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 ...
Classification of Grid Alignment Methods There are two views on microarray grid alignment: • Automation of methods: — Manual (a grid template of spots is manually adjusted) — Semi-automated (manual grid initialization followed by automated refinement) — Fully automated (data driven without any human intervention based on one-time human setup) • Image analysis approach: — Template-based — Data-driven — Affymetrix chips (special case) 30
31 Microarray Grid Alignment: Previous Work Approaches: • The Affymetrix chips approach – — Pros: the alignment problem was simplified and hence the grid alignment became more accurate. — Cons: the Affymetrix technology has been much more expensive than the technology with coated glass slides. • Template-based approach: the most prevalent in existing software packages, e.g., GenePix Pro by Axon Instruments, ScanAlyze or GridOnArray by Scanalytics. — Pros: Incorporates knowledge about ideal grid — Cons: manual alignment • Data-driven approach: — image segmentation — statistical analysis of 1D image projections. — Pros: automatic alignment — Cons: accuracy and robustness, e.g., missing spots, noise
- 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: Grid Alignment: Application Domains
- 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
Classific<strong>at</strong>ion <strong>of</strong> Grid Alignment Methods<br />
There are two views on microarray grid alignment:<br />
• Autom<strong>at</strong>ion <strong>of</strong> methods:<br />
— Manual (a grid templ<strong>at</strong>e <strong>of</strong> spots is manually adjusted)<br />
— Semi-autom<strong>at</strong>ed (manual grid initializ<strong>at</strong>ion followed by<br />
autom<strong>at</strong>ed refinement)<br />
— Fully autom<strong>at</strong>ed (d<strong>at</strong>a driven without any human<br />
intervention based on one-time human setup)<br />
• <strong>Image</strong> analysis approach:<br />
— Templ<strong>at</strong>e-based<br />
— D<strong>at</strong>a-driven<br />
— Affymetrix chips (special case)<br />
30
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