DNA Microarray Image Analysis - University of Illinois at Urbana ...
DNA Microarray Image Analysis - University of Illinois at Urbana ... DNA Microarray Image Analysis - University of Illinois at Urbana ...
14 MICROARRAY IMAGE PROCESSING REQUIREMENTS
Ideal Microarray Image? 1. Ideal cDNA microarray image in terms of its image content: • Deterministic grid geometry • Known background intensity with zero uncertainty • Pre-defined spot shape (morphology) • Constant spot intensity that (a) is different from the background, (b) is directly proportional to the biological phenomenon (up- or –down-regulation), and (c) has zero uncertainty for all spots. Ideal cDNA microarray image content => utopia 2. Ideal cDNA microarray image in terms of statistical confidence: • A very large number of pixels per spot (theoretically it would reach infinity) Constraints: Cost of experiments, image resolution (scanners), storage of extremely high resolution images and other specimen preparation issues 15
- Page 1 and 2: February 4, 2005 DNA Microarray Ima
- Page 3 and 4: Publications • Journals: — Bajc
- Page 5 and 6: Microarray Problem: Major Objective
- Page 7 and 8: Input and Output of Microarray Data
- Page 9 and 10: Types of Expected Microarray Data M
- Page 11 and 12: 11 Microarray Data Processing Workf
- Page 13: DNA Microarray Image Analysis • T
- Page 17 and 18: Microarray Image Technologies • A
- Page 19 and 20: Variations of Grid Geometry • Rot
- Page 21 and 22: Variation of Spot Morphology • Sp
- Page 23 and 24: Examples: Spatially Varying Backgro
- Page 25 and 26: 25 Examples: Spatial Resolution, Li
- Page 27 and 28: IMAGE ANALYSIS: MICROARRAY GRID ALI
- Page 29 and 30: Grid Alignment: Application Domains
- Page 31 and 32: 31 Microarray Grid Alignment: Previ
- Page 33 and 34: Microarray Grid Alignment: Previous
- Page 35 and 36: 35 Grid Alignment Algorithm Overvie
- Page 37 and 38: Image Down-Sampling • Design of r
- Page 39 and 40: Vertical and Horizontal Line Score
- Page 41 and 42: Optional Regularity Enforcement •
- Page 43 and 44: Processing Multiple Grids Line Disc
- Page 45 and 46: Spot Size & Spot Density 45 •Radi
- Page 47 and 48: Missing Spots The fewer the spots i
- Page 49 and 50: Down-sampling •Experimental resul
- Page 51 and 52: Grid Alignment Properties Color Inv
- Page 53 and 54: Multiple Grids: Semi-Automated vs.
- Page 55 and 56: 55 MICROARRAY FOREGROUND SEPARATION
- Page 57 and 58: Foreground Separation Using Spatial
- Page 59 and 60: Foreground Separation Using Intensi
- Page 61 and 62: Foreground Separation From Multi-Ch
- Page 63 and 64: Step 1: Separating Spots from Backg
Ideal <strong>Microarray</strong> <strong>Image</strong>?<br />
1. Ideal c<strong>DNA</strong> microarray image in terms <strong>of</strong> its image content:<br />
• Deterministic grid geometry<br />
• Known background intensity with zero uncertainty<br />
• Pre-defined spot shape (morphology)<br />
• Constant spot intensity th<strong>at</strong> (a) is different from the<br />
background, (b) is directly proportional to the biological<br />
phenomenon (up- or –down-regul<strong>at</strong>ion), and (c) has zero<br />
uncertainty for all spots.<br />
Ideal c<strong>DNA</strong> microarray image content => utopia<br />
2. Ideal c<strong>DNA</strong> microarray image in terms <strong>of</strong> st<strong>at</strong>istical confidence:<br />
• A very large number <strong>of</strong> pixels per spot (theoretically it would<br />
reach infinity)<br />
Constraints: Cost <strong>of</strong> experiments, image resolution (scanners),<br />
storage <strong>of</strong> extremely high resolution images and other<br />
specimen prepar<strong>at</strong>ion issues<br />
15
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