Automatic analysis of DNA microarray images using mathematical morphology
Automatic analysis of DNA microarray images using mathematical morphology
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DOI：
10.1093/bioinformatics/btg057
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发表时间：
2003-03-22
期刊：
影响因子：
5.8
通讯作者：
Serra, J
中科院分区：
文献类型：
--
作者：
Angulo, J;Serra, J
动机：DNA微阵列是一项实验技术，它由数千个离散的DNA序列组成的阵列，这些序列打印在玻璃显微镜载玻片上。图像分析是基因芯片实验的一个重要方面。这一步骤的目的是将斑点的图像缩减到表格中，并测量每个斑点的强度。为了将这项技术应用于实验室工作，高效、准确和自动化的DNA斑点图像分析是必不可少的。结果：我们提出了一套无监督的自动算法，利用对强度变化和伪影都具有鲁棒性的形态算子从DNA微阵列中快速、准确地提取斑点数据。这种方法可以概括为以下几点。最初，网格化算法产生自动分割成点象限的微阵列图像，这些点象限稍后被单独分析。然后分五步完成对SPOT象限图像的分析。首先对光斑进行预量化，计算出光斑尺寸分布规律。其次，使用按区域的形态滤波来执行背景噪声提取。第三，正交格网提供了获得光斑轨迹的第一种方法。第四，利用分水岭变换进行斑点分割或斑点边界定义。第五，检测光斑的轮廓允许信号量化或光斑强度提取；在这方面，研究了噪声模型。该算法已经与ScanAlyze和Genepix两个软件包进行了性能比较，显示了其稳健性和精确度。
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 prequantification, 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.