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Why do indices and coordinates have to be different? Just use the x,y coordinates as your indices. Unless there is some issue like your coordinates can be negative or something.

So the array itself is a representation of the image. One array dimension for each dimension of the image and the value is the color of the pixes.

This will work as i stated in my original post....

That sounds more like what Norm was talking about. One big array where each position represents one pixel then each has a small array of x,y,z coordinates.

Do they need to be in a particular...

Interesting take Norm. I guess we need the question answered...

Are you looking for "an array to hold x,y,z positions" or "a 3D array holding data at position x,y,z"?

This is how it would work