free open source deconvolution

[nikhil]

Hi,

     i need to do a 3-d deconvolution of stacks of fluorescence widefield images,   apart from deconvolution lab by EPFL is there any open source package available  for deconvolution ? Is it possible to write the some algorithms like richardson lucy in matlab for doing 3-d deconvolution ?

[Joel Sheffield]

I have been impressed by the plugins that Bob Dougherty has written --one
generates a theoretical PSF, and the other carries out iterative
deconvolution.  You can find them on the IJ website under his name.  or,
follow this link:  http://www.optinav.com/imagej.html

Joel



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Wed, Feb 25, 2015 at 11:24 PM, nikhil <[hidden email]> wrote:

> Hi,
>
>      i need to do a 3-d deconvolution of stacks of fluorescence widefield
> images,   apart from deconvolution lab by EPFL is there any open source
> package available  for deconvolution ? Is it possible to write the some
> algorithms like richardson lucy in matlab for doing 3-d deconvolution ?
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/free-open-source-deconvolution-tp5011779.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[G. Esteban Fernandez]

I tested all the decon plugins and options available for ImageJ 1-2
years ago and, in my hands for my particular application, Piotr
Wendykier's Parallel Iterative Deconvolution plugin with the WPL
option and a measured PSF worked best
(https://sites.google.com/site/piotrwendykier/software/deconvolution/paralleliterativedeconvolution).
With that I routinely deconvolve 3D+time data taken through a 20x/0.4
LWD lens using a measured PSF cropped to 64x64x123.

AutoQuant AutoDeblur blind decon was better in my tests but it costs
money.  MIPAV is free and apparently employs the same or a similar
blind decon algorithm
(http://mipav.cit.nih.gov/pubwiki/index.php/Microscopy:_Blind_Deconvolution)
but I remember that back then I couldn't get it to run.  I have a
better computer now; I should try MIPAV again....

-Esteban

On Wed, Feb 25, 2015 at 8:48 PM, JOEL B. SHEFFIELD <[hidden email]> wrote:

> I have been impressed by the plugins that Bob Dougherty has written --one
> generates a theoretical PSF, and the other carries out iterative
> deconvolution.  You can find them on the IJ website under his name.  or,
> follow this link:  http://www.optinav.com/imagej.html
>
> Joel
>
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*
>
> On Wed, Feb 25, 2015 at 11:24 PM, nikhil <[hidden email]> wrote:
>
>> Hi,
>>
>>      i need to do a 3-d deconvolution of stacks of fluorescence widefield
>> images,   apart from deconvolution lab by EPFL is there any open source
>> package available  for deconvolution ? Is it possible to write the some
>> algorithms like richardson lucy in matlab for doing 3-d deconvolution ?
>>
>>
>>
>> --
>> View this message in context:
>> http://imagej.1557.x6.nabble.com/free-open-source-deconvolution-tp5011779.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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