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Yes, the correction factor n2/n1 is sufficient for most cases.
(n2 = RI of the sample; n1 = RI of the objective's immersion medium)
There is some residual error in this calculation. If you wanted to be really 
precise, look at this paper: 	Kuypers, L.C., W.F. Decraemer, J.J. Dirckx, and 
J.P. Timmermans, A procedure to determine the correct thickness of an 
object with confocal microscopy in case of refractive index mismatch. J 
Microsc, 2005. 218(Pt 1): p. 68-78.

I have not used Zeiss confocals much in last 20 years, but remember that 
when I worked with Zeiss LSM 10 (yes, before LSM 310 or 210) it actually 
had this correction implemented when you did Z-scans and depth profiling.  

Stan Vitha
Microscopy and Imaging Center
Texas A&M University


On Tue, 5 Apr 2016 20:44:51 +0000, Moulding, Dale 
<[log in to unmask]> wrote:

>Hi Michael,
>Is it just needing correction for refractive index? 660um imaged through 
the glass will be 660 x 1.51 to give the expected 1mm (air to glass RI 
mismatch) and a 1.31 air to water correction in the other set up?
>Cheers
>Dale
>
>
>On 5 Apr 2016, at 21:15, Cammer, Michael 
<[log in to unmask]<mailto:[log in to unmask]>
> wrote:

>
>A few weeks ago there was a discussion here about measuring depth by 
reflectance.
>
>We had a similar issue.  Yes there are "ghost" reflections as we moved 
away from the glass surfaces, but we expected these because of the 3D 
nature of diffraction patterns.
>
>The bigger problem was that the answers we were getting for depth 
measurements were unexpectedly small.
>
>A user came in to image a home built chamber with a glass face.  The 
results we were getting for depth seemed too small.  Therefore, we made a 
chamber with cut glass slides to check this.  A description with pictures etc 
is at http://microscopynotes.com/710/10X_cal_issue/index.html , but here 
is the short version:
>
>When imaged through the glass slide to the coverslip we got the same 
results as imaging through the coverslip to the slide.
>
>When imaging through air or dilute water based dye, we got the same 
results.
>
>My conclusion is that there is a calibration constant off somewhere in the 
confocal system; it's probably just a software problem.
>
>Next call:  Zeiss service.
>
>Regards,
>Michael
>