Hi Kai,
I don't have that as a plugin, but I do have a macro called BG
Subtraction from ROI. Perhaps this is what you're looking for?
--begin code--
// Michael Cammer 20030118
// macros for cleaning up time series data
//---------------------------------------------
// User selects a ROI in the background of a stack.
// This ROI is measured in each slice and the mean value of
each slice is subtracted
// from the correct slice. This corrects for variation in
background value over time.
//Added single slice function and ability to set Stdev c\valkue
macro "BG [F12]" {
currentTitle = getTitle();
currentID=getImageID();
run("Set Measurements...", " mean standard redirect=None
decimal=0");
scaling=3;
//scaling=getNumber("Enter Scaling factor",3)
selectImage(currentID);
if (nSlices>1){
// setSlice(1);
run("Plot Z-axis Profile"); run("Close");
for (i=1; i<=nSlices; i++){
bgmean=getResult("Mean",(i-1));
bgStdev=getResult("StdDev",(nResults-1));
bgTotal=bgmean+(scaling*bgStdev);
selectImage(currentID);
run("Set Slice...", "slice="+i);
run("Select All");
run("Subtract...", "slice value="+bgTotal);}
}
if (nSlices==1) {run("Measure");
selectImage(currentID);
bgmean=getResult("Mean",(nResults-1));
bgStdev=getResult("StdDev",(nResults-1));
bgTotal=bgmean+(scaling*bgStdev);
run("Select All");
run("Subtract...", "value="+bgTotal);
run("Select None");
}
selectWindow("Results");
run("Close");
//showMessage("StDev="+bgStDev+ " Mean BG = "+bgmean);
run("Set Measurements...", " mean redirect=None decimal=0");
run("Select None");
}
--end code--
---- Original message ----
>Date: Mon, 19 Apr 2010 04:04:18 -0400
>From: Kai Fan <
[hidden email]>
>Subject: BG subtraction from ROI
>To:
[hidden email]
>
>Hi,
>
>This question might sound stupid but I have been trying to
find the plugin in ImageJ called "BG subtraction from ROI" but
it's not either in the latest ImageJ version or in the plugin
download website.
>Appreciate anyone who can help. Thanks!
>
>Kai
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