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 ...
34 Grid Alignment Requirements Ideal grid alignment algorithm: • Finds irregularly row- and column-spaced 2D arrays with translational and rotational offsets. • Motivation: The dipping pins bend over time and cause irregularity in a 2D arrangement of the printed spots. Any rotational offset of a slide or dipping pins will cause a rotated 2D grid in a microarray image with respect to the image edge. • Performs alignment on images with any number of input channels. • Motivation: Many image acquisition types. • Is color and spot size independent. • Motivation: Many image acquisition types (color). Preparation steps (spot size). • Is independent of any chosen primitive shape. • Motivation: Technology development, e.g., CLONDIAG chip. • Is parameter “free”. • Motivation: Repeatability without any bias and optimal performance. • Accommodates speed versus accuracy tradeoffs. • Motivation: Inspection versus Analysis
35 Grid Alignment Algorithm Overview
- 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 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: Microarray Grid Alignment: Previous
- 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
34<br />
Grid Alignment Requirements<br />
Ideal grid alignment algorithm:<br />
• Finds irregularly row- and column-spaced 2D arrays with transl<strong>at</strong>ional and<br />
rot<strong>at</strong>ional <strong>of</strong>fsets.<br />
• Motiv<strong>at</strong>ion: The dipping pins bend over time and cause irregularity in a 2D<br />
arrangement <strong>of</strong> the printed spots. Any rot<strong>at</strong>ional <strong>of</strong>fset <strong>of</strong> a slide or dipping pins<br />
will cause a rot<strong>at</strong>ed 2D grid in a microarray image with respect to the image<br />
edge.<br />
• Performs alignment on images with any number <strong>of</strong> input channels.<br />
• Motiv<strong>at</strong>ion: Many image acquisition types.<br />
• Is color and spot size independent.<br />
• Motiv<strong>at</strong>ion: Many image acquisition types (color). Prepar<strong>at</strong>ion steps (spot size).<br />
• Is independent <strong>of</strong> any chosen primitive shape.<br />
• Motiv<strong>at</strong>ion: Technology development, e.g., CLONDIAG chip.<br />
• Is parameter “free”.<br />
• Motiv<strong>at</strong>ion: Repe<strong>at</strong>ability without any bias and optimal performance.<br />
• Accommod<strong>at</strong>es speed versus accuracy trade<strong>of</strong>fs.<br />
• Motiv<strong>at</strong>ion: Inspection versus <strong>Analysis</strong>
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