Re: Parallel Spectral Deconvolution plugin update

Posted by Justin McGrath on Jan 07, 2008; 7:48pm
URL: http://imagej.273.s1.nabble.com/Parallel-Spectral-Deconvolution-plugin-update-tp3697631p3697634.html

How do you determine the PSF?  I was interested in deconvolving a
fluorescence image but wasn't sure how to get the PSF of the
microscope.  Just for grins I cut and pasted an example of an Airy
disk from a journal article and used that.  To my surprise, it worked
pretty well, but there has to be a better way.

Since I know about the optics of the microscope can I calculate the
PSF?  If so, can you point me to some place that explains how?

Justin

On Jan 7, 2008 7:26 AM, Piotr Wendykier <[hidden email]> wrote:

> Dear Christophe,
>
> The short answer is:  yes, it could be used for your Z-stacks,
> and no it is not a totally different kind of deconvolution.
>
> The long answer is harder to explain.  There is just one definition of
> deconvolution, but there are a lot of different methods that can be used
> to actually do the deconvolution. Furthermore, some people use different
> names for essentially the same methods. Why different methods? That's
> hard to explain without using a lot of mathematics. The basic idea is that
> the result produced by deconvolution algorithms depends on the image, the
> noise in the image, and the PSF. One deconvolution method might work well
> for one problem, but not so well for another problem. So it is good to
> try different methods. This plugin uses fairly standard deconvolution
> methods, with two advantages. First, we provide different deconvolution
> methods that you can try with your data -- maybe one will work better
> than another. Second, our methods have been implemented to be very
> efficient on modern multi-core processor machines.
> If you want to know more about these algorithms, I recommend an excellent
> book: "Deblurring Images: Matrices, Spectra, and Filtering" by
> Per Christian Hansen, James G. Nagy, and Dianne P. O'Leary, SIAM 2006.
>
> Piotr
>
> On Jan 7, 2008 4:36 AM, Christophe Leterrier
>
> <[hidden email]> wrote:
> > I went to the plugin homepage, it seems very interesting but it didn't
> > explained what is the use of such a decouvolution... Could someone explain
> > what exactly is this plugin doing ? I'm interested in 3D deconvolution of
> > widefield fluorescence Z-stacks, could this be used for this application or
> > is it a totally different kind of deconvolution ?
> >
> >
> > On Jan 7, 2008 12:10 AM, Piotr Wendykier <[hidden email]> wrote:
> >
> > > Hello,
> > >
> > > I have updated the Parallel Spectral Deconvolution plugin.
> > > The bug causing poor results in all 3D methods with reflexive
> > > boundary conditions has been fixed. Moreover, the source code
> > > has been significantly simplified and the plugin now uses Parallel Colt
> > > 0.2.
> > >
> > > The plugin is available at:
> > >
> > > http://piotr.wendykier.googlepages.com/deconvolution
> > >
> > > Regards,
> > >
> > > Piotr Wendykier
> > >
> >
>