A new method for gridding DNA microarrays

作者：Charalambous Christoforos C; Matsopoulos George K^*

来源：Computers in Biology and Medicine, 2013, 43(10): 1303-1312.

DOI：10.1016/j.compbiomed.2013.06.005

• DNA microarrays
• Distortion
• Image processing
• Gridding
• Alignment
• Template matching
• Correlation coefficients
• Spots detection

In this paper, a new methodological scheme for the gridding of DNA microarrays is proposed. The scheme composes of a series of processes applied sequentially. Each DNA microarray image is pre-processed to remove any noise and the center of each spot is detected using a template matching algorithm. Then, an initial gridding is automatically placed on the DNA microarray image by %26apos;building%26apos; rectangular pyramids around the detected spots%26apos; centers. The gridlines %26quot;move%26quot; between the pyramids, horizontally and vertically, forming this initial grid. Furthermore, a refinement process is applied composing of a five-step approach in order to correct gridding imperfections caused by its initial placement, both in non-spot cases and in more than one spot enclosure cases. The proposed gridding scheme is applied on DNA microarray images under known transformations and on real-world DNA data. Its performance is compared against the projection pursuit method, which is often used due to its speed and simplicity, as well as against a state-of-the-art method, the Optimal Multi-level Thresholding Gridding (OMTG). According to the obtained results, the proposed gridding scheme outperforms both methods, qualitatively and quantitatively.

• 出版日期2013-10-1