DNA Microarray Image Analysis - University of Illinois at Urbana ...

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Microarray Grid Alignment: Objective • The objective of the grid alignment step is to localize a twodimensional (2D) array of spots in a microarray scan before any information is extracted from the spots. • Terminology: A 2D array of spots is also loosely denoted as a grid of spots, while one array of spots among multiple 2D arrays in one microarray scan is often denoted as a block or a sub-array of spots 2D array of spots Sub-array of spots 28
Grid Alignment: Application Domains Application domains for the grid alignment problem: • Animal science and plant science - DNA expression level measurements (Microarray technology) • Chemistry – olfactory sensors based on a number of different chemically responsive dyes deposited on a substrate (e.g., paper, film, silica). The color change of the dyes is determined after exposure to different analytes. The color change after exposure to different analytes can be accurately measured to identify unknown compounds and concentration levels of known compounds. • Crystallography – 2D and 3D structure measurements using X-ray 29
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 and 14: DNA Microarray Image Analysis • T
Page 15 and 16: Ideal Microarray Image? 1. Ideal cD
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: IMAGE ANALYSIS: MICROARRAY GRID ALI
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
Page 65 and 66: Goals and Objectives of Quality Ass
Page 67 and 68: Quality Assessment: Spot Examples
Page 69 and 70: Criteria for Assessing Morphologica
Page 71 and 72: I2K Selecting Valid Pixels - SNR Me
Page 73 and 74: I2K Selecting Valid Pixels - Topolo
Page 75 and 76: 75 MICROARRAY DATA QUANTIFICATION A
Page 77 and 78: Spot Descriptors • Volume of fore
Page 79 and 80:
Visualization of Spot Descriptors S
Page 81 and 82:
Normalization • Normalization usi
Page 83 and 84:
83 MICROARRAY DATA FUSION, ANALYSIS
Page 85 and 86:
Visualization • Data: 3D cubes,di
Page 87 and 88:
Web-Based Documentation 87 http://a
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