03%20image%20proc%201_22_08

03%20image%20proc%201_22_08 - A microarray scanner creates...

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1 1 The Basics of Microarray Image Processing 1/22/2008 2 A microarray scanner creates a digital image of a microarray. ± A digital image is a rectangular array of intensity values. ± Each intensity value corresponds to a pixel . ± The color depth of an image is the number of bits used to store the intensity value of one pixel. ± A color depth of 16 bits/pixel (common for microarray scanners) means that the intensity value of each pixel will be an integer between 0 and 65,535 = 2 16 –1 . ± The number of pixels contained in the digital image is called the resolution . 3 Color Depth=6 Resolution=128 x 128 4 Color Depth=2 Resolution=128 x 128 5 Color Depth=6 Resolution=32 x 32 6 Color Depth=2
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2 7 Image processing for spotted arrays (cDNA and spotted oligo) can be divided into four basic steps: 1. Array localization – find the spots 2. Image segmentation – categorize each pixel as spot signal, background, or other 3. Quantification – assign signal and background values to each spot 4. Spot quality assessment – compute measures of spot quality for each spot Image Processing for Spotted Arrays 8 Image Processing for Spotted Arrays ± These steps are typically carried out with the aid of specialized software and can involve varying degrees of human input. 9
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03%20image%20proc%201_22_08 - A microarray scanner creates...

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