Clear outside tool deleting inside ROI

Hi all

I wonder if anyone can help me. I am having an issue with my ROIs on ImageJ. Once I’ve drawn, combined and saved my ROIs and then I try and clear the background, the Clear Outside command also clears within my ROIs. My ROIs are definitely closed, my background is set to black and my foreground white.

I have tried using ROIs drawn and sent to my computer by another user, and those ROIs work fine – they are not cleared along with the background. I have tried uninstalling and reinstalling Fiji and it is completely up to date on my computer, but still the inside of my ROIs are being cleared with my background. I can’t find anything online with advice about this problem. Does anyone know what might be going wrong?

Any help would be hugely, hugely appreciated.

It would help if you take some screenshots and make a screenshot from the image information (press ‘i’).

It could be that your ROI is nor enabled which is causing this behavior (just a guess).

What happens if you draw a new ROI and use the clear outside action?


Sorry, just posted some screenshots but they were too dim so reposting here.

When I draw a new ROI, the clear outside action still clears the inside of the ROI. This happens with all ROIs drawn on my system but not for the ROI drawn on someone else’s that has been sent to me.

I thought you have sent the ROI and not a new ROI was sent to you to reproduce (I skipped this fact in your first post).

So it might be that your ROI (composite ROI) is wrong.

When I create a hyperstack with a composite ROI the cropping works.

Try to remake you ROI’s individually (add to manager), create a composite ROI (select all single ROI’s and use the action “More->or (Combine)” then press action “Add[t]” to create a composite ROI.

Use the clear outside action with the new composite ROI (select in ROI Manager).

I have managed to sort it - turns out it was something as simple as using the freehand line tool, rather than the freehand selection tool. This meant that clear outside cleared everything except the lines I had drawn, including the inside of my ROI. Thank you for your help anyway!