If you want to use scatter3, you can pass it your x, y, and z vectors which will define where markers will be drawn. Then your temperature data can be used to control the size and/or color of the markers. According to your description, x, y, and z are vectors whereas Temperature is a 3D array. That seems slightly odd, but I suppose plausible. At any rate, you'd need to at least convert that 3D array into a vector before passing it to scatter3: scatter3( x, y, z, [], Temperature(:) );
That makes some assumptions about how the data is actually stored, but it's a best guess based on the information you've given.
If you have a lot of data points, then scatter3 isn't the best option.
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