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I have imported all points of interest (POI) from database to TileMill. The distance between the POIs are a few meters. Thats is why its became ugly looking map. Is there any option that will aggregate POIs those are within 100 or 500 meter?

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I think pre-processing your data using a binning technique would result in a neater map. Mapbox has written a straightforward tutorial that will help a lot. Once you go through the data pre-processing, they explain how to take the output and style it in Tilemill.

http://www.mapbox.com/blog/binning-alternative-point-maps/

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