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Re: Deconvolution advice

Posted by Lutz Schaefer on Oct 02, 2012; 4:40pm
URL: http://confocal-microscopy-list.275.s1.nabble.com/Deconvolution-advice-tp7579090p7579109.html

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Hello all,

Jay is correct, a regularized inverse filter of the separated (shifted)
orders can be used followed by magnitude (and/or linear) reconstruction. To
the best of my knowledge, this principle is implemented in the Zeiss ZEN and
AxioVision software. It is also possible to use a Gauss likelihood iterative
algorithm, but to no advantage as the extracted orders cannot be constrained
to positivity.
A realization of Poisson likelihood will, as Jay says proof difficult, owing
to its inherent nonlinearity.

Best Regards
Lutz

__________________________________
L u t z   S c h a e f e r
Sen. Scientist
Mathematical modeling / Image processing
Advanced Imaging Methodology Consultation
16-715 Doon Village Rd.
Kitchener, ON, N2P 2A2, Canada
Phone/Fax: +1 519 894 8870
Email:     [hidden email]
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--------------------------------------------------
From: "Unruh, Jay" <[hidden email]>
Sent: Tuesday, October 02, 2012 10:17
To: <[hidden email]>
Subject: Re: Deconvolution advice

> *****
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>
> Hi all,
>
> Deconvolution for SIM is a very different story than for other techniques.
> SIM by default uses an inverse filter in its reconstruction to recombine
> the shifted components of the fourier transform without enhancing the high
> frequency noise.  Typical SIM software has a noise parameter for the
> wiener filter.  If you set this filter low, you start to see a rippling
> pattern in the noise and eventually in the high signal regions.  As far as
> I can tell, no one has tried to use more advanced (poisson noise driven)
> algorithms for this problem.
>
> If one assumes that Autoquant is using some variant of the algorithm shown
> in Tim Holmes' Handbook of Biological Confocal  chapter, then this
> algorithm is not immediately applicable to the SIM problem.  The algorithm
> update function involves dividing the original image by the convolved
> object guess and then convolving that ratio with the reflected psf and
> finally multiplying by the object guess.  Given that the raw SIM image is
> actually a frequency modulated image in a particular direction, it is not
> clear how the original ratio would be generated.  Richardson-Lucy has a
> similar problem.  Would you deconvolve before reconstructing?  This is the
> only circumstance under which the noise could be considered poisson.  In
> that case, can the original PSF be used?  I'm not entirely certain that
> the deconvolution would preserve the frequency modulation in the image.
> In addition, the original reconstruction algorithm would require a second
> step of deconvolution during the reconstruction step--not sure how the
> noise parameter should be chosen after initial deconvolution.
>
> Jay
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Gitta Hamel
> Sent: Monday, October 01, 2012 8:42 AM
> To: [hidden email]
> Subject: Re: Deconvolution advice
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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>
> **commercial response**
>
>
> Hello Andrew,
>
> It's fully understandable that people want to know the scientific grounds
> when using Huygens.
>
> For the full list of articles I refer to
> http://www.svi.nl/HuygensReferences at which the relevant papers are at
> the bottom of the page and mostly written during the years 1996-1998.
> There are much more articles that ought to be included so your question
> shows that we must give more attention to this topic.
>
> With best wishes,
>
> Gitta Hamel
>
> ****************************************
> Gitta Hamel
> Managing Director Scientific Volume Imaging bv Developers of the *HUYGENS*
> software The Netherlands
> phone: ++ 31 35 6 42 16 26
> *****************************************
>
>
> ^SVI Customer support: mail us your questions [hidden email]
> <mailto:[hidden email]>or find answers online in our Huygens
> WIKI:www.svi.nl/FrontPage <http://%20www.svi.nl/FrontPage>
>
>
>
> On 09/29/2012 04:00 PM, Gens, John Scott wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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>>
>> Andrew-
>>
>> You might want to get in touch with Jim McNally.  Last I heard he was
>> at NIH-NCI.
>>
>> Some of his older papers on deconvoltion algorithms are below, but he
>> can probably point you towards more recent information.
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/10579932
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/11541650   ( in particular, fig.2
>> compared  a 3D image processed by three different algorithms)
>>
>>
>> Quoting Andrew York <[hidden email]>:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Hello, I'm looking for advice and information about deconvolution,
>>> especially from those with first-hand experience.
>>>
>>> Traditionally, one of the processing steps in structured illumination
>>> microscopy is deconvolution. For our SIM, we decided to use an
>>> open-source
>>> solution:
>>> https://sites.google.com/site/piotrwendykier/software/deconvolution/p
>>> aralleliterativedeconvolution
>>>
>>>
>>> This seemed like a nice tradeoff between reinventing the wheel with
>>> our own deconvolution code, and subjecting ourselves to a 'black box'
>>> closed-source
>>> solution. However, we've recently tried out the Huygens deconvolution
>>> software, and the results seem quite promising, possibly an
>>> improvement over other methods we've tried. I like good images, but I
>>> don't like black boxes, and I like to understand my data processing.
>>>
>>> 1. Is the exact algorithm used in Huygens transparently documented
>>> anywhere? I spent a few hours searching today, but if it's out there,
>>> I missed it.
>>>
>>> 2. Is there a clear winner for deconvolution algorithms? What should
>>> I be using?
>>>
>>> 3. Are there other deconvolution software packages I should consider?
>>> Ideally I'm looking for software based on clearly-documented algorithms.
>>>
>>> Thanks for the help.
>>>
>>> -Andrew York
>>> NIH/NIBIB
>>>
>>
>
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