Re: 3D structured illumination microscopy with an axially moving illumination pattern

Posted by Andrew York on
URL: http://confocal-microscopy-list.275.s1.nabble.com/3D-structured-illumination-microscopy-with-an-axially-moving-illumination-pattern-tp7587343p7587345.html

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Seems like a good opportunity to mention SIM fusion via iterative
deconvolution. It's a very different way of thinking about the problem
compared to Mats's elegant Fourier theory, but it has the advantage that it
doesn't really care what illumination you use, so it's very easy to adapt
to different schemes, including the case of illumination that doesn't
follow the objective.

I wrote up a simple demo to show what I mean:
https://goo.gl/DKaFM3

Let me know if the code and images make sense, and let me know if you spot
any errors.

On Mon, Sep 25, 2017 at 10:45 AM, Reto Fiolka <
[hidden email]> wrote:

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>
> Dear Thomas
>
> If the axial pattern is fixed to the sample, then its "sidebands" need to
> be actively unmixed, i.e. you need additional phase steps along the axial
> pattern orientation and you would need to solve the algebraic equation
> system and move the sidebands to their true location in Fourier space
> numerically.
>
> You can think of it as the same as 2D SIM (phase stepping, unmixing,
> shifting), now just applied to all three dimensions. Therefore all
> information gets passed through the conventional, widefield 3D OTF. This
> means that 3D Nyquist sampling for conventional 3D microscopy is sufficient
> for the raw data. In normal 3D SIM with axial self modulation, you already
> have to apply a higher axial sampling for the final SIM resolution.
>
> You are correct that for Sara's Multifocus SIM you would need axial phase
> steps to unmix the axial information components. A conventional grating
> based setup can not do that (it would need to shift the grating axially
> over large distances in image space or have a phase shifting element for
> the zero diffraction order). Therefore a proper 3D reconstruction was not
> attempted in that work.
>
> Such a system has to my best knowledge not been realized yet, but would
> unlock the full potential of multifocus 3D SIM.
>
> Reto
>
> PS: an interesting situation occurs if you shift the axial illumination
> pattern at a different rate than you make z steps in a normal 3D SIM
> microscope. The axial information, while being the same Fourier
> coefficients, would be shifted to other areas in 3D Fourier space than what
> the normal self demodulation would do.
>