Re: Deconvolution advice

Posted by Gitta Hamel on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Deconvolution-advice-tp7579090p7579105.html

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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

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Managing Director Scientific Volume Imaging bv
Developers of the *HUYGENS* software
The Netherlands
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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 <[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/paralleliterativedeconvolution 
>>
>>
>> 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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