Macro on imageJ, loop does not move to the next ROI

Question

I'm trying to crop sections in an image and then averaging all of them. I'm recycling my previous macros on imageJ. Previous macros work well by doing loops in a list of ROIs. But, for this one, I can't understand why the loop does not move to the next ROI in the list. Instead, I got the job N-times as the number of ROIs I have in the list but the macro uses the first ROI information. This is my macro:

runMacro("OpenROI");
rename("AA");
selectWindow("AA");
n=roiManager("count");

for(i=0;i<n;i++){
    roiManager("select",i);
    run("Copy");
    run("Internal Clipboard");
    rename(i);
}

selectWindow("AA");
run("Close");
run("Images to Stack", "name=Stack title=[] use");
run("Z Project...", "projection=[Average Intensity]");

Someone can catch what am I losing it? Thanks

score 1 · Answer 1 · answered Nov 04 '21 at 20:57

I found a solution, the line:

selectWindow("AA");

must be inside the loop in order to set the ROI on the image. Full code is as follows:

runMacro("OpenROI");
rename("AA");

n=roiManager("count");

for(i=0;i <n; i++){
    selectWindow("AA");
    roiManager("select",i);
    run("Copy");
    run("Internal Clipboard");
    rename(i);
}

selectWindow("AA");
run("Close");
run("Images to Stack", "name=Stack title=[] use");
run("Z Project...", "projection=[Average Intensity]");

Macro on imageJ, loop does not move to the next ROI

1 Answers1