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Re: automate bkg substract from roi

Posted by Wayne Rasband on Jan 04, 2006; 3:12pm
URL: http://imagej.273.s1.nabble.com/automate-bkg-substract-from-roi-tp3704147p3704151.html

Here is another background subtraction macro. With this one, each image
in the stack is corrected by its own calculated background level. Note
that the selection used to calculate the background level can be a
composite (discontinuous) selection created by holding down the shift
key.

     if (selectionType==-1)
        exit("This macro requires an area selection");
     for (i=1; i<=nSlices; i++) {
         setSlice(i);
         getStatistics(area, mean);
         run("Select None");
         run("Subtract...", "value="+mean);
         run("Restore Selection");
     }

-wayne


On Jan 3, 2006, at 4:46 PM, F Javier Diez Guerra wrote:

> At 21:19 03/01/2006, you wrote:
>> Here is a macro that subtracts the mean gray level calculated from
>> user-defined selections that have been added to the ROI Manager. It
>> works with either a single image or a stack.
>>
>>     n = roiManager("count");
>>     if (n==0)
>>         exit("This macro requires at least one ROI Manager entry");
>>     sum = 0;
>>     for (i=0; i<n; i++) {
>>         roiManager("select", i);
>>         getStatistics(area, mean);
>>         sum += mean;
>>     }
>>     average = sum/n;
>>     run("Select None");
>>     run("Subtract...", "stack value="+average);
>>
>> -wayne
>
>
> Wayne,
>
> Thanks very much for the "bkg substract from roi" macro. It works very
> well with single images. However, in stacks it takes the value of bkg
> obtained from the first (or current) image and substracts it to the
> whole set of images in the stack. Since the images within the stack
> share the background roi's areas but have different background levels,
> the background correction is only valid for the first (or current)
> image of the stack.
>
> Is it possible to automate the process so that each image of the stack
> is corrected by its own calculated level of background? Alternatively,
> the stack can be first converted to images, substract background with
> the macro to each image individually and then convert the images back
> to stack.
>
> Best regards
>
>
> F Javier Diez-Guerra, PhD
> Profesor Titular
> Centro de Biologia Molecular Severo Ochoa
> Facultad de Ciencias, Universidad Autónoma
> Ctra Colmenar Viejo Km 15
> Cantoblanco, 28049 Madrid
> SPAIN
>
> phone:  +34 91 4978051
> Fax:      +34 91 4978087
> e-mail: [hidden email]