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Thanks for your persistence in finding a reference Kevin.  I read that
chapter in Pawley early on but didn't see any formulas that I could
quickly use to get numbers for my particular application.

One paper that presents z correction models that I was able to follow
and make an Excel spreadsheet for is:

van Elburg et al. (2007)  Improved correction of axial geometrical
distortion in index-mismatched fluorescent confocal microscopic images
using high-aperture objective lenses.  J. Microscopy 228(1):45-54.

They used "rigorous electromagnetic diffraction theory" to generate
numerical data (as in Egner and Hell's chapter in Pawley) and present
linear and non-linear models, trimmed down to relatively simple
equations, that fit the numbers.  They don't actually present the
rigours of the EM theory, so my mathematically simple mind wasn't
confused.  I don't have the expertise (or time!) to evaulate how good
their models are, but their equations in my spreadsheet churned out
numbers that agree with Table 20.2 and Fig. 20.10 in Pawley's book.
The corrected z-stacks gave results that my user says seem accurate.

If someone ever reads this post who knows more about the paper above
some feedback would be appreciated.

Esteban


On Feb 19, 2008 1:35 AM, Kevin Braeckmans <[log in to unmask]> wrote:
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>
>
>
> Dear all,
>
>
>
> For those interested, a rigorous treatment of how to correct for
> z-measurements in case of a mismatch in refractive indices can be found in
> the Handbook by Pawley, 3rd edition, chapter 20 by Egner and Hell. (I
> believe this chapter is also in the 2nd edition of the Handbook).
>
>
>
> With regard to Esteban's situation (see thread 'How to correct z distance in
> RI mismatch'), yesterday I gave the suggestion to use the geometrical
> formula for an effective NA of approx. 1 (i.e. half the illumination light
> cone). Comparing this with the values reported in table 2 of the chapter by
> Egner and Esteban, a reasonable correspondence is found for a focus depth of
> 15 to 20 micron (less than a micron difference). After that the geometrical
> formula (with adjusted effective NA) does not give an adequate prediction
> anymore. In any case, in this chapter you can find everything needed for
> accurate calculations.
>
>
>
> Best regards,
>
>
>
> Kevin
>
>
>
> Kevin Braeckmans, Ph.D.
>
> Lab. General Biochemistry and Physical Pharmacy
>
> Ghent University
>
> Harelbekestraat 72
>
> 9000 Ghent
>
> Belgium
>
> Tel: +32 (0)9 264.80.78
>
> Fax: +32 (0)9 264.81.89



-- 
G. Esteban Fernandez, Ph.D.
Associate Director
Molecular Cytology Research Core Facility
University of Missouri
1201 E. Rollins St.
Columbia, MO  65211

573-882-4895
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http://www.biotech.missouri.edu/mcc/