ij-macro-programming-workshop
Exercise 21 - Measure the distance of spots to the border of the nucleus
Exercise 21.2 - Remove spots outside the nucleus
Aims:
- threshold images and create binary masks
- use the nucleus mask to remove spots outside the nucleus
Use the DoG function of the last exercise on the green channel of the image in
images/21! Apply an auto-threshold (triangle) and create a binary mask and apply a binary
watershed to separate touching spots!
Apply an auto-threshold on the blue-channel and create a binary mask!
Combine the two binary masks using the Image Calculator with the and-operation to only
keep common areas! Do not close the mask of the nucleus in the macro, we are still going to need
it in the next step.
inputImageID = getImageID();
DoG(1.4, 3);
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function DoG(sigma1, sigma2) {
run("Duplicate...", " ");
bigBlurID = getImageID();
run("Duplicate...", " ");
smallBlurID = getImageID();
run("Gaussian Blur...", "sigma="+sigma1);
selectImage(bigBlurID);
bigBlurTitle = getTitle();
run("Gaussian Blur...", "sigma="+sigma2);
imageCalculator("subtract", smallBlurID, bigBlurID);
close(bigBlurTitle);
}