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There are a couple of versions of this tool. If you use the one from the Processing Toolbox, it will contain distances within the origin points. Instead, use the Distance Matrix tool from the menubar: Vector > Analysis Tools > Distance Matrix This version ignores calculating the distance of the origin points with itself.


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Use the polygon neighbors tool to identify neighbouring cells. The output is a table that lists out all neighbours for each polygon in the input feature class. Relate the output table with the original shapefile using polygon/cell id. When you select a cell with points, you can then easily find its neighbours.



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