Re: automate bkg substract from roi

Posted by F Javier Díez Guerra on Jan 03, 2006; 9:46pm
URL: http://imagej.273.s1.nabble.com/automate-bkg-substract-from-roi-tp3704147p3704150.html

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

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