automate bkg substract from roi

Posted by F Javier Díez Guerra on Jan 01, 2006; 9:29pm
URL: http://imagej.273.s1.nabble.com/automate-bkg-substract-from-roi-tp3704147.html

Dear ImageJ listers,

I wish everybody a better new year 2006.

My question:
Does anybody know of a macro or plugin to automate background substraction
using  mean gray levels calculated from user-defined roi's in a stack? I
have searched in the list archive and found no specific reference or
comment to it.

The purpose is to automate the following manual procedure:

open an image stack (already corrected for uneven illumination)
draw several roi's within dark background areas (must be done manually)
import the roi's in multimeasure plugin
do multimeasure
average the roi mean gray values obtained for each image in the stack
use this number  to process > Math > substract each image in the stack
save the new stack as Vg stack-bkg.tif
repeat again

The stacks contain images obtained from the same microscope field (cultured
cells) captured from different fluorescence channels (red, green).

I appreciate your help.

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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