Usually the software knows the z-step and the x-y resolution and tries to match
them either by interpolating the z-planes of by subsampling the x-y planes.
Our Biorad MRC-600 does the latter.  However, still the PSFs are elongated.
 
We believe this is due to 2 reasons:
The first is that the refractive index is not perfectly matched so the actual s
specimen is smaller than the intended.  This will elongate the object.  Put you
 
The second reason is not that the resolutions are not the same (if you
interpolate properly the can become) but because a confocal microscope
is not perfectly confocal.  A way to check this is to see that the
elongation depends on the size of the apeture in front of the sensor.
if you acquire the PSF of a non-confocal system is not only very
elongated but also has the characteristic ripples which in a confocal
simply do not go through.
 
 
Stamatis Pagakis
Bioengineering
UC davis