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Table of contents
Minimum Spanning Tree Gridding
1: Microarrays (biochips) and Gridding
Canonical Rectangular Microarray
Slide 4
Gridding Some Array/Image Quality Issues
2: Standard Gridding Techniques
Standard Gridding Techniques Spot finding / Centroiding
Standard Gridding Techniques FFT Rotation Determination
Weighted Normalized Cross Correlation WNCC
Standard Gridding Methods “Auto” Correlation
Standard Gridding Methods Fiducial-Less gridding (Radon Xform)
Standard Gridding Methods Gridding Microarrays With Fiducials
Gridding Warped Arrays Graph based Gridding When standard gridding techniques won’t do
MST Gridder A problematic Array
Noob’s Gridder Simple Raster Scan
Connected Component Gridding Def:Graph and Connected Component
Connected Component Gridding Grid as a graph between found spots
Connected Component Gridding The “Flood Fill” Gridder
Connected Component Gridding Breadth First Graph Traversal & Gridder
Connected Component Gridding Graph Breadth First Grid: The Movie
MST Gridding
MST Gridder Quality of edges matters
MST Gridder Def: Spanning Tree (ST)
MST Gridder Def: Minimum Spanning Tree (MST)
MST Gridder Kruskal’s Algorithm
MST Gridder Kruskal’s Algorithm Example
MST Gridding Edge creation from centroids for Kruskal
MST Gridding All Together: Edges To Grid
1) 4 connected weighted edges Input to Kruskal MST Algorithm
2) MST Gridding MST by Kruskal Algorithm: The Movie
3&4) MST Gridding Breadth First MST Gridding: The Movie
MST Gridding Post Processing
MST Gridder Warped Array Result: Example 2
MST Gridder Warped Array Result: Example 3
MST Gridder Warped Array Result: Example 4
MST Gridder Warped Array Result: Example 5
MST Gridder Acre (sub-grid) format (overkill)