Deconvolution Packages

[lechristophe]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear microscopists,

Do anybody have experience on the Deconvolution module offered by
Metamorph Software (Molecular Devices) ? It appears to have two options,
one is blind deconvolution and the other is from a measured PSF. How
about the performance, ease of use, etc ? How does it compare to other
software like Volocity or Huygens ?

Do anybody have a free alternative that I didn't try yet (I know ImageJ
plugins and XCOSM but these are not really usable IMHO...) ?

Thanks for your advices,

Christophe Leterrier

PS/ For commercial replies, I'm in France so be kind enough to tell me
what is your distributor here. Don't hesitate to reply directly to me in
private and send me pdf brochures. Thanks !

[Shalin Mehta]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Hi Christophe,

I am using evaluation versions of Huygen's and Autoquant's X2 now.
 It appears that blind deconvolution and deconvolution with measured PSF work equally well(at least when you are evaluating the algorithms by deconvolving bead images).

 Huygen's allows one to use either theoretical PSF or the measured PSF. I tried deconvolution using measured PSF of spherically aberrated image of beads and symmetry was restored but the noise in the experimental PSF threw up slight artifacts. Autoquant's blind deconvolution worked very well, but their newer version (which seem to have been migrated from earlier platform to .NET) is not that stable in terms of user interface.

I am also curious about  objective ways of comparing deconvolution algorithms when working with real samples.

Cheers,
Shalin

On 10/3/07, Christophe Leterrier <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear microscopists,

Do anybody have experience on the Deconvolution module offered by
Metamorph Software (Molecular Devices) ? It appears to have two options,
one is blind deconvolution and the other is from a measured PSF. How
about the performance, ease of use, etc ? How does it compare to other
software like Volocity or Huygens ?

Do anybody have a free alternative that I didn't try yet (I know ImageJ
plugins and XCOSM but these are not really usable IMHO...) ?

Thanks for your advices,

Christophe Leterrier

PS/ For commercial replies, I'm in France so be kind enough to tell me
what is your distributor here. Don't hesitate to reply directly to me in
private and send me pdf brochures. Thanks !

--
My co-ordinates:
Shalin Mehta, Graduate student
Graduate Programme in Bioengineering, NUS, Singapore
Email: shalin {dot} mehta {at} gmail {dot} com
Blog: electricsbm.blogspot.com
Mobile: [phone]

[Glen MacDonald-2]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

On Oct 3, 2007, at 3:51 AM, Shalin Mehta wrote:
> Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi- 
> bin/wa?S1=confocal Hi Christophe,
>
> I am using evaluation versions of Huygen's and Autoquant's X2 now.
>  It appears that blind deconvolution and deconvolution with  
> measured PSF work equally well(at least when you are evaluating the  
> algorithms by deconvolving bead images).
>
How did you estimate the SNR?  I find that this is an important  
parameter for Huygens.  The blind approaches may be calculating this  
behind the scenes, but I've seen them struggle with very high SNR and  
with very low SNR samples.  SVI suggests several means of doing the  
estimation.  One useful estimate is to take the square root of the  
quotient from dividing the minimum or average of a background region  
into the mean of a region containing signal.
>  Huygen's allows one to use either theoretical PSF or the measured  
> PSF. I tried deconvolution using measured PSF of spherically  
> aberrated image of beads and symmetry was restored but the noise in  
> the experimental PSF threw up slight artifacts. Autoquant's blind  
> deconvolution worked very well, but their newer version (which seem  
> to have been migrated from earlier platform to .NET) is not that  
> stable in terms of user interface.
>
try some pre-stained test slides collecting images with a range of  
SNR.  If you work with thick samples such as organ cultures,  
zebrafish or c. elegans then tests must be made with a similar  
sample, preferably using a reproducible (and simple) label.
> I am also curious about  objective ways of comparing deconvolution  
> algorithms when working with real samples.
>
> Cheers,
> Shalin
>

Regards,
Glen



Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]

************************************************************************
******
The box said "Requires WindowsXP or better", so I bought a Macintosh.
************************************************************************
******

> On 10/3/07, Christophe Leterrier <[hidden email]>  
> wrote: Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Dear microscopists,
>
> Do anybody have experience on the Deconvolution module offered by
> Metamorph Software (Molecular Devices) ? It appears to have two  
> options,
> one is blind deconvolution and the other is from a measured PSF. How
> about the performance, ease of use, etc ? How does it compare to other
> software like Volocity or Huygens ?
>
> Do anybody have a free alternative that I didn't try yet (I know  
> ImageJ
> plugins and XCOSM but these are not really usable IMHO...) ?
>
> Thanks for your advices,
>
> Christophe Leterrier
>
> PS/ For commercial replies, I'm in France so be kind enough to tell me
> what is your distributor here. Don't hesitate to reply directly to  
> me in
> private and send me pdf brochures. Thanks !
>
>
>
> --
> My co-ordinates:
> Shalin Mehta, Graduate student
> Graduate Programme in Bioengineering, NUS, Singapore
> Email: shalin {dot} mehta {at} gmail {dot} com
> Blog: electricsbm.blogspot.com
> Mobile: [phone]