour segmentation can also be solved by working in polar coordinates, calculating the up/downminimal path, which is easily obtained with the generalized distance function. With this model-based technique, the segmentation can be regularised by controlling different elements of the algorithm. According to the spot typology (e.g., doughnut-like or egg-like spots), several minimal paths can be computed to obtain a multi-region segmentation. Moreover, this segmentation is more robust and sensible to weak spots, improving the previous approaches.
Document type :
Journal articles
Complete list of metadata

Cited literature [22 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-00830720
Contributor : Bibliothèque MINES ParisTech Connect in order to contact the contributor
Submitted on : Thursday, June 6, 2013 - 8:49:39 AM
Last modification on : Tuesday, June 21, 2022 - 1:00:20 PM
Long-term archiving on: : Saturday, September 7, 2013 - 4:08:18 AM

File

836-840-1-PB.pdf
Publisher files allowed on an open archive

Identifiers

Citation

Jesus Angulo. Polar Modelling And Segmentation Of Genomic Microarray Spots Using Mathematical Morphology. Image Analysis & Stereology, International Society for Stereology, 2008, 27 (2), pp.107-124. ⟨10.5566/ias.v27.p107-124⟩. ⟨hal-00830720⟩

Share

Metrics

Record views

2863

Files downloads

75