Quadtree

A quadtree is a geometric data structure for storing points in two-dimensional space

R-tree

R-Tree is a popular index structure for spatial data, stored as Minimum Bounding Rectangles (MBRs).

Better perfomance r-tree

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"If you can use a database you can use the point datatype or you can write your own r-tree;when you have many overlapping pins maybe a quadtree from question Creating Map from scanned image |

"You can also try a quadtree it has some from question Optimizing search through large list of lat/long coords to find match |

Indexes faster nearest

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"Quadtree indexes are created from question R-Tree and Quadtree Comparison "R-tree are much from question R-Tree and Quadtree Comparison |

Others

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A quadtree is a from question Find nearest edge in graph |

R-tree are substantially from question R-Tree and Quadtree Comparison |

I use quadtree from question Spatial index with sum and count for C++ |

On the other hand the wikipedia article on r-tree seems from question What spatial indexing algorithm should I use? |