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I have geoTIFF raster with cells size 5x5 m in WGS84. I would like to make a point layer with values from raster. I use ArcMap extension: raster to point, but it makes a point net with size 5x~9 m, not each cells centroids. Do you have some idea why?

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You need to transform your data into a projected coordinate system. Then the resolution of the raster will be in the units of your chosen projection and the conversion from raster to point will work.

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