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Hi Serge,
A while ago I looked in the source code; it appears that the COSM software
(file completeXcosm.cxx) calculates the backprojected pinhole diameter in
mm using this expression
fsize = fsize_/(lm * magY_*1E3) where “fsize_” is the pinhole size in
micrometers entered by the user ("Size" value in the COSM
software), “lm” is lateral magnification of the objective, “magY” is the
magnification of the realy optics in front of the pinhole ("Magnification"
value in the COSM software).
I believe the "Distance" value is relevant only to a spinning disk confocal,
the distance between pinholes.
It was not clear to me whether I should take the shape factor into account
(square pinhole, not circular on most confocals) for PSF generation: either
enter the size reported by the software (length of the square) or calculate a
diameter of a circle of equal area: square pinhole size magnified by 2/sqrt
(PI)?
That's all I have.
I'll be curious to learn more.
Stan Vitha
Microscopy and Imaging Center
Texas A&M University
On Mon, 4 May 2015 16:39:23 -0500, Sergey Tauger
<
[hidden email]> wrote:
>
>Dear All,
>
>There is a whitespace in COSMOS manual on confocal microscope PSF
generation. Could
>somebody please answer these questions:
>1. What are the units of aperture size, dwell distance?
>2. How do distance and magnification correspond to previously defined
values of objective
>magnification and pixel spacing?
>
>Best,
>Serge
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