How do I convert a 3D matrix with data to a 3D coordinate system?

I have a 3D array with intensity values inside of each cell representing a simulation previously conducted. When I perform an imagesc, there is a distinct ellipsoid pattern in my data. My question is: how can I convert all the information stored in the 3D matrix to a 3D coordinate system that has points where the ellipsoid resides in space? Thanks.

[Walter Roberson]

How did you imagesc() a 3D array, unless it just happened to have a third dimension of 3 and so would have been interpreted as an RGB array? imagesc() can only be used on arrays that are either 2 dimensions or are of length 3 in the third dimension.