A fully automatic gridding method for cDNA microarray images

BMC Bioinformatics

Research Article

Luis Rueda¹  Iman Rezaeian¹ 

[1] School of Computer Science, University of Windsor, 401 Sunset Avenue, N9B 3P4, Windsor, Ontario, Canada;

关键词: Radon;    Refinement Procedure;    Correct Number;    Dilution Step;    Spot Detection;   

DOI  :  10.1186/1471-2105-12-113

 received in 2010-09-17, accepted in 2011-04-21,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundProcessing cDNA microarray images is a crucial step in gene expression analysis, since any errors in early stages affect subsequent steps, leading to possibly erroneous biological conclusions. When processing the underlying images, accurately separating the sub-grids and spots is extremely important for subsequent steps that include segmentation, quantification, normalization and clustering.ResultsWe propose a parameterless and fully automatic approach that first detects the sub-grids given the entire microarray image, and then detects the locations of the spots in each sub-grid. The approach, first, detects and corrects rotations in the images by applying an affine transformation, followed by a polynomial-time optimal multi-level thresholding algorithm used to find the positions of the sub-grids in the image and the positions of the spots in each sub-grid. Additionally, a new validity index is proposed in order to find the correct number of sub-grids in the image, and the correct number of spots in each sub-grid. Moreover, a refinement procedure is used to correct possible misalignments and increase the accuracy of the method.ConclusionsExtensive experiments on real-life microarray images and a comparison to other methods show that the proposed method performs these tasks fully automatically and with a very high degree of accuracy. Moreover, unlike previous methods, the proposed approach can be used in various type of microarray images with different resolutions and spot sizes and does not need any parameter to be adjusted.

【 授权许可】

CC BY   
© Rueda and Rezaeian; licensee BioMed Central Ltd. 2011