Applying masks to stack of thresholded images


I am trying to apply selection to a stack of images of objects/cells from 20hr live cell imaging. The cells move, change shape and divide in that time. I created a substack of the channels (red & green) that i want to intensity quantitate. Next applied threshold, fill holes and dilate – applies to all the images in the substack. But when i apply mask,it only applies to the top image. Image calculator/multiply option applies the same mask to all images. How do i apply individual mask to the images in substack so i can apply proper selection for intensity measurements?


Welcome to the forum, @Amnesiac74!

If you have a stack of individual masks​ and a stack of images, and both stacks have the same size, you should be able to combine them with the Image Calculator. Did you try this?


I do not have a stack of individual masks. Is there way to create stack of individual masks without using macros, similar to how individual thresholding can be applied to all the images in the stack? Thanks!