adaptive thresholding allgorithm

[Jin Ming Ji]

Hello!

Does anyone know how to smooth the images by 3x3 pixel averaging by
Image J?

I am also very eager to know if there is a plugin or some software
available to threshold the images in a stack with an adaptive
thresholding algorithm, which will take into account the local intensity
level, as simple thresholding using a constant threshold value did not
give good results due to variable local background.   What I am trying
to do is to segment my images into clearer patches (whose dynamic
behaviors is my study interest) and background.

Thank you,

Mingji



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[Elena Kardash]

Hi, Mingji,
  did you try the smooth command from the process menu? here is the
documentation:
http://rsb.info.nih.gov/ij/docs/menus/process.html

Elena

-------------------

> Hello!
>
> Does anyone know how to smooth the images by 3x3 pixel averaging by
> Image J?
>
> I am also very eager to know if there is a plugin or some software
> available to threshold the images in a stack with an adaptive
> thresholding algorithm, which will take into account the local intensity
> level, as simple thresholding using a constant threshold value did not
> give good results due to variable local background.   What I am trying
> to do is to segment my images into clearer patches (whose dynamic
> behaviors is my study interest) and background.
>
> Thank you,
>
> Mingji
>
>
>
> DISCLAIMER:
> This email is confidential and may be privileged. If you are not the

intended recipient,
please delete it and notify us immediately. Please do not copy or use it for
any purpose,
or disclose its contents to any other person as it may be an offence under the
Official
Secrets Act. Thank you.
>

[Noel BONNET]

3x3 averaging can be performed through Process -> Filter -> Mean.

Some sort of "adaptive thresholding" can be performed with the plug-in
'No-threshold' histogram-based image segmentation available at:
www.univ-reims.fr/INSERM514/ImageJ

but some adaptation will be necessary to make it work on stacks.

Noel

[Gary Chinga]

Take a look at the dynamic thresholding plugin at: http://
www.gcsca.net/IJ/Dynamic.html. The plugin works with stacks and  
perform several smoothing filtering. May need some modifications for  
your purpose.

Gary.



On Jan 31, 2006, at 8:04 AM, Jin Ming Ji wrote:

> Hello!
>
> Does anyone know how to smooth the images by 3x3 pixel averaging by
> Image J?
>
> I am also very eager to know if there is a plugin or some software
> available to threshold the images in a stack with an adaptive
> thresholding algorithm, which will take into account the local  
> intensity
> level, as simple thresholding using a constant threshold value did not
> give good results due to variable local background.   What I am trying
> to do is to segment my images into clearer patches (whose dynamic
> behaviors is my study interest) and background.
>
> Thank you,
>
> Mingji
>
>
>
> DISCLAIMER:
> This email is confidential and may be privileged. If you are not  
> the intended recipient, please delete it and notify us immediately.  
> Please do not copy or use it for any purpose, or disclose its  
> contents to any other person as it may be an offence under the  
> Official Secrets Act. Thank you.
>
>

[Paul M. Wallace]

List:

I am able to apply
Process>Math>Log
to an image with the macro:
Run("Log")

However I am not able to to apply an exponential in the same manner:
Run("Exp")

Is there a call or workaround for this?
-Paul

--
JAN Scientific, Inc.
123 NW 36th St., Ste 235
Seattle, WA 98107
206.632.1814

[Wayne Rasband]

> I am able to apply
> Process>Math>Log
> to an image with the macro:
> Run("Log")
>
> However I am not able to to apply an exponential in the same manner:
> Run("Exp")
>
> Is there a call or workaround for this?

ImageJ 1.35q will have a Process>Math>Exp command. In the meantime, use
this macro code:

       for (y=0; y<getHeight; y++) {
           for (x=0; x<getWidth; x++) {
               putPixel(x, y, exp(getPixel(x, y)));
           }
           if (y%20==0)  showProgress(y, getHeight);
        }
        resetMinAndMax;

-wayne

[Jin Ming Ji]

Thanks Chris, Noel, Wayne and Gary

I know how to do the 3x3 pixel averaging smooth now, which can be done
by either the convolution kernel or mean.  

I am still trying the local adaptive thresholding using the methods
suggested.

Mingji


-----Original Message-----
From: Noel BONNET [mailto:[hidden email]]
Sent: Tuesday, January 31, 2006 6:02 PM
To: [hidden email]; Jin Ming Ji
Cc: Noel BONNET
Subject: Re: adaptive thresholding allgorithm

3x3 averaging can be performed through Process -> Filter -> Mean.

Some sort of "adaptive thresholding" can be performed with the plug-in
'No-threshold' histogram-based image segmentation available at:
www.univ-reims.fr/INSERM514/ImageJ

but some adaptation will be necessary to make it work on stacks.

Noel



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This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person as it may be an offence under the Official Secrets Act. Thank you.