ij-macro-programming-workshop
Exercise 13 - background correction on a stack
Aim:
- apply some of the technics learned in the first part to
correct the background in a time series. Learn how to pass
the value of a variable to a command that is called with
run.
Look at the time-series actine-stack.tif. The base level
of the background varies from frame to frame. Fill in the
gaps in the macro below. It will correct the background in
the time-series, so that the flimmering when watching the
film will disapear.
The user should make a selection on the background before starting the macro.
useful commands:
nSlices- the number of slices in the stacksetSlice(i)- set the current slicegetStatistics(area, mean);run("Select None");run("Restore Selection");run("Subtract...", "value=5 slice");
Your code starts after this line
for (i=1; i<=nSlices; i++) { // iterate over all frames of the time-series
setSlice(i); // set the current slice
getStatistics(area, mean); // get the mean intensity of the current selection (the variable mean will be set to it).
run("Select None"); // remove the current selection before subtracting the mean from the image (otherwise it will just be subtracted from the selection).
run("Subtract...", "value=" + mean + " slice"); // subtract the mean value of the background, measured on the current frame, from the current frame from the
run("Restore Selection"); // restore the original selection of a background region for the next iteration.
}
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The code below is for automatically checking the result. Please ignore it!
run("Select None");
imageId = getImageID();
makeRectangle(530, 30, 78, 430);
run("Plot Z-axis Profile");
plotId = getImageID();
Plot.getValues(x, y);
selectImage(imageId);
run("Select None");
Array.getStatistics(y, min, max, mean, stdDev);
ok = (stdDev<1);
selectImage(plotId);
run("Close");
doCommand("Start Animation [\\]");
if (ok)
showMessage("That's right. Great, you did it!");
else
showMessage("Your result is wrong! Please check your macro and try again!");