PSF into 5 Seidel Aberrations

[Volodymyr Nechyporuk-Zloy]

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Dear Colleagues,

Assuming we have z-stack of 100 beads (200 nm in diameter), how can we
obtain decomposition of PSF into 5 Seidel Aberrations? Is it possible to do
this in ImageJ or Matlab? Can we generate statistics, e.g. standard
deviation of parameters?

Best regards,
Volodymyr

--
Dr. Volodymyr Nechyporuk-Zloy (Imaging Facility Manager)

The Kennedy Institute of RheumatologyUniversity of Oxford, Roosevelt Drive,
Headington, Oxford, OX3 7FY, United Kingdom


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[Reto Fiolka]

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Hi Volodymyr

A common way is to determine the pupil function via phase retrieval from your PSF data.

See Hanser and Gustafsson:

Hanser, B. M., et al. "Phaseretrieved pupil functions in widefield fluorescence
microscopy." Journal of microscopy 216.1 (2004): 32-48.

or

Hanser, Bridget M., et al. "Phase retrieval for high-numerical-aperture optical systems."
Optics letters 28.10 (2003): 801-803.

Phase retrieval is pretty well accepted and I know of groups who used it to characterize
their microscope or determine the influence matrix of an adaptive optics system.

Once you retrieved the pupil function, you can decompose the phase into your basis
function of choice.

I have never used Seidel functions, but Zernike modes are pretty easy to determine with
a function like fminsearch in Matlab. (I would use Matlab for phase retrieval and
decomposition).

Best,
Reto

[Kyle Michael Douglass]

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Hi Volodymyr,
I have also used Hanser's phase retrieval method to calculate
aberrations in the pupil function from intensity stacks and found that
it works reasonably well.

Keep in mind that the 2003 paper is based on scalar diffraction theory.
If you need vector diffraction, you can use the method described in
Hanser's 2004 paper. Someone recently pointed out to me that there is
code freely available to do the vector diffraction calculations, though
I have not personally tried it myself. The address is here:
http://www.nijboerzernike.nl/

Cheers,
Kyle

On 12/07/2015 08:39 PM, Reto Fiolka wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Volodymyr
>
> A common way is to determine the pupil function via phase retrieval from your PSF data.
>
> See Hanser and Gustafsson:
>
> Hanser, B. M., et al. "Phaseretrieved pupil functions in widefield fluorescence
> microscopy." Journal of microscopy 216.1 (2004): 32-48.
>
> or
>
> Hanser, Bridget M., et al. "Phase retrieval for high-numerical-aperture optical systems."
> Optics letters 28.10 (2003): 801-803.
>
> Phase retrieval is pretty well accepted and I know of groups who used it to characterize
> their microscope or determine the influence matrix of an adaptive optics system.
>
> Once you retrieved the pupil function, you can decompose the phase into your basis
> function of choice.
>
> I have never used Seidel functions, but Zernike modes are pretty easy to determine with
> a function like fminsearch in Matlab. (I would use Matlab for phase retrieval and
> decomposition).
>
> Best,
> Reto

--
Kyle M. Douglass, PhD
Post-doctoral researcher
The Laboratory of Experimental Biophysics
EPFL, Lausanne, Switzerland
http://kmdouglass.github.io
http://leb.epfl.ch

[Volodymyr Nechyporuk-Zloy]

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Dear Reto and Kyle,

Thank you very much for the suggestions.

Best regards,
Volodymyr