Microarray Scanner Software Design

Gnenchip image acquisition and chip analysis are the key parts of techniques for genechip and play two important roles in the application of genechip. In this paper, first we accomplish how to control the image acquiring system, and recovery the chip image accurately, aiming for the feature of acquiring course. Then we study the methods of image analysis and data analysis in order to extract the hybridizing intensity and retrieve the biological information.In image acquiring system, we can control the scanner automatically, scanning range can be specified by user. In order to resolve the nonlinear distortion occurring in the course of image acquiring, first we apply affme transformation to adjust image, then recovery image by means of linear interleration algorithms.Some factors such as noise from irregular spots, dust on the slide, and nonspecific hybridization make it difficult to extract data accurately. We use fuzzy mathematical morphology to remove noise and dust which can lower noise successfully and also make up a loss of intensity caused by fluorescence blench.To acquire the target region, we purpose automatic gridding method based on image segmentation for image with irregular spots, it's segmentation through threshold. This method is presented simply and fast. However it's not suitable for spots with asymmetrical intensity. As for images with regular spots , a semi-automatic gridding method is used to improve processing speed, and it can achieve good effect.In the extraction of fluorescent intensity, we discuss background removing, the methods of computing and normalization. According to different gridding methods, diverse computing algorithms are adopted to ensure the accuracy of image analysis.We study the data analysis of expression genechip, put emphasis on the visualization of result.Finally we develop two software, one is ArrayScan 1.0, the other is AnaArray 1.0.