Denoising for confocal images

[Arrate Munoz Barrutia]

Dear all,
Is there any nice plugin to denoise confocal images? Thanks a lot in advance.
Best
Arrate

[Ruy]

Try Process-filters-median. Radius 1 or 2 pixels should do the job.

Good luck

Ruy Jaeger


On 12/8/08 4:26 PM, "Arrate Munoz Barrutia" <[hidden email]> wrote:

> Dear all,
> Is there any nice plugin to denoise confocal images? Thanks a lot in advance.
> Best
> Arrate
>


 ========================================================================
                   Dr. Ruy G. Jaeger, DDS, MSD, PhD
                                Professor
 University of Sao Paulo            Institute of Biomedical Sciences
             Department of Cell and Developmental Biology
                     Av. Prof. Lineu Prestes 1524 
      Rooms 302 (Office and microscopy room) and 405 (Laboratory)   
                         Sao Paulo SP 05508-900
 Phones: 55-11-30918454 (office), 30918034 (Lab)    FAX [phone]
                                BRAZIL
          website: http://www.icb.usp.br/~rgjaeger/index.html
 ========================================================================

[Stephan Preibisch]

Hi Arrate,

I also made good experiences with a small Gaussian filter. But no matter
which filter you use, it is better to use appropriate 3D filters if you
have 3D datasets ... afaik they are not built into ImageJ.

I once wrote a plugin for 3D gaussian convolution:
http://fly.mpi-cbg.de/~preibisch/software.html#Gauss

It maybe uses a bit much memory in 3D, I did not optimize for that...

All the best,
Stephan

> Dear all,
> Is there any nice plugin to denoise confocal images? Thanks a lot in
> advance.
> Best
> Arrate
>

[Gabriel Lapointe]

I usually have good results with the hybrid 3D median filter
http://rsbweb.nih.gov/ij/plugins/hybrid3dmedian.html

Gabriel

Arrate Munoz Barrutia wrote:
> Dear all,
> Is there any nice plugin to denoise confocal images? Thanks a lot in advance.
> Best
> Arrate
>
>  

[Roger Chang-3]

Arrate,
I would definitely use filters to denoise confocal images as the others
have suggested. You may also experiment with ImageJ's Remove Outliers
function (be sure to checkmark the preview checkbox before accepting the
Radius and Threshold inputs). This function can be found under
Process>>Noise>>Remove Outliers.

Hope this suggestion helps.
-Roger Chang
Washington University in St. Louis Biomedical Engineering Department:
Efimov Lab

> Dear all,
> Is there any nice plugin to denoise confocal images? Thanks a lot in
> advance.
> Best
> Arrate
>