subtracting average

[chris elliott]

Hi, I have an avi which i can read withimageJ, but I wanted to calculate
the average intensity at each corresponding pixel, and then subtract
this from each frame. Is there an existing plugin/macro etc to do this?

thanks
chris

[Paul Johnston]

Are you looking for background subtraction?  If so consider the
^Process -> Subtract Background... plugin (that's built-in).

paul

On Fri, Jan 30, 2009 at 2:54 AM, chris elliott <[hidden email]> wrote:
> Hi, I have an avi which i can read withimageJ, but I wanted to calculate the
> average intensity at each corresponding pixel, and then subtract this from
> each frame. Is there an existing plugin/macro etc to do this?
>
> thanks
> chris
>

[David Hovis]

Sounds to me like you want to do Image->Stacks -> Z-project (Average  
Intensity).

Then you can use Process-> Image Calculator... (Image1:Original_Stack,  
Operation: Subtract, Image2: AVG_Original_Stack) to subtract the  
average frame from each frame in the stack.

You'll probably want to use a 32-bit result, as otherwise any value  
less than the average will become zero.

--David


On Jan 30, 2009, at 5:54 AM, chris elliott wrote:

> Hi, I have an avi which i can read withimageJ, but I wanted to  
> calculate the average intensity at each corresponding pixel, and  
> then subtract this from each frame. Is there an existing plugin/
> macro etc to do this?
>
> thanks
> chris