*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

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:[log in to unmask]] On Behalf Of Gitta Hamel
Sent: Monday, October 01, 2012 8:42 AM
To: [log in to unmask]
Subject: Re: Deconvolution advice

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

**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 [log in to unmask] <mailto:[log in to unmask]>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
> *****
>
> 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 <[log in to unmask]>:
>
>> *****
>> 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
>>
>

--
Managing Director

Huygens SVI

tel: +31 (0)35 642 16 26

fax:  +31 (0)35 683 79 71

skype: gittahamel

cell: +31(0)618 021272

Visiting address

Laapersveld 63,
1213 VB Hilversum,
The Netherlands