Saving ROIs in an image sequence

Hello. I’m working on image sequences from 3D datasets. I have manually created a selection on each image of the image stack through the ROI manager and interpolated the (all different) selections. How can I save the images inside the selection and exclude all the rest? I have tried to save as tiff the stack by using the clear outside function beforehand, but that function applies the same selection on all the image stack. Thank you


Perhaps you could write a script to split the stack… overlay the correct ROIs on that image and clear outside… do this for each and the merge them once again? Does that seem feasible for you?

Yes! It worked by working on each selection separately and then saving the modified stack as an image sequence. Good idea, thank you!

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